From noreply at github.com  Wed Jul  1 07:46:19 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 06:46:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] bcba62: Qt6 no longer supports the
 QString().sprintf() fun...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/8886d7-6fc2e4@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bcba62aaaf014951e3bad0f773d2affc10e53f5e
      https://github.com/ehb54/ultrascan3/commit/bcba62aaaf014951e3bad0f773d2affc10e53f5e
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_buffer.cpp
    M utils/us_cfa_data.cpp
    M utils/us_datafiles.cpp
    M utils/us_gzip.cpp
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_model.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_simparms.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_util.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Qt6 no longer supports the QString().sprintf() function. Fixed this issue by replacing it with proper functions


  Commit: 193bcc32a83df8e1f95d41e9dae11a6434da38e7
      https://github.com/ehb54/ultrascan3/commit/193bcc32a83df8e1f95d41e9dae11a6434da38e7
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_dataIO.cpp

  Log Message:
  -----------
  replaced QString::SkipEmptyParts with Qt::SkipEmptyParts


  Commit: 3d82f0921ddc17663db935727e74ac7285150aa4
      https://github.com/ehb54/ultrascan3/commit/3d82f0921ddc17663db935727e74ac7285150aa4
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  replaced toTime_t() with toSecsSinceEpoch() in QDateTime


  Commit: 9842f68622b8822f47a5c2878669890685348af7
      https://github.com/ehb54/ultrascan3/commit/9842f68622b8822f47a5c2878669890685348af7
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  c++17 doesn't support register


  Commit: 68bfa3350ea117e6c8b2a8222fa5c59e2b453cd8
      https://github.com/ehb54/ultrascan3/commit/68bfa3350ea117e6c8b2a8222fa5c59e2b453cd8
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_cfa_data.cpp
    M utils/us_memory.cpp
    M utils/us_project.cpp
    M utils/us_report.cpp
    M utils/us_rotor.cpp
    M utils/us_settings.cpp
    M utils/us_solution.cpp

  Log Message:
  -----------
  replaced QRegExp with QRegularExpression


  Commit: c50c776f797e411dfdf83c69446cba8b40e1a744
      https://github.com/ehb54/ultrascan3/commit/c50c776f797e411dfdf83c69446cba8b40e1a744
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_local_server.h

  Log Message:
  -----------
  add #include <QDebug> to us_local_server.h


  Commit: 2b2e229139b83fd1e2ce99edf290a820df77fe46
      https://github.com/ehb54/ultrascan3/commit/2b2e229139b83fd1e2ce99edf290a820df77fe46
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_cfa_data.cpp

  Log Message:
  -----------
  fixed the issue with adding an integer to a character


  Commit: 84254a6aa4322f882cea6d15ebaa6375c1dd1220
      https://github.com/ehb54/ultrascan3/commit/84254a6aa4322f882cea6d15ebaa6375c1dd1220
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-21 (Mon, 21 Jul 2025)

  Changed paths:
    M utils/us_lamm_astfvm.cpp

  Log Message:
  -----------
  replaced QTime with QElapsedTimer


  Commit: 4469af92492851be98df19fc8d20cbb65cf499f8
      https://github.com/ehb54/ultrascan3/commit/4469af92492851be98df19fc8d20cbb65cf499f8
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_math2.cpp
    M utils/us_math2.h

  Log Message:
  -----------
  Replace qrand/qsrand with std::mt19937 from C++11 <random> library because qrand/qsrand are not supported in Qt.6. Mersenne Twister 19937 generator produces thread-safe random number with quality and performance. QTime::currentTime() is replaced with std::chrono::system_clock to generated an unique random seed with higher precision. std::uniform_real_distribution coupled with std::mt19937 is used to generate uniformly distributed random numbers.


  Commit: 8027aae3133b42fd97a3595a932af099e20d12f9
      https://github.com/ehb54/ultrascan3/commit/8027aae3133b42fd97a3595a932af099e20d12f9
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  QStringRef is deprecated in Qt.6 and is replaced with QStringView


  Commit: c03e53c33a046303a0973d609fb2077954717ba0
      https://github.com/ehb54/ultrascan3/commit/c03e53c33a046303a0973d609fb2077954717ba0
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_astfem_rsa.cpp
    M utils/us_hardware.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  replace qSor with str::sort for vectors of int, double, and QString


  Commit: 3bd31299ae152f354f67673997d47527ee13ab0f
      https://github.com/ehb54/ultrascan3/commit/3bd31299ae152f354f67673997d47527ee13ab0f
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  sorting a vector of US_ZSolute using std::sort is tricky. we should decide what parameter of the US_ZSolute should be used to sort the vector based on. US_ZSolute has x, y, z, c where x, y, and z are the parameters used to make grids for 2DSA. For example s, ff0, and vbar. So they change by analysis. c is the concetration of the species which is used here to sort the sim_vals.zsolutes.


  Commit: 7a6584a8150598a709a9e5cbdd5f057d1822013e
      https://github.com/ehb54/ultrascan3/commit/7a6584a8150598a709a9e5cbdd5f057d1822013e
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  s values of the US_Solute are used to sort the sim_vals.solutes.


  Commit: e057219f4688995edd4d1e7a70929753cceeaa37
      https://github.com/ehb54/ultrascan3/commit/e057219f4688995edd4d1e7a70929753cceeaa37
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  wrong type casting


  Commit: 9bf93b888a0c6283dd4fe50f27a24e7e36847380
      https://github.com/ehb54/ultrascan3/commit/9bf93b888a0c6283dd4fe50f27a24e7e36847380
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_timer.cpp
    M utils/us_timer.h

  Log Message:
  -----------
  replace QTime with QElapsedTimer in US_Timer


  Commit: aa6733cf95d1f98e40f11045c996c2507121e7a7
      https://github.com/ehb54/ultrascan3/commit/aa6733cf95d1f98e40f11045c996c2507121e7a7
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  replace qrand and qsrand with std random generator in US_Crypto


  Commit: 2b97df7f65bfc7e8254d33a7e7e76b1cd949f2ef
      https://github.com/ehb54/ultrascan3/commit/2b97df7f65bfc7e8254d33a7e7e76b1cd949f2ef
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_stiffbase.h

  Log Message:
  -----------
  remove unit macro and instead include <QtGlobal>


  Commit: 6adbbd87bf8462b30588b1c1a70f363f5e33a79f
      https://github.com/ehb54/ultrascan3/commit/6adbbd87bf8462b30588b1c1a70f363f5e33a79f
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  US_DB2::value : we must cast char** to QVarient. QVariant::Invalid is deprecated and replaced with QVariant()


  Commit: 8d6cadc10bcd7d58d1692a6622ecfe2213ce145d
      https://github.com/ehb54/ultrascan3/commit/8d6cadc10bcd7d58d1692a6622ecfe2213ce145d
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  US_BufferComponent::saveToDB should return an Int. I assumed it should be idBufferComponent after trying to save a new buffer component in DB


  Commit: 8c54b51cc75babc28615af49a56735cebb58820a
      https://github.com/ehb54/ultrascan3/commit/8c54b51cc75babc28615af49a56735cebb58820a
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-22 (Tue, 22 Jul 2025)

  Changed paths:
    M utils/us_math2.cpp

  Log Message:
  -----------
  US_Math2::randomize : start with std::random_device to make a random seed. then mixed it with current time to increase the entropy. add process ID. it is important for MPI runs


  Commit: 1e08a16239893c26e56a4ec7a75b078f5e33780a
      https://github.com/ehb54/ultrascan3/commit/1e08a16239893c26e56a4ec7a75b078f5e33780a
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  fixed indentation and not using curly braces for if blocks


  Commit: 5ed9c7f4aaf2812f54ad9f20088fad994ffe685e
      https://github.com/ehb54/ultrascan3/commit/5ed9c7f4aaf2812f54ad9f20088fad994ffe685e
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_project.cpp

  Log Message:
  -----------
  Update utils/us_project.cpp

Fixed by Lukas.

Co-authored-by: Lukas Dobler <69309597+doluk at users.noreply.github.com>


  Commit: e2f82f84ce3688e18ad64b185291442e9ea94c76
      https://github.com/ehb54/ultrascan3/commit/e2f82f84ce3688e18ad64b185291442e9ea94c76
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_report.cpp

  Log Message:
  -----------
  Update utils/us_report.cpp

fixed by Lukas.

Co-authored-by: Lukas Dobler <69309597+doluk at users.noreply.github.com>


  Commit: 40e8280789baf4229426227a497068c6b39ba9f5
      https://github.com/ehb54/ultrascan3/commit/40e8280789baf4229426227a497068c6b39ba9f5
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_project.cpp
    M utils/us_report.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/utils_with_qt6' into utils_with_qt6


  Commit: 2b557d83d4e0c49fb729e8e8674e6743c4aecc15
      https://github.com/ehb54/ultrascan3/commit/2b557d83d4e0c49fb729e8e8674e6743c4aecc15
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_report.cpp

  Log Message:
  -----------
  Update utils/us_report.cpp

fixed by Lukas!

Co-authored-by: Lukas Dobler <69309597+doluk at users.noreply.github.com>


  Commit: c6894a31494ac44b463878e61992d5b5b46bdf06
      https://github.com/ehb54/ultrascan3/commit/c6894a31494ac44b463878e61992d5b5b46bdf06
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_report.cpp

  Log Message:
  -----------
  Update utils/us_report.cpp

fixed by Lukas

Co-authored-by: Lukas Dobler <69309597+doluk at users.noreply.github.com>


  Commit: 56fd87c26d16af03531c1b6170fdeb943b183fe3
      https://github.com/ehb54/ultrascan3/commit/56fd87c26d16af03531c1b6170fdeb943b183fe3
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_report.cpp

  Log Message:
  -----------
  Update utils/us_report.cpp

fixed by Lukas!

Co-authored-by: Lukas Dobler <69309597+doluk at users.noreply.github.com>


  Commit: bf63e374e7bb523a3115699f24919e06d6d969d5
      https://github.com/ehb54/ultrascan3/commit/bf63e374e7bb523a3115699f24919e06d6d969d5
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_rotor.cpp

  Log Message:
  -----------
  Update utils/us_rotor.cpp

fixed by Lukas!

Co-authored-by: Lukas Dobler <69309597+doluk at users.noreply.github.com>


  Commit: 6a79cd3b2725e774c7baef8629a054c7d1d69f89
      https://github.com/ehb54/ultrascan3/commit/6a79cd3b2725e774c7baef8629a054c7d1d69f89
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_report.cpp
    M utils/us_rotor.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/utils_with_qt6' into utils_with_qt6


  Commit: fe388f070d81a3b002b68271f9e02412257c6566
      https://github.com/ehb54/ultrascan3/commit/fe388f070d81a3b002b68271f9e02412257c6566
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_report.cpp
    M utils/us_report.h

  Log Message:
  -----------
  us_report: Move regex to header for reuse across methods


  Commit: 27c40211dc61cbcfab1ddb4f69aa485d05752199
      https://github.com/ehb54/ultrascan3/commit/27c40211dc61cbcfab1ddb4f69aa485d05752199
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_util.cpp

  Log Message:
  -----------
  us_util.cpp: used a clear version of the mid function of QStringList


  Commit: ca93d830d3b4efac58b7dccdd7aed4d78a29c4da
      https://github.com/ehb54/ultrascan3/commit/ca93d830d3b4efac58b7dccdd7aed4d78a29c4da
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  us_solve_sim.cpp: removed lambda function from std:sort since operator< is defined in the header file


  Commit: f7ca0ab961c14253d0133556f4c8b7861f88e13b
      https://github.com/ehb54/ultrascan3/commit/f7ca0ab961c14253d0133556f4c8b7861f88e13b
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_matrix.cpp
    M utils/us_model.cpp

  Log Message:
  -----------
  fixed the indentations and added braced to the 'for' block


  Commit: cf21afee5788075f15e05bd7570b6c4fc9039efe
      https://github.com/ehb54/ultrascan3/commit/cf21afee5788075f15e05bd7570b6c4fc9039efe
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_analyte.cpp

  Log Message:
  -----------
  toLower() method of QString doesn't lower the string in place. it returns another string


  Commit: 67451f3508ad69c38929872ef40a5879cdf64c72
      https://github.com/ehb54/ultrascan3/commit/67451f3508ad69c38929872ef40a5879cdf64c72
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_cfa_data.cpp

  Log Message:
  -----------
  us_cfa_data.cpp: "executing query on QSqlDatabase is deprecated since Qt 6.6 and replace with QSqlQuery::exec() which is also supported by Qt 5.15


  Commit: e7144b1a1b562e27c54200ac0f49145a63741386
      https://github.com/ehb54/ultrascan3/commit/e7144b1a1b562e27c54200ac0f49145a63741386
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  us_xpn_data.cpp: executing a query on QSqlDatabase is deprecated since Qt 6.6 and replace with QSqlQuery::exec() which is also supported by Qt 5.15


  Commit: 6f29f8bb4063ef8150d630adc11c300adf4e69e8
      https://github.com/ehb54/ultrascan3/commit/6f29f8bb4063ef8150d630adc11c300adf4e69e8
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-29 (Tue, 29 Jul 2025)

  Changed paths:
    M utils/us_ana_profile.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  fixed indentations


  Commit: 576eb10a22e9eb49bf735d383045dd6393dcfa08
      https://github.com/ehb54/ultrascan3/commit/576eb10a22e9eb49bf735d383045dd6393dcfa08
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-29 (Tue, 29 Jul 2025)

  Changed paths:
    M utils/us_link_ssl.cpp

  Log Message:
  -----------
  us_link_ssl.cpp: simplified() returns a new QString and it is used to rewrite the client_name


  Commit: 13d43bdb65ac6611ad9b988e2ad7436b880b54f8
      https://github.com/ehb54/ultrascan3/commit/13d43bdb65ac6611ad9b988e2ad7436b880b54f8
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-29 (Tue, 29 Jul 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  us_xpn_data.cpp: comment out unused variables


  Commit: aa5f6484e899c0c16449ced5724171f2423b9091
      https://github.com/ehb54/ultrascan3/commit/aa5f6484e899c0c16449ced5724171f2423b9091
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-29 (Tue, 29 Jul 2025)

  Changed paths:
    M utils/us_stiffbase.h

  Log Message:
  -----------
  us_stiffbase.h: define unit instead of including whole <QtGlobal>


  Commit: 183143d228bceca4560f98403748b98da71763e4
      https://github.com/ehb54/ultrascan3/commit/183143d228bceca4560f98403748b98da71763e4
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-29 (Tue, 29 Jul 2025)

  Changed paths:
    M utils/us_hydrosim.h

  Log Message:
  -----------
  us_hydrosim.h: wrong macro definition


  Commit: 1a25f5daf6d9914b1722f59340428b1cf6204286
      https://github.com/ehb54/ultrascan3/commit/1a25f5daf6d9914b1722f59340428b1cf6204286
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-07-30 (Wed, 30 Jul 2025)

  Changed paths:
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_crc.h
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_dmga_constr.cpp
    M utils/us_dmga_constr.h
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_project.h
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_rotor.h
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution_vals.cpp
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_solve_sim.h
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.h

  Log Message:
  -----------
  removed #include <QtCore> and included only libraraies that are needed


  Commit: 2fe76586f9e2a98de89c1d6bc06a0022bdb059bf
      https://github.com/ehb54/ultrascan3/commit/2fe76586f9e2a98de89c1d6bc06a0022bdb059bf
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_dmga_constr.cpp
    M utils/us_dmga_constr.h
    M utils/us_eprofile.cpp
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.cpp
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_project.h
    M utils/us_protocol_util.cpp
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_rotor.h
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution_vals.cpp
    M utils/us_solve_sim.cpp
    M utils/us_solve_sim.h
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp

  Log Message:
  -----------
  utils: define a new header file named us_utils_qt.h that includes all necessary qt libs needed for utils programs.


  Commit: 5735f4b7432adf3550754e00a6bb68c31620082d
      https://github.com/ehb54/ultrascan3/commit/5735f4b7432adf3550754e00a6bb68c31620082d
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M utils/us_astfem_math.cpp
    M utils/us_astfem_rsa.h
    M utils/us_simparms.cpp

  Log Message:
  -----------
  avoid redefining DbgLv


  Commit: df38a513d0b2e3777b0eb40271eaa9dcbdd91942
      https://github.com/ehb54/ultrascan3/commit/df38a513d0b2e3777b0eb40271eaa9dcbdd91942
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M gui/us_run_details2.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M utils/us_astfem_math.cpp
    M utils/us_math2.h
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  removed min/max macros from us_math2.h and replaced them with std ones everywhere it is called in the gui and programs.


  Commit: 149192ffd8bfd877414dc7bc60ce83e28f77c861
      https://github.com/ehb54/ultrascan3/commit/149192ffd8bfd877414dc7bc60ce83e28f77c861
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-02 (Sat, 02 Aug 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M utils/us_astfem_math.cpp
    M utils/us_solve_sim.cpp
    M utils/us_utils_qt.h

  Log Message:
  -----------
  replaced min/max and std::min/max with qMin/qMax in utils


  Commit: 99328607f509f3624ae4bc675d7661cc8e8fc6f3
      https://github.com/ehb54/ultrascan3/commit/99328607f509f3624ae4bc675d7661cc8e8fc6f3
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-02 (Sat, 02 Aug 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_predict1.cpp
    M gui/us_run_details2.cpp

  Log Message:
  -----------
  replaced min/max and std::min/max with qMin/qMax in libgui


  Commit: fd828f5d6b6dee18437ae035e4deda5963b37160
      https://github.com/ehb54/ultrascan3/commit/fd828f5d6b6dee18437ae035e4deda5963b37160
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-02 (Sat, 02 Aug 2025)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp

  Log Message:
  -----------
  replaced min/max and std::min/max with qMin/qMax in the programs


  Commit: ece28622af778b3b936f5dee16ccac7d5ea2a06b
      https://github.com/ehb54/ultrascan3/commit/ece28622af778b3b936f5dee16ccac7d5ea2a06b
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M utils/us_solve_sim.cpp
    M utils/us_util.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  replace QString().sprintf() with Qt methods


  Commit: 043d903895d150b1718f1de85a5105355f9fc7a6
      https://github.com/ehb54/ultrascan3/commit/043d903895d150b1718f1de85a5105355f9fc7a6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-24 (Fri, 24 Oct 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M README.md
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    A admin/pam/pam_no_ad/Makefile
    A admin/pam/pam_no_ad/README.md
    A admin/pam/pam_no_ad/files/mariadb
    A admin/pam/pam_no_ad/files/php
    A admin/pam/pam_no_ad/files/sssd.conf
    A admin/pam/pam_no_ad/files/system-auth-nosss
    A admin/pam/pam_no_ad/pam_auth_pamtester.php
    A admin/pam/pam_no_ad/pam_auth_test.php
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    M admin/release/ubuntu_qt6/Dockerfile
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    M doc/manual/advanced_config.body
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_choice.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_minimize.cpp
    R gui/us_model_editor.cpp
    R gui/us_model_editor.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.cpp
    M gui/us_model_loader.h
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot3d.cpp
    M gui/us_predict1.cpp
    M gui/us_project_gui.cpp
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_sassoc.h
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_table.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M gui/us_widgets_dialog.h
    M gui/us_window_message.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa_process.cpp
    M programs/us_2dsa/us_2dsa_process.h
    M programs/us_2dsa/us_adv_analysis_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_plot_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    A programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.cpp
    M programs/us_config/us_color.h
    M programs/us_config/us_config.cpp
    M programs/us_config/us_config.h
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_experiment_gui.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_convert/us_select_triples.cpp
    M programs/us_convert/us_select_triples.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.cpp
    M programs/us_density_match/us_remove_models.cpp
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_exclude_profile.cpp
    M programs/us_edit/us_get_edit.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.h
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_globalequil/us_long_messagebox.h
    M programs/us_globalequil/us_model_adpars.cpp
    M programs/us_globalequil/us_model_select.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/dmga_worker.cpp
    M programs/us_mpi_analysis/ga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/parallel_masters.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/pmasters_compjob.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_pcsa/us_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    A programs/us_query_rmsd/CMakeLists.txt
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_experiment_ra.h
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_sync_db.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    A qwtplot3d/CMakeLists.txt
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    M test/modelbuilder/us_modelbuilder.cpp
    M test/utils/CMakeLists.txt
    A test/utils/mock/mock_us_db2.h
    A test/utils/test_mock_us_db2.cpp
    A test/utils/test_us_ana_profile.cpp
    A test/utils/test_us_analyte.cpp
    A test/utils/test_us_astfem_math.cpp
    A test/utils/test_us_buffer.cpp
    A test/utils/test_us_crc.cpp
    A test/utils/test_us_crypto.cpp
    A test/utils/test_us_dataIO.cpp
    M test/utils/test_us_datafiles.cpp
    R test/utils/test_us_datafiles.h
    A test/utils/test_us_db2.cpp
    A test/utils/test_us_math2.cpp
    A test/utils/test_us_matrix.cpp
    A test/utils/test_us_memory.cpp
    A test/utils/test_us_model.cpp
    A test/utils/test_us_project.cpp
    A test/utils/test_us_settings.cpp
    R test/utils/test_us_simparams.cpp
    R test/utils/test_us_simparams.h
    A test/utils/test_us_simparms.cpp
    A test/utils/test_us_stiffbase.cpp
    A test/utils/test_us_time_state.cpp
    A test/utils/test_us_timer.cpp
    M test/utils/test_us_util.cpp
    R test/utils/test_us_util.h
    M test/utils/test_us_utils_main.cpp
    A test/utils/test_us_vector.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3_defines.h
    A us_somo/develop/include/us_band_broaden.h
    M us_somo/develop/include/us_hydrodyn.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_dad.h
    M us_somo/develop/include/us_hydrodyn_hydro.h
    M us_somo/develop/include/us_hydrodyn_hydro_zeno.h
    M us_somo/develop/include/us_hydrodyn_mals.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_buffer.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_ciq.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_movie.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_matrix.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pfortran.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_tar.h
    M us_somo/develop/include/us_tnt_jama.h
    M us_somo/develop/include/us_unicode.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_util.cpp
    A us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_color.cpp
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_ffd.cpp
    M us_somo/develop/src/us_font.cpp
    M us_somo/develop/src/us_fractal_dimension.cpp
    M us_somo/develop/src/us_help.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_load_results_opts.cpp
    M us_somo/develop/src/us_hydrodyn_bd_options.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_advanced.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_powerfit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_movie.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_plots.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dammin_opts.cpp
    M us_somo/develop/src/us_hydrodyn_fractal_dimension.cpp
    M us_somo/develop/src/us_hydrodyn_grid_atob.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate_align.cpp
    M us_somo/develop/src/us_hydrodyn_hydro.cpp
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_mals_movie.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_plots.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_scale.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_movie.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_misc.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pat.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_results.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_buffer_fit.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_buffer_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_ciq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_wheel.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_residuals.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_util.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_imgviewer.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_matrix.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_plot_zoom.cpp
    M us_somo/develop/src/us_pm_fitness.cpp
    M us_somo/develop/src/us_register.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_guinier.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydrate_align.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_grid_atob_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_pat_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_pat.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/src/us_util.cpp
    M us_somo/develop/src/us_zeno_cxx.cpp
    M us_somo/somo/doc/manual/somo/somo-Zeno_optionsNew.png
    M us_somo/somo/doc/manual/somo/somo-main0new.png
    M us_somo/somo/doc/manual/somo/somo-main4.png
    M us_somo/somo/doc/manual/somo/somo.html
    A us_somo/somo/doc/manual/somo/somo_ZENO_correction_warning.png
    M us_somo/somo/doc/manual/somo/somo_cluster_config.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_gzip.cpp
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_project.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_rotor.cpp
    M utils/us_rotor.h
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.cpp
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_solve_sim.h
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into utils_with_qt6


  Commit: 13f6c5148d62ff0f6aa632c3de0bd533453f7365
      https://github.com/ehb54/ultrascan3/commit/13f6c5148d62ff0f6aa632c3de0bd533453f7365
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-26 (Sun, 26 Oct 2025)

  Changed paths:
    M admin/cmake/FindQwt.cmake

  Log Message:
  -----------
  Standardize Qwt environment variable checks and add `QWT_VERSION` and `QWT_QT_VERSION` definitions for improved CMake configuration clarity and maintainability.


  Commit: f6d6012fbc4fdbc543b30a6d3463bddc1673b616
      https://github.com/ehb54/ultrascan3/commit/f6d6012fbc4fdbc543b30a6d3463bddc1673b616
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-26 (Sun, 26 Oct 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M CMakeLists.txt
    M README.md
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    M admin/release/ubuntu_qt6/Dockerfile
    M doc/manual/advanced_config.body
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_plot.cpp
    M gui/us_report_gui.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_second_moment/us_second_moment.cpp
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M utils/us_ana_profile.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h

  Log Message:
  -----------
  Merge pull request #298 from ehb54/main

update qt6-compile


  Commit: b50cca680591c9248bc21802a59b43b0b5b0687b
      https://github.com/ehb54/ultrascan3/commit/b50cca680591c9248bc21802a59b43b0b5b0687b
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-26 (Sun, 26 Oct 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_predict1.cpp
    M gui/us_run_details2.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h

  Log Message:
  -----------
  Merge pull request #299 from samo38/utils_with_qt6

Merge samo38/ultrascan3 at Utils with qt6 into lukas/qt6-compile


  Commit: be440f7beb44ba005109efbf314633c079010602
      https://github.com/ehb54/ultrascan3/commit/be440f7beb44ba005109efbf314633c079010602
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-26 (Sun, 26 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Update CMake to support optional Qt6 usage and modernize Qt library linking

Introduced a `USE_QT6` build option for switching between Qt5 and Qt6. Modernized Qt library linking by standardizing to `Qt::` aliases. Updated all related targets and dependencies for improved flexibility and maintainability.


  Commit: 4c7b899cc2a8e239f5e6e6e210f3f0b28c1d7165
      https://github.com/ehb54/ultrascan3/commit/4c7b899cc2a8e239f5e6e6e210f3f0b28c1d7165
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-26 (Sun, 26 Oct 2025)

  Changed paths:
    M utils/us_crypto.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_project.cpp
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_rotor.cpp
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_util.cpp
    M utils/us_util.h

  Log Message:
  -----------
  Streamline random data initialization and UUID validation

- Removed legacy random generator logic and unnecessary includes in `US_Math2`.
- Unified UUID validation through the addition of `UUID_REGEX` in `US_Util`, eliminating redundant regex definitions.
- Applied `const` correctness and range-based for loops for improved code clarity and maintainability.


  Commit: 401dd595a2ebd258a45c6b6de3a8670368fbff50
      https://github.com/ehb54/ultrascan3/commit/401dd595a2ebd258a45c6b6de3a8670368fbff50
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-26 (Sun, 26 Oct 2025)

  Changed paths:
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp

  Log Message:
  -----------
  Migrate `QGLWidget` to `QOpenGLWidget` for Qt5/Qt6 compatibility

- Replaced `QGLWidget` instances with `QOpenGLWidget` across all affected files to modernize the codebase and ensure compatibility with Qt5 and Qt6.
- Updated `renderPixmap` and `updateGL()` calls to use `grabFramebuffer()` and `update()` respectively for alignment with `QOpenGLWidget` API.
- Adjusted include directives to utilize `QOpenGLFunctions` and `QOpenGLWidget` as needed.
- Refactored constructors to remove deprecated `QGLWidget` parameters, enhancing clarity and maintainability.


  Commit: cdfc55c93b1bfcf85085c81b1008ec8cc5664db5
      https://github.com/ehb54/ultrascan3/commit/cdfc55c93b1bfcf85085c81b1008ec8cc5664db5
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-26 (Sun, 26 Oct 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Modernize Qt library linking and add Qt6 OpenGLWidgets support

- Updated `CMakeLists.txt` to replace `Qt5::` aliases with `Qt::` for library linking.
- Added conditional linking for `Qt::OpenGLWidgets` when `USE_QT6` is enabled.
- Simplified data visualization linking by standardizing to `Qt::DataVisualization`.


  Commit: b0294917db216081128ee6776aa0885343e57fa1
      https://github.com/ehb54/ultrascan3/commit/b0294917db216081128ee6776aa0885343e57fa1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M admin/cmake/FindQwt.cmake

  Log Message:
  -----------
  Modernize `FindQwt.cmake` for dynamic Qt version detection and improved path handling

- Replaced hardcoded Qt version checks with `QT_VERSION_MAJOR` for better flexibility.
- Unified Qwt path suffix definitions to eliminate redundancy.
- Updated Qwt include search logic to enhance maintainability and alignment with current Qt standards.


  Commit: ddfe73b1aa17df2f2421be4328756e27808905c5
      https://github.com/ehb54/ultrascan3/commit/ddfe73b1aa17df2f2421be4328756e27808905c5
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M utils/us_util.h

  Log Message:
  -----------
  Refactor `UUID_REGEX` declaration in `US_Util`

- Moved `UUID_REGEX` from an inline static to a static member for consistency and improved maintainability.


  Commit: 9544a154835325e5c55cd9c951d90b3b563b4b68
      https://github.com/ehb54/ultrascan3/commit/9544a154835325e5c55cd9c951d90b3b563b4b68
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M utils/us_util.cpp

  Log Message:
  -----------
  Add `UUID_REGEX` as a static member in `US_Util`

- Introduced `UUID_REGEX` as a static member for standardized UUID validation.
- Ensures consistency and improves code clarity by centralizing the regular expression definition.


  Commit: be365b4a7833917e7995ff67c206636d31662824
      https://github.com/ehb54/ultrascan3/commit/be365b4a7833917e7995ff67c206636d31662824
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Add conditional handling for `LIBMARIADB` and `LIBMYSQL` SSL options in `US_DB2`

- Introduced checks for `LIBMARIADB` and `LIBMYSQL` to appropriately configure SSL options.
- Ensured `MYSQL_OPT_SSL_VERIFY_SERVER_CERT` is disabled for `LIBMARIADB` and `MYSQL_OPT_SSL_MODE` is set to `SSL_MODE_REQUIRED` for `LIBMYSQL`.
- Improved compatibility and clarity by tailoring SSL behavior based on the library in use.


  Commit: fb1ac1a0cdb0632fb12ea84c6305fc25683502a1
      https://github.com/ehb54/ultrascan3/commit/fb1ac1a0cdb0632fb12ea84c6305fc25683502a1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Add conditional Qt version handling and improve MySQL/MariaDB configuration in CMake

- Introduced `USE_QT6` option to dynamically set `CMAKE_CXX_STANDARD` and related Qt configurations.
- Added `QT_VERSION_MAJOR` and related variables for streamlined Qt version management.
- Enhanced MySQL/MariaDB detection by setting version and module details for improved logging and clarity.
- Updated `googletest` to version `v1.16.0`.


  Commit: f45449d5afe29c6ce2333a490f74d922ca77e56a
      https://github.com/ehb54/ultrascan3/commit/f45449d5afe29c6ce2333a490f74d922ca77e56a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_csv_loader.cpp
    M gui/us_gui_util.cpp
    M gui/us_investigator.cpp
    M gui/us_license.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_mwl_data.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_sassoc.cpp
    M gui/us_sassoc.h
    M gui/us_scan_excl_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.h

  Log Message:
  -----------
  Migrate `QRegExp` to `QRegularExpression` and update deprecated Qt API usage

- Replaced `QRegExp` with `QRegularExpression` across all relevant files for improved performance and modern API compatibility.
- Updated deprecated methods like `setMargin` to `setContentsMargins` and `replace` overloads to use updated syntax.
- Migrated `QGLWidget` to `QOpenGLWidget` for Qt5/Qt6 compatibility.
- Adjusted signals, slots, and method parameters for use with modern Qt data types (`QPointF` replacing `QwtDoublePoint`).
- Removed legacy/deprecated preprocessor macros and redundant Qt4-specific code paths.


  Commit: e0dac0f05cc15e30b37122b5d93220d8ddbd06d6
      https://github.com/ehb54/ultrascan3/commit/e0dac0f05cc15e30b37122b5d93220d8ddbd06d6
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Replace `this` with `parent` in `QMessageBox::critical` calls and update argument handling for clarity and consistency.


  Commit: 229876ffd3dfa190e508942203f782c7ccd3a21c
      https://github.com/ehb54/ultrascan3/commit/229876ffd3dfa190e508942203f782c7ccd3a21c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp

  Log Message:
  -----------
  Replace `QwtDoubleRect` with `QRectF` in `us_show_norm.cpp` for consistency with modern Qt data types.


  Commit: 421adc1b835b9669f6f7be9ff74061f86da49cce
      https://github.com/ehb54/ultrascan3/commit/421adc1b835b9669f6f7be9ff74061f86da49cce
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h

  Log Message:
  -----------
  Replace `setMargin` with `setContentsMargins` and `QwtDoublePoint` with `QPointF` for consistency and modernization of Qt API usage.


  Commit: 2e2a2088ff9f6aa86d3c71efffe1849208b69db0
      https://github.com/ehb54/ultrascan3/commit/2e2a2088ff9f6aa86d3c71efffe1849208b69db0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M programs/main1.inc

  Log Message:
  -----------
  Replace `QRegExp` with `QRegularExpression` in `main1.inc` for modernization and improved Qt API compatibility.


  Commit: 157763286ccf749d9a866acd9608224ab5438fbf
      https://github.com/ehb54/ultrascan3/commit/157763286ccf749d9a866acd9608224ab5438fbf
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  Migrate `QRegExp` to `QRegularExpression` in `us_analysis_profile.cpp` for modernization and updated Qt API compliance.


  Commit: 77d60151680de84d196e426431c20338d7037b75
      https://github.com/ehb54/ultrascan3/commit/77d60151680de84d196e426431c20338d7037b75
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Replace `currentDateTime().toUTC()` with `currentDateTimeUtc()` for improved readability and adherence to modern Qt API usage.


  Commit: e7a18cbf2f5a891d11fb908cf513f60b42d55efd
      https://github.com/ehb54/ultrascan3/commit/e7a18cbf2f5a891d11fb908cf513f60b42d55efd
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M utils/us_util.cpp
    M utils/us_util.h

  Log Message:
  -----------
  - Add `is_valid_uuid` method to validate UUID strings in `US_Util`.


  Commit: 486a15c6851e050314dbf9b610edf75bff9b3b33
      https://github.com/ehb54/ultrascan3/commit/486a15c6851e050314dbf9b610edf75bff9b3b33
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M test/utils/test_us_ana_profile.cpp

  Log Message:
  -----------
  - Add `scan_excl_nth` initialization in `test_us_ana_profile.cpp` for consistency with new profile attributes.


  Commit: 0cd14771ef3d6dd0f08ec30a9a89c7cf8c514488
      https://github.com/ehb54/ultrascan3/commit/0cd14771ef3d6dd0f08ec30a9a89c7cf8c514488
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h

  Log Message:
  -----------
  - Replace `QwtDoubleInterval` with `QwtInterval` and `QwtDoubleRect` with `QRectF` for modernization and alignment with updated Qt data types.
- Add `DbgLv` macro guard in `us_spectrodata.h` for improved debug handling.


  Commit: 50cb408dd7dc30ec665a6b9427e4130a84281578
      https://github.com/ehb54/ultrascan3/commit/50cb408dd7dc30ec665a6b9427e4130a84281578
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp

  Log Message:
  -----------
  - Replace `QwtDoubleInterval` with `QwtInterval` in `us_show_norm.cpp` for modernization and alignment with updated Qt API conventions.


  Commit: 5b11838954d048df7196b7c8e5e0dfe12abc53fc
      https://github.com/ehb54/ultrascan3/commit/5b11838954d048df7196b7c8e5e0dfe12abc53fc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  - Replace `Qt5::DataVisualization` with `Qt::DataVisualization` in `CMakeLists.txt` for compatibility with updated Qt modules.
- Migrate `QRegExp` to `QRegularExpression` in `us_autoflow_analysis.cpp` for modernization and improved Qt API compliance.
- Replace `setTimeSpec` with `setTimeZone` in `us_autoflow_analysis.cpp` to align with updated Qt date/time handling methods.


  Commit: e46a63dcfb8dd94ccad475aedbbc98ad278e9f72
      https://github.com/ehb54/ultrascan3/commit/e46a63dcfb8dd94ccad475aedbbc98ad278e9f72
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h

  Log Message:
  -----------
  - Replace `QwtDoublePoint` with `QPointF` in `us_buoyancy` for consistency with updated Qt API.


  Commit: 8ff50839c50fadd6050274e3c81b116114f8454c
      https://github.com/ehb54/ultrascan3/commit/8ff50839c50fadd6050274e3c81b116114f8454c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_colorgradient/us_colorgradient.cpp

  Log Message:
  -----------
  - Migrate `QRegExp` to `QRegularExpression` in `us_colorgradient.cpp` for modernization and Qt API compliance.
- Add version-specific conditional handling for `pixmap()` method based on Qt 6.6.0+ changes.


  Commit: 938309c9aab5680d097687751e77ba15d86863e5
      https://github.com/ehb54/ultrascan3/commit/938309c9aab5680d097687751e77ba15d86863e5
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt

  Log Message:
  -----------
  - Replace `Qt5::DataVisualization` with `Qt::DataVisualization` in `CMakeLists.txt` for compliance with updated Qt module naming conventions.


  Commit: 578c59683c712c74021c0fc5c8167fc210323b3b
      https://github.com/ehb54/ultrascan3/commit/578c59683c712c74021c0fc5c8167fc210323b3b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h

  Log Message:
  -----------
  - Migrate `qApp->desktop()` to `QGuiApplication::primaryScreen()->availableSize()` for compatibility with updated Qt API.
- Replace `QGLWidget` with `QOpenGLWidget` in `us_vhw_combine` for modern OpenGL rendering.
- Replace `QwtDoublePoint` with `QPointF` in `us_vhw_enhanced` for consistency with updated Qt API.


  Commit: 9fe44e6404df5672fc990058b5e20b4fae28372c
      https://github.com/ehb54/ultrascan3/commit/9fe44e6404df5672fc990058b5e20b4fae28372c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  - Migrate `QRegExp` to `QRegularExpression` across multiple files for modernization and Qt API compliance.
- Replace deprecated `setMargin` with `setContentsMargins` for layout updates.
- Add version-specific handling for Qt 6.7.0+ signal connection changes in `us_grid_editor`.
- Replace `QwtDoubleRect` and `QwtDoubleInterval` with `QRectF` and `QwtInterval` for alignment with updated Qt types.
- Update `qApp->desktop()` to `QGuiApplication::primaryScreen()->availableSize()` for Qt API compatibility.
- Standardize module linking by transitioning `Qt5::DataVisualization` to `Qt::DataVisualization` in `CMakeLists.txt`.
- Improve QMessageBox handling to use modern button enums for consistency.


  Commit: 1ea7d5e3427a6983375833117520b28736d415cf
      https://github.com/ehb54/ultrascan3/commit/1ea7d5e3427a6983375833117520b28736d415cf
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_config/us_color.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.cpp

  Log Message:
  -----------
  - Migrate `QRegExp` to `QRegularExpression` across multiple files for Qt API modernization.
- Replace integer-to-string conversions with `QString::number` for improved readability and consistency.
- Refactor loop structures in `us_color.cpp` to use range-based syntax for clarity and maintainability.


  Commit: 2352815203d49a2c6e25b697186051bfd58c0202
      https://github.com/ehb54/ultrascan3/commit/2352815203d49a2c6e25b697186051bfd58c0202
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_convert/us_convertio.cpp
    M programs/us_convert/us_convertio.h
    M programs/us_convert/us_experiment.cpp
    M programs/us_convert/us_get_run.cpp

  Log Message:
  -----------
  - Migrate `QRegExp` to `QRegularExpression` across multiple files for Qt API modernization and compliance.
- Replace `QwtDoublePoint` with `QPointF` for consistency with updated Qt API.
- Refactor QMessageBox usage to leverage modern button enums for improved readability and consistency.
- Update loop constructs to range-based syntax for better maintainability.
- Replace integer conversions with `QString::number` for enhanced clarity.
- Use `setContentsMargins` instead of deprecated `setMargin` for layout updates.


  Commit: e20a5f10f65643667f1c479c0ffa16f705af3c81
      https://github.com/ehb54/ultrascan3/commit/e20a5f10f65643667f1c479c0ffa16f705af3c81
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h

  Log Message:
  -----------
  - Replace `QwtDoublePoint` with `QPointF` across `us_edit` and `us_edit_scan` for consistency with updated Qt API.
- Migrate `QRegExp` to `QRegularExpression` for modernization and compliance with Qt's updated regex handling.
- Refactor `QMessageBox` usage to use modern button enums for improved readability and maintainability.


  Commit: a9172152f71a9fc276c84b8bfc589d260bc54812
      https://github.com/ehb54/ultrascan3/commit/a9172152f71a9fc276c84b8bfc589d260bc54812
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  - Migrate `QRegExp` to `QRegularExpression` across `us_exp_utils.cpp`, `us_experiment_gui_optima.cpp`, and `us_proto_ranges.cpp` for Qt API modernization and compliance.
- Replace `count()` with `length()` for improved string handling consistency.
- Remove conditional macros for Qt versions under 5 in `us_proto_ranges.cpp`.


  Commit: 39de1a6bf7e20096e8453b36ae974f65e5099375
      https://github.com/ehb54/ultrascan3/commit/39de1a6bf7e20096e8453b36ae974f65e5099375
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h

  Log Message:
  -----------
  - Replace `QGLWidget` with `QOpenGLWidget` in `us_fematch` for modern OpenGL support.
- Migrate `qApp->desktop()` to `QGuiApplication::primaryScreen()->availableSize()` for Qt API compliance.
- Adjust `horizontalAdvance` calculation for proper width computation in `us_fematch.cpp`.
- Update `CMakeLists.txt` to transition from `Qt5::DataVisualization` to `Qt::DataVisualization` for module naming consistency.


  Commit: a414b3d9e1c1a3ecf6e7faa40a690d6b5374ddc0
      https://github.com/ehb54/ultrascan3/commit/a414b3d9e1c1a3ecf6e7faa40a690d6b5374ddc0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h

  Log Message:
  -----------
  - Replace `QwtDoublePoint` with `QPointF` in `us_fit_meniscus` for consistency with updated Qt API.
- Migrate `QRegExp` to `QRegularExpression` in `us_fit_meniscus` for Qt API modernization.
- Update `setTimeSpec` to `setTimeZone` for handling `QDateTime` in `us_fit_meniscus`.
- Replace `QwtDoubleRect` with `QRectF` for alignment with updated Qt types.


  Commit: e696115e11b8585e8722c70ba49b540569cc45ef
      https://github.com/ehb54/ultrascan3/commit/e696115e11b8585e8722c70ba49b540569cc45ef
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h

  Log Message:
  -----------
  Replace `QwtDoublePoint` and `QwtDoubleRect` with `QPointF` and `QRectF` in `us_ga_init` for compliance with updated Qt API.


  Commit: 467a3504c416ef04f3fe56a07b2f38c5a999893e
      https://github.com/ehb54/ultrascan3/commit/467a3504c416ef04f3fe56a07b2f38c5a999893e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h

  Log Message:
  -----------
  - Replace `QwtDoublePoint` with `QPointF` in `us_globalequil` for Qt API compliance
- Refactor `QMessageBox` buttons to use modern enums for clarity and maintainability


  Commit: e9cdd9c03780d1d88ba0125f3ff8e2912d73ec2b
      https://github.com/ehb54/ultrascan3/commit/e9cdd9c03780d1d88ba0125f3ff8e2912d73ec2b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp

  Log Message:
  -----------
  - Migrate `QRegExp` to `QRegularExpression` across `us_mwl_species_fit.cpp` and `us_mwl_sf_plot3d.cpp` for Qt API modernization.
- Replace deprecated `setMargin` with `setContentsMargins` in `us_mwl_sf_plot3d.cpp` for layout updates.
- Standardize module linking in `CMakeLists.txt` by updating `Qt5::DataVisualization` to `Qt::DataVisualization`.
- Add version-specific conditional handling for `QtDataVisualization` to support multiple Qt versions in `us_mwl_sf_plot3d.h`.


  Commit: 2b9bdd7fa0b19e1e8c7dfea72320583edb4e2695
      https://github.com/ehb54/ultrascan3/commit/2b9bdd7fa0b19e1e8c7dfea72320583edb4e2695
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h

  Log Message:
  -----------
  - Replace `QGLWidget` with `QOpenGLWidget` in `us_mwl_spectra` for modern OpenGL support.
- Migrate `QRegExp` to `QRegularExpression` for Qt API modernization.
- Update `qApp->desktop()` to `QGuiApplication::primaryScreen()->availableSize()` for Qt API compliance.
- Refactor `QMessageBox` button usage to modern enums for clarity and maintainability.


  Commit: 809561f9e4d2d107c406d1941d854e3185ca5b9d
      https://github.com/ehb54/ultrascan3/commit/809561f9e4d2d107c406d1941d854e3185ca5b9d
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp

  Log Message:
  -----------
  - Replace `QGLWidget` with `QOpenGLWidget` in `us_mwl_pltctrl` for modern OpenGL support.
- Update `qApp->desktop()` to `QGuiApplication::primaryScreen()->availableSize()` for Qt API compliance.
- Refactor `QMessageBox` buttons to use modern enums for clarity and maintainability.
- Migrate `QRegExp` to `QRegularExpression` in `us_mwlr_viewer` for modernization and alignment with updated Qt API.


  Commit: 50a03c41966f5de28d8e55857c4d3fba43d0eede
      https://github.com/ehb54/ultrascan3/commit/50a03c41966f5de28d8e55857c4d3fba43d0eede
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h

  Log Message:
  -----------
  - Replace `QwtDoubleInterval` with `QwtInterval` for Qt API consistency in `us_mlplot` and `us_rpscan`.
- Migrate `QRegExp` to `QRegularExpression` in `us_mrecs_loader` for API modernization.
- Replace `QwtDoublePoint` with `QPointF` for compliance with updated Qt API in `us_rpscan`.


  Commit: a7974fd35b02afb8c43d4ca3e7fe4c1470a15825
      https://github.com/ehb54/ultrascan3/commit/a7974fd35b02afb8c43d4ca3e7fe4c1470a15825
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h

  Log Message:
  -----------
  - Replace `QRegExp` with `QRegularExpression` across multiple modules for Qt API modernization.
- Replace `QwtDoublePoint` with `QPointF` for compliance with updated Qt API.
- Replace deprecated `setMargin` with `setContentsMargins` for layout updates.
- Add version-specific conditional handling for checkbox state changes to support multiple Qt versions in `us_convert_scan` and `us_add_refScan`.
- Optimize pointer usage in value assignments with `auto` for cleaner code.


  Commit: 5652e0f953bea1e8842e501916ad4a957694aced
      https://github.com/ehb54/ultrascan3/commit/5652e0f953bea1e8842e501916ad4a957694aced
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp

  Log Message:
  -----------
  - Replace deprecated `setMargin` with `setContentsMargins` for layout updates in `us_query_rmsd`.
- Update `CMakeLists.txt` to use `Qt::DataVisualization` for module naming consistency.


  Commit: ae2b63a2218bbfb633e19fbfe81e4beea25d0607
      https://github.com/ehb54/ultrascan3/commit/ae2b63a2218bbfb633e19fbfe81e4beea25d0607
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h

  Log Message:
  -----------
  - Replace `QRegExp` with `QRegularExpression` across multiple files for API modernization.
- Refactor `QMessageBox` button handling to use modern enums for improved clarity and maintainability.
- Replace `QwtDoublePoint` with `QPointF` for compliance with updated Qt API.
- Fix incorrect type conversion using `QString::number` for better error message formatting.


  Commit: 57da4043dd7ac8b393ff14dfdbe9aa3f2f54d222
      https://github.com/ehb54/ultrascan3/commit/57da4043dd7ac8b393ff14dfdbe9aa3f2f54d222
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  - Replace `QRegExp` with `QRegularExpression` for API modernization.
- Update `QString` concatenation with `QString(".")` for consistency.
- Replace `QGLWidget` with `QOpenGLWidget` for modern OpenGL support.
- Update CMakeLists.txt to use `Qt::DataVisualization` for module name consistency.


  Commit: ba1ba9b93065e10cbb86caccc6381e1186e4554b
      https://github.com/ehb54/ultrascan3/commit/ba1ba9b93065e10cbb86caccc6381e1186e4554b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h

  Log Message:
  -----------
  Replace `QwtDoubleRect` with `QRectF` for compliance with updated Qt API in `us_rotor_calibration`.


  Commit: effe6ce3d4d0ef92adeb5f59be87f02d0faa2c14
      https://github.com/ehb54/ultrascan3/commit/effe6ce3d4d0ef92adeb5f59be87f02d0faa2c14
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  - Replace `QwtDoublePoint` with `QPointF` in `us_spectrum` for Qt API compliance.
- Refactor `QMessageBox` button handling to use modern enums for improved clarity.
- Optimize `std::minmax_element` assignments using `auto` for cleaner code.
- Use `qRound` for type consistency in wavelength bounds.
- Replace `<math.h>` with `<cmath>` for modern header usage.


  Commit: 64d8413714c3108f937e8b76b1a8ba3f16c38a4d
      https://github.com/ehb54/ultrascan3/commit/64d8413714c3108f937e8b76b1a8ba3f16c38a4d
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  - Fix incorrect `QMessageBox` button status logic in `us_edit`.


  Commit: deb377ae673f2e29f7a776716672ba7550739a87
      https://github.com/ehb54/ultrascan3/commit/deb377ae673f2e29f7a776716672ba7550739a87
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-02 (Sun, 02 Nov 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  - Add version-specific conditional handling for `setPenWidth` to support multiple Qt versions in `us_xpn_viewer`.


  Commit: fe96d5575a8f88b29c935c3e8c6c33468859f2cf
      https://github.com/ehb54/ultrascan3/commit/fe96d5575a8f88b29c935c3e8c6c33468859f2cf
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project_academic/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    M programs/us_config/us_color.cpp
    A programs/us_convert/CMakeLists.txt
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    A programs/us_pcsa/CMakeLists.txt
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_vhw_combine.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt
    M utils/us_defines.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 4d8935a878d0e3a7a55933b8f1ac3b616f8daf6b
      https://github.com/ehb54/ultrascan3/commit/4d8935a878d0e3a7a55933b8f1ac3b616f8daf6b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp

  Log Message:
  -----------
  - Remove redundant `#endif` directive in `us_show_norm` for improved code cleanliness.


  Commit: 8d6d6c8b7f040da86cab0c2fde8c858b808a8005
      https://github.com/ehb54/ultrascan3/commit/8d6d6c8b7f040da86cab0c2fde8c858b808a8005
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt to use `Qt` namespace for module consistency

- Replace `Qt5::` with `Qt::` in `us3_resources` linking.
- Modify `utils` linking to use `Qt::` for core modules (`Core`, `Xml`, `Network`, `Sql`).


  Commit: 21062f87c59071f5d7763db68f6ee141ccb2bf99
      https://github.com/ehb54/ultrascan3/commit/21062f87c59071f5d7763db68f6ee141ccb2bf99
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Replace `QRegularExpression` with `QStringLiteral` for improved string handling in `us_plot`.


  Commit: c92f56e6242bb4cf31fca9bcaf196c7edfb01846
      https://github.com/ehb54/ultrascan3/commit/c92f56e6242bb4cf31fca9bcaf196c7edfb01846
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp

  Log Message:
  -----------
  Refactor `us_analyte_gui` conditional checks for `isEmpty()` usage

- Replace `size() != 0` with `!isEmpty()` for `seqsmry`.
- Replace `size() == 0` with `isEmpty()` for `descriptions`.


  Commit: 8d796a2e98334176781d581da498b11e1b5f91a4
      https://github.com/ehb54/ultrascan3/commit/8d796a2e98334176781d581da498b11e1b5f91a4
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M gui/us_model_loader.cpp

  Log Message:
  -----------
  Properly convert unix wildcard to regex.


  Commit: 4a82e64bee4952023e898053ce4ad6b68b565b8b
      https://github.com/ehb54/ultrascan3/commit/4a82e64bee4952023e898053ce4ad6b68b565b8b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M gui/us_spectrodata.cpp

  Log Message:
  -----------
  Remove unused `setInterval` calls from `us_spectrodata` for code cleanup.


  Commit: d4094016318557f26afe81290047fe20bdc9a07a
      https://github.com/ehb54/ultrascan3/commit/d4094016318557f26afe81290047fe20bdc9a07a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Update `QRegularExpression` pattern in `us_autoflow_analysis`

- Replace wildcard-to-regex conversion with explicit regex for model descriptions.


  Commit: e1c24e44caea4e7c5e14a3e0a3dffbb464c89871
      https://github.com/ehb54/ultrascan3/commit/e1c24e44caea4e7c5e14a3e0a3dffbb464c89871
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Enable static libs preference and testing in CMake

- Set `US3_PREFER_STATIC` default to ON.
- Introduce `BUILD_TESTING` option, defaulted to ON.
- Replace `US3_BUILD_TESTS` with `BUILD_TESTING` for consistency in testing configurations.


  Commit: 1582fd4d72e144c840fd83c29710ddcca650cfea
      https://github.com/ehb54/ultrascan3/commit/1582fd4d72e144c840fd83c29710ddcca650cfea
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Disable `BUILD_TESTING` by default in CMake configuration


  Commit: d97b94cfc728b74cdc4d22f4294fba7444bd03fd
      https://github.com/ehb54/ultrascan3/commit/d97b94cfc728b74cdc4d22f4294fba7444bd03fd
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_experiment.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_datafiles.cpp
    M utils/us_report.h

  Log Message:
  -----------
  Refactor and optimize code for improved readability and functionality

- Simplify `QFileInfo` instantiation in `us_mwl_species_fit`.
- Optimize `QString::number` usage with `rightJustified` in `us_datafiles`.
- Update regex patterns in `us_fit_meniscus` and `us_autoflow_analysis` to improve readability and functionality.
- Use `QTimeZone::utc()` instead of string-based UTC for consistency in multiple files.
- Mark `QRegularExpression` instances as `static` for efficiency in `us_xpn_viewer`.
- Refactor `QRegularExpression` matching logic to use `QString::indexOf` for improved clarity and performance.
- Adjust spacing and alignment in headers for consistent formatting.


  Commit: 25c3b692febb46e387afcec3bd534dcbebe88222
      https://github.com/ehb54/ultrascan3/commit/25c3b692febb46e387afcec3bd534dcbebe88222
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

  Changed paths:
    M gui.pri
    M gui/libus_gui.pro
    M qwtplot3d/qwtplot3d.pro

  Log Message:
  -----------
  Add `openglwidgets` to project dependencies

- Include `openglwidgets` in `qwtplot3d.pro` to enhance OpenGL functionality.
- Add `openglwidgets` to `gui.pri` for GUI consistency.
- Update `libus_gui.pro` with `openglwidgets` for improved feature support.


  Commit: fbd81603bae2e97d470b843b3572f7146ca3f896
      https://github.com/ehb54/ultrascan3/commit/fbd81603bae2e97d470b843b3572f7146ca3f896
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Fix logic error in `us_convert_gui` runID validation

- Correct `QRegularExpression` match condition by adding negation to properly validate `runID`.


  Commit: 429e64f9ebb3a40388adb92d281281e9cf91c572
      https://github.com/ehb54/ultrascan3/commit/429e64f9ebb3a40388adb92d281281e9cf91c572
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

  Changed paths:
    M qwtplot3d/src/qwt3d_label.cpp

  Log Message:
  -----------
  Update QT version check in `qwt3d_label.cpp`

- Modify QT version comparison logic to use `QT_VERSION_CHECK` for improved readability and maintainability.


  Commit: 5357385a614755a654c3bd5aaf8e001b508a7849
      https://github.com/ehb54/ultrascan3/commit/5357385a614755a654c3bd5aaf8e001b508a7849
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

  Changed paths:
    M gui.pri
    M gui/libus_gui.pro
    M qwtplot3d/qwtplot3d.pro

  Log Message:
  -----------
  Add conditional `openglwidgets` inclusion based on Qt version

- Update `qwtplot3d.pro` to include `openglwidgets` only for Qt versions greater than 5.99.
- Adjust `gui.pri` to conditionally add `openglwidgets` for improved flexibility with Qt versions.
- Modify `libus_gui.pro` to include `openglwidgets` dependency based on the Qt version.


  Commit: c96c66f46ba9f308354280592e406997830bdcd3
      https://github.com/ehb54/ultrascan3/commit/c96c66f46ba9f308354280592e406997830bdcd3
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-10 (Mon, 10 Nov 2025)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Update version check for qmake in makeall.sh


  Commit: 61217222a10d435ddf1cd4ad032ba4e6bd865c52
      https://github.com/ehb54/ultrascan3/commit/61217222a10d435ddf1cd4ad032ba4e6bd865c52
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-10 (Mon, 10 Nov 2025)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Merge pull request #307 from ehb54/ehb54-patch-4

Update version check for qmake in makeall.sh


  Commit: 910f23c2f12c7bfa2cff364725d6e6b07dc3735f
      https://github.com/ehb54/ultrascan3/commit/910f23c2f12c7bfa2cff364725d6e6b07dc3735f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-12 (Wed, 12 Nov 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Fix size of returned QByteArray for US_DB2::mysqlEscapeString

Refactor mysqlEscapeString to use constData for input and adjust resizing logic.


  Commit: 0587da27d11a47a031a2345ea944e5b52923bd00
      https://github.com/ehb54/ultrascan3/commit/0587da27d11a47a031a2345ea944e5b52923bd00
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-13 (Thu, 13 Nov 2025)

  Changed paths:
    M gui/us_gui_util.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h

  Log Message:
  -----------
  Refactor `US_SpectrogramData` and update raster handling

- Rename `initRaster` to `getRaster` and update method signature to be `const`. This helps to avoid confusion with the QwtRasterData::initRaster, which has different functionality.
- Add conditional `setInterval` calls for compatibility with older `Qwt` versions.
- Adjust `value` method to use `const` arguments and override specifier.
- Refactor `boundingRect` to remove unnecessary `#if` conditions.
- Update references to renamed `getRaster` method in related files.


  Commit: 49e82b3ef6a8a4567a4da2dd86bd2ea24263c28d
      https://github.com/ehb54/ultrascan3/commit/49e82b3ef6a8a4567a4da2dd86bd2ea24263c28d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-13 (Thu, 13 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h

  Log Message:
  -----------
  [Qt5/Qt6]GMP : 5. ANALYSIS -- fix 'Show oerlay' & 'Delete' buttons behavior in Qt6 builds...


  Commit: 39a4c51ee0332b7bc85d5ad3215f311df748b287
      https://github.com/ehb54/ultrascan3/commit/39a4c51ee0332b7bc85d5ad3215f311df748b287
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h

  Log Message:
  -----------
  Refactor signal mapping logic in `us_autoflow_analysis` and `us_analysis_profile`

- Replace `QSignalMapper` usage with lambda-based connections for better readability and modern Qt practices.
- Remove obsolete `QSignalMapper` declarations and related code in headers for cleanup.


  Commit: 57bf3bd1f029bc588861ddbc4b027a9227ba29ef
      https://github.com/ehb54/ultrascan3/commit/57bf3bd1f029bc588861ddbc4b027a9227ba29ef
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-15 (Sat, 15 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 9717b5a3c53ea980931ab8abd9723d89c4678375
      https://github.com/ehb54/ultrascan3/commit/9717b5a3c53ea980931ab8abd9723d89c4678375
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Replace leftRef with left


  Commit: 7ac7f3643ac686e016a4c0bda79f188aefc06933
      https://github.com/ehb54/ultrascan3/commit/7ac7f3643ac686e016a4c0bda79f188aefc06933
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M utils/us_db2.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Update `value` method to return default `QVariant`

- Replace `QVariant::Invalid` with default `QVariant()` in `US_DB2::value` method to align with modern QVariant usage.
- Update method documentation in `us_db2.h` to reflect the change.


  Commit: 6334d8a547ec98d53ccca0926c511a7554263428
      https://github.com/ehb54/ultrascan3/commit/6334d8a547ec98d53ccca0926c511a7554263428
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Uncomment `column_indexes` calls in `us_xpn_data.cpp` to enable proper column index retrieval logic.


  Commit: 72306fcec7a1e4c91c96c06a871d7f0478ac8964
      https://github.com/ehb54/ultrascan3/commit/72306fcec7a1e4c91c96c06a871d7f0478ac8964
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  GMP : 2.LIVE_UPDATE -- check for positiveness of the vacuum value before updatign GUI...


  Commit: 9d2cd0b12aa0e908db8596ec4688818c8a8b669e
      https://github.com/ehb54/ultrascan3/commit/9d2cd0b12aa0e908db8596ec4688818c8a8b669e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #318 from ehb54/main

Update lukas/qt6-compile with main


  Commit: 1687a57993f87b8937fdcf06045e10225b504ca6
      https://github.com/ehb54/ultrascan3/commit/1687a57993f87b8937fdcf06045e10225b504ca6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  CodeQl action: Add qt6 containers for gui and mpi

Updated branches for pull requests and enabled additional Qt6 containers.


  Commit: 06815f05ab2f337ae26ce8382ddaf80069e0e931
      https://github.com/ehb54/ultrascan3/commit/06815f05ab2f337ae26ce8382ddaf80069e0e931
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M CMakeLists.txt
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    M gui/libus_gui.pro
    M gui/us_combined_plots_parms_gui.cpp
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: c7cd4ad5a59edf9e177e82908100cf3fe0247d5c
      https://github.com/ehb54/ultrascan3/commit/c7cd4ad5a59edf9e177e82908100cf3fe0247d5c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-03 (Wed, 03 Dec 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_experiment.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 3e70e06b8a38cdc3ce1ed864e58449d0b843b23e
      https://github.com/ehb54/ultrascan3/commit/3e70e06b8a38cdc3ce1ed864e58449d0b843b23e
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-04 (Thu, 04 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_experiment.cpp
    M utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: eacada70d7c465b727dd7db3997339c6bd9bf1f5
      https://github.com/ehb54/ultrascan3/commit/eacada70d7c465b727dd7db3997339c6bd9bf1f5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: c90cc6690c06b1be85cf82126319a190c30d6505
      https://github.com/ehb54/ultrascan3/commit/c90cc6690c06b1be85cf82126319a190c30d6505
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-10 (Wed, 10 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    M vcpkg.json

  Log Message:
  -----------
  Enhance CMake configuration for Qt5 and Qt6 support, update vcpkg dependencies, and remove obsolete Qwt port files


  Commit: 560d7338f7f1ce606716df47c6d22e66427dc74b
      https://github.com/ehb54/ultrascan3/commit/560d7338f7f1ce606716df47c6d22e66427dc74b
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json

  Log Message:
  -----------
  Add overlay ports for `qwtplot3d` with support for `qwt-6-3-0-qt5` and `qwt-6-3-0-qt6` dependencies


  Commit: e4b7267d108684864f940f5d9f7c82d6ce506dcf
      https://github.com/ehb54/ultrascan3/commit/e4b7267d108684864f940f5d9f7c82d6ce506dcf
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json

  Log Message:
  -----------
  Add overlay port for `qwt-6-3-0-qt5` with vcpkg configuration and patches


  Commit: fc1bfc04d0d7d5c090981678b554ca62175aa77b
      https://github.com/ehb54/ultrascan3/commit/fc1bfc04d0d7d5c090981678b554ca62175aa77b
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json

  Log Message:
  -----------
  Add overlay port for `qt5-multimedia` with vcpkg configuration and patches


  Commit: b83a3e819e759f5ad754a562142575e7105c00ed
      https://github.com/ehb54/ultrascan3/commit/b83a3e819e759f5ad754a562142575e7105c00ed
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt

  Log Message:
  -----------
  Remove redundant `find_package(Qt5)` calls in `CMakeLists.txt` across multiple programs.


  Commit: 84cbc6c9c0d0d6d9564567e1fce4b84ae3e4cdd1
      https://github.com/ehb54/ultrascan3/commit/84cbc6c9c0d0d6d9564567e1fce4b84ae3e4cdd1
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Add conditional check for `Qt::Test` target alias creation in `CMakeLists.txt`


  Commit: 7485285209c8c4fbb5e9311a6765cf10f58d76c0
      https://github.com/ehb54/ultrascan3/commit/7485285209c8c4fbb5e9311a6765cf10f58d76c0
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M CMakePresets.json
    M vcpkg.json

  Log Message:
  -----------
  Add support for Qwt 6.1.6 and 6.3.0 configurations with updated vcpkg features and CMake presets

- Enhance `vcpkg.json` with new features for Qwt 6.1.6 and 6.3.0.
- Update `CMakePresets.json` to include custom presets for different Qwt versions across platforms.
- Refactor preset definitions for improved clarity and platform specificity.


  Commit: 05fcfe57f6acbc11cc86599a4c6cd79df932904e
      https://github.com/ehb54/ultrascan3/commit/05fcfe57f6acbc11cc86599a4c6cd79df932904e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M CMakePresets.json

  Log Message:
  -----------
  Add new `base-qt5-qwt616` preset and refactor Qt5 Qwt6.1.6 platform-specific presets to inherit from it


  Commit: b6d77d788c73d678ed8809aef7927dde929b92a3
      https://github.com/ehb54/ultrascan3/commit/b6d77d788c73d678ed8809aef7927dde929b92a3
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json

  Log Message:
  -----------
  Simplify `vcpkg.json` dependencies for `qwt-6-3-0-qt5` by consolidating `qt5-base` features


  Commit: 279b0ac8ed33b11b36efd374afe030708a44c890
      https://github.com/ehb54/ultrascan3/commit/279b0ac8ed33b11b36efd374afe030708a44c890
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake

  Log Message:
  -----------
  Update `qwt-6-3-0-qt5` overlay port: add Qt5 configuration handling and Qwt version file generation.


  Commit: e7f44af75262b12412c8808ae922b043a0e320a7
      https://github.com/ehb54/ultrascan3/commit/e7f44af75262b12412c8808ae922b043a0e320a7
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    M buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    M buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json

  Log Message:
  -----------
  Update `qwtplot3d-qwt-6-3-0-qt6` overlay port: migrate from Qt5 to Qt6 dependencies and configuration


  Commit: 52fd18139fe6586687ec67848b932163ac7cd15c
      https://github.com/ehb54/ultrascan3/commit/52fd18139fe6586687ec67848b932163ac7cd15c
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json

  Log Message:
  -----------
  Add new `qwt-6-3-0-qt6` overlay port with Qt6 dependencies, patches, and vcpkg configuration files.


  Commit: ef4652ce8e31076480754ee2ff0a89ff6c6b53c9
      https://github.com/ehb54/ultrascan3/commit/ef4652ce8e31076480754ee2ff0a89ff6c6b53c9
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M CMakePresets.json
    M vcpkg.json

  Log Message:
  -----------
  Update `vcpkg.json` and `CMakePresets.json` to switch `qwt` dependency to `qwt-6-3-0-qt6` and enable `USE_QT6` environment variable


  Commit: adaa5f90545392fdf74a3f76281146b1f49ea877
      https://github.com/ehb54/ultrascan3/commit/adaa5f90545392fdf74a3f76281146b1f49ea877
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M programs/us_fit_meniscus/CMakeLists.txt

  Log Message:
  -----------
  Remove redundant `us_gui_static` dependency from `us_fit_meniscus` CMakeLists as already included in us_program_common


  Commit: 28970f647dfa973602f796e7db4dba84cfd53485
      https://github.com/ehb54/ultrascan3/commit/28970f647dfa973602f796e7db4dba84cfd53485
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json

  Log Message:
  -----------
  Add `qt5-tools` overlay port with vcpkg configuration, patches, and build options for `qdoc` and `libclang`.


  Commit: 51f4446a7d6c46e6e5bc231625d0f3598c64e0e8
      https://github.com/ehb54/ultrascan3/commit/51f4446a7d6c46e6e5bc231625d0f3598c64e0e8
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake

  Log Message:
  -----------
  Comment out `REMOVE_RECURSE` directive for debug include files in `qwt-6-1-6` overlay port.


  Commit: 824917fd842361f25a320716b60f4d663c40d36f
      https://github.com/ehb54/ultrascan3/commit/824917fd842361f25a320716b60f4d663c40d36f
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.h
    M gui/us_csv_loader.h
    M gui/us_experiment_gui.h
    M gui/us_get_run.h
    M gui/us_intensity.h
    M gui/us_select_triples.h
    M gui/us_selectbox.h

  Log Message:
  -----------
  Mark GUI classes with `US_GUI_EXTERN` for consistent symbol export.


  Commit: fa485869e37155a7a3bd6abc2d8b62d3290b94e3
      https://github.com/ehb54/ultrascan3/commit/fa485869e37155a7a3bd6abc2d8b62d3290b94e3
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Add GLU library linkage for Windows in GUI CMake configuration


  Commit: 7e1b604be12be95c4434659ce535bf7ec2f2b1f5
      https://github.com/ehb54/ultrascan3/commit/7e1b604be12be95c4434659ce535bf7ec2f2b1f5
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Refactor `us_program_common` GUI linkage logic in CMake for better TARGET handling
Prevent linking against static and dynamic us_gui library at the same time


  Commit: f09d400fba032d067a391cdb44bc8b24adfc62cd
      https://github.com/ehb54/ultrascan3/commit/f09d400fba032d067a391cdb44bc8b24adfc62cd
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M utils/us_convert.h
    M utils/us_convertio.h
    M utils/us_experiment.h

  Log Message:
  -----------
  Mark utility classes with `US_UTIL_EXTERN` for consistent symbol export.


  Commit: d3e888e267c9caf78859338a6f1cf719327ad232
      https://github.com/ehb54/ultrascan3/commit/d3e888e267c9caf78859338a6f1cf719327ad232
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: df86df9039cb75f8b70c9f3cb92badd78dd35e1b
      https://github.com/ehb54/ultrascan3/commit/df86df9039cb75f8b70c9f3cb92badd78dd35e1b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Refactor `us_program_common` CMake linkage for UltraScan3::Resources. Prevent compiler from dropping resources
- Add support for `WHOLE_ARCHIVE` linking with CMake 3.24+
- Implement fallbacks for older CMake versions, including MSVC, Apple, and GNU toolchains.


  Commit: dce480bd9c76222754a2255a237d20ac5c3f261e
      https://github.com/ehb54/ultrascan3/commit/dce480bd9c76222754a2255a237d20ac5c3f261e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  - Add `us_utils` dependency to GUI CMake configuration
- Update `target_link_libraries` for consistent usage of `UltraScan3::Utils`


  Commit: 0c53e87884daba86bbf95aa2933e8b49c0d5a6ec
      https://github.com/ehb54/ultrascan3/commit/0c53e87884daba86bbf95aa2933e8b49c0d5a6ec
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M gui/us_images.cpp
    M gui/us_images.h

  Log Message:
  -----------
  Prevent unavailable images, in case the compiler dropped the resources by dynamically loading the image resource once(mutex protected)
- Add `ensure_us3_gui_images_resources` to initialize resources in `US_Images`
- Update image methods to ensure resources are loaded before use


  Commit: bffcbf60b9a2fc282367921d2a94834e17e20bd0
      https://github.com/ehb54/ultrascan3/commit/bffcbf60b9a2fc282367921d2a94834e17e20bd0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  Update symbol visibility macros for consistent exports for non windows builds to prevent visibility issues.

- Add `__attribute__((visibility("default")))` for GCC/Clang support in `US_EXPORT` and `US_IMPORT`.
- Update `US_UTIL_EXTERN` and `US_GUI_EXTERN` to utilize `US_EXPORT` for consistency.


  Commit: d9f790e9a362a42951e9673084733e3e75a7447a
      https://github.com/ehb54/ultrascan3/commit/d9f790e9a362a42951e9673084733e3e75a7447a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  - Safeguard against missing splash image by enforcing minimum dimensions.
- Refactor splash screen rendering to use `QImage` for modern, flexible painting.
- Ensure graceful handling when the splash image resource is unavailable.


  Commit: 11a7a7c669bebe3a734cbf8dbd09b73332f55e39
      https://github.com/ehb54/ultrascan3/commit/11a7a7c669bebe3a734cbf8dbd09b73332f55e39
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake

  Log Message:
  -----------
  Clean up unused compiler flags in qt5-tools portfile.


  Commit: 446270b10005ff9807a4bfc2ec2c3e4efde6ad18
      https://github.com/ehb54/ultrascan3/commit/446270b10005ff9807a4bfc2ec2c3e4efde6ad18
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    A admin/cmake/triplets/x64-mingw-dynamic.cmake

  Log Message:
  -----------
  Add x64 MinGW dynamic triplet configuration for Vcpkg


  Commit: 6b0a884bca62b0406762f7868cbe06fc14cff07f
      https://github.com/ehb54/ultrascan3/commit/6b0a884bca62b0406762f7868cbe06fc14cff07f
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_minimize.cpp
    M gui/us_new_spectrum.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M utils/us_analyte.cpp
    M utils/us_archive.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.cpp
    M utils/us_extern.h
    M utils/us_gzip.cpp
    M utils/us_matrix.cpp
    M utils/us_solution.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  - Replace `and`/`or` with standard logical operators `&&`/`||` for consistency and clarity.
- Modernize usage of `QVector` for thread management and dynamic arrays.
- Introduce portability enhancements for platform-specific file operations (`us_open`, `_unlink`, etc.).
- Add missing header guards for floating-point limits (`FLT_MIN`/`FLT_MAX`).
- Standardize debug error outputs with severity levels.


  Commit: b45e442ac95cf354da0c836fb3a70941b58de387
      https://github.com/ehb54/ultrascan3/commit/b45e442ac95cf354da0c836fb3a70941b58de387
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  - Modernize and standardize CMake configuration
  - Add custom Vcpkg triplets and overlay ports for dynamic builds.
  - Refactor compiler flags and definitions for platform-specific optimizations.
  - Improve handling of debug options and static/dynamic library configurations.
  - Enhance Qwt library detection with support for both manual and unofficial configurations.
  - Introduce platform-specific linking and compile options for portability improvements.


  Commit: f1abbfab8dc3387d589172ab2defbf2d4349605e
      https://github.com/ehb54/ultrascan3/commit/f1abbfab8dc3387d589172ab2defbf2d4349605e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Toggle default library preference to shared in CMake configuration (`US3_PREFER_STATIC` set to OFF).


  Commit: 1d6b2a17ebace2b32b7a84a8656e3f43c9efa8b4
      https://github.com/ehb54/ultrascan3/commit/1d6b2a17ebace2b32b7a84a8656e3f43c9efa8b4
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  mod: revision script to use git commit date and time


  Commit: df7167edd6a9b16ffefe2e44baa1c668c1d55308
      https://github.com/ehb54/ultrascan3/commit/df7167edd6a9b16ffefe2e44baa1c668c1d55308
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into 670-bug-us_revisionh-dependency-issue


  Commit: 463a20612262393b49dd4ca80148e0c0fcbeb108
      https://github.com/ehb54/ultrascan3/commit/463a20612262393b49dd4ca80148e0c0fcbeb108
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M programs/us/revision.sh
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: cmake update to use git commit date and time


  Commit: 89f3f3c6557b041b72007f43decf13f661ceae2e
      https://github.com/ehb54/ultrascan3/commit/89f3f3c6557b041b72007f43decf13f661ceae2e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: filename reverted


  Commit: fa23140e88f25ada59996ff8f6496603dd6007ff
      https://github.com/ehb54/ultrascan3/commit/fa23140e88f25ada59996ff8f6496603dd6007ff
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 6d0e037362d1d3eee6b34d6c87fecb03ed56bc35
      https://github.com/ehb54/ultrascan3/commit/6d0e037362d1d3eee6b34d6c87fecb03ed56bc35
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M admin/cmake/GenerateVersion.cmake
    M programs/us/revision.sh

  Log Message:
  -----------
  fix: only show delta on tracked file changes


  Commit: 8cd2500e840339baf525a08fb150964ec3355fc0
      https://github.com/ehb54/ultrascan3/commit/8cd2500e840339baf525a08fb150964ec3355fc0
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: check tracked file changes


  Commit: 107cb20eb507bf616842dd36d780663f6d20549a
      https://github.com/ehb54/ultrascan3/commit/107cb20eb507bf616842dd36d780663f6d20549a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: remove build term from splash


  Commit: 040225ce1b554cde2af83441f8507e05ef14962b
      https://github.com/ehb54/ultrascan3/commit/040225ce1b554cde2af83441f8507e05ef14962b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M admin/cmake/GenerateVersion.cmake
    M programs/us/revision.sh

  Log Message:
  -----------
  fix: time was not in utc


  Commit: ef6f3bd3f96408decfe78facbf37acadc5834997
      https://github.com/ehb54/ultrascan3/commit/ef6f3bd3f96408decfe78facbf37acadc5834997
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png

  Log Message:
  -----------
  mod: icons remove border


  Commit: b18cfde249b29b29b8733d537141a5ff3524407f
      https://github.com/ehb54/ultrascan3/commit/b18cfde249b29b29b8733d537141a5ff3524407f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: update about info


  Commit: df5ad6ee3ef0ca36aa3672b571d5cccea0856c20
      https://github.com/ehb54/ultrascan3/commit/df5ad6ee3ef0ca36aa3672b571d5cccea0856c20
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

  Changed paths:
    M gui/CMakeLists.txt
    M gui/fix-mac-make.sh
    R gui/images.qrc
    M gui/libus_gui.pro
    M gui/qrc_make_adds.txt
    M gui/us_images.cpp

  Log Message:
  -----------
  - Replace `images.qrc` with dynamically generated `us3_gui_images.qrc`.
- Update build scripts and resource initialization to reference `us3_gui_images.qrc`.
- Refactor resource handling to dynamically load and ensure `us3_gui_images` via mutex.


  Commit: 5b2c72b8ee1af841045b5f6f313d4a390fa6e786
      https://github.com/ehb54/ultrascan3/commit/5b2c72b8ee1af841045b5f6f313d4a390fa6e786
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  Change runType assignment from values to keys


  Commit: 002ebf147e17b71a02f0e188dcae6b32673bf8ed
      https://github.com/ehb54/ultrascan3/commit/002ebf147e17b71a02f0e188dcae6b32673bf8ed
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

  Changed paths:
    M programs/us_legacy_converter/us_legacy_converter.cpp

  Log Message:
  -----------
  Change runtype assignment from values to keys


  Commit: 4fed5b3095bfd9af12a2b2847249679052409da9
      https://github.com/ehb54/ultrascan3/commit/4fed5b3095bfd9af12a2b2847249679052409da9
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp

  Log Message:
  -----------
  Merge pull request #338 from ehb54/lukas/legacy_data_import

Fix import from legacy data


  Commit: d12fcee27d2fff7ad77065cf179b4e8d647f974c
      https://github.com/ehb54/ultrascan3/commit/d12fcee27d2fff7ad77065cf179b4e8d647f974c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 7c33cc761e271a6cb89b3002c67bfd0ac5f406c9
      https://github.com/ehb54/ultrascan3/commit/7c33cc761e271a6cb89b3002c67bfd0ac5f406c9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-20 (Sat, 20 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  add: additional authors


  Commit: 81762adc9c91ecd4d3dc952103b1a5581d137609
      https://github.com/ehb54/ultrascan3/commit/81762adc9c91ecd4d3dc952103b1a5581d137609
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-20 (Sat, 20 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp

  Log Message:
  -----------
  Merge branch 'main' into 670-bug-us_revisionh-dependency-issue


  Commit: 4f98a669ba7fb1c53dcba4599de894533ddc8c57
      https://github.com/ehb54/ultrascan3/commit/4f98a669ba7fb1c53dcba4599de894533ddc8c57
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-22 (Mon, 22 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M programs/us/revision.sh
    M programs/us/us.cpp

  Log Message:
  -----------
  Merge pull request #336 from ehb54/670-bug-us_revisionh-dependency-issue

git commit date and time


  Commit: bf5c7965f6f3cd30fdee0ceb9181c5b0b0e32cd6
      https://github.com/ehb54/ultrascan3/commit/bf5c7965f6f3cd30fdee0ceb9181c5b0b0e32cd6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-23 (Tue, 23 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M programs/us/revision.sh
    M programs/us/us.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: aede93a36fbddcb60733fc4e45b3004b66b19a48
      https://github.com/ehb54/ultrascan3/commit/aede93a36fbddcb60733fc4e45b3004b66b19a48
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M doc/manual/advanced_config.body
    M utils/us_db2.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Refactor SSL configuration in `us_db2.cpp`:

- Consolidate SSL setup logic into a new `configure_ssl` method.
- Replace duplicate SSL configuration code with reusable function calls.
- Introduce error handling improvements for SSL setup failures.
- Update parameter naming for clarity (`error` ? `err`).
- Update documentation and references to reflect changes.


  Commit: fcf3e8e8b9e4b5b5aa785821478f592275934728
      https://github.com/ehb54/ultrascan3/commit/fcf3e8e8b9e4b5b5aa785821478f592275934728
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M utils/us_convert.h
    M utils/us_convertio.h
    M utils/us_experiment.h
    M utils/us_extern.h

  Log Message:
  -----------
  Add `US_UTIL_EXTERN` for symbol export in utility classes and update platform-specific macros

- Modify utility class declarations (`US_ConvertIO`, `US_Experiment`, `US_Convert`) to use `US_UTIL_EXTERN` for proper symbol visibility.
- Update `us_extern.h` to define `US_EXPORT`, `US_IMPORT`, `US_UTIL_EXTERN`, and `US_GUI_EXTERN` with platform-specific logic (e.g., GCC/Clang).
- Ensure uniform handling of visibility attributes for non-Windows platforms.


  Commit: f14b93b09219d242683cc79f118ed78165295074
      https://github.com/ehb54/ultrascan3/commit/f14b93b09219d242683cc79f118ed78165295074
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Add symbolic link creation for `etc` directory and enhance QWT and LibArchive handling in `CMakeLists.txt`


  Commit: a481bc52de8cafaf54b7ee05b3cbf34c9436ccf4
      https://github.com/ehb54/ultrascan3/commit/a481bc52de8cafaf54b7ee05b3cbf34c9436ccf4
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Add dependencies for `us_program_common` to ensure proper build order in `CMakeLists.txt`


  Commit: 4330e56111ecdc006e03c30b0b7a5bb3f7224af0
      https://github.com/ehb54/ultrascan3/commit/4330e56111ecdc006e03c30b0b7a5bb3f7224af0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.h
    M gui/us_experiment_gui.h
    M gui/us_get_run.h

  Log Message:
  -----------
  Apply `US_GUI_EXTERN` to GUI class declarations for symbol export

- Update `US_ExperimentGui`, `US_GetRun`, and `US_ConvertGui` to use `US_GUI_EXTERN` for improved symbol visibility across platforms.


  Commit: f719fc16c1a026b10e81214fe3eb53eceefcc9b3
      https://github.com/ehb54/ultrascan3/commit/f719fc16c1a026b10e81214fe3eb53eceefcc9b3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Add dependencies for `us_utils_static` in `CMakeLists.txt` based on build type


  Commit: 33e95b20a5d83c4901b1665caec7acef9fa29388
      https://github.com/ehb54/ultrascan3/commit/33e95b20a5d83c4901b1665caec7acef9fa29388
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Set minimum TLS version for database connection

Add support for setting minimum TLS version to 1.2 in database connection.


  Commit: b2c3bf47409e753c9fc19a553f4443b14abe8ac5
      https://github.com/ehb54/ultrascan3/commit/b2c3bf47409e753c9fc19a553f4443b14abe8ac5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Cleanup


  Commit: 67c9dc8ad7b8bf0a6c8a59f471aa11ef5e9f66d8
      https://github.com/ehb54/ultrascan3/commit/67c9dc8ad7b8bf0a6c8a59f471aa11ef5e9f66d8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M utils/ius_db2.h

  Log Message:
  -----------
  Fix parameter name from 'error' to 'err'


  Commit: e7e29ef2a51a257c10d7ec02322012a83e9b8a6b
      https://github.com/ehb54/ultrascan3/commit/e7e29ef2a51a257c10d7ec02322012a83e9b8a6b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M test/utils/test_us_simparms.cpp

  Log Message:
  -----------
  Prevent accessing the second channel in a one channel centerpiece crashing the test

Previously the test passed, because the missing etc files caused a flow in which no error was thrown. By symlinking the etc files properly, this caused now a crash


  Commit: 4f95fa8faa841098f4fadc4563e8b664c4d36ff0
      https://github.com/ehb54/ultrascan3/commit/4f95fa8faa841098f4fadc4563e8b664c4d36ff0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M test/utils/test_us_ana_profile.cpp

  Log Message:
  -----------
  Fix tests crashing because of the scan_excl_nth being incorrectly initialized and updated. Enable skipped tests again


  Commit: c8038ba4c78146998ebf7d9e1d4a27e7923c4224
      https://github.com/ehb54/ultrascan3/commit/c8038ba4c78146998ebf7d9e1d4a27e7923c4224
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Update `us_utils` to enforce symbol visibility and linking options in `CMakeLists.txt`

- Add platform-specific `target_compile_options` and `target_link_options` for consistent symbol export behavior on UNIX and macOS.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 57c8faa142074cd9d1149d209ba558df01e04afc
      https://github.com/ehb54/ultrascan3/commit/57c8faa142074cd9d1149d209ba558df01e04afc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_csv_loader.h
    M gui/us_intensity.h
    M gui/us_new_spectrum.h
    M gui/us_plot.h
    M gui/us_project_gui.h
    M gui/us_sassoc.h
    M gui/us_select_triples.h
    M gui/us_selectbox.h
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Apply `US_GUI_EXTERN` for symbol export in GUI class declarations

- Modify multiple GUI classes across headers to use `US_GUI_EXTERN` for improved symbol visibility and cross-platform compatibility.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: f5c7a43636c8b135356628aa4a5377c3a67c8d3c
      https://github.com/ehb54/ultrascan3/commit/f5c7a43636c8b135356628aa4a5377c3a67c8d3c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Exclude qmake-generated files from GUI source list in `CMakeLists.txt`

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: abc1f5a67e0e5f4d76be0643a3b95f266bb188a2
      https://github.com/ehb54/ultrascan3/commit/abc1f5a67e0e5f4d76be0643a3b95f266bb188a2
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Add qmake-compatible compiler flags and optional LTO for Release builds in `CMakeLists.txt`

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 9f528bb04373eeae038dd1dded810eb09a4bffce
      https://github.com/ehb54/ultrascan3/commit/9f528bb04373eeae038dd1dded810eb09a4bffce
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-30 (Tue, 30 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M gui/CMakeLists.txt
    M gui/fix-mac-make.sh
    R gui/images.qrc
    M gui/libus_gui.pro
    M gui/qrc_make_adds.txt
    M gui/us_convert_gui.cpp
    M gui/us_images.cpp
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M scripts/build.sh

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/lukas/qt6-compile' into lukas/qt6-compile


  Commit: 1e5681139c0d0adaa2d2bdcccadac62e0bae14cc
      https://github.com/ehb54/ultrascan3/commit/1e5681139c0d0adaa2d2bdcccadac62e0bae14cc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-30 (Tue, 30 Dec 2025)

  Changed paths:
    M CMakePresets.json

  Log Message:
  -----------
  Add VCPKG_TARGET_TRIPLET for Linux dynamic build


  Commit: a6e20929d725c26226a09f3ee3eb6e316f6c7bca
      https://github.com/ehb54/ultrascan3/commit/a6e20929d725c26226a09f3ee3eb6e316f6c7bca
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-31 (Wed, 31 Dec 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Refine TLS cipher suite definition for enhanced security and backward compatibility in `us_db2.cpp`

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 2f810aea610fcf3b7cb7a997124f039b15910e6c
      https://github.com/ehb54/ultrascan3/commit/2f810aea610fcf3b7cb7a997124f039b15910e6c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-01-03 (Sat, 03 Jan 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.h
    M gui/us_csv_loader.h
    M gui/us_experiment_gui.h
    M gui/us_get_run.h
    M gui/us_intensity.h
    M gui/us_new_spectrum.h
    M gui/us_plot.h
    M gui/us_project_gui.h
    M gui/us_sassoc.h
    M gui/us_select_triples.h
    M gui/us_selectbox.h
    M gui/us_solution_gui.h
    M programs/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_simparms.cpp
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/us_convert.h
    M utils/us_convertio.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_experiment.h
    M utils/us_extern.h

  Log Message:
  -----------
  Merge pull request #339 from ehb54/lukas/db_connection

Fix: Database Connection for newer Openssl versions, CMake Fixes backport from #300


  Commit: 16fff1967916e35010b79c2cb31ce5dd7b6ad445
      https://github.com/ehb54/ultrascan3/commit/16fff1967916e35010b79c2cb31ce5dd7b6ad445
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-04 (Sun, 04 Jan 2026)

  Changed paths:
    M CMakeLists.txt
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_new_spectrum.h
    M gui/us_plot.h
    M gui/us_project_gui.h
    M gui/us_sassoc.h
    M gui/us_selectbox.h
    M gui/us_solution_gui.h
    M programs/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_simparms.cpp
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/us_db2.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 0fff32bdf5c6c15bf3b0bf96bff3858766e852fb
      https://github.com/ehb54/ultrascan3/commit/0fff32bdf5c6c15bf3b0bf96bff3858766e852fb
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-04 (Sun, 04 Jan 2026)

  Changed paths:
    M CMakeLists.txt
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_new_spectrum.h
    M gui/us_plot.h
    M gui/us_project_gui.h
    M gui/us_sassoc.h
    M gui/us_selectbox.h
    M gui/us_solution_gui.h
    M programs/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_simparms.cpp
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/us_db2.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/lukas/qt6-compile' into lukas/qt6-compile

# Conflicts:
#	CMakeLists.txt


  Commit: 097713e62433c13a0975a8293196807afdd01662
      https://github.com/ehb54/ultrascan3/commit/097713e62433c13a0975a8293196807afdd01662
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-05 (Mon, 05 Jan 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP: 4.EDIT -- when reading Apofile's data for Scan Exclusions, check that every nth scan not be 0 (or unset) as this cased crash; this is possible for earlier protocols ...


  Commit: 76602d4c7069e7ac4f15daa401a4141301be567f
      https://github.com/ehb54/ultrascan3/commit/76602d4c7069e7ac4f15daa401a4141301be567f
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h

  Log Message:
  -----------
  Rename QLabel variables to `lbl_` prefixed names for improved consistency in `us_font` files


  Commit: c5cb34c47426c0e89f1647e0c4ddf40b49bba8c6
      https://github.com/ehb54/ultrascan3/commit/c5cb34c47426c0e89f1647e0c4ddf40b49bba8c6
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.h

  Log Message:
  -----------
  Add conditional inclusion of `<unistd.h>` for non-Windows platforms in `us_com_project_gui.h`


  Commit: 7e965475eb967de0e24a23b867b67eca4685713a
      https://github.com/ehb54/ultrascan3/commit/7e965475eb967de0e24a23b867b67eca4685713a
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  Add conditional inclusion of `<unistd.h>` for non-Windows platforms across multiple GUI header files for cross-platform compatibility


  Commit: d7b2cf305764fd93ba923b2b98e9a436417ac9a4
      https://github.com/ehb54/ultrascan3/commit/d7b2cf305764fd93ba923b2b98e9a436417ac9a4
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Comment out obsolete `#warning` directive in `us_experiment_gui_optima.cpp`.


  Commit: e943dc2efed0e478563fa973b843f70fc5ba105b
      https://github.com/ehb54/ultrascan3/commit/e943dc2efed0e478563fa973b843f70fc5ba105b
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_fds_filemanager/us_fds_filemanager.cpp

  Log Message:
  -----------
  Replace raw arrays with `QVector` in `us_fds_filemanager.cpp` for better safety and modern C++ compliance.


  Commit: 65b2c4babd29d6c22d7c987982d51584c12e9e18
      https://github.com/ehb54/ultrascan3/commit/65b2c4babd29d6c22d7c987982d51584c12e9e18
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Add qwtplot3d library to CMakeLists.txt and define compile options for Windows


  Commit: d0403e79ea82d05f7f9d003d4163516a58258953
      https://github.com/ehb54/ultrascan3/commit/d0403e79ea82d05f7f9d003d4163516a58258953
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M CMakePresets.json

  Log Message:
  -----------
  Update `CMakePresets.json` to adjust MinGW conditions and set VCPKG triplet for Windows builds


  Commit: e8640132887a70936b99095e9102ce2986b71157
      https://github.com/ehb54/ultrascan3/commit/e8640132887a70936b99095e9102ce2986b71157
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M gui/us_passwd.cpp

  Log Message:
  -----------
  e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 5d33eb2aef8c3f0f5a4a29b87448ad208d81984c
      https://github.com/ehb54/ultrascan3/commit/5d33eb2aef8c3f0f5a4a29b87448ad208d81984c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M gui/us_passwd.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  [MORE ]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 545ae8d4a3ff14a6e315409e923b9ca41076e9b6
      https://github.com/ehb54/ultrascan3/commit/545ae8d4a3ff14a6e315409e923b9ca41076e9b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp

  Log Message:
  -----------
  [MORE 2]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 5558bbe9b28475c555cb94973cef193f29f11804
      https://github.com/ehb54/ultrascan3/commit/5558bbe9b28475c555cb94973cef193f29f11804
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp

  Log Message:
  -----------
  [MORE 2a]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: a136b59f67c8fda1ee6311db7c67cdb3517544ad
      https://github.com/ehb54/ultrascan3/commit/a136b59f67c8fda1ee6311db7c67cdb3517544ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp

  Log Message:
  -----------
  [MORE 3]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 3fb85fd790fba2583aed0262d1610aed737a512b
      https://github.com/ehb54/ultrascan3/commit/3fb85fd790fba2583aed0262d1610aed737a512b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp

  Log Message:
  -----------
  [MORE 3 Plus audit Trail]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 358fa3127df640b71b730a1a59a36c30ef57b35c
      https://github.com/ehb54/ultrascan3/commit/358fa3127df640b71b730a1a59a36c30ef57b35c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [MORE 5 Plus audit Trail]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 3c5adbaa5801cf489f6544623e8dc23ae51cd3aa
      https://github.com/ehb54/ultrascan3/commit/3c5adbaa5801cf489f6544623e8dc23ae51cd3aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp

  Log Message:
  -----------
  [MORE 6 Plus audit Trail]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 17fefbf81659578b2696e6810bc983a49dba5f16
      https://github.com/ehb54/ultrascan3/commit/17fefbf81659578b2696e6810bc983a49dba5f16
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp

  Log Message:
  -----------
  [MORE 7 Plus audit Trail & page pagination]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: e72f2c1d666e58f670d0013e78ee4e271a5a09ea
      https://github.com/ehb54/ultrascan3/commit/e72f2c1d666e58f670d0013e78ee4e271a5a09ea
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-06 (Tue, 06 Jan 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp

  Log Message:
  -----------
  [MORE 8 Plus audit Trail & page pagination]e-Sigs -- work on adding and passing reviewers' decision on GMP report's Approval/rejection during e-signing...


  Commit: 7c2bec78b6a0198397031c56ec411a9252f04000
      https://github.com/ehb54/ultrascan3/commit/7c2bec78b6a0198397031c56ec411a9252f04000
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-07 (Wed, 07 Jan 2026)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  Replace `_unlink` and `_chmod` with `unlink` and `chmod` for better cross-platform compatibility in `us_gzip.cpp`. Adjust Windows platform checks and migrate from `strcpy_s` to `qstrcpy`.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 81f59a21d854bfa0653cad7c542f1628fc95f5c0
      https://github.com/ehb54/ultrascan3/commit/81f59a21d854bfa0653cad7c542f1628fc95f5c0
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-07 (Wed, 07 Jan 2026)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  Fix preprocessor directive syntax for Windows


  Commit: 7e2f5851c9e0ed47372d1a4dbaa935ea883e0344
      https://github.com/ehb54/ultrascan3/commit/7e2f5851c9e0ed47372d1a4dbaa935ea883e0344
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-08 (Thu, 08 Jan 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h

  Log Message:
  -----------
  GMP | R&D programs -- ask user to confirm when exiting programs...


  Commit: 6ab3d3a27c0adc9dd654816240703b36ef05041a
      https://github.com/ehb54/ultrascan3/commit/6ab3d3a27c0adc9dd654816240703b36ef05041a
  Author: reecemartin48 <135046110+reecemartin48 at users.noreply.github.com>
  Date:   2026-01-09 (Fri, 09 Jan 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Merge pull request #340 from ehb54/alexey-dev-issue683

GMP: 4.EDIT -- when reading Apofile's data for Scan Exclusions, check hat every nth scan not be 0?


  Commit: bf59fbfb33cc0ddcf42f5117bbff6eaef6036a21
      https://github.com/ehb54/ultrascan3/commit/bf59fbfb33cc0ddcf42f5117bbff6eaef6036a21
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-09 (Fri, 09 Jan 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: aed7d9e140bfd8c59caf4d90b56d30499024e416
      https://github.com/ehb54/ultrascan3/commit/aed7d9e140bfd8c59caf4d90b56d30499024e416
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-09 (Fri, 09 Jan 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  [1]GMP | R&D programs -- ask user to confirm when exiting programs...


  Commit: ba140a214b0d6d3fc51e620ce4ff61a50b60e25b
      https://github.com/ehb54/ultrascan3/commit/ba140a214b0d6d3fc51e620ce4ff61a50b60e25b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-09 (Fri, 09 Jan 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP REPORTER -- remove words GMP/non-GMP from the report's title...


  Commit: 67bed35c012990f32e1177e301a57f38a0be05cb
      https://github.com/ehb54/ultrascan3/commit/67bed35c012990f32e1177e301a57f38a0be05cb
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue685


  Commit: f2bcdfb5fcaaa18ac852db80e31ae2ae040ce293
      https://github.com/ehb54/ultrascan3/commit/f2bcdfb5fcaaa18ac852db80e31ae2ae040ce293
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M gui/us_passwd.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #342 from ehb54/alexey-dev-issue685

Ability to Approve/Reject GMP Report


  Commit: 02db8f53be150d60db90c37a4e0c475cd504f56f
      https://github.com/ehb54/ultrascan3/commit/02db8f53be150d60db90c37a4e0c475cd504f56f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: 6566c1e0ad133c8c15008fd0e2f4a43859041b55
      https://github.com/ehb54/ultrascan3/commit/6566c1e0ad133c8c15008fd0e2f4a43859041b55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M gui/us_passwd.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #343 from ehb54/main

Mergre main into alexey-dev-issue686


  Commit: 7a461d6cea4628319290da95d5c6c492351180d5
      https://github.com/ehb54/ultrascan3/commit/7a461d6cea4628319290da95d5c6c492351180d5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  [1]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: 62a2f6d78b1b3a37da1c632202cdd1636a4f4675
      https://github.com/ehb54/ultrascan3/commit/62a2f6d78b1b3a37da1c632202cdd1636a4f4675
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [2]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: 8ecfc1e4707734ef1629523538d1f29fb3c746d4
      https://github.com/ehb54/ultrascan3/commit/8ecfc1e4707734ef1629523538d1f29fb3c746d4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [3]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: 80b29b38504deabfcb19d6fdbbb717792d272854
      https://github.com/ehb54/ultrascan3/commit/80b29b38504deabfcb19d6fdbbb717792d272854
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [3a]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: bd65902237ae82e5d31925e019e8f9e46b8a82f1
      https://github.com/ehb54/ultrascan3/commit/bd65902237ae82e5d31925e019e8f9e46b8a82f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-12 (Mon, 12 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [4]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: 7dbe9b8fd7641fa17a63d54c921656eeb30d5fd3
      https://github.com/ehb54/ultrascan3/commit/7dbe9b8fd7641fa17a63d54c921656eeb30d5fd3
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-13 (Tue, 13 Jan 2026)

  Changed paths:
    M gui/us_passwd.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 99f7a546ebbe56580b7a5acbdcc6f1a44846f48c
      https://github.com/ehb54/ultrascan3/commit/99f7a546ebbe56580b7a5acbdcc6f1a44846f48c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-13 (Tue, 13 Jan 2026)

  Changed paths:
    M vcpkg.json

  Log Message:
  -----------
  Modify libmariadb entry in vcpkg.json

Updated libmariadb entry to include OpenSSL feature.


  Commit: d6d2c153d89a845bbb50690d1899b07822d11881
      https://github.com/ehb54/ultrascan3/commit/d6d2c153d89a845bbb50690d1899b07822d11881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-13 (Tue, 13 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [5]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: c9ffc7bb6a1b7994c962acc20945815e005d7613
      https://github.com/ehb54/ultrascan3/commit/c9ffc7bb6a1b7994c962acc20945815e005d7613
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-13 (Tue, 13 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [5a]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: d2f2efb71959e6ff1b77154dc50f8c96f466c3c1
      https://github.com/ehb54/ultrascan3/commit/d2f2efb71959e6ff1b77154dc50f8c96f466c3c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-13 (Tue, 13 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [5b]GMP | R&D -- work towards reusing R&D protocols in the GMP framework...


  Commit: bdbf60172638a38747bb896bbfa77852048c6975
      https://github.com/ehb54/ultrascan3/commit/bdbf60172638a38747bb896bbfa77852048c6975
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-01-13 (Tue, 13 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #345 from ehb54/alexey-dev-issue686

Re-using R&D protocols within GMP framework


  Commit: 04998c2c159ca9f4460261a09011f715b9ded19e
      https://github.com/ehb54/ultrascan3/commit/04998c2c159ca9f4460261a09011f715b9ded19e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-14 (Wed, 14 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 9752dedd7ae38964191197fad9f8eaeb9202531e
      https://github.com/ehb54/ultrascan3/commit/9752dedd7ae38964191197fad9f8eaeb9202531e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-14 (Wed, 14 Jan 2026)

  Changed paths:
    M gui/us_passwd.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #346 from ehb54/main

Mearging main into alexey-dev-issue678


  Commit: 757ef23c2df62c066267d68db70f6fc9703a0a8e
      https://github.com/ehb54/ultrascan3/commit/757ef23c2df62c066267d68db70f6fc9703a0a8e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-15 (Thu, 15 Jan 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  [2]GMP | R&D programs -- ask user to confirm when exiting programs...


  Commit: bcfaf8d580319bb94d276b9d596e151a25a3073c
      https://github.com/ehb54/ultrascan3/commit/bcfaf8d580319bb94d276b9d596e151a25a3073c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-16 (Fri, 16 Jan 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h

  Log Message:
  -----------
  Merge pull request #341 from ehb54/alexey-dev-issue678

GMP | R&D programs -- ask user to confirm when exiting programs...


  Commit: 582f7ac94ec640640bd27629202501de235af605
      https://github.com/ehb54/ultrascan3/commit/582f7ac94ec640640bd27629202501de235af605
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-16 (Fri, 16 Jan 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: b7ef6c746a0255676ccbfb6b665b6333622e83d4
      https://github.com/ehb54/ultrascan3/commit/b7ef6c746a0255676ccbfb6b665b6333622e83d4
  Author: Saeed <github.com/samo38>
  Date:   2026-01-19 (Mon, 19 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  us_integral: added vbar distro


  Commit: c013ad257122d7f5757b2be16917f314b10b7ffc
      https://github.com/ehb54/ultrascan3/commit/c013ad257122d7f5757b2be16917f314b10b7ffc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-21 (Wed, 21 Jan 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/db_connection_windows_vcpkg


  Commit: 766ea78bd149f180ca7b2a9369bd3382148de76b
      https://github.com/ehb54/ultrascan3/commit/766ea78bd149f180ca7b2a9369bd3382148de76b
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #344 from ehb54/lukas/db_connection_windows_vcpkg

Modify libmariadb entry in vcpkg.json


  Commit: cd149cc300c321fffa47638394bd915a7ca258c9
      https://github.com/ehb54/ultrascan3/commit/cd149cc300c321fffa47638394bd915a7ca258c9
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


  Commit: 209dba0c4bb17c8a404318b57d5826131665157f
      https://github.com/ehb54/ultrascan3/commit/209dba0c4bb17c8a404318b57d5826131665157f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/FindQwt.cmake
    A admin/cmake/triplets/x64-mingw-dynamic.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    M gui.pri
    M gui/CMakeLists.txt
    M gui/fix-mac-make.sh
    R gui/images.qrc
    M gui/libus_gui.pro
    M gui/qrc_make_adds.txt
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_get_run.cpp
    M gui/us_gui_util.cpp
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_investigator.cpp
    M gui/us_license.cpp
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_mwl_data.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_sassoc.h
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.h
    M makeall.sh
    M programs/CMakeLists.txt
    M programs/main1.inc
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #300 from ehb54/lukas/qt6-compile

Update ultrascan to build with qt5.15.10+ or qt6.8.+ and qwt6.1.6 or qwt6.3.0


  Commit: edfe3d93736f4d21d05015dba6216a7c07cfb618
      https://github.com/ehb54/ultrascan3/commit/edfe3d93736f4d21d05015dba6216a7c07cfb618
  Author: Saeed <github.com/samo38>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  add R(h) rb


  Commit: 101862e8adaad3ad184dd77cd388423c467368a7
      https://github.com/ehb54/ultrascan3/commit/101862e8adaad3ad184dd77cd388423c467368a7
  Author: Saeed <github.com/samo38>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/FindQwt.cmake
    A admin/cmake/triplets/x64-mingw-dynamic.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    M gui.pri
    M gui/CMakeLists.txt
    M gui/fix-mac-make.sh
    R gui/images.qrc
    M gui/libus_gui.pro
    M gui/qrc_make_adds.txt
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_get_run.cpp
    M gui/us_gui_util.cpp
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_investigator.cpp
    M gui/us_license.cpp
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_mwl_data.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_sassoc.h
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.h
    M makeall.sh
    M programs/CMakeLists.txt
    M programs/main1.inc
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    M vcpkg.json

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into us_integral


  Commit: 1adf73f1c4c9bfe5776f65ecae19294163ba1237
      https://github.com/ehb54/ultrascan3/commit/1adf73f1c4c9bfe5776f65ecae19294163ba1237
  Author: Saeed <github.com/samo38>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  add hr vectors


  Commit: 2542899201e17dd085de687f6fdfe671fa123bdb
      https://github.com/ehb54/ultrascan3/commit/2542899201e17dd085de687f6fdfe671fa123bdb
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    A doc/manual/source/#Makefile#
    A doc/manual/source/2dsa/2dsa_adv.rst
    A doc/manual/source/2dsa/2dsa_analys.rst
    A doc/manual/source/2dsa/2dsa_main.rst
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  Log Message:
  -----------
  ACAB doubled


  Commit: 99f518f577e8ff84c28cc02f3e3bd6cdb3fcacd1
      https://github.com/ehb54/ultrascan3/commit/99f518f577e8ff84c28cc02f3e3bd6cdb3fcacd1
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-01-22 (Thu, 22 Jan 2026)

  Changed paths:
    A .github/workflows/bump-version.yml

  Log Message:
  -----------
  add: bump version workflow


  Commit: 0f3650c4ac72c937a21c2c1b00a9fcf2bbcd9c8d
      https://github.com/ehb54/ultrascan3/commit/0f3650c4ac72c937a21c2c1b00a9fcf2bbcd9c8d
  Author: Saeed <github.com/samo38>
  Date:   2026-01-23 (Fri, 23 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  calculate rh from D


  Commit: e0bb671ae974157fb37d82c7884427498e944172
      https://github.com/ehb54/ultrascan3/commit/e0bb671ae974157fb37d82c7884427498e944172
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-01-23 (Fri, 23 Jan 2026)

  Changed paths:
    A .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #348 from ehb54/691-request-update-workflow-to-add-version-file-and-update-version-in-us_defines

Add bump version workflow


  Commit: 000572b4470833c4cd55dc8c07bfe30eadfb08f0
      https://github.com/ehb54/ultrascan3/commit/000572b4470833c4cd55dc8c07bfe30eadfb08f0
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-01-24 (Sat, 24 Jan 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Bump version to 4.1.0


  Commit: a71ddd5aa108ec9bc41b90b64fc57f365032083f
      https://github.com/ehb54/ultrascan3/commit/a71ddd5aa108ec9bc41b90b64fc57f365032083f
  Author: Saeed <github.com/samo38>
  Date:   2026-01-26 (Mon, 26 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  replace S_Solute with SolParam


  Commit: efe498c83cd9b87e53393725e527abdfe2e4036f
      https://github.com/ehb54/ultrascan3/commit/efe498c83cd9b87e53393725e527abdfe2e4036f
  Author: Saeed <github.com/samo38>
  Date:   2026-01-26 (Mon, 26 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  recalc r_h


  Commit: 8ba90ba55aa38fa0756457d800cf859cfbbb5c78
      https://github.com/ehb54/ultrascan3/commit/8ba90ba55aa38fa0756457d800cf859cfbbb5c78
  Author: Saeed <github.com/samo38>
  Date:   2026-01-26 (Mon, 26 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  calculate rh from f in meter


  Commit: 1775a16ed46b3e795b72a8c39e85c37e084c347e
      https://github.com/ehb54/ultrascan3/commit/1775a16ed46b3e795b72a8c39e85c37e084c347e
  Author: Saeed <github.com/samo38>
  Date:   2026-01-26 (Mon, 26 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  edit x axis labels


  Commit: 2f0b65d3035c4164a71480a60c692161bf64ab2c
      https://github.com/ehb54/ultrascan3/commit/2f0b65d3035c4164a71480a60c692161bf64ab2c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-01-26 (Mon, 26 Jan 2026)

  Changed paths:
    A .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge branch 'main' into us_integral


  Commit: e08ce06ec32dbd266cd302dda037f3f30e0f364c
      https://github.com/ehb54/ultrascan3/commit/e08ce06ec32dbd266cd302dda037f3f30e0f364c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-01-26 (Mon, 26 Jan 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  Merge pull request #347 from samo38/us_integral

us_integral: added vbar distribution


  Commit: 0ca5c3f6f16b6c2e357c2eca631eee2e5d894a4f
      https://github.com/ehb54/ultrascan3/commit/0ca5c3f6f16b6c2e357c2eca631eee2e5d894a4f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-01-28 (Wed, 28 Jan 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  GMP and R&D | 1. EXP:Ranges -- fix error in the Manula Wavelength Slector syntax...


  Commit: 96ee714e450f03998ba02aaaf514f1a350da0197
      https://github.com/ehb54/ultrascan3/commit/96ee714e450f03998ba02aaaf514f1a350da0197
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-02 (Mon, 02 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h

  Log Message:
  -----------
  GMP | 8. AProfile: Report | ReportItems -- work on adding an option to upload from .gadistro & .sol_integ.stats files...


  Commit: ec1ef5551bdd7381fd14863e3ad0cddd7474237b
      https://github.com/ehb54/ultrascan3/commit/ec1ef5551bdd7381fd14863e3ad0cddd7474237b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-02 (Mon, 02 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [ further wirk, bugs fixed]GMP | 8. AProfile: Report | ReportItems -- work on adding an option to upload from .gadistro & .sol_integ.stats files...


  Commit: 1bed32fbf1b5865f9d4241da389cd51fc7502286
      https://github.com/ehb54/ultrascan3/commit/1bed32fbf1b5865f9d4241da389cd51fc7502286
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-02 (Mon, 02 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [ further work, multiple files checks]GMP | 8. AProfile: Report | ReportItems -- work on adding an option to upload from .gadistro & .sol_integ.stats files...


  Commit: 84ab1b719ee2bb0d31cf0c1b50bb2d0c702c3b06
      https://github.com/ehb54/ultrascan3/commit/84ab1b719ee2bb0d31cf0c1b50bb2d0c702c3b06
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-02 (Mon, 02 Feb 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  Merge pull request #352 from ehb54/main

Add main to alexey-dev-issue693


  Commit: 2c019fc6878b57e1c32eaffbe63a5e91f774116d
      https://github.com/ehb54/ultrascan3/commit/2c019fc6878b57e1c32eaffbe63a5e91f774116d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-02 (Mon, 02 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [ 11a further work, multiple files checks]GMP | 8. AProfile: Report | ReportItems -- work on adding an option to upload from .gadistro & .sol_integ.stats files...


  Commit: d1e2cfa1ac60af4aadf7b43609bce67db0172b7e
      https://github.com/ehb54/ultrascan3/commit/d1e2cfa1ac60af4aadf7b43609bce67db0172b7e
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-02-03 (Tue, 03 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h

  Log Message:
  -----------
  Merge pull request #353 from ehb54/alexey-dev-issue693

Alexey dev issue693: GMP : AProfile: Reports -- read from gadistro & stats files...


  Commit: 754919623caf6fd45a51f5727822cfac0020d4e7
      https://github.com/ehb54/ultrascan3/commit/754919623caf6fd45a51f5727822cfac0020d4e7
  Author: Saeed Mortezazadeh <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-02-03 (Tue, 03 Feb 2026)

  Changed paths:
    M gui/us_csv_loader.cpp
    M utils/us_csv_data.cpp

  Log Message:
  -----------
  csv loader: remove strict rules from ASCII checking


  Commit: ce46d86dbadf1a938281bae38ce621b26a5de8a3
      https://github.com/ehb54/ultrascan3/commit/ce46d86dbadf1a938281bae38ce621b26a5de8a3
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-02-05 (Thu, 05 Feb 2026)

  Changed paths:
    M gui/us_csv_loader.cpp
    M utils/us_csv_data.cpp

  Log Message:
  -----------
  Merge pull request #354 from samo38/issue_721

csv loader: remove strict rules to check ASCII


  Commit: d287d24ac45d15c14c50dffde79d3abcf44e1c47
      https://github.com/ehb54/ultrascan3/commit/d287d24ac45d15c14c50dffde79d3abcf44e1c47
  Author: Saeed <github.com/samo38>
  Date:   2026-02-06 (Fri, 06 Feb 2026)

  Changed paths:
    M gui/us_spectrodata.h

  Log Message:
  -----------
  us_spectrodata: add hydrodynamic radius to S_Solute


  Commit: 1a9eda0deabbf567b25ddd721c01232463c6d549
      https://github.com/ehb54/ultrascan3/commit/1a9eda0deabbf567b25ddd721c01232463c6d549
  Author: Saeed <github.com/samo38>
  Date:   2026-02-06 (Fri, 06 Feb 2026)

  Changed paths:
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  us_integral: replace SolParam with S_Solute


  Commit: da3fc554ce97a1be8cfe7b62337d78d92604161f
      https://github.com/ehb54/ultrascan3/commit/da3fc554ce97a1be8cfe7b62337d78d92604161f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Add unit tests for regex pattern validation across multiple directories using Google Test.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: cb515698419c2bb2848d269cceca3d7868746844
      https://github.com/ehb54/ultrascan3/commit/cb515698419c2bb2848d269cceca3d7868746844
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Remove unused QRegularExpression instance in `us_astfem_sim.cpp` for cleanup.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: b0ac1a3cb666e4f4b25c1365edc8d5c5e4f6bacf
      https://github.com/ehb54/ultrascan3/commit/b0ac1a3cb666e4f4b25c1365edc8d5c5e4f6bacf
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Fix regex pattern

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 6576b55edf442a9f5bbf1a514fdf3c8b7d0aacb4
      https://github.com/ehb54/ultrascan3/commit/6576b55edf442a9f5bbf1a514fdf3c8b7d0aacb4
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Fix regex pattern to escape hyphen in `us_experiment_gui_optima.cpp`.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 6e7d30e0ef299014a0c9cb9ef1946d1a47fb0a7c
      https://github.com/ehb54/ultrascan3/commit/6e7d30e0ef299014a0c9cb9ef1946d1a47fb0a7c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Enhance regex validation test to handle multiple root directories.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 08cb8eff95cbb8854677c23f9a6feaf2cb8a3cf0
      https://github.com/ehb54/ultrascan3/commit/08cb8eff95cbb8854677c23f9a6feaf2cb8a3cf0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M gui/us_model_loader.cpp

  Log Message:
  -----------
  Refactor `mflt1` handling in `us_model_loader.cpp` to improve readability and maintainability with explicit regex variable.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 5078a8d03fd2b3aa46a05080799be0a7160b8ebf
      https://github.com/ehb54/ultrascan3/commit/5078a8d03fd2b3aa46a05080799be0a7160b8ebf
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Improve regex patterns in `test_us_regex.cpp` by refining matching groups and simplify logic using `US3_SOURCE_DIR`.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 209a54e72c0504fe6f76815b7942f5a22fd234f0
      https://github.com/ehb54/ultrascan3/commit/209a54e72c0504fe6f76815b7942f5a22fd234f0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Remove unused `#include <QDebug>` from `test_us_regex.cpp`.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 9242af2cd2230eee60f31dfeb847dc9f5e8d5f7f
      https://github.com/ehb54/ultrascan3/commit/9242af2cd2230eee60f31dfeb847dc9f5e8d5f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Improve regex pattern in `us_proto_ranges.cpp` by adding anchors to validate the entire input string.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 265038699620b8b1a90c53f84efb775c87a8d9f8
      https://github.com/ehb54/ultrascan3/commit/265038699620b8b1a90c53f84efb775c87a8d9f8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-08 (Sun, 08 Feb 2026)

  Changed paths:
    M gui/us_csv_loader.cpp
    M utils/us_csv_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qregularexpression


  Commit: 2ea487199988c676fcc1964a6f46d839a5923f6e
      https://github.com/ehb54/ultrascan3/commit/2ea487199988c676fcc1964a6f46d839a5923f6e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-09 (Mon, 09 Feb 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP | 6. Report | GMP Reporter -- do not treat models for triples unselected via MWL settings in AProfile...


  Commit: 61e17120bfea3d3fe14220a8a0813e06f91b405e
      https://github.com/ehb54/ultrascan3/commit/61e17120bfea3d3fe14220a8a0813e06f91b405e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-09 (Mon, 09 Feb 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  GMP | 6. Report | GMP Reporter -- [test for exclusion from replicas averages ] do not treat models for triples unselected via MWL settings in AProfile...


  Commit: bc93bdb1ac483145af191042bca04ce2dae6160c
      https://github.com/ehb54/ultrascan3/commit/bc93bdb1ac483145af191042bca04ce2dae6160c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-09 (Mon, 09 Feb 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP | 6. Report | GMP Reporter -- [test for exclusion from replicas averages ] do not treat models for triples unselected via MWL settings in AProfile...


  Commit: f422eaebafa361f357d0b27d3f56d3f4d3247f8e
      https://github.com/ehb54/ultrascan3/commit/f422eaebafa361f357d0b27d3f56d3f4d3247f8e
  Author: Saeed <github.com/samo38>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h

  Log Message:
  -----------
  us_ga_init: add Rh


  Commit: 64aaf14c987aa4ffd38f3384794e8d48c9db4550
      https://github.com/ehb54/ultrascan3/commit/64aaf14c987aa4ffd38f3384794e8d48c9db4550
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  GMP | 6. Report | GMP Reporter -- debugs...


  Commit: 0948900b5205298e629f088eb4065f427533405a
      https://github.com/ehb54/ultrascan3/commit/0948900b5205298e629f088eb4065f427533405a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  [1]GMP | 6. Report | GMP Reporter -- debugs...


  Commit: dea86432abbfcb78b4a27b2d6ff3e2598049a457
      https://github.com/ehb54/ultrascan3/commit/dea86432abbfcb78b4a27b2d6ff3e2598049a457
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp

  Log Message:
  -----------
  [3]GMP | 6. Report | GMP Reporter -- debugs...


  Commit: 460d442cc51bf15666694018e83b32f67ad3b7d3
      https://github.com/ehb54/ultrascan3/commit/460d442cc51bf15666694018e83b32f67ad3b7d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp

  Log Message:
  -----------
  [44]GMP | 6. Report | GMP Reporter -- debugs...


  Commit: dd8f0db7bde551fdadeb9537b163c89d4a92c354
      https://github.com/ehb54/ultrascan3/commit/dd8f0db7bde551fdadeb9537b163c89d4a92c354
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp

  Log Message:
  -----------
  [55]GMP | 6. Report | GMP Reporter -- debugs...


  Commit: 7b19d82c50ea2091a5f5505be3dcc5dc6c68c1f2
      https://github.com/ehb54/ultrascan3/commit/7b19d82c50ea2091a5f5505be3dcc5dc6c68c1f2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M gui/us_csv_loader.cpp
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M utils/us_csv_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue696


  Commit: 03cfa5a45de626720e1950e9f8175c43f8f4eeda
      https://github.com/ehb54/ultrascan3/commit/03cfa5a45de626720e1950e9f8175c43f8f4eeda
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: dataDisk -- preclude uploading data with mismatching wvls in A/B channels of each cell ..


  Commit: 4aea2b2f6186986e0fd3ad290cfeaa1377b10159
      https://github.com/ehb54/ultrascan3/commit/4aea2b2f6186986e0fd3ad290cfeaa1377b10159
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-10 (Tue, 10 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge pull request #351 from ehb54/alexey-dev-issue696

GMP and R&D | 1. EXP:Ranges -- fix error in the Manula Wavelength Selector syntax


  Commit: 3f5f87a55d56cc92cf12660f817aac9818f146c2
      https://github.com/ehb54/ultrascan3/commit/3f5f87a55d56cc92cf12660f817aac9818f146c2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qregularexpression


  Commit: c15785325aacd959a7751c0d680b21526c3d13c2
      https://github.com/ehb54/ultrascan3/commit/c15785325aacd959a7751c0d680b21526c3d13c2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Remove unused QRegularExpression definition

Removed commented-out QRegularExpression for range matching.


  Commit: 7dd74a941f99399277845ebc113b332cb11a6c83
      https://github.com/ehb54/ultrascan3/commit/7dd74a941f99399277845ebc113b332cb11a6c83
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_fit_meniscus/CMakeLists.txt

  Log Message:
  -----------
  Refactor CMakeLists.txt for us_fit_meniscus

Updated the CMake configuration to simplify the build process by removing conditional library builds and directly linking the executable to the common library.


  Commit: c0861a3c61ea3133bd02b3dd1974217fa41b6ccb
      https://github.com/ehb54/ultrascan3/commit/c0861a3c61ea3133bd02b3dd1974217fa41b6ccb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP | 1. EXP.: dataDisk -- set all tabs but few to readonly upon dataDisk upload; unset when dataDisk uncheched ..


  Commit: 51825487cf5107edca76f02968f26dd1d142173d
      https://github.com/ehb54/ultrascan3/commit/51825487cf5107edca76f02968f26dd1d142173d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.: dataDisk -- set all tabs but few to readonly upon dataDisk upload; unset when dataDisk uncheched ..


  Commit: b4b6df18011d41ed7209dca2fa4580a93512d976
      https://github.com/ehb54/ultrascan3/commit/b4b6df18011d41ed7209dca2fa4580a93512d976
  Author: Saeed <github.com/samo38>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  us_ga_init/us_solutedata: add Hr to the report file


  Commit: a10c820b1808470ff1529c74ae9e8cbb6f2db80f
      https://github.com/ehb54/ultrascan3/commit/a10c820b1808470ff1529c74ae9e8cbb6f2db80f
  Author: Saeed <github.com/samo38>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h

  Log Message:
  -----------
  us_ddist_combine: add Rh to the discrete distributions program


  Commit: 3e454dd1eca619263c23dc1206fe22fb60c737c4
      https://github.com/ehb54/ultrascan3/commit/3e454dd1eca619263c23dc1206fe22fb60c737c4
  Author: Saeed <github.com/samo38>
  Date:   2026-02-11 (Wed, 11 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_699


  Commit: 9e51cdcfa43a81f4121dea2aa9d99d5f9cfe7d05
      https://github.com/ehb54/ultrascan3/commit/9e51cdcfa43a81f4121dea2aa9d99d5f9cfe7d05
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-12 (Thu, 12 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: 8.AProfile:2DSA -- remove check for metadata in customgrid models in GMP...


  Commit: 482dbb495512e7628e78756240055909d096c476
      https://github.com/ehb54/ultrascan3/commit/482dbb495512e7628e78756240055909d096c476
  Author: Saeed <github.com/samo38>
  Date:   2026-02-12 (Thu, 12 Feb 2026)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp

  Log Message:
  -----------
  us nm unit for hydrodynamic radius


  Commit: 679d24e59f88ba1d091f5f2d7025cebce66847a2
      https://github.com/ehb54/ultrascan3/commit/679d24e59f88ba1d091f5f2d7025cebce66847a2
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-13 (Fri, 13 Feb 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Adjust button sizes in `us_plot.cpp` to improve UI consistency. Add missing size configurations for `btnCMap`.


  Commit: 9c4bc4cfdbca84956e3698eae833736bd38049ec
      https://github.com/ehb54/ultrascan3/commit/9c4bc4cfdbca84956e3698eae833736bd38049ec
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-13 (Fri, 13 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h

  Log Message:
  -----------
  Refactor `US_AnalysisBase2` to improve readability and maintainability:

- Replace raw arrays with `QVector` for `x_weights` and `y_weights`.
- Use `QSignalBlocker` to simplify signal connection management.
- Switch from old-style signal/slot syntax to the new syntax.
- Add `reset_data` and `reset_gui` methods to centralize reset logic.
- Update function parameters to use `const` where applicable.
- Improve code consistency with `nullptr` and `static_cast`.


  Commit: 53e206359e71440d79578430acdebaef4dcaedf0
      https://github.com/ehb54/ultrascan3/commit/53e206359e71440d79578430acdebaef4dcaedf0
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-13 (Fri, 13 Feb 2026)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h

  Log Message:
  -----------
  Add `reset`, `reset_data`, and `reset_gui` methods to `US_2dsa`. Refactor signal/slot connections to new-style syntax for improved clarity and maintainability.


  Commit: 7947fe35531e4787b56f263dd0789b40f196dc98
      https://github.com/ehb54/ultrascan3/commit/7947fe35531e4787b56f263dd0789b40f196dc98
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-13 (Fri, 13 Feb 2026)

  Changed paths:
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h

  Log Message:
  -----------
  Refactor `US_Dcdt` for signal/slot modernization and reset logic centralization:

- Refactor signal/slot connections to use the new-style syntax.
- Add `reset_data` and `reset_gui` methods for better modularity.
- Replace repetitive signal blocking with `QSignalBlocker`.


  Commit: aa8931a16cb3c1b35e26f7ae7c12d77303de7449
      https://github.com/ehb54/ultrascan3/commit/aa8931a16cb3c1b35e26f7ae7c12d77303de7449
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-13 (Fri, 13 Feb 2026)

  Changed paths:
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h

  Log Message:
  -----------
  Add `reset`, `reset_data`, and `reset_gui` methods to `US_MwlSpeciesFit` for centralized reset logic.


  Commit: c220871ce8f2a92cd7d0599e8f3f1c8d9d5ca440
      https://github.com/ehb54/ultrascan3/commit/c220871ce8f2a92cd7d0599e8f3f1c8d9d5ca440
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-13 (Fri, 13 Feb 2026)

  Changed paths:
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h

  Log Message:
  -----------
  Add `reset`, `reset_data`, and `reset_gui` methods to `US_SecondMoment` for centralized reset logic.


  Commit: 66ad967703fe072619f70bd88332a44b08f6deb7
      https://github.com/ehb54/ultrascan3/commit/66ad967703fe072619f70bd88332a44b08f6deb7
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-13 (Fri, 13 Feb 2026)

  Changed paths:
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h

  Log Message:
  -----------
  Add `reset`, `reset_data`, and `reset_gui` methods to `US_vHW_Enhanced` for centralized reset logic. Refactor signal/slot connections to new-style syntax for improved readability.


  Commit: 07467629be5a04d4391038f9c0928e1801bea687
      https://github.com/ehb54/ultrascan3/commit/07467629be5a04d4391038f9c0928e1801bea687
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M gui/us_model_loader.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Merge pull request #355 from ehb54/lukas/qregularexpression

Add test case for QRegularExpression


  Commit: a4ef846e1efc8c0c36fd8ba95a8624abe699b90d
      https://github.com/ehb54/ultrascan3/commit/a4ef846e1efc8c0c36fd8ba95a8624abe699b90d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M gui/us_model_loader.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_fit_meniscus


  Commit: 276cc3fe3d26224cab52f0f3f4300685881cb7b0
      https://github.com/ehb54/ultrascan3/commit/276cc3fe3d26224cab52f0f3f4300685881cb7b0
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M gui/us_model_loader.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue727


  Commit: 2fd6c045e09af67fd040a1060e4511630131160d
      https://github.com/ehb54/ultrascan3/commit/2fd6c045e09af67fd040a1060e4511630131160d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_fit_meniscus/CMakeLists.txt

  Log Message:
  -----------
  Merge pull request #360 from ehb54/lukas/us_fit_meniscus

Refactor CMakeLists.txt for us_fit_meniscus


  Commit: 8c56b13faf08fbb28cae8ccf6065281505773c75
      https://github.com/ehb54/ultrascan3/commit/8c56b13faf08fbb28cae8ccf6065281505773c75
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M gui/us_model_loader.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue722


  Commit: b88e3e9b8bf9b260bb39b1506d42a8109999484f
      https://github.com/ehb54/ultrascan3/commit/b88e3e9b8bf9b260bb39b1506d42a8109999484f
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M gui/us_model_loader.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue726


  Commit: d33d111549b1ef2ab5c3c1fb0221d0d4051f5c45
      https://github.com/ehb54/ultrascan3/commit/d33d111549b1ef2ab5c3c1fb0221d0d4051f5c45
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge pull request #359 from ehb54/alexey-dev-issue722

GMP | 1. EXP.: dataDisk -- preclude uploading data with mismatching wavelengths in A/B channels


  Commit: 0bd3d78bdfcabdbfcf26427148b6c46ba5e35ab0
      https://github.com/ehb54/ultrascan3/commit/0bd3d78bdfcabdbfcf26427148b6c46ba5e35ab0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fit_meniscus/CMakeLists.txt

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue727


  Commit: 74decf93e5b0bcb0d14c8b1c478c7ea142927592
      https://github.com/ehb54/ultrascan3/commit/74decf93e5b0bcb0d14c8b1c478c7ea142927592
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue726


  Commit: e2958af17ebf6efb9e81b1f388d776e1ca4e57c9
      https://github.com/ehb54/ultrascan3/commit/e2958af17ebf6efb9e81b1f388d776e1ca4e57c9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  Merge pull request #363 from ehb54/alexey-dev-issue726

GMP | 1. EXP.: 8.AProfile:2DSA -- remove check for metadata in customGrid models uploaded


  Commit: 146c6530464ca618ee4f58a94b04927bbc7bd34a
      https://github.com/ehb54/ultrascan3/commit/146c6530464ca618ee4f58a94b04927bbc7bd34a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue727


  Commit: 0b9cfd848d0d53888d6c22853966518f5b088fe7
      https://github.com/ehb54/ultrascan3/commit/0b9cfd848d0d53888d6c22853966518f5b088fe7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M gui/us_model_loader.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Merge pull request #357 from ehb54/main

main to here


  Commit: d874c292e59932a8d126026910cca00d4279ae90
      https://github.com/ehb54/ultrascan3/commit/d874c292e59932a8d126026910cca00d4279ae90
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge pull request #361 from ehb54/alexey-dev-issue727

Alexey dev issue727: ReadOnly tabs when dataDisk in GMP


  Commit: b005ec4151340cdf16ce95a47c930d0807c6fc40
      https://github.com/ehb54/ultrascan3/commit/b005ec4151340cdf16ce95a47c930d0807c6fc40
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-02-14 (Sat, 14 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue724


  Commit: 49e66ee799500b45cb201876615b40b4ea9e3bd9
      https://github.com/ehb54/ultrascan3/commit/49e66ee799500b45cb201876615b40b4ea9e3bd9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-15 (Sun, 15 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #356 from ehb54/alexey-dev-issue724

GMP | 6. Report | GMP Reporter -- do not treat models for triples unselected in MWL settings as missed


  Commit: c9c647fe4dee50482fd482171b83783d3fae427c
      https://github.com/ehb54/ultrascan3/commit/c9c647fe4dee50482fd482171b83783d3fae427c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-15 (Sun, 15 Feb 2026)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  GMP | 5. ANALSYSI | 6. REPORT -- for fit_meniscus_And_bottom option, make sure to capture mode of meniscus update in 5. ANALAYSIS|FITMEN stage - best fit, or manual update, pass to User Interations section of the Rpeort as well as to audit trail...


  Commit: 0500c3350c3437732e0d9ed656185a5e32ca2584
      https://github.com/ehb54/ultrascan3/commit/0500c3350c3437732e0d9ed656185a5e32ca2584
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.h

  Log Message:
  -----------
  Make `reset_data` and `reset_gui` non-virtual in `US_AnalysisBase2` to simplify inheritance structure.


  Commit: 074e12d4c448250dccba1b236d2f887b14cd26f0
      https://github.com/ehb54/ultrascan3/commit/074e12d4c448250dccba1b236d2f887b14cd26f0
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp

  Log Message:
  -----------
  Simplify `reset_gui` in `US_2dsa` by removing redundant `nullptr` assignments.


  Commit: 643926ae3cc32d094e7feda27fe58bc9099818ef
      https://github.com/ehb54/ultrascan3/commit/643926ae3cc32d094e7feda27fe58bc9099818ef
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_pcsa/us_pcsa.cpp

  Log Message:
  -----------
  Refactor `US_pcsa` signal/slot connections to use new-style syntax for improved readability and maintainability.


  Commit: 0667d84eda957989a0d1072815ced463ad60dd21
      https://github.com/ehb54/ultrascan3/commit/0667d84eda957989a0d1072815ced463ad60dd21
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_pcsa/us_pcsa.cpp

  Log Message:
  -----------
  Refactor `US_pcsa` to modernize signal/slot connections with new-style syntax for improved clarity and maintainability.


  Commit: 90e550a3655c4e118231ecaaf412f1844d959f34
      https://github.com/ehb54/ultrascan3/commit/90e550a3655c4e118231ecaaf412f1844d959f34
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h

  Log Message:
  -----------
  Refactor `US_pcsa` to replace raw pointer `te_results` with `QPointer` for improved memory management and safety.


  Commit: 8a1a27c3f2cbf5cd2341fe453c6d33a6fe6f5182
      https://github.com/ehb54/ultrascan3/commit/8a1a27c3f2cbf5cd2341fe453c6d33a6fe6f5182
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h

  Log Message:
  -----------
  Refactor `US_pcsa` to remove unused `child_closed` slot and redundant signal/slot connections. Adjust pointer initialization for improved clarity and use `clear()` for better reset logic.


  Commit: 2e87560345745184b24f6b1adc221a84a71ba937
      https://github.com/ehb54/ultrascan3/commit/2e87560345745184b24f6b1adc221a84a71ba937
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h

  Log Message:
  -----------
  Add `reset`, `reset_data`, and `reset_gui` methods to `US_pcsa` for centralized reset logic.


  Commit: 915e9c1eeea05f71a9a76779507fc00a9f7c0cf1
      https://github.com/ehb54/ultrascan3/commit/915e9c1eeea05f71a9a76779507fc00a9f7c0cf1
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_pcsa/us_pcsa.cpp

  Log Message:
  -----------
  Refactor `US_pcsa` for improved readability and maintainability: update conditional checks, initialize variables with modern syntax, and streamline GUI reset logic.


  Commit: f7feea2e4e70bf2d86cf344797d74e454c074bf1
      https://github.com/ehb54/ultrascan3/commit/f7feea2e4e70bf2d86cf344797d74e454c074bf1
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.cpp

  Log Message:
  -----------
  Refactor `US_AnalysisBase2`: remove redundant `const` in `QDir` declaration and increase precision for `vbar` field display.


  Commit: 7bc3455e432949e1baf6f295e3c3e2918ea647cd
      https://github.com/ehb54/ultrascan3/commit/7bc3455e432949e1baf6f295e3c3e2918ea647cd
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp

  Log Message:
  -----------
  Refactor `US_MwlSpeciesFit`: enhance `reset_data` by clearing additional containers and initializing `us_gmp_auto_mode` to `false`.


  Commit: 45ebb0d251485129fedf336ed7fe31f374d468b8
      https://github.com/ehb54/ultrascan3/commit/45ebb0d251485129fedf336ed7fe31f374d468b8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M gui/us_model_loader.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    A test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_analysis_base_reset_button


  Commit: 7e1223aebe668ca75e872f8f2096bff99af80529
      https://github.com/ehb54/ultrascan3/commit/7e1223aebe668ca75e872f8f2096bff99af80529
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp

  Log Message:
  -----------
  Refactor `US_2dsa`: enhance `reset_data` by initializing `dset` and appending it to `dsets`.


  Commit: 7ad4a9ea5ad1ded27de94a0da82a9a2a240a01f4
      https://github.com/ehb54/ultrascan3/commit/7ad4a9ea5ad1ded27de94a0da82a9a2a240a01f4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us/CMakeLists.txt

  Log Message:
  -----------
  Update Windows icon resource path in CMakeLists.txt


  Commit: 19e226c14175154289a18157f2ec01fee0d0092c
      https://github.com/ehb54/ultrascan3/commit/19e226c14175154289a18157f2ec01fee0d0092c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Enable BigObj format for large files in CMake

Added support for BigObj format in MSVC and GCC/Clang compilers for large files.


  Commit: 34e1f1f692d84430b5d47ba46266add455f73b66
      https://github.com/ehb54/ultrascan3/commit/34e1f1f692d84430b5d47ba46266add455f73b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Add link options for Windows Release builds

Add Windows-specific link options for Release builds to suppress console window


  Commit: 82c31c25f15c5c68ad67fa5c4f6adcae251c7ddd
      https://github.com/ehb54/ultrascan3/commit/82c31c25f15c5c68ad67fa5c4f6adcae251c7ddd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  [1]GMP | 5. ANALSYSI | 6. REPORT -- for fit_meniscus_And_bottom option, make sure to capture mode of meniscus update in 5. ANALAYSIS|FITMEN stage - best fit, or manual update, pass to User Interations section of the Rpeort as well as to audit trail...


  Commit: 85154b5fde5b9b552646f5bd6334c86faa744dac
      https://github.com/ehb54/ultrascan3/commit/85154b5fde5b9b552646f5bd6334c86faa744dac
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.cpp

  Log Message:
  -----------
  Add null check for dbP in disk_controls condition


  Commit: 1abad2a8d207a4293111f589493d27d7d093b877
      https://github.com/ehb54/ultrascan3/commit/1abad2a8d207a4293111f589493d27d7d093b877
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add BigObj compile options for us_utils_static


  Commit: 02b8e6a74eda39a2f7930e2a161c0a91392fff6d
      https://github.com/ehb54/ultrascan3/commit/02b8e6a74eda39a2f7930e2a161c0a91392fff6d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_plot.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h

  Log Message:
  -----------
  Merge pull request #364 from ehb54/lukas/us_analysis_base_reset_button

Analysis programs reset button


  Commit: 8816a556aaf04bde3c1bf2d4a8ae26ea83682e81
      https://github.com/ehb54/ultrascan3/commit/8816a556aaf04bde3c1bf2d4a8ae26ea83682e81
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_plot.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/cmake_fixes


  Commit: c3f92aa4906fca184b43069e3fcf49aa9c65aa9d
      https://github.com/ehb54/ultrascan3/commit/c3f92aa4906fca184b43069e3fcf49aa9c65aa9d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-16 (Mon, 16 Feb 2026)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h

  Log Message:
  -----------
  [2]GMP | 5. ANALSYSI | 6. REPORT -- for fit_meniscus_And_bottom option, make sure to capture mode of meniscus update in 5. ANALAYSIS|FITMEN stage - best fit, or manual update, pass to User Interations section of the Rpeort as well as to audit trail...


  Commit: 1aabf75b57be7e0c7096cab60625574e0b688794
      https://github.com/ehb54/ultrascan3/commit/1aabf75b57be7e0c7096cab60625574e0b688794
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-17 (Tue, 17 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Merge pull request #365 from ehb54/lukas/cmake_fixes

Lukas/cmake fixes


  Commit: 678ff7f6c7bed9024cc5f25e855c87b95ed0db50
      https://github.com/ehb54/ultrascan3/commit/678ff7f6c7bed9024cc5f25e855c87b95ed0db50
  Author: Saeed Mortezazadeh <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-02-17 (Tue, 17 Feb 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h

  Log Message:
  -----------
  us_ga_init: replace plot checkboxs with radiobuttons


  Commit: 7ce3e54ec1ff65f0e3dbbccd1119349c41eeb9a8
      https://github.com/ehb54/ultrascan3/commit/7ce3e54ec1ff65f0e3dbbccd1119349c41eeb9a8
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-02-17 (Tue, 17 Feb 2026)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_plot.cpp
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue736


  Commit: 8fc7603a80492999df59ceed6230f0534734c5d8
      https://github.com/ehb54/ultrascan3/commit/8fc7603a80492999df59ceed6230f0534734c5d8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-17 (Tue, 17 Feb 2026)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h

  Log Message:
  -----------
  Merge pull request #366 from ehb54/alexey-dev-issue736

User Interactions for 5. ANALYSIS : FITMEN in the GMP report & Audit Trail in case of 'Fit Maniscus & Bottom' option


  Commit: 3902c84e081fd344c94094e6e7c120a10bf3c40f
      https://github.com/ehb54/ultrascan3/commit/3902c84e081fd344c94094e6e7c120a10bf3c40f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-18 (Wed, 18 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h

  Log Message:
  -----------
  GMP | 1. EXP. [Gen., 2DSA, PCSA] -- remove Varying Vbar & cons.f/f0 fields in 2DSA; field validators in all tabs....


  Commit: 327e1e2fcb6c942e05029608fbe46152c3027639
      https://github.com/ehb54/ultrascan3/commit/327e1e2fcb6c942e05029608fbe46152c3027639
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-18 (Wed, 18 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP | 1. EXP. : dataDist -- do not impose check for mismatched A/B channs. wvls. for S-data, and singe-channel RA data....


  Commit: c9c5a8725b6a56caf94ad54e46417d544ae8c914
      https://github.com/ehb54/ultrascan3/commit/c9c5a8725b6a56caf94ad54e46417d544ae8c914
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-18 (Wed, 18 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    A admin/cmake/toolchain-macos.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    M programs/us/CMakeLists.txt
    M scripts/build.sh

  Log Message:
  -----------
  mod: remove alpha folder and update macos build


  Commit: ca2d76006ab1d5031061c41da2fdb082b475438e
      https://github.com/ehb54/ultrascan3/commit/ca2d76006ab1d5031061c41da2fdb082b475438e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-18 (Wed, 18 Feb 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: update environment variable echo statement


  Commit: 12375251f49081bbf84273353a7d7dba7dfa1cde
      https://github.com/ehb54/ultrascan3/commit/12375251f49081bbf84273353a7d7dba7dfa1cde
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    A admin/cmake/toolchain-macos.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    M programs/us/CMakeLists.txt
    M scripts/build.sh

  Log Message:
  -----------
  Merge pull request #369 from ehb54/629-request-remove-alpha-folder-from-ultrascan3-repo

Remove Alpha Folder


  Commit: d787112c42145adc032e986e17be63d8efd5dfda
      https://github.com/ehb54/ultrascan3/commit/d787112c42145adc032e986e17be63d8efd5dfda
  Author: Saeed <github.com/samo38>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h

  Log Message:
  -----------
  add check_draw_btn


  Commit: ba06a7cd941b1bb63391e1fba5d30baf782f4d3e
      https://github.com/ehb54/ultrascan3/commit/ba06a7cd941b1bb63391e1fba5d30baf782f4d3e
  Author: Saeed <github.com/samo38>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    A admin/cmake/toolchain-macos.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_model_loader.cpp
    M gui/us_plot.cpp
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M scripts/build.sh
    A test/utils/test_us_regex.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_699


  Commit: 0e8e23a92b9a25ccfdbb4c7644d30119ab521a43
      https://github.com/ehb54/ultrascan3/commit/0e8e23a92b9a25ccfdbb4c7644d30119ab521a43
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    A admin/cmake/toolchain-macos.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    M programs/us/CMakeLists.txt
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue718


  Commit: ac5f152ac8ba6b0d7f9a65d40f3b7556bc970cee
      https://github.com/ehb54/ultrascan3/commit/ac5f152ac8ba6b0d7f9a65d40f3b7556bc970cee
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  GMP | R&D  -- connect Help btn to help()....


  Commit: 05244eacbe440afd5348b931a95305443dd6673d
      https://github.com/ehb54/ultrascan3/commit/05244eacbe440afd5348b931a95305443dd6673d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  GMP | 8. AProf.:Report  -- shift tille for Pseudo3D plots up a bit...


  Commit: 9f65eb0ffed3357339a3500e400ea119f9827144
      https://github.com/ehb54/ultrascan3/commit/9f65eb0ffed3357339a3500e400ea119f9827144
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h

  Log Message:
  -----------
  Merge pull request #367 from ehb54/alexey-dev-issue718

GMP | 1. EXP. [Gen., 2DSA, PCSA] -- remove Varying Vbar & cons.f/f0 from 2DSA settings; add validators for all numeric fields in Gen.,2DSA,PCSA


  Commit: fb0e5c780bc7aa696e368d9f6d46b22688fe5707
      https://github.com/ehb54/ultrascan3/commit/fb0e5c780bc7aa696e368d9f6d46b22688fe5707
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-19 (Thu, 19 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  GMP | 7. Ranges.: Gary's selector  -- tried to address increments in selections...


  Commit: a6fe9c7b13c638a88e1390c744efd98cbec59acf
      https://github.com/ehb54/ultrascan3/commit/a6fe9c7b13c638a88e1390c744efd98cbec59acf
  Author: Saeed Mortezazadeh <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  add anno_label(int) to us_ga_init


  Commit: 8617cadc6147eda447864b6626622e9bffa4128e
      https://github.com/ehb54/ultrascan3/commit/8617cadc6147eda447864b6626622e9bffa4128e
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    A doc/manual/source/_static/images/bad_grid.png
    A doc/manual/source/_static/images/beck_convert-2.png
    A doc/manual/source/_static/images/beck_converter.png
    A doc/manual/source/_static/images/good_grid.png
    A doc/manual/source/_static/images/grid-setup.png
    A doc/manual/source/_static/images/mwlr_spectra_3d.png
    A doc/manual/source/_static/images/mwlr_spectra_cont.png
    A doc/manual/source/_static/images/mwlr_spectra_f.png
    A doc/manual/source/_static/images/mwlr_spectra_o.png
    A doc/manual/source/_static/images/mwlr_spectra_save.png
    A doc/manual/source/_static/images/set-zvalue.png
    A doc/manual/source/_static/images/xpn_viewer-loaded.png
    A doc/manual/source/_static/images/xpn_viewer-saved.png
    A doc/manual/source/_static/images/xpn_viewer.png
    A doc/manual/source/_static/images/zvalue_eq.png
    M doc/manual/source/beckman_openauc.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/index.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/mwl_species_fit.rst
    M doc/manual/source/mwl_species_sim.rst
    M doc/manual/source/mwl_spectra.rst
    M doc/manual/source/predict1.rst
    M doc/manual/source/ramp_data.rst
    M doc/manual/source/tmp.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  WALICAFB


  Commit: 779bf5e32b16d7eddc415ecc2fe90709ac0026b9
      https://github.com/ehb54/ultrascan3/commit/779bf5e32b16d7eddc415ecc2fe90709ac0026b9
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    A .github/workflows/bump-version.yml
    M CMakeLists.txt
    M CMakePresets.json
    A admin/cmake/toolchain-macos.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_csv_loader.cpp
    M gui/us_model_loader.cpp
    M gui/us_plot.cpp
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M scripts/build.sh
    A test/utils/test_us_regex.cpp
    M utils/CMakeLists.txt
    M utils/us_csv_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into haben-Dev


  Commit: 935d35d3bb247201260925626ead40c7e5911908
      https://github.com/ehb54/ultrascan3/commit/935d35d3bb247201260925626ead40c7e5911908
  Author: Saeed <github.com/samo38>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h

  Log Message:
  -----------
  add help button to the us_legacy_converter


  Commit: a39e0c3fc901b37000aa384dff633eca9b5f21cc
      https://github.com/ehb54/ultrascan3/commit/a39e0c3fc901b37000aa384dff633eca9b5f21cc
  Author: Saeed <github.com/samo38>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h

  Log Message:
  -----------
  us_query_rmsd: add help button


  Commit: bb36da7046d87e90154684ecee5a92e3521fb317
      https://github.com/ehb54/ultrascan3/commit/bb36da7046d87e90154684ecee5a92e3521fb317
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    A admin/cmake/toolchain-macos.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    M programs/us/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue742


  Commit: 9332b11c468511b91b824048956f411d88e92ba2
      https://github.com/ehb54/ultrascan3/commit/9332b11c468511b91b824048956f411d88e92ba2
  Author: Saeed <github.com/samo38>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  add help buttons


  Commit: 2786677b0b7c3dcd1f55bf7fb1c7a78257a3bada
      https://github.com/ehb54/ultrascan3/commit/2786677b0b7c3dcd1f55bf7fb1c7a78257a3bada
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge pull request #368 from ehb54/alexey-dev-issue742

GMP | 1. EXP. : dataDist -- do not impose check for mismatched A/B channs wvl for S-data


  Commit: 3ca613086ee315038618d9ce0a642da1999e7608
      https://github.com/ehb54/ultrascan3/commit/3ca613086ee315038618d9ce0a642da1999e7608
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue746


  Commit: 67ca8b752f82ede833bb3f16e6e3f2f00801a3b5
      https://github.com/ehb54/ultrascan3/commit/67ca8b752f82ede833bb3f16e6e3f2f00801a3b5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue515


  Commit: d0890b9202cd432e88acb5573eb12401399ac6df
      https://github.com/ehb54/ultrascan3/commit/d0890b9202cd432e88acb5573eb12401399ac6df
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-20 (Fri, 20 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue702


  Commit: 624105a44700833dbabe95610557269b85c9d938
      https://github.com/ehb54/ultrascan3/commit/624105a44700833dbabe95610557269b85c9d938
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge pull request #372 from ehb54/alexey-dev-issue702

GMP | 7. Ranges.: Gary's selector  -- tried to address increments in wvl selections?


  Commit: 649a36c3a6bfc1942f2c116a43de591572e959a5
      https://github.com/ehb54/ultrascan3/commit/649a36c3a6bfc1942f2c116a43de591572e959a5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue515


  Commit: 253e03b46f36753d81db75a92dcf958d768d29f1
      https://github.com/ehb54/ultrascan3/commit/253e03b46f36753d81db75a92dcf958d768d29f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  [1]GMP | R&D  -- connect Help btn to help()....


  Commit: 739bde48ce1e5596b769170a179b245bced40541
      https://github.com/ehb54/ultrascan3/commit/739bde48ce1e5596b769170a179b245bced40541
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
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  Merge branch 'main' into alexey-dev-issue746


  Commit: 2ea90efd5a9ebebf0c1fcef7291f0c14a0a853b6
      https://github.com/ehb54/ultrascan3/commit/2ea90efd5a9ebebf0c1fcef7291f0c14a0a853b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  Merge pull request #371 from ehb54/alexey-dev-issue515

GMP | 8. AProf.:Report  -- shift tille for Pseudo3D plots up a bit...


  Commit: 5c69cacb804711a2e1fc839a8bf716a778945747
      https://github.com/ehb54/ultrascan3/commit/5c69cacb804711a2e1fc839a8bf716a778945747
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue746


  Commit: 7bf106993a8f72d94033f56ec908772b1087c0ef
      https://github.com/ehb54/ultrascan3/commit/7bf106993a8f72d94033f56ec908772b1087c0ef
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
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    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
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    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
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    R doc/manual/images/manage_data.png
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    R doc/manual/images/manage_data_cmenu-1.png
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    R doc/manual/images/manage_data_pasw.png
    R doc/manual/images/manage_data_sync.png
    R doc/manual/images/manage_data_thelp-1.png
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    R doc/manual/images/master-pw.png
    R doc/manual/images/model_editor.png
    R doc/manual/images/mwlr_view_3dplot.png
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    R doc/manual/index.body
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    R doc/manual/mainstyle.css
    R doc/manual/make-docs.sh
    R doc/manual/make-html.sh
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    R doc/manual/make-wraps.sh
    R doc/manual/manage_data.body
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    R doc/manual/select_runs.body
    R doc/manual/simparams.body
    R doc/manual/somo.body
    R doc/manual/source/#Makefile#
    M doc/manual/source/conf.py
    R doc/manual/source/make.bat
    M doc/manual/source/requirements.txt
    R doc/manual/template.img.body
    R doc/manual/tidy.conf
    R doc/manual/time_derivative.body
    R doc/manual/ultrascan3.txt
    R doc/manual/us_buffer.body
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    R doc/manual/us_fds_filemanager.body
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    R doc/manual/us_project.body
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    R doc/manual/uscol.body
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    R doc/manual/vhw_combine.body
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    R doc/manual/vhw_enhanced.body
    R doc/manual/wrapped-images.lst
    M gui/us_help.cpp
    M makeall.sh
    M scripts/build.sh
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  mod: delete legacy help, integrate sphinx help


  Commit: 3d08b0b47f4e2317e53a69e11dc522f164182ec7
      https://github.com/ehb54/ultrascan3/commit/3d08b0b47f4e2317e53a69e11dc522f164182ec7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake

  Log Message:
  -----------
  mod: release only build for macos


  Commit: 7d351ae823d28a24be8d1406165cb8c4887fb1e7
      https://github.com/ehb54/ultrascan3/commit/7d351ae823d28a24be8d1406165cb8c4887fb1e7
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M gui/us_report_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: c8f871714964df445fd9b6dac06aa954bcc04d69
      https://github.com/ehb54/ultrascan3/commit/c8f871714964df445fd9b6dac06aa954bcc04d69
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-02-21 (Sat, 21 Feb 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge pull request #370 from ehb54/alexey-dev-issue746

GMP | R&D  -- connect Help btn to help()....


  Commit: 8eb6af8dac0c0037f48381a8383228ef7f55a358
      https://github.com/ehb54/ultrascan3/commit/8eb6af8dac0c0037f48381a8383228ef7f55a358
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-22 (Sun, 22 Feb 2026)

  Changed paths:
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    R etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm

  Log Message:
  -----------
  mod: remove gmp icons


  Commit: ed169be467f3b5054b1675c832cee30a332f58e1
      https://github.com/ehb54/ultrascan3/commit/ed169be467f3b5054b1675c832cee30a332f58e1
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-02-22 (Sun, 22 Feb 2026)

  Changed paths:
    A .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/FindQwt.cmake
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/toolchain-macos.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/x64-mingw-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    M doc/manual/advanced_config.body
    M gui.pri
    M gui/CMakeLists.txt
    M gui/fix-mac-make.sh
    R gui/images.qrc
    M gui/libus_gui.pro
    M gui/qrc_make_adds.txt
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_get_run.cpp
    M gui/us_get_run.h
    M gui/us_gui_util.cpp
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.cpp
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_mwl_data.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_new_spectrum.h
    M gui/us_passwd.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_project_gui.h
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_sassoc.h
    M gui/us_select_triples.h
    M gui/us_selectbox.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.h
    M makeall.sh
    M programs/CMakeLists.txt
    M programs/main1.inc
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    M scripts/build.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_simparms.cpp
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_experiment.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into 666-bug-icons-dont-fill-space-on-new-macos


  Commit: a69727d693e60c02d3b9c4db2e16387437816ce5
      https://github.com/ehb54/ultrascan3/commit/a69727d693e60c02d3b9c4db2e16387437816ce5
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-23 (Mon, 23 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    A admin/cmake/triplets/arm64-windows.cmake
    M gui/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.ps1
    M vcpkg.json

  Log Message:
  -----------
  Windows ARM64 build fixes: triplet, export macros, windeployqt


  Commit: 84d482ad6f56b2e3acc6c957d97719052eaefbd7
      https://github.com/ehb54/ultrascan3/commit/84d482ad6f56b2e3acc6c957d97719052eaefbd7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-23 (Mon, 23 Feb 2026)

  Changed paths:
    M CMakePresets.json
    R admin/cmake/toolchain-macos.cmake
    A admin/cmake/toolchain.cmake
    A scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    R vcpkg

  Log Message:
  -----------
  mod: add build for windows script and standardize linux and macos build


  Commit: d0f42eef0df776ad01ea51cc7505eeb80878b2d8
      https://github.com/ehb54/ultrascan3/commit/d0f42eef0df776ad01ea51cc7505eeb80878b2d8
  Author: Saeed <github.com/samo38>
  Date:   2026-02-23 (Mon, 23 Feb 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  us_spectrum: removed unnecessary widgets


  Commit: e43bca35c3066c669ca922450241c6bdf5b4de40
      https://github.com/ehb54/ultrascan3/commit/e43bca35c3066c669ca922450241c6bdf5b4de40
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-23 (Mon, 23 Feb 2026)

  Changed paths:
    M scripts/build.ps1

  Log Message:
  -----------
  fix: processor core check


  Commit: 70a4fd76fe5b6edf065fdf2b5f5ba0bcedb2165e
      https://github.com/ehb54/ultrascan3/commit/70a4fd76fe5b6edf065fdf2b5f5ba0bcedb2165e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-23 (Mon, 23 Feb 2026)

  Changed paths:
    M admin/cmake/toolchain.cmake

  Log Message:
  -----------
  fix: remove force


  Commit: 6d4f2ac655f09a8a6b067f5a54b974908ab10aaf
      https://github.com/ehb54/ultrascan3/commit/6d4f2ac655f09a8a6b067f5a54b974908ab10aaf
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-23 (Mon, 23 Feb 2026)

  Changed paths:
    M admin/cmake/toolchain.cmake

  Log Message:
  -----------
  fix: linux arm64 now handled correctly


  Commit: 534da76a2eb5090416dc3e2fa4416db272ac9b91
      https://github.com/ehb54/ultrascan3/commit/534da76a2eb5090416dc3e2fa4416db272ac9b91
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-02-24 (Tue, 24 Feb 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: 98c5f9693e9265ed8f1515603098010def86eb70
      https://github.com/ehb54/ultrascan3/commit/98c5f9693e9265ed8f1515603098010def86eb70
  Author: Saeed <github.com/samo38>
  Date:   2026-02-24 (Tue, 24 Feb 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  rename labels


  Commit: 0880dfb2dd0e8e00e5613ff36d94c03e11edd27c
      https://github.com/ehb54/ultrascan3/commit/0880dfb2dd0e8e00e5613ff36d94c03e11edd27c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-24 (Tue, 24 Feb 2026)

  Changed paths:
    M CMakePresets.json
    M admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake

  Log Message:
  -----------
  fix: linux arm64 dynamic and config path added


  Commit: 95f4bf13cb912979ba31f07969ede459ee9a3cfb
      https://github.com/ehb54/ultrascan3/commit/95f4bf13cb912979ba31f07969ede459ee9a3cfb
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-24 (Tue, 24 Feb 2026)

  Changed paths:
    M etc/etc_belongs_list.txt
    A etc/us3-GMP-icon-128x128.ico
    A etc/us3-GMP-icon-128x128.png
    A etc/us3-GMP-icon-128x128.xpm
    A etc/us3-GMP-icon-32x32.ico
    A etc/us3-GMP-icon-32x32.png
    A etc/us3-GMP-icon-32x32.xpm
    A etc/us3-GMP-icon-48x48.ico
    A etc/us3-GMP-icon-48x48.png
    A etc/us3-GMP-icon-48x48.xpm

  Log Message:
  -----------
  fix: returned gmp icons back to branch because at least one is used us_comproject.desktop:Icon=/opt/ultrascan3/etc/us3-GMP-icon-128x128.png


  Commit: d28e726d4e40aae7be0f55ed03c1e7fe45e36d00
      https://github.com/ehb54/ultrascan3/commit/d28e726d4e40aae7be0f55ed03c1e7fe45e36d00
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-24 (Tue, 24 Feb 2026)

  Changed paths:
    M doc/manual/source/colorgradient.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/mwl_spectra.rst
    M doc/manual/source/mwlr_viewer.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/requirements.txt
    M doc/manual/source/us_project.rst
    M doc/manual/source/vhw_combine.rst

  Log Message:
  -----------
  mod: migrate to sphinx-design from subfigure


  Commit: 8cef6842fe3282a17f7fe6a11688d966a17b86da
      https://github.com/ehb54/ultrascan3/commit/8cef6842fe3282a17f7fe6a11688d966a17b86da
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-02-25 (Wed, 25 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    R admin/cmake/toolchain-macos.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M programs/us/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #337 from ehb54/666-bug-icons-dont-fill-space-on-new-macos

New Icons


  Commit: 63ddc08f86dd138595c248e3ec8653b3e4640132
      https://github.com/ehb54/ultrascan3/commit/63ddc08f86dd138595c248e3ec8653b3e4640132
  Author: ehb <ehb at ehbs-MacBook-Pro.local>
  Date:   2026-02-25 (Wed, 25 Feb 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  restore macx:LIBS, expected for OSX package pipeline


  Commit: 42f2fd0ef0f999defd30ec52c17df8d7acf8ccef
      https://github.com/ehb54/ultrascan3/commit/42f2fd0ef0f999defd30ec52c17df8d7acf8ccef
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-02-25 (Wed, 25 Feb 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  add VER to qwtplot3d


  Commit: f22ac1211864fd6e1e0f4bd0ab603df9a6703163
      https://github.com/ehb54/ultrascan3/commit/f22ac1211864fd6e1e0f4bd0ab603df9a6703163
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M utils/us_astfem_math.cpp
    M utils/us_cfa_data.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Add support for `TIMESTATE_TYPE` and `IMPORT_TYPE` in `US_TimeState`: introduce enums, accessor methods, and XML serialization logic.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 92969167df27d9df138b7faee2cb16d988228790
      https://github.com/ehb54/ultrascan3/commit/92969167df27d9df138b7faee2cb16d988228790
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Refactor `US_AstfemMath`: add parameter names to function signatures, update `check_acceleration` to include optional `timestate` argument, and adjust related logic.


  Commit: 8318d566a89cb3e06093e1d79d56d11d3488103a
      https://github.com/ehb54/ultrascan3/commit/8318d566a89cb3e06093e1d79d56d11d3488103a
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    R admin/cmake/toolchain-macos.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M programs/us/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: 4bb72c42f9441f20b9b825741d31d186a728fe4c
      https://github.com/ehb54/ultrascan3/commit/4bb72c42f9441f20b9b825741d31d186a728fe4c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_csv_loader.cpp
    M gui/us_model_loader.cpp
    M gui/us_plot.cpp
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    A test/utils/test_us_regex.cpp
    M utils/CMakeLists.txt
    M utils/us_csv_data.cpp
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into ticket_747


  Commit: 89b7691a714d92e99e335e23378d225aa3b1b536
      https://github.com/ehb54/ultrascan3/commit/89b7691a714d92e99e335e23378d225aa3b1b536
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  fix revision.sh checks osx/linux compat.


  Commit: b1b7791e9c3922286c2d9d56c2f0a378911720ee
      https://github.com/ehb54/ultrascan3/commit/b1b7791e9c3922286c2d9d56c2f0a378911720ee
  Author: Saeed <github.com/samo38>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h

  Log Message:
  -----------
  add Rh to us_pseudo3d_combine


  Commit: bd32e3b102e354732b319bc5687719785b83d3f2
      https://github.com/ehb54/ultrascan3/commit/bd32e3b102e354732b319bc5687719785b83d3f2
  Author: Saeed <github.com/samo38>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    R admin/cmake/toolchain-macos.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/us_report_gui.cpp
    M programs/us/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_699


  Commit: 8c545d6f5c77a42afc10d3badcaa8f9b34866f2d
      https://github.com/ehb54/ultrascan3/commit/8c545d6f5c77a42afc10d3badcaa8f9b34866f2d
  Author: Saeed <github.com/samo38>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    R admin/cmake/toolchain-macos.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/us_report_gui.cpp
    M programs/us/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_748


  Commit: 38b548536c2c0458b2cc85f5663ca56eb9538f3f
      https://github.com/ehb54/ultrascan3/commit/38b548536c2c0458b2cc85f5663ca56eb9538f3f
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M gui/us_spectrodata.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h

  Log Message:
  -----------
  Merge pull request #362 from samo38/ticket_699

Ticket 699: adding Hydrodynamic radius to additional plotting programs


  Commit: 572bb723ed591be3225aacbdbc387c93c17ca792
      https://github.com/ehb54/ultrascan3/commit/572bb723ed591be3225aacbdbc387c93c17ca792
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-02-26 (Thu, 26 Feb 2026)

  Changed paths:
    M gui/us_spectrodata.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-670


  Commit: 6dd71c26fbdb258b25259c7c5e41be982d54a809
      https://github.com/ehb54/ultrascan3/commit/6dd71c26fbdb258b25259c7c5e41be982d54a809
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-27 (Fri, 27 Feb 2026)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Refactor US_Crypto for AES-256-GCM encryption


  Commit: 1461b65d9eae700e3429db2b7c19c35361fea861
      https://github.com/ehb54/ultrascan3/commit/1461b65d9eae700e3429db2b7c19c35361fea861
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-27 (Fri, 27 Feb 2026)

  Changed paths:
    M utils/us_crypto.h

  Log Message:
  -----------
  Add decryptLegacy function and update decrypt signature


  Commit: ed2647558eb754fa66c8e7d52d3f0b8efac2c53c
      https://github.com/ehb54/ultrascan3/commit/ed2647558eb754fa66c8e7d52d3f0b8efac2c53c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-27 (Fri, 27 Feb 2026)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  Update encryption tests to expect invalid results


  Commit: 27402a271781fa16ae00a693e5ce8e3f06e8e33e
      https://github.com/ehb54/ultrascan3/commit/27402a271781fa16ae00a693e5ce8e3f06e8e33e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-27 (Fri, 27 Feb 2026)

  Changed paths:
    M utils/us_crypto.h

  Log Message:
  -----------
  Fix parameter description for decrypt functions


  Commit: 344a4930c5819ebfd2875eccc84d0a44a446ee31
      https://github.com/ehb54/ultrascan3/commit/344a4930c5819ebfd2875eccc84d0a44a446ee31
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-27 (Fri, 27 Feb 2026)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Fix encryption finalization logic in us_crypto.cpp


  Commit: 817a32ad7fe5e5c35ec0479673a2f4c20a7a8e3c
      https://github.com/ehb54/ultrascan3/commit/817a32ad7fe5e5c35ec0479673a2f4c20a7a8e3c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-02-27 (Fri, 27 Feb 2026)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Fix tag data retrieval in EVP_CIPHER_CTX_ctrl


  Commit: 85100ef73842bc75a8f210f7b9038301adae82db
      https://github.com/ehb54/ultrascan3/commit/85100ef73842bc75a8f210f7b9038301adae82db
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-02-27 (Fri, 27 Feb 2026)

  Changed paths:
    M gui/us_spectrodata.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: 7f63285b165bc88c2a317f9f368082e0d24d8861
      https://github.com/ehb54/ultrascan3/commit/7f63285b165bc88c2a317f9f368082e0d24d8861
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-28 (Sat, 28 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    A admin/cmake/MacDeploy.cmake
    R buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    R buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    R buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    R buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    M doc/manual/CMakeLists.txt
    A doc/manual/StageAssistant.cmake
    M doc/manual/source/mwl_spectra.rst
    M gui/CMakeLists.txt
    M gui/us_help.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M qwtplot3d/CMakeLists.txt
    M scripts/build.sh
    M vcpkg.json

  Log Message:
  -----------
  fix: fix qt help search and implement dmg


  Commit: 8e3d67b30d1a4eaf6faf0d18d80a835288ee5ae7
      https://github.com/ehb54/ultrascan3/commit/8e3d67b30d1a4eaf6faf0d18d80a835288ee5ae7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-02-28 (Sat, 28 Feb 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    R admin/cmake/toolchain-macos.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/us_spectrodata.h
    M programs/us/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M vcpkg.json

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/527-enhancement-sphinx-migration-2' into 527-enhancement-sphinx-migration-2

# Conflicts:
#	.gitignore
#	scripts/build.sh


  Commit: ef3356b450a93ec526f92ee27da0a9bfcfa9c04a
      https://github.com/ehb54/ultrascan3/commit/ef3356b450a93ec526f92ee27da0a9bfcfa9c04a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-01 (Sun, 01 Mar 2026)

  Changed paths:
    M LICENSE.txt

  Log Message:
  -----------
  fix: text was original utf-8 so quotes became questions marks with ascii tool. Changed ? to ascii quotes.


  Commit: 096f3590c1a57a798a0c13863e80d333a690b4cf
      https://github.com/ehb54/ultrascan3/commit/096f3590c1a57a798a0c13863e80d333a690b4cf
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-02 (Mon, 02 Mar 2026)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Fix type casting for GCM tag data


  Commit: ca6f560338cfe03c4fa0e60bb95577b526dbf2ed
      https://github.com/ehb54/ultrascan3/commit/ca6f560338cfe03c4fa0e60bb95577b526dbf2ed
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-02 (Mon, 02 Mar 2026)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Fix type casting for GCM tag in us_crypto.cpp


  Commit: 82c2dc2269b90376cf1f69ca3f88b4bee38c641e
      https://github.com/ehb54/ultrascan3/commit/82c2dc2269b90376cf1f69ca3f88b4bee38c641e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-02 (Mon, 02 Mar 2026)

  Changed paths:
    R admin/cmake/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M scripts/build.sh

  Log Message:
  -----------
  add: launcher and packaging step


  Commit: 88ef4e481d1b4ea751d997b156e3782f1befce93
      https://github.com/ehb54/ultrascan3/commit/88ef4e481d1b4ea751d997b156e3782f1befce93
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-02 (Mon, 02 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/toolchain.cmake
    M doc/manual/CMakeLists.txt
    M doc/manual/StageAssistant.cmake

  Log Message:
  -----------
  add: working qt6 build and install


  Commit: 5ee4575063fb99b0b70eb335bc0d88e3a903b857
      https://github.com/ehb54/ultrascan3/commit/5ee4575063fb99b0b70eb335bc0d88e3a903b857
  Author: Saeed <github.com/samo38>
  Date:   2026-03-03 (Tue, 03 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  us_spectrum: update GUI and DataProfile


  Commit: d864a615e96c4dd2c66a738120c35c6eb556d647
      https://github.com/ehb54/ultrascan3/commit/d864a615e96c4dd2c66a738120c35c6eb556d647
  Author: Saeed <github.com/samo38>
  Date:   2026-03-03 (Tue, 03 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  us_spectrum: use minmax


  Commit: 644141ae003ec988b86eb7b01c1e21cf208b0dac
      https://github.com/ehb54/ultrascan3/commit/644141ae003ec988b86eb7b01c1e21cf208b0dac
  Author: Saeed <github.com/samo38>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    M gui/us_spectrodata.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_748


  Commit: d1215ab67e2f9e4aa0bcf349eac8da7f58a9be6a
      https://github.com/ehb54/ultrascan3/commit/d1215ab67e2f9e4aa0bcf349eac8da7f58a9be6a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm

  Log Message:
  -----------
  mod: update 128x128 us-gmp icon and remove others


  Commit: ff02149480e771cbc205a241cee2322ae52a5ea3
      https://github.com/ehb54/ultrascan3/commit/ff02149480e771cbc205a241cee2322ae52a5ea3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    R propignore
    R proppng
    R proptext

  Log Message:
  -----------
  mod: delete svn files


  Commit: 0d744f1905b897d66da68befb43637e8ac4cd7bc
      https://github.com/ehb54/ultrascan3/commit/0d744f1905b897d66da68befb43637e8ac4cd7bc
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    R README.linguist
    M gui/libus_gui.pro
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    R qwtplot3d/lingua_de.ts
    M utils/libus_utils.pro

  Log Message:
  -----------
  mod: remove deprecated translation files and settings


  Commit: 04583d8a1b0bcf01875f31b93a12343610284126
      https://github.com/ehb54/ultrascan3/commit/04583d8a1b0bcf01875f31b93a12343610284126
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake

  Log Message:
  -----------
  add: windows installer


  Commit: 20b958cec1d253988daedd88a2fec65efd28448d
      https://github.com/ehb54/ultrascan3/commit/20b958cec1d253988daedd88a2fec65efd28448d
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    M scripts/build.ps1

  Log Message:
  -----------
  add: pkg command to build.ps1


  Commit: 722ffd5c4e0c7d1f2f2c27127e065270ae3c7598
      https://github.com/ehb54/ultrascan3/commit/722ffd5c4e0c7d1f2f2c27127e065270ae3c7598
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm

  Log Message:
  -----------
  Merge pull request #380 from ehb54/773-request-update-us-3-gmp-icons

Icon Maintenance


  Commit: 47dbf4a3837c551d64f6436f25aa7f5f7d482fad
      https://github.com/ehb54/ultrascan3/commit/47dbf4a3837c551d64f6436f25aa7f5f7d482fad
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into 775-bug-svn-files


  Commit: 93fb5f9f839b1aea6d85ed568acc18030ebed5c1
      https://github.com/ehb54/ultrascan3/commit/93fb5f9f839b1aea6d85ed568acc18030ebed5c1
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into 756-bug-translation-maintenance


  Commit: fe5370afd345acf40744a8c872c09eef88887bba
      https://github.com/ehb54/ultrascan3/commit/fe5370afd345acf40744a8c872c09eef88887bba
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    R propignore
    R proppng
    R proptext

  Log Message:
  -----------
  Merge pull request #381 from ehb54/775-bug-svn-files

Remove Legacy SVN Files


  Commit: b1b7bdf318164406971f4188a7b3cf8b0aacbbaa
      https://github.com/ehb54/ultrascan3/commit/b1b7bdf318164406971f4188a7b3cf8b0aacbbaa
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into 756-bug-translation-maintenance


  Commit: 90e9cf2eb989a85420f4668067092a143d4457a9
      https://github.com/ehb54/ultrascan3/commit/90e9cf2eb989a85420f4668067092a143d4457a9
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    R README.linguist
    M gui/libus_gui.pro
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    R qwtplot3d/lingua_de.ts
    M utils/libus_utils.pro

  Log Message:
  -----------
  Merge pull request #382 from ehb54/756-bug-translation-maintenance

Translation File Maintenance


  Commit: 2698e05dd320a374785cab43ed05a52db3c5c3a7
      https://github.com/ehb54/ultrascan3/commit/2698e05dd320a374785cab43ed05a52db3c5c3a7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/windows/WinPkg.cmake
    M scripts/build.ps1

  Log Message:
  -----------
  fix: missing programs in installer package


  Commit: 499648d1ea27751d008981e0d9f1447cfbef7072
      https://github.com/ehb54/ultrascan3/commit/499648d1ea27751d008981e0d9f1447cfbef7072
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-04 (Wed, 04 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M scripts/build.ps1

  Log Message:
  -----------
  fix: missing sphinx on windows build


  Commit: 300852b8d51c2733817729fab46d6d0e68f5e717
      https://github.com/ehb54/ultrascan3/commit/300852b8d51c2733817729fab46d6d0e68f5e717
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    R README.linguist
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/libus_gui.pro
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    R propignore
    R proppng
    R proptext
    R qwtplot3d/lingua_de.ts
    M utils/libus_utils.pro

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_crypto_buffer_overflow


  Commit: 2fcc6637f35ea3ab3c8e1450a06b60932d033f1b
      https://github.com/ehb54/ultrascan3/commit/2fcc6637f35ea3ab3c8e1450a06b60932d033f1b
  Author: Saeed <samo38:github>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  us_spectrum: update


  Commit: 9c62b533654400def76e5db0eb8c8f4924ff66d1
      https://github.com/ehb54/ultrascan3/commit/9c62b533654400def76e5db0eb8c8f4924ff66d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    R README.linguist
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/libus_gui.pro
    M gui/us_spectrodata.h
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    R propignore
    R proppng
    R proptext
    R qwtplot3d/lingua_de.ts
    M utils/libus_utils.pro

  Log Message:
  -----------
  Merge pull request #383 from ehb54/main

Update feature branch to main


  Commit: 0f7d005ceda3b8031c1180200237d736f60a1b4c
      https://github.com/ehb54/ultrascan3/commit/0f7d005ceda3b8031c1180200237d736f60a1b4c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h

  Log Message:
  -----------
  Merge pull request #379 from ehb54/lukas/us_crypto_buffer_overflow

us_crypto: Avoid buffer overflow, support longer passwords, introduce safer encryption


  Commit: 780dac6301b72554362f7cc2944a17a6c64d2aa5
      https://github.com/ehb54/ultrascan3/commit/780dac6301b72554362f7cc2944a17a6c64d2aa5
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M utils/us_astfem_math.cpp

  Log Message:
  -----------
  Refactor `US_AstfemMath`: improve low acceleration rate handling by adding corrections for slow experiments and original `timestate` checks.


  Commit: 01be09bde2a7cc42512e4a4f215108a9419c0d32
      https://github.com/ehb54/ultrascan3/commit/01be09bde2a7cc42512e4a4f215108a9419c0d32
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M gui/us_convert_gui.h

  Log Message:
  -----------
  Add `prepareTimeState` method and integrate `US_TimeState` into `US_ConvertGui`


  Commit: e0424b860fb5077ab33b7e5db663b721da5ba290
      https://github.com/ehb54/ultrascan3/commit/e0424b860fb5077ab33b7e5db663b721da5ba290
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  Refactor `US_ConvertGui`: implement `prepareTimeState` for streamlined time state preparation and integrate into speed step processing logic.


  Commit: 97b756dde416093dc9c7bb730c4958161c0e0232
      https://github.com/ehb54/ultrascan3/commit/97b756dde416093dc9c7bb730c4958161c0e0232
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/timestate


  Commit: b2c2afd33a8ed941e547021628bcb32abea1675a
      https://github.com/ehb54/ultrascan3/commit/b2c2afd33a8ed941e547021628bcb32abea1675a
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    R README.linguist
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/libus_gui.pro
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    R propignore
    R proppng
    R proptext
    R qwtplot3d/lingua_de.ts
    M test/utils/test_us_crypto.cpp
    M utils/libus_utils.pro
    M utils/us_crypto.cpp
    M utils/us_crypto.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-670


  Commit: ea9b77b204f53d6694d97541134564d0606916a3
      https://github.com/ehb54/ultrascan3/commit/ea9b77b204f53d6694d97541134564d0606916a3
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  Refactor `US_ConvertGui`: streamline file handling logic in time state preparation and enable GUI button state based on file existence.


  Commit: 11fa3a30cb824bce1c32920aa3a6b2c307f54f1a
      https://github.com/ehb54/ultrascan3/commit/11fa3a30cb824bce1c32920aa3a6b2c307f54f1a
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M utils/us_astfem_math.cpp

  Log Message:
  -----------
  Refactor `US_AstfemMath`: replace `qDebug` with `DbgLv` for consistent debug logging.


  Commit: 5eb4adb03f6cf6e0ab2a6163a5d614d3b034d383
      https://github.com/ehb54/ultrascan3/commit/5eb4adb03f6cf6e0ab2a6163a5d614d3b034d383
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M test/utils/test_us_time_state.cpp

  Log Message:
  -----------
  Update `test_us_time_state`: adjust expected version to `2.2` in origin test.


  Commit: 41a6910c567f5d60a14f6a802af0a1134eef03c4
      https://github.com/ehb54/ultrascan3/commit/41a6910c567f5d60a14f6a802af0a1134eef03c4
  Author: Saeed <samo38:github>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  add argsort and sort functions


  Commit: bc8f22c93dcad653e16c52717a9386d9a99c67c9
      https://github.com/ehb54/ultrascan3/commit/bc8f22c93dcad653e16c52717a9386d9a99c67c9
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M programs/us_config/us_admin.cpp

  Log Message:
  -----------
  Refactor password re-encryption logic


  Commit: 93b2e5a2535f0de5b6fe2b4384a60d509571f6d4
      https://github.com/ehb54/ultrascan3/commit/93b2e5a2535f0de5b6fe2b4384a60d509571f6d4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M programs/us_config/us_admin.cpp

  Log Message:
  -----------
  Check for empty cipherHex and optimize database loop

Added a check for empty cipherHex before decryption and modified the database loop to use a reference.


  Commit: 6a9245189a1804e4557df78035f6f4401a5883ea
      https://github.com/ehb54/ultrascan3/commit/6a9245189a1804e4557df78035f6f4401a5883ea
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-05 (Thu, 05 Mar 2026)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_adv.rst
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    M doc/manual/source/3d_plot.rst
    R doc/manual/source/_static/custom.css
    R doc/manual/source/_static/images/2dsa_3dplot.png
    R doc/manual/source/_static/images/2dsa_advan.png
    R doc/manual/source/_static/images/2dsa_analvv.png
    R doc/manual/source/_static/images/2dsa_analys.png
    R doc/manual/source/_static/images/2dsa_main-c.png
    R doc/manual/source/_static/images/2dsa_main-o.png
    R doc/manual/source/_static/images/2dsa_resplot.png
    R doc/manual/source/_static/images/D20W_bar.png
    R doc/manual/source/_static/images/MW-bar.png
    R doc/manual/source/_static/images/RINplot.png
    R doc/manual/source/_static/images/TINplot.png
    R doc/manual/source/_static/images/UltraScan-logo.png
    R doc/manual/source/_static/images/add_RIN-TIN.png
    R doc/manual/source/_static/images/add_RIN.png
    R doc/manual/source/_static/images/add_TIN.png
    R doc/manual/source/_static/images/advanced_config.png
    R doc/manual/source/_static/images/analyte_details.png
    R doc/manual/source/_static/images/analyte_edit.png
    R doc/manual/source/_static/images/analyte_edit_spec.png
    R doc/manual/source/_static/images/analyte_new_sequence.png
    R doc/manual/source/_static/images/analyte_newc.png
    R doc/manual/source/_static/images/analyte_newd.png
    R doc/manual/source/_static/images/analyte_newp.png
    R doc/manual/source/_static/images/analyte_selectc.png
    R doc/manual/source/_static/images/analyte_selectd.png
    R doc/manual/source/_static/images/analyte_selectp.png
    R doc/manual/source/_static/images/analyte_sequence.png
    R doc/manual/source/_static/images/analyte_settings.png
    R doc/manual/source/_static/images/analyte_spec-gui.png
    R doc/manual/source/_static/images/analyte_specmenu.png
    R doc/manual/source/_static/images/analyte_spectrum.png
    R doc/manual/source/_static/images/analytes.png
    R doc/manual/source/_static/images/associations.png
    R doc/manual/source/_static/images/astfem_sim.png
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    A doc/manual/source/images/us_extinction-0.png
    A doc/manual/source/images/us_extinction-00.png
    A doc/manual/source/images/us_extinction-000.png
    A doc/manual/source/images/us_extinction-1.png
    A doc/manual/source/images/us_extinction-2.png
    A doc/manual/source/images/us_extinction-3.png
    A doc/manual/source/images/us_fds_filemanager-0.png
    A doc/manual/source/images/us_fds_filemanager-1.png
    A doc/manual/source/images/us_fds_filemanager-2.png
    A doc/manual/source/images/us_fds_filemanager-3.png
    A doc/manual/source/images/us_fds_filemanager-4.png
    A doc/manual/source/images/us_investigator-2.png
    A doc/manual/source/images/us_investigator.png
    A doc/manual/source/images/us_modelmetrics-0.png
    A doc/manual/source/images/us_modmet_report.png
    A doc/manual/source/images/us_project.png
    A doc/manual/source/images/us_project1.png
    A doc/manual/source/images/us_project2.png
    A doc/manual/source/images/us_project3.png
    A doc/manual/source/images/us_project_add-supdata.png
    A doc/manual/source/images/us_project_edit-supdata.png
    A doc/manual/source/images/us_project_web.png
    A doc/manual/source/images/us_project_webed.png
    A doc/manual/source/images/us_solution1.png
    A doc/manual/source/images/us_solution2.png
    A doc/manual/source/images/us_solution3.png
    A doc/manual/source/images/us_spectrum-0.png
    A doc/manual/source/images/us_spectrum-1.png
    A doc/manual/source/images/us_spectrum-load.png
    A doc/manual/source/images/usfont-1.png
    A doc/manual/source/images/usfont-2.png
    A doc/manual/source/images/vhw_combine-combo.png
    A doc/manual/source/images/vhw_combine-envel.png
    A doc/manual/source/images/vhw_combine-selrun.png
    A doc/manual/source/images/vhw_combine.png
    A doc/manual/source/images/vhw_distribution.png
    A doc/manual/source/images/vhw_enh_groups.png
    A doc/manual/source/images/vhw_enh_groups.png6-33-11.png
    A doc/manual/source/images/vhw_enh_groups_res.png
    A doc/manual/source/images/vhw_enhanced.png
    A doc/manual/source/images/vhw_histogram.png
    A doc/manual/source/images/xpn_viewer-loaded.png
    A doc/manual/source/images/xpn_viewer-saved.png
    A doc/manual/source/images/xpn_viewer.png
    A doc/manual/source/images/zvalue_eq.png
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/model_editor.rst
    M doc/manual/source/mwl_spectra.rst
    M doc/manual/source/mwlr_viewer.rst
    M doc/manual/source/pcsa/index.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_adv.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_mlines.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pcsa/pcsa_rpscan.rst
    M doc/manual/source/predict1.rst
    M doc/manual/source/predict2.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/register.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/requirements.txt
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/sassoc.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/temp.txt
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/tmst_viewer.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_extinction.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_modelmetrics.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_distrib_plot.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  fix: change qthelp url to use manual instead of doc, use right project structure for images and update links


  Commit: dd6f8d6767fa98ae4f35d21e7e5411f7f1f1eb17
      https://github.com/ehb54/ultrascan3/commit/dd6f8d6767fa98ae4f35d21e7e5411f7f1f1eb17
  Author: Saeed <samo38:github>
  Date:   2026-03-06 (Fri, 06 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  use Microsoft format, add overlap function


  Commit: e9f9ae1d960fb6e262803ee6b522247b68cf8894
      https://github.com/ehb54/ultrascan3/commit/e9f9ae1d960fb6e262803ee6b522247b68cf8894
  Author: Saeed <samo38:github>
  Date:   2026-03-06 (Fri, 06 Mar 2026)

  Changed paths:
    R README.linguist
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/libus_gui.pro
    M gui/us_spectrodata.h
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    R propignore
    R proppng
    R proptext
    R qwtplot3d/lingua_de.ts
    M test/utils/test_us_crypto.cpp
    M utils/libus_utils.pro
    M utils/us_crypto.cpp
    M utils/us_crypto.h

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_747


  Commit: b33c9b1cddd853e103542e10c4328830fc59e944
      https://github.com/ehb54/ultrascan3/commit/b33c9b1cddd853e103542e10c4328830fc59e944
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-06 (Fri, 06 Mar 2026)

  Changed paths:
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M doc/manual/CMakeLists.txt
    R doc/manual/StageAssistant.cmake
    M programs/us/CMakeLists.txt
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  mod: windows and macos qt assistant fix


  Commit: adb74a9f1e5a1e238c264228544137f56a4125b5
      https://github.com/ehb54/ultrascan3/commit/adb74a9f1e5a1e238c264228544137f56a4125b5
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-06 (Fri, 06 Mar 2026)

  Changed paths:
    M scripts/build.ps1

  Log Message:
  -----------
  fix: builddir set at the beginning


  Commit: cea2ea0e77baf6dbcc9097b3062ede36ca70f800
      https://github.com/ehb54/ultrascan3/commit/cea2ea0e77baf6dbcc9097b3062ede36ca70f800
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-06 (Fri, 06 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M doc/manual/CMakeLists.txt
    M scripts/build.ps1

  Log Message:
  -----------
  fix: windows path issues


  Commit: 99a443309500f6d44fde4d4ba640770dfadeec24
      https://github.com/ehb54/ultrascan3/commit/99a443309500f6d44fde4d4ba640770dfadeec24
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-06 (Fri, 06 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M doc/manual/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp

  Log Message:
  -----------
  fix: windows missing dll


  Commit: 32f3fd93bf886595a3d9b9b0335a74cf5645913a
      https://github.com/ehb54/ultrascan3/commit/32f3fd93bf886595a3d9b9b0335a74cf5645913a
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Initialize `tsobj` with `TIMESTATE_TYPE::ORIGINAL` in `US_TimeState`.


  Commit: f6095ff611d0c2f9f6a04567e6f2a74535dd45fd
      https://github.com/ehb54/ultrascan3/commit/f6095ff611d0c2f9f6a04567e6f2a74535dd45fd
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Initialize `tsobj` with `TIMESTATE_TYPE::ORIGINAL` in `us_xpn_data`.


  Commit: 399ad6ee7636d4885c37adff02b723d1e6af48c9
      https://github.com/ehb54/ultrascan3/commit/399ad6ee7636d4885c37adff02b723d1e6af48c9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    M scripts/build.sh
    M utils/CMakeLists.txt

  Log Message:
  -----------
  add: linux cmake packaging


  Commit: c3215226c1e826bd7c620115a98fe3694cfe771e
      https://github.com/ehb54/ultrascan3/commit/c3215226c1e826bd7c620115a98fe3694cfe771e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M scripts/build.sh
    M utils/us_memory.cpp

  Log Message:
  -----------
  fix: cross platform page size


  Commit: 16d1f75e51f11ad87c8f18b11e0a8a2bb755ea44
      https://github.com/ehb54/ultrascan3/commit/16d1f75e51f11ad87c8f18b11e0a8a2bb755ea44
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/build.ps1
    M scripts/build.sh
    M vcpkg.json

  Log Message:
  -----------
  fix: assistant on linux


  Commit: 4cff648f9ba827db6e67e9cedb1a93953e8a0f76
      https://github.com/ehb54/ultrascan3/commit/4cff648f9ba827db6e67e9cedb1a93953e8a0f76
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M test/utils/test_us_time_state.cpp
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_cfa_data.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #384 from ehb54/lukas/timestate

Add TIMESTATE_TYPE and IMPORT_TYPE support with refactorings


  Commit: 5ab554ce68ae411774740695115c51b480df8c8a
      https://github.com/ehb54/ultrascan3/commit/5ab554ce68ae411774740695115c51b480df8c8a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  fix: vcpkg cache clear


  Commit: a8b6e9963d8ed447dc737af6b4e3b69c3894945f
      https://github.com/ehb54/ultrascan3/commit/a8b6e9963d8ed447dc737af6b4e3b69c3894945f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  fix: vcpkg cache clear fix


  Commit: 19f656eb532b2218880402623455153763d66d50
      https://github.com/ehb54/ultrascan3/commit/19f656eb532b2218880402623455153763d66d50
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  fix: assistant now copied to bin on dev build


  Commit: 75e0dc23de6fbdd330b322115c640d973e916d02
      https://github.com/ehb54/ultrascan3/commit/75e0dc23de6fbdd330b322115c640d973e916d02
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  fix: assistant find update


  Commit: 57f162e692e1a548bb426454e7e768e6f68b1bc4
      https://github.com/ehb54/ultrascan3/commit/57f162e692e1a548bb426454e7e768e6f68b1bc4
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: program path issue


  Commit: 4700970e14e8ef1bf44b3fe91efd8dbcd15ba544
      https://github.com/ehb54/ultrascan3/commit/4700970e14e8ef1bf44b3fe91efd8dbcd15ba544
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  fix: assistant not found


  Commit: 14d6c7e63b928fb3a73559fdafa9426502eda98c
      https://github.com/ehb54/ultrascan3/commit/14d6c7e63b928fb3a73559fdafa9426502eda98c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  fix: guard specific macos required tools


  Commit: 1c6be4ed0464373db7a5a1a6a780f17bc12dbcf5
      https://github.com/ehb54/ultrascan3/commit/1c6be4ed0464373db7a5a1a6a780f17bc12dbcf5
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake

  Log Message:
  -----------
  fix: missing library in pkg


  Commit: 216860fe02c9358e021e6a54b84aa2aa0e462a99
      https://github.com/ehb54/ultrascan3/commit/216860fe02c9358e021e6a54b84aa2aa0e462a99
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  fix: rcc error


  Commit: be038ad56e172897c3f18b8a1319fced62a708a0
      https://github.com/ehb54/ultrascan3/commit/be038ad56e172897c3f18b8a1319fced62a708a0
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/packaging/linux/LinuxDeploy.cmake

  Log Message:
  -----------
  fix: update plugin directory


  Commit: 87c38bbe59db529cf02b7887c7bfe57ebc8e62da
      https://github.com/ehb54/ultrascan3/commit/87c38bbe59db529cf02b7887c7bfe57ebc8e62da
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-07 (Sat, 07 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake

  Log Message:
  -----------
  add: readme


  Commit: 75648618e7f79fde451a6e9f2cf9023d8ed19140
      https://github.com/ehb54/ultrascan3/commit/75648618e7f79fde451a6e9f2cf9023d8ed19140
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-08 (Sun, 08 Mar 2026)

  Changed paths:
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h

  Log Message:
  -----------
  Add `load_timestate` methods to `US_ConvertScan` for handling time state from disk or database.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: fb3e874b186e61a3c3b696be002fa6134d681c4e
      https://github.com/ehb54/ultrascan3/commit/fb3e874b186e61a3c3b696be002fa6134d681c4e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-08 (Sun, 08 Mar 2026)

  Changed paths:
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h

  Log Message:
  -----------
  Merge pull request #386 from ehb54/lukas/us_pseudo_absorbance_timestate

us_pseudo_absorbance: transfer timestate


  Commit: f4323bc883bb8996c6e627bfb9b8295063ef176f
      https://github.com/ehb54/ultrascan3/commit/f4323bc883bb8996c6e627bfb9b8295063ef176f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-08 (Sun, 08 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    M programs/CMakeLists.txt
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M scripts/build.sh

  Log Message:
  -----------
  fix: hpc build


  Commit: c515903ce23bec6067e47ed10ae663518f3de230
      https://github.com/ehb54/ultrascan3/commit/c515903ce23bec6067e47ed10ae663518f3de230
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-08 (Sun, 08 Mar 2026)

  Changed paths:
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  mod: use all cores with CI runners


  Commit: 7a8a012754d242634bca20501e1a1c94be231d6c
      https://github.com/ehb54/ultrascan3/commit/7a8a012754d242634bca20501e1a1c94be231d6c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-08 (Sun, 08 Mar 2026)

  Changed paths:
    M CMakePresets.json
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  fix: CI runners and hpc build


  Commit: 5277352caa620430b2bf8a580f9f10d43218d930
      https://github.com/ehb54/ultrascan3/commit/5277352caa620430b2bf8a580f9f10d43218d930
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-08 (Sun, 08 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  fix: not all dependencies found


  Commit: 60b1b16425fcda080aea3bfac20f1abad9e8bc32
      https://github.com/ehb54/ultrascan3/commit/60b1b16425fcda080aea3bfac20f1abad9e8bc32
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-08 (Sun, 08 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  fix: dependenies added


  Commit: 97cbb1a37275a33ef389b6fc7c2132ed4aaf52f4
      https://github.com/ehb54/ultrascan3/commit/97cbb1a37275a33ef389b6fc7c2132ed4aaf52f4
  Author: Saeed <samo38:github>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  us_spectrum: large updates


  Commit: 15ea3878148a0987efd94cdedb07b9e3db570cfd
      https://github.com/ehb54/ultrascan3/commit/15ea3878148a0987efd94cdedb07b9e3db570cfd
  Author: Saeed <samo38:github>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  finish the fit function


  Commit: 1c6be507a58b5e30438f1565b772e544ee297d86
      https://github.com/ehb54/ultrascan3/commit/1c6be507a58b5e30438f1565b772e544ee297d86
  Author: Saeed <samo38:github>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  improve find_lambda function


  Commit: 3b29d9afdd3d29c7e33af7f0b989ccf1c642bc8c
      https://github.com/ehb54/ultrascan3/commit/3b29d9afdd3d29c7e33af7f0b989ccf1c642bc8c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    A scripts/bootstrap-deps.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  fix: bootstrap deps


  Commit: 4975707ad3f001539ceeea7d716043118c23d07a
      https://github.com/ehb54/ultrascan3/commit/4975707ad3f001539ceeea7d716043118c23d07a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    M scripts/bootstrap-deps.sh

  Log Message:
  -----------
  fix: qt5 tools overlay


  Commit: e7e0613e5d7d234f835e4e9490416e0a7f5b9803
      https://github.com/ehb54/ultrascan3/commit/e7e0613e5d7d234f835e4e9490416e0a7f5b9803
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M scripts/bootstrap-deps.sh
    M scripts/bootstrap-macos.sh
    M scripts/build.sh
    A us-build

  Log Message:
  -----------
  add: bash wrapper


  Commit: b93b52b3acb64a650854a16f3983473f49becee9
      https://github.com/ehb54/ultrascan3/commit/b93b52b3acb64a650854a16f3983473f49becee9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M scripts/build.ps1

  Log Message:
  -----------
  mod: make profile positional for powershell


  Commit: dfec7b06f5af8e9ad31d7b4c682197a103bd5fb1
      https://github.com/ehb54/ultrascan3/commit/dfec7b06f5af8e9ad31d7b4c682197a103bd5fb1
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M scripts/bootstrap-windows.ps1
    M scripts/build.bat

  Log Message:
  -----------
  fix: convert -- pkg to - pkg for windows


  Commit: 2f98f90faa5b640815d571359919c09034a266c1
      https://github.com/ehb54/ultrascan3/commit/2f98f90faa5b640815d571359919c09034a266c1
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M scripts/bootstrap-windows.ps1

  Log Message:
  -----------
  fix: getwin


  Commit: 7249d6b2d508075f65d61b2643639c789db68d8e
      https://github.com/ehb54/ultrascan3/commit/7249d6b2d508075f65d61b2643639c789db68d8e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-09 (Mon, 09 Mar 2026)

  Changed paths:
    M scripts/bootstrap-windows.ps1

  Log Message:
  -----------
  fix: add chocolatey fallback for ci


  Commit: fd116b43987cda26a351438dcd70082a7c27ce17
      https://github.com/ehb54/ultrascan3/commit/fd116b43987cda26a351438dcd70082a7c27ce17
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-03-10 (Tue, 10 Mar 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M test/utils/test_us_time_state.cpp
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_cfa_data.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-670


  Commit: 12ffcd24c66797e3e2d49303bce6232cc9c13d7c
      https://github.com/ehb54/ultrascan3/commit/12ffcd24c66797e3e2d49303bce6232cc9c13d7c
  Author: Saeed <github.com/samo38>
  Date:   2026-03-10 (Tue, 10 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  us_spectrum: finilized the widget


  Commit: 21473e24e6f59d7d4edaba9f4ea29e1174a8f579
      https://github.com/ehb54/ultrascan3/commit/21473e24e6f59d7d4edaba9f4ea29e1174a8f579
  Author: Saeed <github.com/samo38>
  Date:   2026-03-10 (Tue, 10 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  reformat some lines


  Commit: 55d03f81788bc585236ce0b642d89abc3293ad3a
      https://github.com/ehb54/ultrascan3/commit/55d03f81788bc585236ce0b642d89abc3293ad3a
  Author: Saeed <github.com/samo38>
  Date:   2026-03-10 (Tue, 10 Mar 2026)

  Changed paths:
    R README.linguist
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/libus_gui.pro
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    R propignore
    R proppng
    R proptext
    R qwtplot3d/lingua_de.ts
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_time_state.cpp
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_748


  Commit: c3dd2ab6d66893c243fe40ba02010696a7b78d52
      https://github.com/ehb54/ultrascan3/commit/c3dd2ab6d66893c243fe40ba02010696a7b78d52
  Author: Saeed <github.com/samo38>
  Date:   2026-03-10 (Tue, 10 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  reformat comments


  Commit: 74f3ba1cd3b6646dce0b4638c98b2707dff60f2e
      https://github.com/ehb54/ultrascan3/commit/74f3ba1cd3b6646dce0b4638c98b2707dff60f2e
  Author: Saeed <github.com/samo38>
  Date:   2026-03-10 (Tue, 10 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  us_spectrum.h: removed us_math2.h


  Commit: 1dbeb030075307c5652d506be95a2186a0c22724
      https://github.com/ehb54/ultrascan3/commit/1dbeb030075307c5652d506be95a2186a0c22724
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Refactor `US_Plot`: enhance double-click interactions, add zoom configuration, and improve curve/axis management with event filter.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 72c834e6d8fa6d6cd9d3b1d1eb90cc7410670c01
      https://github.com/ehb54/ultrascan3/commit/72c834e6d8fa6d6cd9d3b1d1eb90cc7410670c01
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h

  Log Message:
  -----------
  Add "Click Exclusion Mode" in `US_Edit` with hover tooltips and enhanced scan selection functionality.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: ced5c0cf9086f5a21a308bcb214f061a75e89aab
      https://github.com/ehb54/ultrascan3/commit/ced5c0cf9086f5a21a308bcb214f061a75e89aab
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Add null pointer check for `plot->getZoomer()` in `US_Edit` to prevent potential crashes.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: b5607cb3d6296c0e48283cc6dd1a804c051dd8d9
      https://github.com/ehb54/ultrascan3/commit/b5607cb3d6296c0e48283cc6dd1a804c051dd8d9
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Remove redundant state machine changes in "Click Exclusion Mode" toggle of `US_Edit`.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: d548b54d3bbac75ffbf270b99643e5cf26257968
      https://github.com/ehb54/ultrascan3/commit/d548b54d3bbac75ffbf270b99643e5cf26257968
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M gui/us_plot.h

  Log Message:
  -----------
  Initialize members in `CurveDistance` struct with default values to improve stability and prevent undefined behavior.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: f3e23f8189d66b9641b37fb2c54b38119d2ef2ec
      https://github.com/ehb54/ultrascan3/commit/f3e23f8189d66b9641b37fb2c54b38119d2ef2ec
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Refactor `US_Plot`: add new double-click connections, refactor axis configuration, and enhance zoomer signal handling.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: d73cc2971816653d17d72f1785291c00b96b0c8b
      https://github.com/ehb54/ultrascan3/commit/d73cc2971816653d17d72f1785291c00b96b0c8b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Update `US_Plot::createZoomer` to adjust `US_Zoomer` constructor arguments for axis configuration.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 45140eeddd64e45d6b5c87061f79c9aefc3ce25e
      https://github.com/ehb54/ultrascan3/commit/45140eeddd64e45d6b5c87061f79c9aefc3ce25e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    M programs/us/revision.sh
    M scripts/build.ps1

  Log Message:
  -----------
  fix: windows CI vcpkg cache usage


  Commit: 1ec6ec52d283b6c710abe095ebcad82139a64ae3
      https://github.com/ehb54/ultrascan3/commit/1ec6ec52d283b6c710abe095ebcad82139a64ae3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M CMakePresets.json
    M scripts/build.sh

  Log Message:
  -----------
  add: macos intel build


  Commit: 39ad33c5c781b0f007822456803df7d591795fe7
      https://github.com/ehb54/ultrascan3/commit/39ad33c5c781b0f007822456803df7d591795fe7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M scripts/build.ps1

  Log Message:
  -----------
  fix: vcpkg CI handling


  Commit: 7fad3a4dfaa187ad4eb94554cedbe3ec6cf56773
      https://github.com/ehb54/ultrascan3/commit/7fad3a4dfaa187ad4eb94554cedbe3ec6cf56773
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M programs/us_mpi_analysis/revision.sh

  Log Message:
  -----------
  fix: change revision to git_revision to be consistent with other programs


  Commit: b4417a6bfd0cfcc840668d21e88718e957734e47
      https://github.com/ehb54/ultrascan3/commit/b4417a6bfd0cfcc840668d21e88718e957734e47
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    R README.linguist
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/libus_gui.pro
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    R propignore
    R proppng
    R proptext
    R qwtplot3d/lingua_de.ts
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_time_state.cpp
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: f0c8ede548bfb3a6f2380059dd1aacf09c6a7883
      https://github.com/ehb54/ultrascan3/commit/f0c8ede548bfb3a6f2380059dd1aacf09c6a7883
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M scripts/bootstrap-macos.sh

  Log Message:
  -----------
  fix: add missing dependencies


  Commit: 09eeb4bec49931c943f732f024f1166b882c3e3a
      https://github.com/ehb54/ultrascan3/commit/09eeb4bec49931c943f732f024f1166b882c3e3a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    R README.linguist
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/libus_gui.pro
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_config/us_config.pro
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    R propignore
    R proppng
    R proptext
    R qwtplot3d/lingua_de.ts
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_time_state.cpp
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/527-enhancement-sphinx-migration-2' into 527-enhancement-sphinx-migration-2


  Commit: 51ba58286eaaa41af877ff9330d19560633e1c16
      https://github.com/ehb54/ultrascan3/commit/51ba58286eaaa41af877ff9330d19560633e1c16
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M scripts/bootstrap-macos.sh

  Log Message:
  -----------
  fix: add missing dependencies


  Commit: 21a5f4a7ad52a67040b9426ed30a082038813498
      https://github.com/ehb54/ultrascan3/commit/21a5f4a7ad52a67040b9426ed30a082038813498
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: reduce linux disk space usage


  Commit: 12b7e30a17e5c86f8e9d4960f7e8da86d67b3b4f
      https://github.com/ehb54/ultrascan3/commit/12b7e30a17e5c86f8e9d4960f7e8da86d67b3b4f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: removed vcpkg folder creation


  Commit: ece15a944fb55077213717e00f084056004367a7
      https://github.com/ehb54/ultrascan3/commit/ece15a944fb55077213717e00f084056004367a7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-11 (Wed, 11 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/windows/WinDeploy.cmake

  Log Message:
  -----------
  mod: change qt warnings an error to force build to stop


  Commit: 466789a804273570c11c7cb44bf28924caa363df
      https://github.com/ehb54/ultrascan3/commit/466789a804273570c11c7cb44bf28924caa363df
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M test/utils/test_us_time_state.cpp
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_cfa_data.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/masterpassword_change


  Commit: 80474c759ff865d72c8c6043ba64d38bf98e1e15
      https://github.com/ehb54/ultrascan3/commit/80474c759ff865d72c8c6043ba64d38bf98e1e15
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: reduce to 2 cores for ubuntu


  Commit: ae52535acb54fede063aaaefd18be0c4ec92474b
      https://github.com/ehb54/ultrascan3/commit/ae52535acb54fede063aaaefd18be0c4ec92474b
  Author: Saeed <samo38:github>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M test/utils/test_us_time_state.cpp
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_cfa_data.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_747


  Commit: 2e81015b2e85d24c6d0619f563c9053fcb5de9e1
      https://github.com/ehb54/ultrascan3/commit/2e81015b2e85d24c6d0619f563c9053fcb5de9e1
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge pull request #373 from samo38/ticket_747

Ticket 747: add US_Help to us_legacy_converter, us_query_rmsd, us_extinction, us_spectrum, us_ramp


  Commit: e9f0952dea5d8bb82a866082b546997a3e457ec4
      https://github.com/ehb54/ultrascan3/commit/e9f0952dea5d8bb82a866082b546997a3e457ec4
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-670


  Commit: c4af75ba6a8e299d819034f87528f9d6997e469f
      https://github.com/ehb54/ultrascan3/commit/c4af75ba6a8e299d819034f87528f9d6997e469f
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: 0f81d3f0d1fb567b1e570ed90147a17f49e57c1f
      https://github.com/ehb54/ultrascan3/commit/0f81d3f0d1fb567b1e570ed90147a17f49e57c1f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/windows/WinDeploy.cmake
    R scripts/bootstrap-deps.sh
    A scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/build.sh
    M utils/CMakeLists.txt
    M vcpkg.json

  Log Message:
  -----------
  mod: move checks to bootstrap


  Commit: 4ff50388194860753c3e8bc4d697e944ce0f1641
      https://github.com/ehb54/ultrascan3/commit/4ff50388194860753c3e8bc4d697e944ce0f1641
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-12 (Thu, 12 Mar 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/527-enhancement-sphinx-migration-2' into 527-enhancement-sphinx-migration-2


  Commit: 73d3d9961c360d61b70b25d54f762c7f7435325e
      https://github.com/ehb54/ultrascan3/commit/73d3d9961c360d61b70b25d54f762c7f7435325e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/masterpassword_change


  Commit: a54f8e2bc39c26f3e2f95dae43da15eb743e4d25
      https://github.com/ehb54/ultrascan3/commit/a54f8e2bc39c26f3e2f95dae43da15eb743e4d25
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_edit_scan_exclude_click


  Commit: 82349a16124679984a45c562feb3f2583dbdb531
      https://github.com/ehb54/ultrascan3/commit/82349a16124679984a45c562feb3f2583dbdb531
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: add platform safe check


  Commit: 8fbf539a26017728861e732dc1d18eb23eb5767b
      https://github.com/ehb54/ultrascan3/commit/8fbf539a26017728861e732dc1d18eb23eb5767b
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Include OpenSSL applink for MSVC on Windows

Add OpenSSL applink shim for MSVC on Windows.


  Commit: 062c3d2366cc1939df31abf0a90ee9aa81093ffe
      https://github.com/ehb54/ultrascan3/commit/062c3d2366cc1939df31abf0a90ee9aa81093ffe
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M utils/us_timer.h

  Log Message:
  -----------
  Replace 'using namespace std' with std:: in us_timer.h

Prevent windows specific type definition conflicts caused by using namespace std;


  Commit: d285dea10ab7bcc93c14b4f74e336121a728f25a
      https://github.com/ehb54/ultrascan3/commit/d285dea10ab7bcc93c14b4f74e336121a728f25a
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M vcpkg.json

  Log Message:
  -----------
  Update builtin-baseline version in vcpkg.json


  Commit: 2528e2d95ef721c90585880700173e01e85eaa41
      https://github.com/ehb54/ultrascan3/commit/2528e2d95ef721c90585880700173e01e85eaa41
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/us/CMakeLists.txt

  Log Message:
  -----------
  Enhance CMakeLists for Qt6 post-build handling

Added post-build commands for Qt6 integration in Debug and Release modes.


  Commit: 52e46a6c204f209f206de1b17187485510b50872
      https://github.com/ehb54/ultrascan3/commit/52e46a6c204f209f206de1b17187485510b50872
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/us/CMakeLists.txt

  Log Message:
  -----------
  Refactor post-build commands for Qt6 on Windows


  Commit: 428287d058712bdf7736b86456a19b29730bec50
      https://github.com/ehb54/ultrascan3/commit/428287d058712bdf7736b86456a19b29730bec50
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M utils/us_timer.h

  Log Message:
  -----------
  Add map include to us_timer.h


  Commit: b1e9456925a223045bd903ef52c4096e0e3675dc
      https://github.com/ehb54/ultrascan3/commit/b1e9456925a223045bd903ef52c4096e0e3675dc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  Add OpenSSL applink condition for MSVC on Windows


  Commit: 844f0378f9d93d9976788b58bd853ff5baafd865
      https://github.com/ehb54/ultrascan3/commit/844f0378f9d93d9976788b58bd853ff5baafd865
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...


  Commit: ef226636cf28fac5f0b62c8cc7535c518336f7cd
      https://github.com/ehb54/ultrascan3/commit/ef226636cf28fac5f0b62c8cc7535c518336f7cd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-13 (Fri, 13 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp

  Log Message:
  -----------
  [1]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...


  Commit: 008ab8725529f70ff36e4845202c893ddb0e4213
      https://github.com/ehb54/ultrascan3/commit/008ab8725529f70ff36e4845202c893ddb0e4213
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp

  Log Message:
  -----------
  [2]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...


  Commit: cee06353e7b931a3f580d1bffbeb9f2326d63532
      https://github.com/ehb54/ultrascan3/commit/cee06353e7b931a3f580d1bffbeb9f2326d63532
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp

  Log Message:
  -----------
  [3]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...


  Commit: d9676faa3a7a6a92c56faa175bcd24c240a39b0d
      https://github.com/ehb54/ultrascan3/commit/d9676faa3a7a6a92c56faa175bcd24c240a39b0d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M utils/us_timer.h
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #389 from ehb54/lukas/qt6-msvc

CMake Qt6 windows compile MSVC


  Commit: 5c16c03541cbbc99e4d1d5e6304244b7c5cd261d
      https://github.com/ehb54/ultrascan3/commit/5c16c03541cbbc99e4d1d5e6304244b7c5cd261d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M utils/us_timer.h
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into lukas/masterpassword_change


  Commit: ffaae2039c0f2f0337ba9cde3e4667ade9f04c5c
      https://github.com/ehb54/ultrascan3/commit/ffaae2039c0f2f0337ba9cde3e4667ade9f04c5c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M utils/us_timer.h
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_edit_scan_exclude_click


  Commit: 5d9bc472d7f67b7cc2de87cfa943d8db9b3bc1c5
      https://github.com/ehb54/ultrascan3/commit/5d9bc472d7f67b7cc2de87cfa943d8db9b3bc1c5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp

  Log Message:
  -----------
  [4]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...


  Commit: f403e0ca772e609f1f064e09815e424e676e96ba
      https://github.com/ehb54/ultrascan3/commit/f403e0ca772e609f1f064e09815e424e676e96ba
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  Fix methodChanged to suppress signal and reset checkboxes


  Commit: 4c67ee8e4cb27a2a60a41177608c3cf2565db76a
      https://github.com/ehb54/ultrascan3/commit/4c67ee8e4cb27a2a60a41177608c3cf2565db76a
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_plot3d.cpp

  Log Message:
  -----------
  Remove redundant assignment to tdata

Prevent memory corruption


  Commit: 6437b90d6e57f06e5aafbea01753415627877e6b
      https://github.com/ehb54/ultrascan3/commit/6437b90d6e57f06e5aafbea01753415627877e6b
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp

  Log Message:
  -----------
  Update condition for vbar20 comparison


  Commit: 4c73a0c1ae974bfad85180a15588c4203f772bae
      https://github.com/ehb54/ultrascan3/commit/4c73a0c1ae974bfad85180a15588c4203f772bae
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  Fix typo in comment and streamline methodChanged


  Commit: 24cd6bc5d78c14e84c05915d5b043c7628d0c084
      https://github.com/ehb54/ultrascan3/commit/24cd6bc5d78c14e84c05915d5b043c7628d0c084
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_plot3d.cpp

  Log Message:
  -----------
  Merge pull request #391 from ehb54/lukas/us_mwl_spectra_3dplot_reversey

Remove redundant assignment to tdata


  Commit: cd22d118497ba373e73cde824f09464646c78f6e
      https://github.com/ehb54/ultrascan3/commit/cd22d118497ba373e73cde824f09464646c78f6e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_plot3d.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_analyte_protein_vbar_no_sequence


  Commit: a92e13702d0a02ed4fddd7be57df0c9ec134c449
      https://github.com/ehb54/ultrascan3/commit/a92e13702d0a02ed4fddd7be57df0c9ec134c449
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp

  Log Message:
  -----------
  Merge pull request #392 from ehb54/lukas/us_analyte_protein_vbar_no_sequence

Update condition for vbar20 comparison


  Commit: 648e2c616df93b8cb3f16672c3315e44e99a1cdd
      https://github.com/ehb54/ultrascan3/commit/648e2c616df93b8cb3f16672c3315e44e99a1cdd
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_plot3d.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_ddist_combine_all_checkbox


  Commit: 524fb756825b453194c34611c2ce7624e62f7f53
      https://github.com/ehb54/ultrascan3/commit/524fb756825b453194c34611c2ce7624e62f7f53
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_plot3d.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_edit_scan_exclude_click


  Commit: 45a5699260fb89e53971aee6bbf0b5f13d1b40fa
      https://github.com/ehb54/ultrascan3/commit/45a5699260fb89e53971aee6bbf0b5f13d1b40fa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_plot3d.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/masterpassword_change


  Commit: 8a2d982f8e8906a85bfe363487622d59a1ff361e
      https://github.com/ehb54/ultrascan3/commit/8a2d982f8e8906a85bfe363487622d59a1ff361e
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_plot3d.cpp
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M utils/us_timer.h
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: 6d361b64fc8f314fe8399f028d2c79ef9d0e417b
      https://github.com/ehb54/ultrascan3/commit/6d361b64fc8f314fe8399f028d2c79ef9d0e417b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: clean after build set


  Commit: 5b81b9c41fc973670663047afba591d6edaa898c
      https://github.com/ehb54/ultrascan3/commit/5b81b9c41fc973670663047afba591d6edaa898c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/windows/WinDeploy.cmake

  Log Message:
  -----------
  fix: packaging


  Commit: 10e620037c83dddc66d518ab28e33eb36c3e3c17
      https://github.com/ehb54/ultrascan3/commit/10e620037c83dddc66d518ab28e33eb36c3e3c17
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-14 (Sat, 14 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_plot3d.cpp
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M utils/us_timer.h
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-670


  Commit: 07c6d8042bd25e59ca20ca5bd16ed3b6ff8b321c
      https://github.com/ehb54/ultrascan3/commit/07c6d8042bd25e59ca20ca5bd16ed3b6ff8b321c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-15 (Sun, 15 Mar 2026)

  Changed paths:
    M programs/us_config/us_admin.cpp

  Log Message:
  -----------
  Merge pull request #385 from ehb54/lukas/masterpassword_change

Refactor password re-encryption logic


  Commit: ed3ecfca235f46d9da27159afb01288bbcb42cd4
      https://github.com/ehb54/ultrascan3/commit/ed3ecfca235f46d9da27159afb01288bbcb42cd4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-15 (Sun, 15 Mar 2026)

  Changed paths:
    M programs/us_config/us_admin.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_ddist_combine_all_checkbox


  Commit: 3e5bea2d6f8973b1443f2db3438bbbcfe128378f
      https://github.com/ehb54/ultrascan3/commit/3e5bea2d6f8973b1443f2db3438bbbcfe128378f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-15 (Sun, 15 Mar 2026)

  Changed paths:
    M programs/us_config/us_admin.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_edit_scan_exclude_click


  Commit: 3afad49842a3c53daabf741428b683cb8e86837c
      https://github.com/ehb54/ultrascan3/commit/3afad49842a3c53daabf741428b683cb8e86837c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-15 (Sun, 15 Mar 2026)

  Changed paths:
    M programs/us_config/us_admin.cpp

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: afdf12344c5555d4130fa310bf352f2c27bbdadc
      https://github.com/ehb54/ultrascan3/commit/afdf12344c5555d4130fa310bf352f2c27bbdadc
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-15 (Sun, 15 Mar 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/qttools.disable/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools.disable/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools.disable/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools.disable/windeployqt.debug.bat
    R buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    R buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat

  Log Message:
  -----------
  test remove qttools overlay


  Commit: 691c2112f822e5f82f6f153dbb8d568663367a2c
      https://github.com/ehb54/ultrascan3/commit/691c2112f822e5f82f6f153dbb8d568663367a2c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-15 (Sun, 15 Mar 2026)

  Changed paths:
    M programs/us_config/us_admin.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/527-enhancement-sphinx-migration-2' into 527-enhancement-sphinx-migration-2


  Commit: 447c06a32ef5ade7850e1391500673c408a9c5e4
      https://github.com/ehb54/ultrascan3/commit/447c06a32ef5ade7850e1391500673c408a9c5e4
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Refactor `US_Zoomer` and `US_DoubleClickEventFilter`: enhance zoom base initialization, update rubber band/tracker pen settings, and improve double-click handling for axes and curves.


  Commit: a73d1f0d1b712c4345cbd63219466ef87ccabfdb
      https://github.com/ehb54/ultrascan3/commit/a73d1f0d1b712c4345cbd63219466ef87ccabfdb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [5]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...


  Commit: 28dafe4f6fe91d2a19d25a13dca2a9700c8524c1
      https://github.com/ehb54/ultrascan3/commit/28dafe4f6fe91d2a19d25a13dca2a9700c8524c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  [6]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...


  Commit: 88e5262aa244a552236f70eb1b00274e245d2f90
      https://github.com/ehb54/ultrascan3/commit/88e5262aa244a552236f70eb1b00274e245d2f90
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [6a]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...ush


  Commit: 5e19ef3b84e9f0542544c16ad99f1909133b6197
      https://github.com/ehb54/ultrascan3/commit/5e19ef3b84e9f0542544c16ad99f1909133b6197
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [6b]GMP: Report -- test inclusion of the replica groups consisting of 1 channel only into Report...ush


  Commit: cfd2bf22ab1f023d0f1bf0c3677f13218d99b4e3
      https://github.com/ehb54/ultrascan3/commit/cfd2bf22ab1f023d0f1bf0c3677f13218d99b4e3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_plot3d.cpp
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us_config/us_admin.cpp
    M utils/us_timer.h
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #393 from ehb54/main

Merge main into alexey-dev-issue785


  Commit: 5304d85db5ed89082fe2cf86d0fd9f3f3fbd65c3
      https://github.com/ehb54/ultrascan3/commit/5304d85db5ed89082fe2cf86d0fd9f3f3fbd65c3
  Author: Saeed <github.com/samo38>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_plot3d.cpp
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us_config/us_admin.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_ramp_gui.h
    M utils/us_timer.h
    M vcpkg.json

  Log Message:
  -----------
  merge upstream/main , resolved conflicts


  Commit: 5fbfc3b610b9edaa535c2cdde484daba5a1f6d23
      https://github.com/ehb54/ultrascan3/commit/5fbfc3b610b9edaa535c2cdde484daba5a1f6d23
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/windows/WinDeploy.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    M buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    M scripts/bootstrap-windows.ps1
    M scripts/build.ps1

  Log Message:
  -----------
  fix: restore patch for qt5-tools


  Commit: ee9314b8a10555d579148933ce5fb59dc77f25a5
      https://github.com/ehb54/ultrascan3/commit/ee9314b8a10555d579148933ce5fb59dc77f25a5
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M scripts/bootstrap-windows.ps1

  Log Message:
  -----------
  fix: nasm check and add supporting dlls to installation


  Commit: f9860bd8d1ac6f5c5c4a4b0dd90e3cb7f09bd131
      https://github.com/ehb54/ultrascan3/commit/f9860bd8d1ac6f5c5c4a4b0dd90e3cb7f09bd131
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-16 (Mon, 16 Mar 2026)

  Changed paths:
    M scripts/build.ps1
    M vcpkg.json

  Log Message:
  -----------
  mod: check path length is too long on qt 5


  Commit: 4365eb02a1c29a38a42fe848da39deab69e67715
      https://github.com/ehb54/ultrascan3/commit/4365eb02a1c29a38a42fe848da39deab69e67715
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    R buildsys/vcpkg/overlay-ports/qttools.disable/devendor-litehtml.patch
    R buildsys/vcpkg/overlay-ports/qttools.disable/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qttools.disable/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qttools.disable/windeployqt.debug.bat

  Log Message:
  -----------
  del: remove unused overlay


  Commit: c9f9553d1be9cca2abdbef64d64daa2688c9b977
      https://github.com/ehb54/ultrascan3/commit/c9f9553d1be9cca2abdbef64d64daa2688c9b977
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  Merge pull request #390 from ehb54/lukas/us_ddist_combine_all_checkbox

Change behavior of all button in combine discrete distributions


  Commit: 50ee53da3e470361bd6a9fa94454856cc21660a1
      https://github.com/ehb54/ultrascan3/commit/50ee53da3e470361bd6a9fa94454856cc21660a1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_edit_scan_exclude_click


  Commit: c6c251770d12273ef8519ef12212ecaf90df9c8a
      https://github.com/ehb54/ultrascan3/commit/c6c251770d12273ef8519ef12212ecaf90df9c8a
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h

  Log Message:
  -----------
  Merge pull request #388 from ehb54/lukas/us_edit_scan_exclude_click

Refactor US_Plot interactions and enhance US_Edit functionality


  Commit: efe1a2ba8b277a19ae50d1262c14239f9f9dac81
      https://github.com/ehb54/ultrascan3/commit/efe1a2ba8b277a19ae50d1262c14239f9f9dac81
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  add: missing linux packages libsm-dev libice-dev


  Commit: 84f1faaa0819a233d3023bd3ae0d75d2ccaf6430
      https://github.com/ehb54/ultrascan3/commit/84f1faaa0819a233d3023bd3ae0d75d2ccaf6430
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json

  Log Message:
  -----------
  add: port overlay for linux arm fix


  Commit: aae4ac3a14f0a1c0ce391cedb1844ac845045869
      https://github.com/ehb54/ultrascan3/commit/aae4ac3a14f0a1c0ce391cedb1844ac845045869
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Change encryption finalization to decryption


  Commit: 9454cb777d85cb65835ea5eb51fc05bc18d58e78
      https://github.com/ehb54/ultrascan3/commit/9454cb777d85cb65835ea5eb51fc05bc18d58e78
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  Implement EncryptDecryptTest for US_Crypto

Add unit test for encryption and decryption consistency


  Commit: 2c028de85502d48e60a380c61b93dc7a7e2f7727
      https://github.com/ehb54/ultrascan3/commit/2c028de85502d48e60a380c61b93dc7a7e2f7727
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  Add unit test for encryption with different passwords


  Commit: ac1ca1f8183d056ed7e98541ac5ac52d725b33f8
      https://github.com/ehb54/ultrascan3/commit/ac1ca1f8183d056ed7e98541ac5ac52d725b33f8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP-ABDE: Ranges & Upload check for ext. profiles -- while situations when extinction profiles for one or more analytes do not cover all wvls in Ranges are caught, the message is misleading and does not provide a hint for inability to proceed; capture exact message at the stage of living 7. Ranges panel & pass to Upload tab before enabling run submission...


  Commit: 8ba4b05b7f14586d7e527145ba6c464fd3dc3e4d
      https://github.com/ehb54/ultrascan3/commit/8ba4b05b7f14586d7e527145ba6c464fd3dc3e4d
  Author: Saeed <github.com/samo38>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  add wavelength limit picker, add checkbox for db loadings


  Commit: efd337809634d3a364046f3a040862ce1b2a81f4
      https://github.com/ehb54/ultrascan3/commit/efd337809634d3a364046f3a040862ce1b2a81f4
  Author: Saeed <github.com/samo38>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_748


  Commit: b94ce34c55dd06ddc8ccfbb1239c262fe1c9cd52
      https://github.com/ehb54/ultrascan3/commit/b94ce34c55dd06ddc8ccfbb1239c262fe1c9cd52
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Merge pull request #395 from ehb54/lukas/us_crypto_decrypt_fix

Change encryption finalization to decryption


  Commit: d6c8bb86eb4e77d526599971c15a35328a4927d8
      https://github.com/ehb54/ultrascan3/commit/d6c8bb86eb4e77d526599971c15a35328a4927d8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue791


  Commit: e163509a00c5876ac83d78f14c8a969dae251b75
      https://github.com/ehb54/ultrascan3/commit/e163509a00c5876ac83d78f14c8a969dae251b75
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue785


  Commit: 501adedca88f7d331c3a70d62c04cc4992f86979
      https://github.com/ehb54/ultrascan3/commit/501adedca88f7d331c3a70d62c04cc4992f86979
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    M programs/us/CMakeLists.txt
    M scripts/build.sh

  Log Message:
  -----------
  add: overlay port for qttools


  Commit: e1e93704ad79bf8d43c6c4eba74a4c90b1dc1fdf
      https://github.com/ehb54/ultrascan3/commit/e1e93704ad79bf8d43c6c4eba74a4c90b1dc1fdf
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: ce7a1d14ace3b2d645b17aeab7be4f3fb881ff7b
      https://github.com/ehb54/ultrascan3/commit/ce7a1d14ace3b2d645b17aeab7be4f3fb881ff7b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #394 from ehb54/alexey-dev-issue785

Alexey dev issue785: Show sigle-channel-replica group info in the Average over Replicas Section of the Report


  Commit: e6579802fd032cde1c91863e8af0b2885d936062
      https://github.com/ehb54/ultrascan3/commit/e6579802fd032cde1c91863e8af0b2885d936062
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-17 (Tue, 17 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue791


  Commit: d0eb3d3a8f27a33f4dc6b857f1a2ddcb6c52af5d
      https://github.com/ehb54/ultrascan3/commit/d0eb3d3a8f27a33f4dc6b857f1a2ddcb6c52af5d
  Author: Saeed <github.com/samo38>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_748


  Commit: 563c55a8a0ccb209a43dc363ec87842b0f4d6489
      https://github.com/ehb54/ultrascan3/commit/563c55a8a0ccb209a43dc363ec87842b0f4d6489
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge pull request #387 from samo38/ticket_748

Ticket 748: Enhance Spectrum Decomposition GUI and functionality


  Commit: 3fef021d4fad55bc1bb07521af0bff3e7ac12095
      https://github.com/ehb54/ultrascan3/commit/3fef021d4fad55bc1bb07521af0bff3e7ac12095
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue791


  Commit: cb192562f44149651f3157090d395a05f79da39e
      https://github.com/ehb54/ultrascan3/commit/cb192562f44149651f3157090d395a05f79da39e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #396 from ehb54/alexey-dev-issue791

GMP-ABDE: Ranges & Upload check for ext. profiles -- while situations?


  Commit: b1fbfbcbd47cd296b70ccd6ac9178c4efd6b4a4e
      https://github.com/ehb54/ultrascan3/commit/b1fbfbcbd47cd296b70ccd6ac9178c4efd6b4a4e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP-dataDisk -- enable centerpiece selection in Cells if dataDisk...


  Commit: a3b6b6a58f4f1d94a9268cc04a014d3ce1a1471e
      https://github.com/ehb54/ultrascan3/commit/a3b6b6a58f4f1d94a9268cc04a014d3ce1a1471e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-dataDisk -- enable centerpiece selection in Cells if dataDisk...


  Commit: 992f15191ea67cf8c4dc85736429ab5939967d2f
      https://github.com/ehb54/ultrascan3/commit/992f15191ea67cf8c4dc85736429ab5939967d2f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [2]GMP-dataDisk -- enable centerpiece selection in Cells if dataDisk...


  Commit: 50c4d0f4452a8f5f8052b4e63ae06abb11f8fe89
      https://github.com/ehb54/ultrascan3/commit/50c4d0f4452a8f5f8052b4e63ae06abb11f8fe89
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-18 (Wed, 18 Mar 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]GMP-dataDisk -- enable centerpiece selection in Cells if dataDisk...


  Commit: 81695e7ad3f97f7cd46fe42d8148a8911fc3fc43
      https://github.com/ehb54/ultrascan3/commit/81695e7ad3f97f7cd46fe42d8148a8911fc3fc43
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge branch 'main' into 527-enhancement-sphinx-migration-2


  Commit: bed8960f5d491db022be512a82491fc248abcbf9
      https://github.com/ehb54/ultrascan3/commit/bed8960f5d491db022be512a82491fc248abcbf9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M doc/manual/CMakeLists.txt
    M doc/manual/README.md
    M doc/manual/source/conf.py
    M programs/us/CMakeLists.txt

  Log Message:
  -----------
  mod: PR comments addressed


  Commit: 5205cb5542bd366b63909189ac9691c6473fc071
      https://github.com/ehb54/ultrascan3/commit/5205cb5542bd366b63909189ac9691c6473fc071
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M test/utils/test_us_crypto.cpp
    M utils/us_crypto.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/527-enhancement-sphinx-migration-2' into 527-enhancement-sphinx-migration-2


  Commit: 76e772666ba74f76a6d525444b9c0cd8f9d01e76
      https://github.com/ehb54/ultrascan3/commit/76e772666ba74f76a6d525444b9c0cd8f9d01e76
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M doc/manual/CMakeLists.txt

  Log Message:
  -----------
  fix: skip subdirectory doc/manual if hpc or documentation off


  Commit: abe431ae514b67270d74e84b599ef069673c1164
      https://github.com/ehb54/ultrascan3/commit/abe431ae514b67270d74e84b599ef069673c1164
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h

  Log Message:
  -----------
  GMP-ABDE -- 4. EDIT points addressed for ticket #792...


  Commit: b1c5c0de414d093440081fca1a975a4e1118a9d1
      https://github.com/ehb54/ultrascan3/commit/b1c5c0de414d093440081fca1a975a4e1118a9d1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1]GMP-ABDE -- 4. EDIT points addressed for ticket #792...


  Commit: c53782335d3f1e5fc4fc2ea6f97ee3d64c79389b
      https://github.com/ehb54/ultrascan3/commit/c53782335d3f1e5fc4fc2ea6f97ee3d64c79389b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]GMP-ABDE -- 4. EDIT points addressed for ticket #792...


  Commit: 672254d0e59b1e555aa0aa2506e7871bb188c5d4
      https://github.com/ehb54/ultrascan3/commit/672254d0e59b1e555aa0aa2506e7871bb188c5d4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-19 (Thu, 19 Mar 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]GMP-ABDE -- 4. EDIT points addressed for ticket #792...


  Commit: 05b438d52cffda88429e278cae66fead57b193ec
      https://github.com/ehb54/ultrascan3/commit/05b438d52cffda88429e278cae66fead57b193ec
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M CMakePresets.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    R doc/manual/source/conf.py-orig.081225
    M gui/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp

  Log Message:
  -----------
  fix: Reformat CMakePresets.json to multi-line style; add US3_NO_DB=ON to all HPC
     presets; fix GLU elseif(UNIX) branch; drop dead Windows assistant path check.


  Commit: 21882cd1fd05a489de72b721e1e4bebaa8fb9ac5
      https://github.com/ehb54/ultrascan3/commit/21882cd1fd05a489de72b721e1e4bebaa8fb9ac5
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M doc/manual/CMakeLists.txt
    M programs/us/CMakeLists.txt

  Log Message:
  -----------
  fix: pr comments


  Commit: 39a94736afc6e6b1450549833138c494fc1ff36b
      https://github.com/ehb54/ultrascan3/commit/39a94736afc6e6b1450549833138c494fc1ff36b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M doc/manual/Makefile

  Log Message:
  -----------
  fix: make all moved to top


  Commit: 5470c9ac380ea0b9e9e522bcb85e831bf0e466fd
      https://github.com/ehb54/ultrascan3/commit/5470c9ac380ea0b9e9e522bcb85e831bf0e466fd
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Enforce analyte for solution in us_solution_gui


  Commit: cb5e49b544fddf3329fd8662619f4a524628a69e
      https://github.com/ehb54/ultrascan3/commit/cb5e49b544fddf3329fd8662619f4a524628a69e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Update comments, fix function signature


  Commit: 01301f4fb775a852d7048cf88a308ff8dd796f5a
      https://github.com/ehb54/ultrascan3/commit/01301f4fb775a852d7048cf88a308ff8dd796f5a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp

  Log Message:
  -----------
  GMP-ABDE -- 5. Analysis addressed for ticket #792...


  Commit: 3ba588420b506827b73516e8dfa8cd4ae9b2ff28
      https://github.com/ehb54/ultrascan3/commit/3ba588420b506827b73516e8dfa8cd4ae9b2ff28
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp

  Log Message:
  -----------
  [2]GMP-ABDE -- 5. Analysis addressed for ticket #792...


  Commit: 55ad77b5ea4726efff74c2e3da2b763af7b12070
      https://github.com/ehb54/ultrascan3/commit/55ad77b5ea4726efff74c2e3da2b763af7b12070
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-20 (Fri, 20 Mar 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M doc/manual/CMakeLists.txt

  Log Message:
  -----------
  fix: presets


  Commit: ad1ceab5b0c51349e506ad4feebf2d0e9442b18f
      https://github.com/ehb54/ultrascan3/commit/ad1ceab5b0c51349e506ad4feebf2d0e9442b18f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-21 (Sat, 21 Mar 2026)

  Changed paths:
    M gui/us_solution_gui.cpp

  Log Message:
  -----------
  Show warning before accepting a solution without analyte or common vbar


  Commit: 7bfe32ca6b7830a5b30fc3e995feb35daccc7460
      https://github.com/ehb54/ultrascan3/commit/7bfe32ca6b7830a5b30fc3e995feb35daccc7460
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-21 (Sat, 21 Mar 2026)

  Changed paths:
    M utils/us_astfem_rsa.cpp

  Log Message:
  -----------
  Add band_forming check for low concentration flag


  Commit: fb3b2bbbe972a00864dd68b72b5da64234516056
      https://github.com/ehb54/ultrascan3/commit/fb3b2bbbe972a00864dd68b72b5da64234516056
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-21 (Sat, 21 Mar 2026)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Fix y-axis scale for band-forming plots


  Commit: 8aeda75b69a9c2d9df2af035ea7265bb93bdacef
      https://github.com/ehb54/ultrascan3/commit/8aeda75b69a9c2d9df2af035ea7265bb93bdacef
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-21 (Sat, 21 Mar 2026)

  Changed paths:
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A pkg/macos/README.md

  Log Message:
  -----------
  mod: readmes


  Commit: 81c3a3a5d2a743645b19098027b58ecdc429d634
      https://github.com/ehb54/ultrascan3/commit/81c3a3a5d2a743645b19098027b58ecdc429d634
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-03-22 (Sun, 22 Mar 2026)

  Changed paths:
    R doc/manual/source/2dsa/2dsa_adv.rst
    R doc/manual/source/2dsa/2dsa_analys.rst
    R doc/manual/source/2dsa/2dsa_main.rst
    R doc/manual/source/2dsa/index.rst
    R doc/manual/source/3d_plot.rst
    R doc/manual/source/analyte/analyte_edit.rst
    R doc/manual/source/analyte/analyte_new.rst
    R doc/manual/source/analyte/analyte_select.rst
    R doc/manual/source/analyte/analyte_settings.rst
    R doc/manual/source/analyte/index.rst
    R doc/manual/source/associations.rst
    R doc/manual/source/astfem_sim.rst
    R doc/manual/source/beckman_openauc.rst
    R doc/manual/source/buffer/buffer_edit.rst
    R doc/manual/source/buffer/buffer_new.rst
    R doc/manual/source/buffer/buffer_select.rst
    R doc/manual/source/buffer/buffer_settings.rst
    R doc/manual/source/buffer/index.rst
    R doc/manual/source/buoyancy_editor.rst
    R doc/manual/source/colorgradient.rst
    R doc/manual/source/combine_models.rst
    R doc/manual/source/common_dialogs.rst
    R doc/manual/source/components.rst
    R doc/manual/source/config.rst
    R doc/manual/source/convert.rst
    R doc/manual/source/ddist_combine.rst
    R doc/manual/source/dens_match.rst
    R doc/manual/source/dmga_init.rst
    R doc/manual/source/dmga_init_constr.rst
    R doc/manual/source/experiment/cells.rst
    R doc/manual/source/experiment/general.rst
    R doc/manual/source/experiment/import.rst
    R doc/manual/source/experiment/index.rst
    R doc/manual/source/experiment/liveupdate.rst
    R doc/manual/source/experiment/optics.rst
    R doc/manual/source/experiment/range.rst
    R doc/manual/source/experiment/rotor.rst
    R doc/manual/source/experiment/solutions.rst
    R doc/manual/source/experiment/speeds.rst
    R doc/manual/source/experiment/submit.rst
    R doc/manual/source/export_legacy.rst
    R doc/manual/source/fe_match/fe_match_adv.rst
    R doc/manual/source/fe_match/fe_match_main.rst
    R doc/manual/source/fe_match/fe_match_simulate.rst
    R doc/manual/source/fe_match/index.rst
    R doc/manual/source/fit_meniscus.rst
    R doc/manual/source/ga_initialize.rst
    R doc/manual/source/gmp/gmp.rst
    R doc/manual/source/gmp/gmp_audit_trail.rst
    R doc/manual/source/gmp/gmp_automation.rst
    R doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    R doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    R doc/manual/source/gmp/gmp_data_acquisition/index.rst
    R doc/manual/source/gmp/gmp_protocol_development.rst
    R doc/manual/source/gmp/gmp_report_generator.rst
    R doc/manual/source/gmp/gmp_signature.rst
    R doc/manual/source/gmp/index.rst
    R doc/manual/source/grid_editor.rst
    R doc/manual/source/idist_combine.rst
    R doc/manual/source/images/2dsa_3dplot.png
    R doc/manual/source/images/2dsa_advan.png
    R doc/manual/source/images/2dsa_analvv.png
    R doc/manual/source/images/2dsa_analys.png
    R doc/manual/source/images/2dsa_main-c.png
    R doc/manual/source/images/2dsa_main-o.png
    R doc/manual/source/images/2dsa_resplot.png
    R doc/manual/source/images/D20W_bar.png
    R doc/manual/source/images/MW-bar.png
    R doc/manual/source/images/RINplot.png
    R doc/manual/source/images/TINplot.png
    R doc/manual/source/images/UltraScan-logo.png
    R doc/manual/source/images/add_RIN-TIN.png
    R doc/manual/source/images/add_RIN.png
    R doc/manual/source/images/add_TIN.png
    R doc/manual/source/images/advanced_config.png
    R doc/manual/source/images/analyte_details.png
    R doc/manual/source/images/analyte_edit.png
    R doc/manual/source/images/analyte_edit_spec.png
    R doc/manual/source/images/analyte_new_sequence.png
    R doc/manual/source/images/analyte_newc.png
    R doc/manual/source/images/analyte_newd.png
    R doc/manual/source/images/analyte_newp.png
    R doc/manual/source/images/analyte_selectc.png
    R doc/manual/source/images/analyte_selectd.png
    R doc/manual/source/images/analyte_selectp.png
    R doc/manual/source/images/analyte_sequence.png
    R doc/manual/source/images/analyte_settings.png
    R doc/manual/source/images/analyte_spec-gui.png
    R doc/manual/source/images/analyte_specmenu.png
    R doc/manual/source/images/analyte_spectrum.png
    R doc/manual/source/images/analytes.png
    R doc/manual/source/images/associations.png
    R doc/manual/source/images/astfem_sim.png
    R doc/manual/source/images/bad_grid.png
    R doc/manual/source/images/beck_convert-2.png
    R doc/manual/source/images/beck_converter.png
    R doc/manual/source/images/bitmap.png
    R doc/manual/source/images/buffer_edit.png
    R doc/manual/source/images/buffer_edit_setting.png
    R doc/manual/source/images/buffer_edit_spectrum.png
    R doc/manual/source/images/buffer_info.png
    R doc/manual/source/images/buffer_manage_spectrum.png
    R doc/manual/source/images/buffer_new.png
    R doc/manual/source/images/buffer_new_spectrum.png
    R doc/manual/source/images/buffer_select.png
    R doc/manual/source/images/buffer_settings.png
    R doc/manual/source/images/buffer_spectrum.png
    R doc/manual/source/images/cfa_view-loadauc.png
    R doc/manual/source/images/cfa_view-loadraw.png
    R doc/manual/source/images/cfa_view-main.png
    R doc/manual/source/images/cfa_view-statsauc.png
    R doc/manual/source/images/cfa_view-statsraw.png
    R doc/manual/source/images/color-1.png
    R doc/manual/source/images/color-2.png
    R doc/manual/source/images/color-a.png
    R doc/manual/source/images/color-b.png
    R doc/manual/source/images/colorgrad1.png
    R doc/manual/source/images/colorgradient/col1_colgen.png
    R doc/manual/source/images/colorgradient/col1_colgen_Fe_match.png
    R doc/manual/source/images/colorgradient/col1_colgen_GA.png
    R doc/manual/source/images/colorgradient/col2_colgen.png
    R doc/manual/source/images/colorgradient/colorgrad.png
    R doc/manual/source/images/colorgradient/colorgradient_main.png
    R doc/manual/source/images/colorgradient/components.png
    R doc/manual/source/images/colorgradient/model_editor.png
    R doc/manual/source/images/combine_models-idedit.png
    R doc/manual/source/images/combine_models-save.png
    R doc/manual/source/images/combine_models.png
    R doc/manual/source/images/components.png
    R doc/manual/source/images/config.png
    R doc/manual/source/images/config1.png
    R doc/manual/source/images/config2.png
    R doc/manual/source/images/config_plot.png
    R doc/manual/source/images/convert-RIdata.png
    R doc/manual/source/images/convert-exclude.png
    R doc/manual/source/images/convert-experiment.png
    R doc/manual/source/images/convert-mwl.png
    R doc/manual/source/images/convert-seltrip.png
    R doc/manual/source/images/convert-subset.png
    R doc/manual/source/images/convert-tolerance.png
    R doc/manual/source/images/convert.png
    R doc/manual/source/images/custom_grid-1.png
    R doc/manual/source/images/custom_grid.png
    R doc/manual/source/images/data_converter.png
    R doc/manual/source/images/data_loader-edits.png
    R doc/manual/source/images/data_loader-trips.png
    R doc/manual/source/images/data_loader.png
    R doc/manual/source/images/database.png
    R doc/manual/source/images/ddist_combine-selrun.png
    R doc/manual/source/images/ddist_combine.png
    R doc/manual/source/images/densmatch_main.png
    R doc/manual/source/images/densmatch_mpars_completed.png
    R doc/manual/source/images/densmatch_mpars_empty.png
    R doc/manual/source/images/densmatch_rmvmodels.png
    R doc/manual/source/images/edit_buffer_spec_menu.png
    R doc/manual/source/images/eq1-mean.png
    R doc/manual/source/images/eq2-skew.png
    R doc/manual/source/images/eq3-kurtosis.png
    R doc/manual/source/images/eq4-moments.png
    R doc/manual/source/images/eq5-variance.png
    R doc/manual/source/images/eq6-stddev.png
    R doc/manual/source/images/eq7-probsigma.png
    R doc/manual/source/images/eq8-confidence.png
    R doc/manual/source/images/experiment_cells.png
    R doc/manual/source/images/experiment_general.png
    R doc/manual/source/images/experiment_optics.png
    R doc/manual/source/images/experiment_overview.png
    R doc/manual/source/images/experiment_photomult.png
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  Log Message:
  -----------
  mod: removed documentation.


  Commit: f448548065ff12b1c240270de9d4827cf5f51a79
      https://github.com/ehb54/ultrascan3/commit/f448548065ff12b1c240270de9d4827cf5f51a79
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-24 (Tue, 24 Mar 2026)

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    R doc/manual/images/pcsa_resplot.png
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    R doc/manual/images/vhw_enh_groups.png
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    R doc/manual/index.body
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    R doc/manual/mainstyle.css
    R doc/manual/make-docs.sh
    R doc/manual/make-html.sh
    R doc/manual/make-qdocs.sh
    R doc/manual/make-wraps.sh
    R doc/manual/manage_data.body
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    R doc/manual/manage_data_thelp.body
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    R doc/manual/select_edits.body
    R doc/manual/select_runs.body
    R doc/manual/simparams.body
    R doc/manual/somo.body
    A doc/manual/source/_static/css/custom.css
    A doc/manual/source/_static/js/language_data.js
    A doc/manual/source/_static/js/sphinx_highlight.js
    A doc/manual/source/conf.py
    A doc/manual/source/index.rst
    A doc/manual/source/requirements.txt
    R doc/manual/template.img.body
    R doc/manual/tidy.conf
    R doc/manual/time_derivative.body
    R doc/manual/ultrascan3.txt
    R doc/manual/us_buffer.body
    R doc/manual/us_edit.body
    R doc/manual/us_edit_mwl.body
    R doc/manual/us_equiltime.body
    R doc/manual/us_fds_filemanager.body
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    R doc/manual/us_project.body
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    R doc/manual/uscol.body
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    R doc/manual/vhw_combine.body
    R doc/manual/vhw_distrib_plot.body
    R doc/manual/vhw_enhanced.body
    R doc/manual/wrapped-images.lst
    M gui/CMakeLists.txt
    M gui/us_help.cpp
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M qwtplot3d/CMakeLists.txt
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    M scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    A us-build
    M utils/CMakeLists.txt
    M utils/us_memory.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #374 from ehb54/527-enhancement-sphinx-migration-2

Integrate Sphinx Document Generation


  Commit: 0a9196aea05b0dc1c6f984302c09ffefa32db302
      https://github.com/ehb54/ultrascan3/commit/0a9196aea05b0dc1c6f984302c09ffefa32db302
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-03-24 (Tue, 24 Mar 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M admin/cmake/toolchain.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
    R doc/manual/buffer_new.body
    R doc/manual/buffer_select.body
    R doc/manual/buffer_settings.body
    R doc/manual/cfa_viewer.body
    R doc/manual/colorgradient.body
    R doc/manual/combine_models.body
    R doc/manual/components.body
    R doc/manual/config.body
    R doc/manual/config2.body
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    R doc/manual/convert-seltrip.body
    R doc/manual/convert.body
    R doc/manual/data_loader.body
    R doc/manual/database_config.body
    R doc/manual/ddist_combine.body
    R doc/manual/dens_match.body
    R doc/manual/dens_match_mparam.body
    R doc/manual/dens_match_rmvmods.body
    R doc/manual/experiment/experiment_cells.body
    R doc/manual/experiment/experiment_general.body
    R doc/manual/experiment/experiment_photomult.body
    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
    R doc/manual/fe_match/fe_match_lddat.body
    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
    R doc/manual/ga_initialize.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
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    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
    R doc/manual/images/color-1.png
    R doc/manual/images/color-2.png
    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
    R doc/manual/images/colorgrad1.png
    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
    R doc/manual/images/combine_models.png
    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
    R doc/manual/images/config2.png
    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
    R doc/manual/images/densmatch_mpars_empty.png
    R doc/manual/images/densmatch_rmvmodels.png
    R doc/manual/images/eq1-mean.png
    R doc/manual/images/eq2-skew.png
    R doc/manual/images/eq3-kurtosis.png
    R doc/manual/images/eq4-moments.png
    R doc/manual/images/eq5-variance.png
    R doc/manual/images/eq6-stddev.png
    R doc/manual/images/eq7-probsigma.png
    R doc/manual/images/eq8-confidence.png
    R doc/manual/images/experiment_cells.png
    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
    R doc/manual/images/fe_match_adv.png
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    A doc/manual/source/_static/css/custom.css
    A doc/manual/source/_static/js/language_data.js
    A doc/manual/source/_static/js/sphinx_highlight.js
    A doc/manual/source/conf.py
    A doc/manual/source/index.rst
    A doc/manual/source/requirements.txt
    R doc/manual/template.img.body
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    M gui/CMakeLists.txt
    M gui/us_help.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_config/us_admin.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M qwtplot3d/CMakeLists.txt
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    M scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    M test/utils/test_us_crypto.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/us_crypto.cpp
    M utils/us_memory.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-670


  Commit: a3d889c69f7012ff5840a86814780d3490d5ea2a
      https://github.com/ehb54/ultrascan3/commit/a3d889c69f7012ff5840a86814780d3490d5ea2a
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-03-24 (Tue, 24 Mar 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  Merge pull request #377 from ehb54/ehb54-issue-670

fix revision.sh checks osx/linux compat.


  Commit: aba103e8cab9d71929941aa888ae3aae0872e049
      https://github.com/ehb54/ultrascan3/commit/aba103e8cab9d71929941aa888ae3aae0872e049
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-24 (Tue, 24 Mar 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M admin/cmake/toolchain.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
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    M gui/CMakeLists.txt
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    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
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    M programs/us_mpi_analysis/2dsa_worker.cpp
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    M utils/us_memory.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_solution_analyte


  Commit: aece3e3e7171e4b42fde89c87820aa518fb4315c
      https://github.com/ehb54/ultrascan3/commit/aece3e3e7171e4b42fde89c87820aa518fb4315c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-24 (Tue, 24 Mar 2026)

  Changed paths:
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    M .gitignore
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    M LICENSE.txt
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    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
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    A admin/cmake/packaging/macos/StageAssistantDev.cmake
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    M admin/cmake/toolchain.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
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    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
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    A doc/manual/source/_static/css/custom.css
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    A doc/manual/source/conf.py
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    M gui/CMakeLists.txt
    M gui/us_help.cpp
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
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    M qwtplot3d/CMakeLists.txt
    A scripts/bootstrap-linux.sh
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    A scripts/bootstrap.bat
    M scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    A us-build
    M utils/CMakeLists.txt
    M utils/us_memory.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_astfem_sim_bfe_fix


  Commit: e219670a84259a14eabcbd6567f410caa19460e4
      https://github.com/ehb54/ultrascan3/commit/e219670a84259a14eabcbd6567f410caa19460e4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-26 (Thu, 26 Mar 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Fix makeall.sh permissions


  Commit: ffbfc46c1f6425db8f285c8ebfe83093848eb1b6
      https://github.com/ehb54/ultrascan3/commit/ffbfc46c1f6425db8f285c8ebfe83093848eb1b6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-26 (Thu, 26 Mar 2026)

  Changed paths:
    M qmakeall.sh

  Log Message:
  -----------
  Fix qmakeall.sh permissions


  Commit: ce69cccd373c62d3682696c7c1e3afbec47ca21c
      https://github.com/ehb54/ultrascan3/commit/ce69cccd373c62d3682696c7c1e3afbec47ca21c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-27 (Fri, 27 Mar 2026)

  Changed paths:
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Merge pull request #397 from ehb54/lukas/us_solution_analyte

Enforce analyte for solution in us_solution_gui


  Commit: cdf7099448e0de34a4e877280839f6acfacf5596
      https://github.com/ehb54/ultrascan3/commit/cdf7099448e0de34a4e877280839f6acfacf5596
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-27 (Fri, 27 Mar 2026)

  Changed paths:
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_astfem_sim_bfe_fix


  Commit: b543a92af379330a545e7dcc63e12daaf3d45239
      https://github.com/ehb54/ultrascan3/commit/b543a92af379330a545e7dcc63e12daaf3d45239
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-27 (Fri, 27 Mar 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP-ABDE -- 4. EDIT typo fixed...


  Commit: abf971e0666fcec75923b6219b9033864ede6e45
      https://github.com/ehb54/ultrascan3/commit/abf971e0666fcec75923b6219b9033864ede6e45
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-03-27 (Fri, 27 Mar 2026)

  Changed paths:
    M makeall.sh
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M qmakeall.sh
    M utils/us_astfem_rsa.cpp

  Log Message:
  -----------
  Merge pull request #399 from ehb54/lukas/us_astfem_sim_bfe_fix

Add band-forming check and fix y-axis scale for plots


  Commit: 407aa2fbe647825650959edafde01a47e49ac0a4
      https://github.com/ehb54/ultrascan3/commit/407aa2fbe647825650959edafde01a47e49ac0a4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-03-27 (Fri, 27 Mar 2026)

  Changed paths:
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    M .gitignore
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    M CMakePresets.json
    M LICENSE.txt
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
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    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
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    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M admin/cmake/toolchain.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
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    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
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    M doc/manual/CMakeLists.txt
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    R doc/manual/advanced_config.body
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    R doc/manual/us_modelmetrics.body
    R doc/manual/us_project.body
    R doc/manual/us_solution.body
    R doc/manual/uscol.body
    R doc/manual/uscolor2.body
    R doc/manual/usfont.body
    R doc/manual/usfont2.body
    R doc/manual/vhw_combine.body
    R doc/manual/vhw_distrib_plot.body
    R doc/manual/vhw_enhanced.body
    R doc/manual/wrapped-images.lst
    M gui/CMakeLists.txt
    M gui/us_help.cpp
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    M scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    A us-build
    M utils/CMakeLists.txt
    M utils/us_astfem_rsa.cpp
    M utils/us_memory.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #401 from ehb54/main

pull main into alexey-dev-issue792


  Commit: 82d4d191eb9afe4cf103b3792c6730f51eb8bafa
      https://github.com/ehb54/ultrascan3/commit/82d4d191eb9afe4cf103b3792c6730f51eb8bafa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-02 (Thu, 02 Apr 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h

  Log Message:
  -----------
  GMP-ABDE -- 4. EDIT: ask user if only last scan was selected for each channel before accepting new edit parameters...


  Commit: e58b784f94dc22571d37ac77acdc90c148ee0004
      https://github.com/ehb54/ultrascan3/commit/e58b784f94dc22571d37ac77acdc90c148ee0004
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-02 (Thu, 02 Apr 2026)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge pull request #398 from ehb54/alexey-dev-issue792

Alexey dev issue792: GMP-ABDE & dataDisk changes


  Commit: 94b9a553e412fb675ba67eea2c9f665b6207233d
      https://github.com/ehb54/ultrascan3/commit/94b9a553e412fb675ba67eea2c9f665b6207233d
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
    M doc/manual/CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists to use `${SPHINX_PROJECT}` variables for Qt help file generation paths (`.qhp` and `.qhcp`).

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: e2d7da6bbf9fcc62e4bfa452f5ec19623488611e
      https://github.com/ehb54/ultrascan3/commit/e2d7da6bbf9fcc62e4bfa452f5ec19623488611e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
    M doc/manual/source/requirements.txt

  Log Message:
  -----------
  Add `sphinxcontrib-qthelp` and `myst-parser` to documentation requirements for Qt help and Markdown support.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 1e69c5071f55b5bc4963bc33c54c1f5978d9a86f
      https://github.com/ehb54/ultrascan3/commit/1e69c5071f55b5bc4963bc33c54c1f5978d9a86f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Enhance Sphinx configuration: add version metadata generation from Git, update QtHelp/HTML output, and refine documentation structure.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 64293373d85c1dd99096806b49351207ccc8fcbd
      https://github.com/ehb54/ultrascan3/commit/64293373d85c1dd99096806b49351207ccc8fcbd
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
    M doc/manual/source/index.rst

  Log Message:
  -----------
  Expand UltraScan-III documentation: add comprehensive structure, improve navigation with toctree captions, and include download link for PDF manual.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 4996aa594c1ed86a6a18b51f4a2e7f2f312ba230
      https://github.com/ehb54/ultrascan3/commit/4996aa594c1ed86a6a18b51f4a2e7f2f312ba230
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 518c1ee39c53443282fc68ec37cc855b2e5aa4f0
      https://github.com/ehb54/ultrascan3/commit/518c1ee39c53443282fc68ec37cc855b2e5aa4f0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
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  Log Message:
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  Update Sphinx configuration: adjust LaTeX preamble for header height and standardize document titles across output formats.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 2946f944109702806ad7b25d283b258d3702adfa
      https://github.com/ehb54/ultrascan3/commit/2946f944109702806ad7b25d283b258d3702adfa
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 34d316c7e97fcdabcf86b0939a85e834d6d878f6
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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  Fix typo in vHW documentation: correct "Wieschet" to "Weischet".

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 56e8463890e60e8501b4233fb88a6dd74f0e39f4
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: ff5165410e579e9e3bf489cf74532942d4dd1b6d
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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  Revise configuration documentation: clarify directory descriptions, standardize terminology, improve debugging/debug level explanations, and update Optima panel section with centered image and corrected details.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 9d89cccbd5d1edac19f5118f9f73b017b4b62768
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  Log Message:
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Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 20e6e37595eff7fcd8c617c1ae65f049be8e60f5
      https://github.com/ehb54/ultrascan3/commit/20e6e37595eff7fcd8c617c1ae65f049be8e60f5
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
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  Log Message:
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  Add Sphinx transform for auto-generating index entries from section titles.


  Commit: 78763cd74bcca991929a7dc53e314e9e61a755b6
      https://github.com/ehb54/ultrascan3/commit/78763cd74bcca991929a7dc53e314e9e61a755b6
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
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  Log Message:
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  Update Sphinx configuration: add `auto_index` extension and adjust sys.path setup for dynamic module resolution.


  Commit: e67f33a49e896d701d7a71317d8d8b2dcebb45a9
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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  Update Optima configuration images in documentation: delete outdated file and revise new image.


  Commit: a0df61141d5869a4c8d57ccdaf8896b84fbf1add
      https://github.com/ehb54/ultrascan3/commit/a0df61141d5869a4c8d57ccdaf8896b84fbf1add
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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  Standardize header formatting in configuration documentation: adjust underline lengths and update section titles for consistency.


  Commit: 20a795daec1d9d2b8a1e99a9522c5b0f39516f9f
      https://github.com/ehb54/ultrascan3/commit/20a795daec1d9d2b8a1e99a9522c5b0f39516f9f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-03 (Fri, 03 Apr 2026)

  Changed paths:
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  Log Message:
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  Update Sphinx configuration: fix sys.path insertion to correctly add the current directory.

Signed-off-by: doluk <69309597+doluk at users.noreply.github.com>


  Commit: 7022886ca10e06e291974dd36c40d68886f97592
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: fec01135a70f30bb6fe279c6355c6d8d46e50f02
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  Date:   2026-04-03 (Fri, 03 Apr 2026)

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  Log Message:
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Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: 213c7d1f346ca9afa40c688dc5d4daae4e55d79f
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  Date:   2026-04-04 (Sat, 04 Apr 2026)

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  Log Message:
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  Remove unused `custom.css` file and retain only essential styles in `custom.css` for cleaner documentation styling.


  Commit: f31826280b208f87c2044d91ceed9b3b725941b8
      https://github.com/ehb54/ultrascan3/commit/f31826280b208f87c2044d91ceed9b3b725941b8
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  Date:   2026-04-04 (Sat, 04 Apr 2026)

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  Log Message:
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  Commit: 0d8aa5eb3868f4fa28393c667f367905088267c1
      https://github.com/ehb54/ultrascan3/commit/0d8aa5eb3868f4fa28393c667f367905088267c1
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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  Log Message:
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  Add support for qthelp exclusive css file


  Commit: 50222b23f0a251076777810ba005c924ef2ddb00
      https://github.com/ehb54/ultrascan3/commit/50222b23f0a251076777810ba005c924ef2ddb00
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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  Log Message:
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  Add `qthelp.css` file to define default styling for QtHelp documentation


  Commit: 86fcf7036c1ad44220fbb6544552d2e7458fd76e
      https://github.com/ehb54/ultrascan3/commit/86fcf7036c1ad44220fbb6544552d2e7458fd76e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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  Log Message:
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  Standardize help text and add debug text options in configuration documentation.


  Commit: 38351d9b483d34b0d464cdc0a02cf4d0c711a5f0
      https://github.com/ehb54/ultrascan3/commit/38351d9b483d34b0d464cdc0a02cf4d0c711a5f0
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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  Log Message:
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  Refine `auto_index` title processing: improve whitespace handling, enhance dimensional notation standardization, and ensure title case consistency.


  Commit: 881728a585525975764e48eb87de544e1a8f5ed6
      https://github.com/ehb54/ultrascan3/commit/881728a585525975764e48eb87de544e1a8f5ed6
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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  Log Message:
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  Standardize section headers and titles in FE Match documentation for consistency and improve formatting.


  Commit: 278eeecf4ee5b0f5e03bbcd8eae65e831f15837b
      https://github.com/ehb54/ultrascan3/commit/278eeecf4ee5b0f5e03bbcd8eae65e831f15837b
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_distrib_plot.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
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  Standardize "van Holde-Weischet" terminology across documentation for improved consistency.


  Commit: 99bbe83fea89b40008e71864323759b4a75ff8cb
      https://github.com/ehb54/ultrascan3/commit/99bbe83fea89b40008e71864323759b4a75ff8cb
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/start_page-rpt.rst

  Log Message:
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  Standardize section headers, titles, and dimensional notations in documentation for improved formatting and consistency.


  Commit: 75a2cca73b6cec686f996d57da668814a975dfc6
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  Date:   2026-04-04 (Sat, 04 Apr 2026)

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  Log Message:
  -----------
  Merge pull request #402 from ehb54/lukas/manual

Add sphinx manual


  Commit: dd51d90b60e4fd6785c98531588a585dc0fb34ed
      https://github.com/ehb54/ultrascan3/commit/dd51d90b60e4fd6785c98531588a585dc0fb34ed
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
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    A doc/manual/source/vhw_enhanced.rst
    A doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  Merge pull request #404 from ehb54/main

update demeler-doc1 to main


  Commit: cd2bc2e7c99e075b63a282c8e687e6d0e111670d
      https://github.com/ehb54/ultrascan3/commit/cd2bc2e7c99e075b63a282c8e687e6d0e111670d
  Author: Demeler <demeler at uslims.uleth.ca>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
    M doc/manual/source/fit_meniscus.rst

  Log Message:
  -----------
  Modify capitalization in fit meniscus


  Commit: cc049b493eb8cb3409dd4d22051e345fd80c7982
      https://github.com/ehb54/ultrascan3/commit/cc049b493eb8cb3409dd4d22051e345fd80c7982
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-04-04 (Sat, 04 Apr 2026)

  Changed paths:
    M doc/manual/source/fit_meniscus.rst

  Log Message:
  -----------
  Merge pull request #405 from ehb54/demeler-doc1

Demeler doc1


  Commit: 11572ca66d369080b73f5925c9b46c3b7200c538
      https://github.com/ehb54/ultrascan3/commit/11572ca66d369080b73f5925c9b46c3b7200c538
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/source/index.rst

  Log Message:
  -----------
  Update Sphinx build system: include `auto_index.py`, link PDF manual in HTML, and clean PDF on `make clean`.


  Commit: e2fbf48c659f3fad2922c9067a43f1b3bdc0ec5e
      https://github.com/ehb54/ultrascan3/commit/e2fbf48c659f3fad2922c9067a43f1b3bdc0ec5e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Update LaTeX configuration: set `latex_use_xindy` to False and redefine font settings for better Unicode handling and compatibility.


  Commit: 78d927e26195be17b4a8ff09959676a6247bcb34
      https://github.com/ehb54/ultrascan3/commit/78d927e26195be17b4a8ff09959676a6247bcb34
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Ensure zoom stack initialization on zoom button press


  Commit: dcc8ccbdac5394275563aeee0c8c523a6df45589
      https://github.com/ehb54/ultrascan3/commit/dcc8ccbdac5394275563aeee0c8c523a6df45589
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Refactor zoom logic to handle null plots and absolute values


  Commit: f7169d62eaece4fd69dd8f88ab06432a8bb390f0
      https://github.com/ehb54/ultrascan3/commit/f7169d62eaece4fd69dd8f88ab06432a8bb390f0
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    A test/utils/test_us_help_pages.cpp

  Log Message:
  -----------
  Add unit test for validating existence of help pages and refactor zoom stack initialization for improved consistency.


  Commit: a542b58b077c8629e05993705eb0967c8e2ed720
      https://github.com/ehb54/ultrascan3/commit/a542b58b077c8629e05993705eb0967c8e2ed720
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Update .gitignore to exclude `doc/manual/build`


  Commit: 3841b3da9b269c931e61bd8332217ea7edafa5ce
      https://github.com/ehb54/ultrascan3/commit/3841b3da9b269c931e61bd8332217ea7edafa5ce
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M utils/CMakeLists.txt
    M utils/us_extern.h

  Log Message:
  -----------
  Add static library support: define `US_UTIL_STATIC` and conditionally update `us_extern.h`.


  Commit: 8bd5bb513393dabe50c036ffbfe60f96a6b3ca21
      https://github.com/ehb54/ultrascan3/commit/8bd5bb513393dabe50c036ffbfe60f96a6b3ca21
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M utils/us_buffer.h

  Log Message:
  -----------
  Initialize `grad_form` flag to `false` in `us_buffer.h`.


  Commit: 923260944deb1b79e310ceb98a16effa5b5090ca
      https://github.com/ehb54/ultrascan3/commit/923260944deb1b79e310ceb98a16effa5b5090ca
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_get_run.h
    M gui/us_load_auc.h
    M gui/us_model_loader.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
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    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h

  Log Message:
  -----------
  Update help file paths for improved documentation consistency and organization.


  Commit: 78e6d90c9756f558dd3c67e03ec447dbaa996a8a
      https://github.com/ehb54/ultrascan3/commit/78e6d90c9756f558dd3c67e03ec447dbaa996a8a
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  Let github action only build the documnetaion with the qthelp builder, because latex dependencies are currently missing


  Commit: 05eb1370b6158124bcafd398fef77466e66be0aa
      https://github.com/ehb54/ultrascan3/commit/05eb1370b6158124bcafd398fef77466e66be0aa
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Remove feature commit in wrong branch


  Commit: 18c02644a764f585fd585e1af1c21e4d5790b60c
      https://github.com/ehb54/ultrascan3/commit/18c02644a764f585fd585e1af1c21e4d5790b60c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Merge pull request #406 from ehb54/lukas/us_plot_zoom_qwt616

Ensure zoom stack initialization on zoom button press


  Commit: 3c1312a39ac562248315fb410c301c9d8eab79f5
      https://github.com/ehb54/ultrascan3/commit/3c1312a39ac562248315fb410c301c9d8eab79f5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/manual_test/make


  Commit: 99fc3a66c861b6275cedd397bfd03e34e85d9435
      https://github.com/ehb54/ultrascan3/commit/99fc3a66c861b6275cedd397bfd03e34e85d9435
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    A .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Add GitHub Actions workflow for Sphinx documentation build


  Commit: 5fa677c2afd3175fa29a37165561f4125a867c5d
      https://github.com/ehb54/ultrascan3/commit/5fa677c2afd3175fa29a37165561f4125a867c5d
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Refactor Sphinx GitHub Actions workflow: replace deprecated problem matcher usage, streamline build commands, and add error handling.


  Commit: b91a5ae2fecdc63970efdf031426e000eff8cc6e
      https://github.com/ehb54/ultrascan3/commit/b91a5ae2fecdc63970efdf031426e000eff8cc6e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    A .github/sphinx-matcher.json

  Log Message:
  -----------
  Add Sphinx problem matcher configuration for GitHub Actions


  Commit: 45da34200ce91a23a4f1f8d168e7a1ee612b03b5
      https://github.com/ehb54/ultrascan3/commit/45da34200ce91a23a4f1f8d168e7a1ee612b03b5
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Annotate Sphinx build warnings in GitHub Actions workflow and update qthelp build step for improved error handling.


  Commit: f3750319ef93a4a4b5f925ffaa38acd1ebb8f6f5
      https://github.com/ehb54/ultrascan3/commit/f3750319ef93a4a4b5f925ffaa38acd1ebb8f6f5
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Replace custom Sphinx warning annotation script with `sphinx-doc/github-problem-matcher` for streamlined GitHub Actions workflow.


  Commit: bc2b74fbb9b5698c8269f2d6b060ce420ab6697a
      https://github.com/ehb54/ultrascan3/commit/bc2b74fbb9b5698c8269f2d6b060ce420ab6697a
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    R .github/sphinx-matcher.json

  Log Message:
  -----------
  Remove obsolete Sphinx problem matcher configuration from GitHub Actions.


  Commit: 715a3fd86ec9bdb692b3e1fa0ce393a86548c213
      https://github.com/ehb54/ultrascan3/commit/715a3fd86ec9bdb692b3e1fa0ce393a86548c213
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
  -----------
  Fix triplicates to triples


  Commit: f1b1aba77a1f2da432e6262d842221eb275d2dd0
      https://github.com/ehb54/ultrascan3/commit/f1b1aba77a1f2da432e6262d842221eb275d2dd0
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    A doc/manual/source/_static/images/dmga-save.png
    A doc/manual/source/_static/images/dmga.png
    A doc/manual/source/_static/images/dmga_constr.png
    A doc/manual/source/_static/images/fe_dmga_adv.png
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  update to latest


  Commit: ff98f3a480b918b42a59334bc0506f87b59b5a37
      https://github.com/ehb54/ultrascan3/commit/ff98f3a480b918b42a59334bc0506f87b59b5a37
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M programs/us_integral/us_delete_models.h

  Log Message:
  -----------
  first link change -  integral


  Commit: 584135021b461a9f753c2ac63b2f37df4cd85b0b
      https://github.com/ehb54/ultrascan3/commit/584135021b461a9f753c2ac63b2f37df4cd85b0b
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/delseltrip.png
    M doc/manual/source/common_dialogs.rst
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  update us_experiment show.help


  Commit: 8e3da82ae6b7563f455e97718bb1f335a1c9bfcc
      https://github.com/ehb54/ultrascan3/commit/8e3da82ae6b7563f455e97718bb1f335a1c9bfcc
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  Standardize terminology: replace "Triplicates" with "Triples" across documentation for clarity and consistency.


  Commit: 7128a07267ee0a0fd7913ea221c2cd891b7099a8
      https://github.com/ehb54/ultrascan3/commit/7128a07267ee0a0fd7913ea221c2cd891b7099a8
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    M test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Improve test failure messages: use `ADD_FAILURE_AT` for precise file/line annotation and enhance regex and help file error clarity


  Commit: 9cf710938424ec4c02179f22bb8da50b226085c6
      https://github.com/ehb54/ultrascan3/commit/9cf710938424ec4c02179f22bb8da50b226085c6
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Add GoogleTest problem matcher to GitHub Actions workflows for enhanced test failure annotation


  Commit: d849477c413c4de8c709970000b9beed563952aa
      https://github.com/ehb54/ultrascan3/commit/d849477c413c4de8c709970000b9beed563952aa
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    M programs/us_2dsa/us_2dsa.h
    M programs/us_config/us_color.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h

  Log Message:
  -----------
  unit test link updates


  Commit: ba9907ccbb59086289b70ee897744f22b939a693
      https://github.com/ehb54/ultrascan3/commit/ba9907ccbb59086289b70ee897744f22b939a693
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/select_prefilt.png
    M doc/manual/source/common_dialogs.rst
    M gui/us_select_edits.h
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_font.cpp

  Log Message:
  -----------
  unit tests help link update


  Commit: 9a107befce5878fa969190700c2a2f6ef48ce068
      https://github.com/ehb54/ultrascan3/commit/9a107befce5878fa969190700c2a2f6ef48ce068
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A doc/manual/source/analysprof_general.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/convert.rst
    A doc/manual/source/ramp_data.rst
    A doc/manual/source/us_administrator.rst
    M doc/manual/source/us_edit.rst
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_config/us_advanced.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_ramp/us_experiment_gui_ra.h

  Log Message:
  -----------
  updates


  Commit: 6fe43510daa8d32555c611669eaa32ab11da07ff
      https://github.com/ehb54/ultrascan3/commit/6fe43510daa8d32555c611669eaa32ab11da07ff
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/edit_exclude_scan.png
    A doc/manual/source/_static/images/edit_scan.png

  Log Message:
  -----------
  images


  Commit: 290b3ed2436ce1c133fb54567579f869c3e2ea70
      https://github.com/ehb54/ultrascan3/commit/290b3ed2436ce1c133fb54567579f869c3e2ea70
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M doc/manual/source/dens_match.rst
    M programs/us_density_match/us_model_params.h

  Log Message:
  -----------
  update link


  Commit: 6242d49b69ff170e32c1fd9ada173147b3744e39
      https://github.com/ehb54/ultrascan3/commit/6242d49b69ff170e32c1fd9ada173147b3744e39
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A doc/manual/source/global_equil.rst
    M doc/manual/source/us_edit.rst

  Log Message:
  -----------
  update


  Commit: 0924fcb4af9a8403c404ace536fffa1cf6209b6f
      https://github.com/ehb54/ultrascan3/commit/0924fcb4af9a8403c404ace536fffa1cf6209b6f
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/index.rst
    M doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_pcsa/us_mlplot.h

  Log Message:
  -----------
  unit test


  Commit: c8515e182cb1cddab6d51258efd8a99f97c8c667
      https://github.com/ehb54/ultrascan3/commit/c8515e182cb1cddab6d51258efd8a99f97c8c667
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M .github/gtest-us.json

  Log Message:
  -----------
  Fix matcher


  Commit: ff35eb4d37eed1d9a2fdd2200d69a00adfcdb41c
      https://github.com/ehb54/ultrascan3/commit/ff35eb4d37eed1d9a2fdd2200d69a00adfcdb41c
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/index.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_select.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/components.rst
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dens_match.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/experiment/cells.rst
    M doc/manual/source/experiment/optics.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/submit.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/model_editor.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_adv.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/rotor.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/vhw_enhanced.rst
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_pcsa/us_mrecs_loader.h

  Log Message:
  -----------
  sphynx links


  Commit: 287fbcbd18bec2e702fabfb4298a69a0b62ee537
      https://github.com/ehb54/ultrascan3/commit/287fbcbd18bec2e702fabfb4298a69a0b62ee537
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M .gitignore
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/_static/images/delseltrip.png
    A doc/manual/source/_static/images/dmga-save.png
    A doc/manual/source/_static/images/dmga.png
    A doc/manual/source/_static/images/dmga_constr.png
    A doc/manual/source/_static/images/edit_exclude_scan.png
    A doc/manual/source/_static/images/edit_scan.png
    A doc/manual/source/_static/images/fe_dmga_adv.png
    A doc/manual/source/_static/images/select_prefilt.png
    A doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_select.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/components.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dens_match.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/cells.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/optics.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/submit.rst
    M doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    A doc/manual/source/global_equil.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/model_editor.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_adv.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    A doc/manual/source/ramp_data.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/rotor.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    A doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_get_run.h
    M gui/us_load_auc.h
    M gui/us_model_loader.h
    M gui/us_select_edits.h
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.h
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    A test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp
    M utils/CMakeLists.txt
    M utils/us_buffer.h
    M utils/us_extern.h

  Log Message:
  -----------
  Merge pull request #408 from ehb54/lukas/manual_test/make

Enhance documentation build system and improve Unicode handling


  Commit: 29678f933d80ecac003838e4bde2c37a65512482
      https://github.com/ehb54/ultrascan3/commit/29678f933d80ecac003838e4bde2c37a65512482
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  GMP  -- additional check for the protocol internals equality before submitting GMP run: check for operator (and revs & approvers)...


  Commit: 77adb01c3a9c4133da796314b1007c031f6dd089
      https://github.com/ehb54/ultrascan3/commit/77adb01c3a9c4133da796314b1007c031f6dd089
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-10 (Fri, 10 Apr 2026)

  Changed paths:
    M doc/manual/source/config.rst

  Log Message:
  -----------
  check new branch


  Commit: 0a0e0eca8a8da8aa4db25e74431e3d89b5808edb
      https://github.com/ehb54/ultrascan3/commit/0a0e0eca8a8da8aa4db25e74431e3d89b5808edb
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-10 (Fri, 10 Apr 2026)

  Changed paths:

  Log Message:
  -----------
  Merge pull request #410 from ehb54/main

Merge pull request #408 from ehb54/lukas/manual_test/make


  Commit: d2c99821961553c3153b8d32337f97b7511bcf81
      https://github.com/ehb54/ultrascan3/commit/d2c99821961553c3153b8d32337f97b7511bcf81
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/rotor_calibration.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  triplicates


  Commit: 6b12d783265172c421a37e224b8adad3f695e245
      https://github.com/ehb54/ultrascan3/commit/6b12d783265172c421a37e224b8adad3f695e245
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst

  Log Message:
  -----------
  minor missplacing


  Commit: c1845c6f4b9734df2f812c0b62d782d4f2609c9a
      https://github.com/ehb54/ultrascan3/commit/c1845c6f4b9734df2f812c0b62d782d4f2609c9a
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst

  Log Message:
  -----------
  minor


  Commit: 999f5967cfac93e336d82d6d37f650a584730945
      https://github.com/ehb54/ultrascan3/commit/999f5967cfac93e336d82d6d37f650a584730945
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/vhw_combine.rst

  Log Message:
  -----------
  ref and doc updates


  Commit: 5442f4062fa7bdbd225d10d4108a9913de662afe
      https://github.com/ehb54/ultrascan3/commit/5442f4062fa7bdbd225d10d4108a9913de662afe
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/_static/images/load_us3.png
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
  -----------
  referencing


  Commit: 5d940737536ba92999909c398bc2c791d46ffd4d
      https://github.com/ehb54/ultrascan3/commit/5d940737536ba92999909c398bc2c791d46ffd4d
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  referencing update


  Commit: 792ea02cbd0b900f1898086c35fa6b3c11e54201
      https://github.com/ehb54/ultrascan3/commit/792ea02cbd0b900f1898086c35fa6b3c11e54201
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/config.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  reference update 2


  Commit: 54a049bf6cfd4facaa834f4e91979253d3aa6b86
      https://github.com/ehb54/ultrascan3/commit/54a049bf6cfd4facaa834f4e91979253d3aa6b86
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    A doc/manual/source/_static/images/cmenu_help.png
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
  -----------
  sphinx-build -M linkcheck /source /build -q --keep-going  + DMGA protocol


  Commit: 5ec1de61dba0f60ca68a98e66e6f8098e0d70384
      https://github.com/ehb54/ultrascan3/commit/5ec1de61dba0f60ca68a98e66e6f8098e0d70384
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  manual name change


  Commit: 73e408bbda42ba6961f01111ffb11b59c8976fce
      https://github.com/ehb54/ultrascan3/commit/73e408bbda42ba6961f01111ffb11b59c8976fce
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/index.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst

  Log Message:
  -----------
  minor updates


  Commit: aadeecb1340fbe3c58273b592171ad822dbd05dd
      https://github.com/ehb54/ultrascan3/commit/aadeecb1340fbe3c58273b592171ad822dbd05dd
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/index.rst

  Log Message:
  -----------
  minor updates in Index


  Commit: 26b3afbb4f6320ad269fb86433af8187d3a79256
      https://github.com/ehb54/ultrascan3/commit/26b3afbb4f6320ad269fb86433af8187d3a79256
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/reporter_comrep.png
    M doc/manual/source/index.rst
    M doc/manual/source/reporter.rst

  Log Message:
  -----------
  These MINOR changes are killing me


  Commit: c35c8a4a2d552e064e5d40205f75deef685d0d6e
      https://github.com/ehb54/ultrascan3/commit/c35c8a4a2d552e064e5d40205f75deef685d0d6e
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/fe_match/index.rst

  Log Message:
  -----------
  Minoooor


  Commit: abf6f6f3682a1676d7d1e8f7dd0f02419fb1954f
      https://github.com/ehb54/ultrascan3/commit/abf6f6f3682a1676d7d1e8f7dd0f02419fb1954f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-15 (Wed, 15 Apr 2026)

  Changed paths:
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge pull request #409 from ehb54/alexey-dev-issue814

GMP  -- additional check for the protocol internals equality before submitting GMP runs: operator(s)


  Commit: 79bb847a03d6a66112ac96beede10610bbba2246
      https://github.com/ehb54/ultrascan3/commit/79bb847a03d6a66112ac96beede10610bbba2246
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Ensure zoom check considers spectrogram items in `us_plot.cpp`


  Commit: 0d3c4779cd3d7e85fc5bc4ad7e449a6afcaf99ff
      https://github.com/ehb54/ultrascan3/commit/0d3c4779cd3d7e85fc5bc4ad7e449a6afcaf99ff
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Refactor signal-slot connections in `us_pseudo3d_combine.cpp` to use modern `&QButtonGroup::idReleased` syntax.


  Commit: e3131079c98204bcde4f43e59bc6114c81d4d6bd
      https://github.com/ehb54/ultrascan3/commit/e3131079c98204bcde4f43e59bc6114c81d4d6bd
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Refactor signal-slot connections in `us_pseudo3d_combine.cpp` to use modern syntax for improved readability and maintainability.


  Commit: c85594c8e6e1edab8b7adae963da46ffe5913fc6
      https://github.com/ehb54/ultrascan3/commit/c85594c8e6e1edab8b7adae963da46ffe5913fc6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h

  Log Message:
  -----------
  Model Selector  -- allow Accept for GMP-generated models...


  Commit: 6bcf83da27c47886d434f95cb5c8b5b393efcc79
      https://github.com/ehb54/ultrascan3/commit/6bcf83da27c47886d434f95cb5c8b5b393efcc79
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-20 (Mon, 20 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_spectrum.rst

  Log Message:
  -----------
  us_buoyancy introduction, Us_spectrum introduction,images and application updated.


  Commit: b5159ec368c6454947e70949aaffbdde6b41c221
      https://github.com/ehb54/ultrascan3/commit/b5159ec368c6454947e70949aaffbdde6b41c221
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-20 (Mon, 20 Apr 2026)

  Changed paths:
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge branch 'main' into haben/docs-crosslinking


  Commit: 0d231234973612a639bab8cf3fc26fb81c88717f
      https://github.com/ehb54/ultrascan3/commit/0d231234973612a639bab8cf3fc26fb81c88717f
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-20 (Mon, 20 Apr 2026)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  Merge pull request #412 from ehb54/haben/docs-crosslinking

Document cross linking, manual help buttons and new pages added.


  Commit: 47638222ab16a5ea91b3b1574d03c5038374b2a4
      https://github.com/ehb54/ultrascan3/commit/47638222ab16a5ea91b3b1574d03c5038374b2a4
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-21 (Tue, 21 Apr 2026)

  Changed paths:
    M doc/manual/source/start_page-mw.rst

  Log Message:
  -----------
  replaced old image in doc


  Commit: 1fece8e1783a00b7b4b2d53c0d3fb24784b20678
      https://github.com/ehb54/ultrascan3/commit/1fece8e1783a00b7b4b2d53c0d3fb24784b20678
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-21 (Tue, 21 Apr 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into haben/docs-crosslinking


  Commit: c0dbe2538c5177518ec31c51efdbe5540a5df70d
      https://github.com/ehb54/ultrascan3/commit/c0dbe2538c5177518ec31c51efdbe5540a5df70d
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-21 (Tue, 21 Apr 2026)

  Changed paths:
    M doc/manual/source/start_page-mw.rst

  Log Message:
  -----------
  Merge pull request #415 from ehb54/haben/docs-crosslinking

replaced old image in doc


  Commit: 0d1643338fa17f6186a4ad8679ba4cccf89fd394
      https://github.com/ehb54/ultrascan3/commit/0d1643338fa17f6186a4ad8679ba4cccf89fd394
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_pseudo3d_combine


  Commit: eca543a22ebb2991eb0b445f72e347063fbc8c72
      https://github.com/ehb54/ultrascan3/commit/eca543a22ebb2991eb0b445f72e347063fbc8c72
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  standardize reference section formatting in start_page.rst and start_page-mw.rst


  Commit: a4f1f53d77b4eb249b8afb6b09bf96f052e25542
      https://github.com/ehb54/ultrascan3/commit/a4f1f53d77b4eb249b8afb6b09bf96f052e25542
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix VERSION file path, change default version from unknown to 4.1.0-dev, refactor release construction


  Commit: db21d0c5a194f41886b613e65623c07d2bc40f9d
      https://github.com/ehb54/ultrascan3/commit/db21d0c5a194f41886b613e65623c07d2bc40f9d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M utils/us_defines.h

  Log Message:
  -----------
  add conditional definitions for US_Version and US_Description in us_defines.h


  Commit: 9cbcea1782add3926f1f936aa6696c0e418a0a33
      https://github.com/ehb54/ultrascan3/commit/9cbcea1782add3926f1f936aa6696c0e418a0a33
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  add __pycache__ to .gitignore


  Commit: 102b83ab79cfa7cf1af1b528d6422565dd8b4bba
      https://github.com/ehb54/ultrascan3/commit/102b83ab79cfa7cf1af1b528d6422565dd8b4bba
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix spacing for no local changes


  Commit: ffce8c0558eef867b786192bfa509ba0b615e715
      https://github.com/ehb54/ultrascan3/commit/ffce8c0558eef867b786192bfa509ba0b615e715
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M utils/us_defines.h

  Log Message:
  -----------
  Remove version and description guards in us_defines.h


  Commit: 36dc1785d98214993d36bfc9d3b4d8274ddf93ba
      https://github.com/ehb54/ultrascan3/commit/36dc1785d98214993d36bfc9d3b4d8274ddf93ba
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Update path comment for VERSION file location


  Commit: 8cf8988f671379dcf266a35155e091020469e547
      https://github.com/ehb54/ultrascan3/commit/8cf8988f671379dcf266a35155e091020469e547
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp

  Log Message:
  -----------
  Refactor signal-slot connections across multiple modules to use modern syntax for improved readability and maintainability.


  Commit: e55fdb6a821372263be14ebfd0bd4debd621c904
      https://github.com/ehb54/ultrascan3/commit/e55fdb6a821372263be14ebfd0bd4debd621c904
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Ensure axis checks account for spectrogram items in `us_plot.cpp`


  Commit: 33967fac5d6dd4415b67c2e8bc928de7aad9504b
      https://github.com/ehb54/ultrascan3/commit/33967fac5d6dd4415b67c2e8bc928de7aad9504b
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M programs/us_pcsa/us_analysis_control_pc.cpp

  Log Message:
  -----------
  Refactor signal-slot connections in `us_analysis_control_pc.cpp` to use modern syntax for improved readability and maintainability.


  Commit: 3c2f9d3ede41ffdcd79d070e45afb8a238e729fb
      https://github.com/ehb54/ultrascan3/commit/3c2f9d3ede41ffdcd79d070e45afb8a238e729fb
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Simplify lambda expressions in `us_pseudo3d_combine.cpp` by removing redundant `&` capture.


  Commit: c20633e9c5e7406950dbc174cae33f60cb8c2d17
      https://github.com/ehb54/ultrascan3/commit/c20633e9c5e7406950dbc174cae33f60cb8c2d17
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Remove future annotations import

Removed future annotations import from conf.py.


  Commit: 60491d8fe675ed9c20c175e16153aa1a2f594186
      https://github.com/ehb54/ultrascan3/commit/60491d8fe675ed9c20c175e16153aa1a2f594186
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Add __pycache__ to .gitignore


  Commit: 2cb09af8870f32c9aa5e3463851c91e6741e0bdd
      https://github.com/ehb54/ultrascan3/commit/2cb09af8870f32c9aa5e3463851c91e6741e0bdd
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/source/conf.py
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  Merge pull request #416 from ehb54/lukas/manual_versioning

Standardize formatting and update versioning in manual


  Commit: eba2b0e533d5a81cad63c0edd5319256ba404cdd
      https://github.com/ehb54/ultrascan3/commit/eba2b0e533d5a81cad63c0edd5319256ba404cdd
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/source/conf.py
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_pseudo3d_combine


  Commit: 46ff46e5434d882cb83343ffd5b854bf6f41f7d1
      https://github.com/ehb54/ultrascan3/commit/46ff46e5434d882cb83343ffd5b854bf6f41f7d1
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue819


  Commit: bf1f52b701e7d998a5d22f3fb3cfac685fe25b11
      https://github.com/ehb54/ultrascan3/commit/bf1f52b701e7d998a5d22f3fb3cfac685fe25b11
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-25 (Sat, 25 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge pull request #413 from ehb54/lukas/us_pseudo3d_combine

Lukas/us pseudo3d combine


  Commit: 409fa95fadf7055d7f1a80221d9570136a3c74ea
      https://github.com/ehb54/ultrascan3/commit/409fa95fadf7055d7f1a80221d9570136a3c74ea
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-22 (Fri, 22 May 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-dataDisk: 1.EXP.: 4. Cells --  Fix logic for changing centerpieces only for cells uploaded from data-from-diks; depending on rotor choice, if uploaded data contains counter-balancing cell, then mirror centerpieces; if no counter-balancing cell exists, do not trigger mirroring, keep cell disabled...


  Commit: c2f09171367a1f7251e1b6c2f115e67a2ec2aa7e
      https://github.com/ehb54/ultrascan3/commit/c2f09171367a1f7251e1b6c2f115e67a2ec2aa7e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-23 (Sat, 23 May 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M scripts/build.sh

  Log Message:
  -----------
  Fix: MariaDB Connector/C auth plugin packaging for Windows and Linux desktop deploys


  Commit: 955a18e6afbf33a71fb3cb653635e8a1fdcba309
      https://github.com/ehb54/ultrascan3/commit/955a18e6afbf33a71fb3cb653635e8a1fdcba309
  Author: Saeed <github.com/samo38>
  Date:   2026-05-25 (Mon, 25 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  us_extinction_gui: load multiple files to the target list in the us_extinction


  Commit: 8ffe17a2ff45c1bd98abb4f443c8e85a44607408
      https://github.com/ehb54/ultrascan3/commit/8ffe17a2ff45c1bd98abb4f443c8e85a44607408
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-25 (Mon, 25 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected...


  Commit: d65cc7b90bd9cfd09a504b97d1e991b5e9709798
      https://github.com/ehb54/ultrascan3/commit/d65cc7b90bd9cfd09a504b97d1e991b5e9709798
  Author: Saeed <github.com/samo38>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  fix the ct_plt range for D values


  Commit: 70c051b3319c22d073aec3e7963574dd431d374b
      https://github.com/ehb54/ultrascan3/commit/70c051b3319c22d073aec3e7963574dd431d374b
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge pull request #421 from samo38/ticket_821

ticket 821: load multiple files in the Spectra Fitter


  Commit: 47568edd1c571d37f6d337dac8403bf2b63355a7
      https://github.com/ehb54/ultrascan3/commit/47568edd1c571d37f6d337dac8403bf2b63355a7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue847


  Commit: 9caa64325023045f92d621ea29c7c24238abe010
      https://github.com/ehb54/ultrascan3/commit/9caa64325023045f92d621ea29c7c24238abe010
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue845


  Commit: 3f5b75b4f2c1f0e13c26e4f5200970f1a849ccce
      https://github.com/ehb54/ultrascan3/commit/3f5b75b4f2c1f0e13c26e4f5200970f1a849ccce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  [Warning message edited]Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected...


  Commit: 8b4bb030d983d019042fbafc5db11ecddb4cef59
      https://github.com/ehb54/ultrascan3/commit/8b4bb030d983d019042fbafc5db11ecddb4cef59
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  [Warning message edited]Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected...


  Commit: 4c2a5827c767a8efdf04d90f65582b75aa7b8f7b
      https://github.com/ehb54/ultrascan3/commit/4c2a5827c767a8efdf04d90f65582b75aa7b8f7b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge branch 'alexey-dev-issue845' of github.com:ehb54/ultrascan3 into alexey-dev-issue845


  Commit: e41650e2a92988aaf178bb235f6fd635ae7732a5
      https://github.com/ehb54/ultrascan3/commit/e41650e2a92988aaf178bb235f6fd635ae7732a5
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-05-27 (Wed, 27 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  Merge pull request #422 from ehb54/alexey-dev-issue845

Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected.


  Commit: 3c4763f65a21b749bfe07dc42e2128122b695384
      https://github.com/ehb54/ultrascan3/commit/3c4763f65a21b749bfe07dc42e2128122b695384
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-05-27 (Wed, 27 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue847


  Commit: 2d6c96d3534c682e0f41a653e60626ac9ca3cda5
      https://github.com/ehb54/ultrascan3/commit/2d6c96d3534c682e0f41a653e60626ac9ca3cda5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-27 (Wed, 27 May 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  1. EXP. setup for: GMP | R&D | Protocol Dev. -- (1) Previous Panel: disable when 1st tab index; (2) Next Panel: disable when last tab index; Enable both buttons otherwise...


  Commit: 336ecdb767221596e40fe03b4109ae958a244155
      https://github.com/ehb54/ultrascan3/commit/336ecdb767221596e40fe03b4109ae958a244155
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge pull request #420 from ehb54/alexey-dev-issue847

GMP-dataDisk: 1.EXP.: 4. Cells --  Fix logic for changing centerpiece?


  Commit: 4271414177534df7efc4fa581c55c7156f3ddabd
      https://github.com/ehb54/ultrascan3/commit/4271414177534df7efc4fa581c55c7156f3ddabd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue855


  Commit: 128150af07823bd4765583981c14e72a886ececb
      https://github.com/ehb54/ultrascan3/commit/128150af07823bd4765583981c14e72a886ececb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_plot.cpp
    M gui/us_properties.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue819


  Commit: ac4b2e251a870242701d557b0f9fb1bde83f1ba1
      https://github.com/ehb54/ultrascan3/commit/ac4b2e251a870242701d557b0f9fb1bde83f1ba1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge pull request #424 from ehb54/alexey-dev-issue855

1. EXP. setup for: GMP | R&D | Protocol Dev. -- Previous Panel & Next Panel buttons


  Commit: 4d55ef620df76f15f779937d88eae46dc5476934
      https://github.com/ehb54/ultrascan3/commit/4d55ef620df76f15f779937d88eae46dc5476934
  Author: Saeed <github.com/samo38>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  us_pseudo3d_combine.cpp: update ct range


  Commit: bfbbceba435317993ba1177f8d6ed0a5810550da
      https://github.com/ehb54/ultrascan3/commit/bfbbceba435317993ba1177f8d6ed0a5810550da
  Author: Saeed <github.com/samo38>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  update ct range


  Commit: 3650572bd17f9308587dfbf1d1410498922d61fc
      https://github.com/ehb54/ultrascan3/commit/3650572bd17f9308587dfbf1d1410498922d61fc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP: 2. Rotor/Labs  : in a non-typical situation where oper. or revs. or appr, lists are empty, disable Add to List button...


  Commit: fada6882842c5ae682cd424efd87744e75cace23
      https://github.com/ehb54/ultrascan3/commit/fada6882842c5ae682cd424efd87744e75cace23
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge pull request #426 from ehb54/alexey-dev-issue857

GMP: 2. Rotor/Labs  tab: Add to List bttns


  Commit: a2adfa71f41c800e6f524a3cc455920214b68843
      https://github.com/ehb54/ultrascan3/commit/a2adfa71f41c800e6f524a3cc455920214b68843
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue819


  Commit: 7d69bb500e80be10d428dd0e6858038dfd36f238
      https://github.com/ehb54/ultrascan3/commit/7d69bb500e80be10d428dd0e6858038dfd36f238
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h

  Log Message:
  -----------
  Merge pull request #414 from ehb54/alexey-dev-issue819

Model Selector  -- allow Accept for GMP-generated models...


  Commit: 081a9573c4b25b4a1160d69485efb294378d580d
      https://github.com/ehb54/ultrascan3/commit/081a9573c4b25b4a1160d69485efb294378d580d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge branch 'main' into t842_gaplot


  Commit: 3e9d2e13ca1148add7cf8287085ba3db3a5863c2
      https://github.com/ehb54/ultrascan3/commit/3e9d2e13ca1148add7cf8287085ba3db3a5863c2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Refactor default database selection process

Refactor database selection logic to avoid redundant calls and improve clarity.


  Commit: c4f9c771e1b24dc0e93e5dca2db4cdb010f1dc9e
      https://github.com/ehb54/ultrascan3/commit/c4f9c771e1b24dc0e93e5dca2db4cdb010f1dc9e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Update database selection logic for default DB


  Commit: 88b1ac951023136e21e2f1ab0c2fd000ad06eac8
      https://github.com/ehb54/ultrascan3/commit/88b1ac951023136e21e2f1ab0c2fd000ad06eac8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Delete .github/workflows/unit-tests.yml


  Commit: 59261739cdcce7bb342cec6d0eca84439819b56d
      https://github.com/ehb54/ultrascan3/commit/59261739cdcce7bb342cec6d0eca84439819b56d
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt

  Log Message:
  -----------
  Fix: Copy MariaDB auth plugins to build directory for development


  Commit: 8b547ef902833338a45d98fe066ac0c767fdf626
      https://github.com/ehb54/ultrascan3/commit/8b547ef902833338a45d98fe066ac0c767fdf626
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Fix: Add US3 version string to Linux deployment CMake configuration


  Commit: 845441e33ec92b9dc3657f2b7871f2183122a73b
      https://github.com/ehb54/ultrascan3/commit/845441e33ec92b9dc3657f2b7871f2183122a73b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M scripts/build.ps1

  Log Message:
  -----------
  Fix: Enhance Windows deployment process for Qt tools in CMake and PowerShell scripts


  Commit: cae5416d082d2ffb9ce37e3299da1d6ba4818688
      https://github.com/ehb54/ultrascan3/commit/cae5416d082d2ffb9ce37e3299da1d6ba4818688
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/toolchain.cmake
    M scripts/build.ps1

  Log Message:
  -----------
  Fix: Improve windeployqt handling for Windows ARM64 and x64 builds in CMake


  Commit: ffe103a9cda3bf0765d63babc1383b5b73c60f00
      https://github.com/ehb54/ultrascan3/commit/ffe103a9cda3bf0765d63babc1383b5b73c60f00
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Merge pull request #429 from ehb54/lukas/unit_test_v1_removal

Delete .github/workflows/unit-tests.yml


  Commit: ba2e69f89d211b977e99532f5a2ee4f5635fe241
      https://github.com/ehb54/ultrascan3/commit/ba2e69f89d211b977e99532f5a2ee4f5635fe241
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    M scripts/build.ps1

  Log Message:
  -----------
  Fix: Enhance build script for Windows by adding build type handling and ensuring full build before packaging


  Commit: 07ebae5c1a9fb79e304cf43ad4969948dbf53c1f
      https://github.com/ehb54/ultrascan3/commit/07ebae5c1a9fb79e304cf43ad4969948dbf53c1f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    M CMakeLists.txt
    M programs/us/us.cpp

  Log Message:
  -----------
  Fix: Copy MariaDB auth plugins to build directory for Windows development


  Commit: 4d0251f74bed05cb83787a04885731d3b152f4b5
      https://github.com/ehb54/ultrascan3/commit/4d0251f74bed05cb83787a04885731d3b152f4b5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M gui/us_extinction_gui.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_properties.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into 840-bug-cmake-build---mariadb-plugin-missing-macos


  Commit: ce276826700547ec7106f9d689b8d998e2001315
      https://github.com/ehb54/ultrascan3/commit/ce276826700547ec7106f9d689b8d998e2001315
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot at users.noreply.github.com>


  Commit: 48619c5707bd21b1fca1d26626f0d42608ec56a7
      https://github.com/ehb54/ultrascan3/commit/48619c5707bd21b1fca1d26626f0d42608ec56a7
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot at users.noreply.github.com>


  Commit: 7c437d150e86857f0f355ba642049e8298aa2967
      https://github.com/ehb54/ultrascan3/commit/7c437d150e86857f0f355ba642049e8298aa2967
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  Merge pull request #428 from ehb54/840-bug-cmake-build---mariadb-plugin-missing

Fix: MariaDB Connector/C auth plugin packaging for Windows and Linux ?


  Commit: c9483a2b187a96210afec12c05ea37f140d27c77
      https://github.com/ehb54/ultrascan3/commit/c9483a2b187a96210afec12c05ea37f140d27c77
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_config_db


  Commit: 77b0d98c96b9428b9058a18a1cde8a5234fd77de
      https://github.com/ehb54/ultrascan3/commit/77b0d98c96b9428b9058a18a1cde8a5234fd77de
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-06-03 (Wed, 03 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Merge pull request #427 from ehb54/lukas/us_config_db

Refactor default database selection process


  Commit: 8109d2d1f8a808b98af3173590fdf0a1bd470a4a
      https://github.com/ehb54/ultrascan3/commit/8109d2d1f8a808b98af3173590fdf0a1bd470a4a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-03 (Wed, 03 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  GMP, Prot_devel, utils/xpn_data : remove unused function, ensure xpn (optima) host is configured during xpn->connect...


  Commit: 25fa9df5a94aabc9a5a53be7d6e15d767a17c238
      https://github.com/ehb54/ultrascan3/commit/25fa9df5a94aabc9a5a53be7d6e15d767a17c238
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-04 (Thu, 04 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #430 from ehb54/alexey-dev-issue872

GMP, Prot_devel, utils/xpn_data : remove unused function, ensure xpn host is configured?


  Commit: 6cf1e2de27f3dc7a74383050c085f36898bb156b
      https://github.com/ehb54/ultrascan3/commit/6cf1e2de27f3dc7a74383050c085f36898bb156b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  GMP, R&D -- correct interplay between scan counts, scan interval, minimum scan interval in 3. Sppeds and 7. Ranges ...


  Commit: 5ce35ace4e6f0bd6eb3de4111d93a0c754c613e8
      https://github.com/ehb54/ultrascan3/commit/5ce35ace4e6f0bd6eb3de4111d93a0c754c613e8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  GMP, R&D -- The first sentence after Attention should not have started with a period. Line should have started with "Please..."....


  Commit: 439bf47d73c1de196a1c091f8629403731ac42e6
      https://github.com/ehb54/ultrascan3/commit/439bf47d73c1de196a1c091f8629403731ac42e6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  Merge pull request #432 from ehb54/alexey-dev-issue873

GMP, R&D -- The first sentence after Attention should not have started with a period. Line should have started with "Please..."....


  Commit: c70b0809570e8451264f061bfddbf0d90ed7d45b
      https://github.com/ehb54/ultrascan3/commit/c70b0809570e8451264f061bfddbf0d90ed7d45b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue874


  Commit: ab4e29f258a4a76852473bb029a8d05af5101e3b
      https://github.com/ehb54/ultrascan3/commit/ab4e29f258a4a76852473bb029a8d05af5101e3b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-07 (Sun, 07 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge pull request #431 from ehb54/alexey-dev-issue874

GMP, R&D -- correct interplay between scan counts, scan interval, min. scan interval


  Commit: b3e1c3148e849dfa0bb3115413e07983b919844e
      https://github.com/ehb54/ultrascan3/commit/b3e1c3148e849dfa0bb3115413e07983b919844e
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  add a label to show the buffer manual state


  Commit: f9dc1123f5d504527a1a5a5f98992c035cda5368
      https://github.com/ehb54/ultrascan3/commit/f9dc1123f5d504527a1a5a5f98992c035cda5368
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 372d4a9b863855920c8f9fcc63e1e874250bcdae
      https://github.com/ehb54/ultrascan3/commit/372d4a9b863855920c8f9fcc63e1e874250bcdae
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  auto scale xy after selecting a new parameter


  Commit: c00094277c02fa9f1bbf1ea45e6c392960605b9e
      https://github.com/ehb54/ultrascan3/commit/c00094277c02fa9f1bbf1ea45e6c392960605b9e
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M gui/us_extinction_gui.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_properties.cpp
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: f28a5e62b10d404ecce483e3109f42b1623253c4
      https://github.com/ehb54/ultrascan3/commit/f28a5e62b10d404ecce483e3109f42b1623253c4
  Author: Saeed <github.com/samo38>
  Date:   2026-06-09 (Tue, 09 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  fixed type cast warnings in us_mpi_analysis.cpp, ga_worker.cpp


  Commit: f3611e7f434e44d3d1c61e7d0e945a94035388f9
      https://github.com/ehb54/ultrascan3/commit/f3611e7f434e44d3d1c61e7d0e945a94035388f9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge pull request #435 from samo38/t861_security_warn

clean security warnings


  Commit: f80b73498a4973369419673e90274f59d9b598b3
      https://github.com/ehb54/ultrascan3/commit/f80b73498a4973369419673e90274f59d9b598b3
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 3dddb9117fd90c1f6e1fdeec16f309bcc7b74a10
      https://github.com/ehb54/ultrascan3/commit/3dddb9117fd90c1f6e1fdeec16f309bcc7b74a10
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: bde95ecaf2c093c38c510529ade5c772aeb0d058
      https://github.com/ehb54/ultrascan3/commit/bde95ecaf2c093c38c510529ade5c772aeb0d058
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 5be7ae9df7ec29fa88487a9dc72834ca6c3ab515
      https://github.com/ehb54/ultrascan3/commit/5be7ae9df7ec29fa88487a9dc72834ca6c3ab515
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_config/us_newxpnhost_db.cpp

  Log Message:
  -----------
  US_Config:Intruments -- incorporate test_Connectivity into Save routing, remove extra connectivity check step...


  Commit: 32473b578707e256cf293eb356d873413dd769b6
      https://github.com/ehb54/ultrascan3/commit/32473b578707e256cf293eb356d873413dd769b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_config/us_newxpnhost_db.cpp

  Log Message:
  -----------
  Merge pull request #436 from ehb54/alexey-dev-issue882

US_Config:Intruments -- incorporate test_Connectivity into Save routing


  Commit: 4aec245df7e6c8b1e030e812298d6cba7cab845e
      https://github.com/ehb54/ultrascan3/commit/4aec245df7e6c8b1e030e812298d6cba7cab845e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  GMP: 2. LIVE_UPDATE -- spelling error fixed...


  Commit: 12f71524c0445a97e2b0b1aaf3d53f6736ea6301
      https://github.com/ehb54/ultrascan3/commit/12f71524c0445a97e2b0b1aaf3d53f6736ea6301
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  GMP: -- modify message for marking run as FAILED/NPT FAILED...


  Commit: 3c7169cde650dedca3d3402f744d3253f88868d5
      https://github.com/ehb54/ultrascan3/commit/3c7169cde650dedca3d3402f744d3253f88868d5
  Author: Saeed <github.com/samo38>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 1be10ca817665f8309bb3df08852200424397547
      https://github.com/ehb54/ultrascan3/commit/1be10ca817665f8309bb3df08852200424397547
  Author: Saeed <github.com/samo38>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/t842_gaplot' into t842_gaplot


  Commit: 6a2abeacf5fcb63c4355bea33d0a8665ebf1aea3
      https://github.com/ehb54/ultrascan3/commit/6a2abeacf5fcb63c4355bea33d0a8665ebf1aea3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  GMP main window -- modify text in the upper textarea...


  Commit: 3fbee9fcc1783c2c585c16e2fe0cdb6c22982a61
      https://github.com/ehb54/ultrascan3/commit/3fbee9fcc1783c2c585c16e2fe0cdb6c22982a61
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  [1]GMP main window -- modify text in the upper textarea...


  Commit: 290881f0fb957f5129113ca6c0d363cda44d453e
      https://github.com/ehb54/ultrascan3/commit/290881f0fb957f5129113ca6c0d363cda44d453e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge pull request #437 from ehb54/alexey-dev-issue885

GMP: 2. LIVE_UPDATE -- spelling error fixed...


  Commit: 51eac7bb6878f0d5e5b586795486cea3043d3d0c
      https://github.com/ehb54/ultrascan3/commit/51eac7bb6878f0d5e5b586795486cea3043d3d0c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue887


  Commit: 27153f63f856b1d20b1465999a14d3e3281e707a
      https://github.com/ehb54/ultrascan3/commit/27153f63f856b1d20b1465999a14d3e3281e707a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue886


  Commit: 4241a57028574e3cd23f3c3291191974fc72a7f5
      https://github.com/ehb54/ultrascan3/commit/4241a57028574e3cd23f3c3291191974fc72a7f5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge pull request #438 from ehb54/alexey-dev-issue887

GMP: -- modify message for marking run as FAILED/NOT FAILED...


  Commit: 5b1e1e57275a9d2d7788c8c73c68af8bffc728aa
      https://github.com/ehb54/ultrascan3/commit/5b1e1e57275a9d2d7788c8c73c68af8bffc728aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue886


  Commit: 1b9d32c8d947abd0215b70dbe7495fc98759a47b
      https://github.com/ehb54/ultrascan3/commit/1b9d32c8d947abd0215b70dbe7495fc98759a47b
  Author: Saeed <github.com/samo38>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  update the ct range by data


  Commit: 1f2dea5900a814f27165ae2bc9b401c3dfee187c
      https://github.com/ehb54/ultrascan3/commit/1f2dea5900a814f27165ae2bc9b401c3dfee187c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge pull request #439 from ehb54/alexey-dev-issue886

GMP main window -- modify text in the upper textarea...


  Commit: 5e1874151de9b54802972297c327c677ea4ed1c9
      https://github.com/ehb54/ultrascan3/commit/5e1874151de9b54802972297c327c677ea4ed1c9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: cbb216d0d629fbbe7c3294431c08f61989b2e7a2
      https://github.com/ehb54/ultrascan3/commit/cbb216d0d629fbbe7c3294431c08f61989b2e7a2
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  upadte ct x and y in the set_limits()


  Commit: 67a4d242dabc14876d9354b93434c818b5baf7ec
      https://github.com/ehb54/ultrascan3/commit/67a4d242dabc14876d9354b93434c818b5baf7ec
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M gui/us_spectrodata.cpp

  Log Message:
  -----------
  in the setRaster function, if xrng becomes 0, xinc becomes INF. The same approach for xrng is applied here.


  Commit: 6f904c41c021e36595b930817137f19ef8ccce19
      https://github.com/ehb54/ultrascan3/commit/6f904c41c021e36595b930817137f19ef8ccce19
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  connect the replot_data function to the pb_refresh


  Commit: c24e05faa744af2d76beb4c61148bc79fa771670
      https://github.com/ehb54/ultrascan3/commit/c24e05faa744af2d76beb4c61148bc79fa771670
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  fixed the issue with draw bins manually


  Commit: 959da46aacd3efb25d3f0a0009e3da52819f733b
      https://github.com/ehb54/ultrascan3/commit/959da46aacd3efb25d3f0a0009e3da52819f733b
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: 32feaefb494d632b390d9acb54c6daefdd47089b
      https://github.com/ehb54/ultrascan3/commit/32feaefb494d632b390d9acb54c6daefdd47089b
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  set range of ct by data


  Commit: 9c70967b72e22425120bb3e0971e49e2cab828a2
      https://github.com/ehb54/ultrascan3/commit/9c70967b72e22425120bb3e0971e49e2cab828a2
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 0678091c6b8ea3a347d8bda5c1f8887a6d3ee65b
      https://github.com/ehb54/ultrascan3/commit/0678091c6b8ea3a347d8bda5c1f8887a6d3ee65b
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Merge pull request #433 from samo38/t870_buffer

Add buffer manual state to the Buffer and Solution GUI


  Commit: 075459dfc9537700e37aba51b3f8a5bb57c3c1c6
      https://github.com/ehb54/ultrascan3/commit/075459dfc9537700e37aba51b3f8a5bb57c3c1c6
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_select_item.cpp
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 16547f24596d6f1a1c6e10976383ed8bc2b74819
      https://github.com/ehb54/ultrascan3/commit/16547f24596d6f1a1c6e10976383ed8bc2b74819
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  Merge pull request #425 from samo38/t842_gaplot

ticket 842: GA plot range issue


  Commit: a7cbce78277c83da3570ae8b311270ecf88d59a5
      https://github.com/ehb54/ultrascan3/commit/a7cbce78277c83da3570ae8b311270ecf88d59a5
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: c7efd6ac8d78505ee8782507280e4a224fd9e858
      https://github.com/ehb54/ultrascan3/commit/c7efd6ac8d78505ee8782507280e4a224fd9e858
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge pull request #423 from samo38/ticket_822_pseudo3d_plot

ticket_822: us_pseudo3d_combine manually diffusion plotting issue


  Commit: 1eb5f81fa55c76e1991446dfaaafd472f62ff46f
      https://github.com/ehb54/ultrascan3/commit/1eb5f81fa55c76e1991446dfaaafd472f62ff46f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: 8285d5c355b2c8730c274762fd27522a30d3cd18
      https://github.com/ehb54/ultrascan3/commit/8285d5c355b2c8730c274762fd27522a30d3cd18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [2: select Project, do not enable tabs]GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: 245d4309e28c9db90cffbef3cb981c97b69a9b4a
      https://github.com/ehb54/ultrascan3/commit/245d4309e28c9db90cffbef3cb981c97b69a9b4a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue891


  Commit: 7870bc0e407e502ff7e3dac5490ba89f35c0a24b
      https://github.com/ehb54/ultrascan3/commit/7870bc0e407e502ff7e3dac5490ba89f35c0a24b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge pull request #440 from ehb54/alexey-dev-issue891

GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk selected to prevent user-filled protocol creation


  Commit: 04bc610b180db0057d777dd09625732e535d15d1
      https://github.com/ehb54/ultrascan3/commit/04bc610b180db0057d777dd09625732e535d15d1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Protocol-Developer: remove v.0,1 from the window title ...


  Commit: aabf6395ab17f75fe98ee8a1856d0df8163ac5a0
      https://github.com/ehb54/ultrascan3/commit/aabf6395ab17f75fe98ee8a1856d0df8163ac5a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge pull request #442 from ehb54/alexey-dev-issue890

Protocol-Developer: remove v.0,1 from the window title ...


  Commit: c01e1313f848d52ba4e9f5c91129eac8c54f2b4d
      https://github.com/ehb54/ultrascan3/commit/c01e1313f848d52ba4e9f5c91129eac8c54f2b4d
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  fix: Update bump PR commit SHA in workflow configuration


  Commit: 52cc7dc3a6bb04f611fd929cf3e9a34d8ff69e1c
      https://github.com/ehb54/ultrascan3/commit/52cc7dc3a6bb04f611fd929cf3e9a34d8ff69e1c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #444 from ehb54/898-update-bump-pr-commit-sha-ultrascan3

Update workflow configuration for commit SHA bump


  Commit: bbe49a767b0802c2c444243ec79fb5dbeeaf2d14
      https://github.com/ehb54/ultrascan3/commit/bbe49a767b0802c2c444243ec79fb5dbeeaf2d14
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/bump-version.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
    R doc/manual/buffer_new.body
    R doc/manual/buffer_select.body
    R doc/manual/buffer_settings.body
    R doc/manual/cfa_viewer.body
    R doc/manual/colorgradient.body
    R doc/manual/combine_models.body
    R doc/manual/components.body
    R doc/manual/config.body
    R doc/manual/config2.body
    R doc/manual/convert-experiment.body
    R doc/manual/convert-seltrip.body
    R doc/manual/convert.body
    R doc/manual/data_loader.body
    R doc/manual/database_config.body
    R doc/manual/ddist_combine.body
    R doc/manual/dens_match.body
    R doc/manual/dens_match_mparam.body
    R doc/manual/dens_match_rmvmods.body
    R doc/manual/experiment/experiment_cells.body
    R doc/manual/experiment/experiment_general.body
    R doc/manual/experiment/experiment_photomult.body
    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
    R doc/manual/fe_match/fe_match_lddat.body
    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
    R doc/manual/ga_initialize.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
    R doc/manual/images/color-1.png
    R doc/manual/images/color-2.png
    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
    R doc/manual/images/colorgrad1.png
    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
    R doc/manual/images/combine_models.png
    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
    R doc/manual/images/config2.png
    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
    R doc/manual/images/densmatch_mpars_empty.png
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    M gui/us_help.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.cpp
    M gui/us_model_loader.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_rotor_gui.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    R qwtplot3d/lingua_de.ts
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_extern.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_memory.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_solve_sim.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: e7fc39e0ded8d0a6cfe774a4c39f42f3e26ec5c2
      https://github.com/ehb54/ultrascan3/commit/e7fc39e0ded8d0a6cfe774a4c39f42f3e26ec5c2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro
    M local.pri.template

  Log Message:
  -----------
  Fix macx build: guard -lqwtplot3d self-link and add -lus_utils to libus_gui

local.pri.template: split -lqwtplot3d onto a guarded line so that
when qwtplot3d itself is being built it does not try to link against
its own not-yet-existing library (ld: library not found for -lqwtplot3d).

gui/libus_gui.pro: add macx LIBS += -lus_utils so that the symbols
moved into libus_gui in Nov 2025 (us_csv_loader, us_convert_gui,
us_extinction_gui, etc.) can resolve against libus_utils at link time.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: c81d8b70460860507d201fd8243784999eddf69b
      https://github.com/ehb54/ultrascan3/commit/c81d8b70460860507d201fd8243784999eddf69b
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-907


  Commit: 36f036553bd505b52b7b696575355f3d715ab159
      https://github.com/ehb54/ultrascan3/commit/36f036553bd505b52b7b696575355f3d715ab159
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro
    M local.pri.template

  Log Message:
  -----------
  Merge pull request #446 from ehb54/ehb54-issue-907

Fix macx build: guard -lqwtplot3d self-link and add -lus_utils to libus_gui


  Commit: c7fe1d915db484906fa21f7fdb059dd46ca14e3d
      https://github.com/ehb54/ultrascan3/commit/c7fe1d915db484906fa21f7fdb059dd46ca14e3d
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Delete doc/manual/source/__pycache__/auto_index.cpython-39.pyc


  Commit: 8ed782c9a9b80ae3e81e35cfb88056da7f66986b
      https://github.com/ehb54/ultrascan3/commit/8ed782c9a9b80ae3e81e35cfb88056da7f66986b
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Add Python bytecode files to .gitignore


  Commit: 02b1998e8c4e4190087e112ea223ffc452d892c1
      https://github.com/ehb54/ultrascan3/commit/02b1998e8c4e4190087e112ea223ffc452d892c1
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Merge pull request #447 from ehb54/ehb54-issue-908

Remove Python bytecode files and update .gitignore


  Commit: 2b7ce8e951545aceafde79228ff691ba4b5b2961
      https://github.com/ehb54/ultrascan3/commit/2b7ce8e951545aceafde79228ff691ba4b5b2961
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  revision.sh: limit ? marker to source code file changes only

Previously git diff checked all tracked files, causing the LOCAL_CHANGES
? symbol to appear whenever build scripts, .pri files, or other non-source
files differed from upstream ? including during normal packaging builds.

Restrict the check to file types that produce compiled output:
*.h, *.cpp, *.ui (Qt Designer), *.qrc (Qt resources).

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: a1bf5d7f2eb4649cd5167b42db38d5c6e4aa4d0d
      https://github.com/ehb54/ultrascan3/commit/a1bf5d7f2eb4649cd5167b42db38d5c6e4aa4d0d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  revision.sh: fix pathspec scope for source-file delta check

git diff pathspecs with bare globs (*.h) only match within the current
directory, not repo-wide. Since the script cd's to programs/us/, the
check was missing changes in gui/, utils/, etc.

Fix by running git -C from the repo root so all subdirectories are covered.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 325d0cbff2d496aaf6a42add91e63d096b0e9d26
      https://github.com/ehb54/ultrascan3/commit/325d0cbff2d496aaf6a42add91e63d096b0e9d26
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-909


  Commit: c4a785babca12aa43bf7f624928fa31cf97da1f4
      https://github.com/ehb54/ultrascan3/commit/c4a785babca12aa43bf7f624928fa31cf97da1f4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  Merge pull request #448 from ehb54/ehb54-issue-909

revision.sh: limit ? marker to source code file changes only


  Commit: 45ef026ad65a694d99671bd358216a9d7f7330d3
      https://github.com/ehb54/ultrascan3/commit/45ef026ad65a694d99671bd358216a9d7f7330d3
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/bump-version.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M admin/cmake/toolchain.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
    R doc/manual/buffer_new.body
    R doc/manual/buffer_select.body
    R doc/manual/buffer_settings.body
    R doc/manual/cfa_viewer.body
    R doc/manual/colorgradient.body
    R doc/manual/combine_models.body
    R doc/manual/components.body
    R doc/manual/config.body
    R doc/manual/config2.body
    R doc/manual/convert-experiment.body
    R doc/manual/convert-seltrip.body
    R doc/manual/convert.body
    R doc/manual/data_loader.body
    R doc/manual/database_config.body
    R doc/manual/ddist_combine.body
    R doc/manual/dens_match.body
    R doc/manual/dens_match_mparam.body
    R doc/manual/dens_match_rmvmods.body
    R doc/manual/experiment/experiment_cells.body
    R doc/manual/experiment/experiment_general.body
    R doc/manual/experiment/experiment_photomult.body
    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
    R doc/manual/fe_match/fe_match_lddat.body
    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
    R doc/manual/ga_initialize.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
    R doc/manual/images/color-1.png
    R doc/manual/images/color-2.png
    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
    R doc/manual/images/colorgrad1.png
    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
    R doc/manual/images/combine_models.png
    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
    R doc/manual/images/config2.png
    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
    R doc/manual/images/densmatch_mpars_empty.png
    R doc/manual/images/densmatch_rmvmodels.png
    R doc/manual/images/eq1-mean.png
    R doc/manual/images/eq2-skew.png
    R doc/manual/images/eq3-kurtosis.png
    R doc/manual/images/eq4-moments.png
    R doc/manual/images/eq5-variance.png
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    A doc/manual/source/xpn_viewer.rst
    R doc/manual/template.img.body
    R doc/manual/tidy.conf
    R doc/manual/time_derivative.body
    R doc/manual/ultrascan3.txt
    R doc/manual/us_buffer.body
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    R doc/manual/vhw_combine.body
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    R doc/manual/wrapped-images.lst
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
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    R etc/us3-GMP-icon-48x48.xpm
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_get_run.h
    M gui/us_help.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_properties.cpp
    M gui/us_rotor_gui.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M local.pri.template
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
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    A pkg/macos/resources/Welcome.txt.in
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    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    R qwtplot3d/lingua_de.ts
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    M scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_extern.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_memory.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_solve_sim.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-766


  Commit: 3ba8a99c404673869fe12bb20bdfd05fc1cbb9e9
      https://github.com/ehb54/ultrascan3/commit/3ba8a99c404673869fe12bb20bdfd05fc1cbb9e9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  remove redundant macx{} block in libus_gui.pro

The single-line macx: LIBS already covers this; the block added in
the prior commit was duplicate.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 5b846ae2ba06a1fe8922ca5463989738b9ac9388
      https://github.com/ehb54/ultrascan3/commit/5b846ae2ba06a1fe8922ca5463989738b9ac9388
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  Merge pull request #375 from ehb54/ehb54-issue-766

fix win32 gui link: add version suffix to -lqwtplot3d


  Commit: e42355993bdf8df5f59068aae970ffe9d7447c95
      https://github.com/ehb54/ultrascan3/commit/e42355993bdf8df5f59068aae970ffe9d7447c95
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    M gui/libus_gui.pro
    M local.pri.template
    M programs/us/revision.sh

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: 4102be089f9a53763e66d2b41a5d7ff0a81baee9
      https://github.com/ehb54/ultrascan3/commit/4102be089f9a53763e66d2b41a5d7ff0a81baee9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Fix linux.pl package name generation for new version/revision header format

us_revision.h no longer has a single REVISION field; it now has separate
BUILDNUM/GIT_REVISION/REVISION_DATE/LOCAL_CHANGES fields. The old
"grep REVISION" matched both GIT_REVISION and REVISION_DATE, producing a
multi-line value that broke the generated package directory name and the
shell commands built from it (used by both the redhat and ubuntu release
Dockerfiles). Build the package name from US_Version (utils/us_defines.h)
and BUILDNUM instead.

Fixes ehb54/ultrascan-tickets#910


  Commit: 22905927a67f8bb8637ed325009771296c5b9052
      https://github.com/ehb54/ultrascan3/commit/22905927a67f8bb8637ed325009771296c5b9052
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge pull request #451 from ehb54/ehb54-issue-910

Fix linux.pl package name generation for new version/revision header format


  Commit: 3c4a6a12de6f56ab3ccb0e05512fe01538445686
      https://github.com/ehb54/ultrascan3/commit/3c4a6a12de6f56ab3ccb0e05512fe01538445686
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Fix CodeQL build-target detection: == is not valid in POSIX sh [ ]

The "Calculate Build Targets" step runs under sh (dash), where [ ] only
supports = not ==. Every [ "$X" == "true" ] test errored as "unexpected
operator" and was treated as false, so the full-rebuild branch never ran
even on a push to main with FORCE_ALL=true. This meant CodeQL's analysis
database only ever contained whichever programs happened to be touched
by a given push's diff, causing already-open alerts in untouched files
(e.g. us_spectrum.cpp) to flap between Fixed/Reappeared across unrelated
PRs without the underlying code ever changing.

Fixes ehb54/ultrascan-tickets#911


  Commit: 2bb70f296f3ecc8f762152da20c145583f3d4fc1
      https://github.com/ehb54/ultrascan3/commit/2bb70f296f3ecc8f762152da20c145583f3d4fc1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  Fix remaining CodeQL security alerts: int-multiplication overflow + format arg

Same pattern as PR #435: cast one multiplication operand to qsizetype
before sizing a QVector, so the multiply itself doesn't happen in (32-bit)
int before widening. Also fixes a %d/qsizetype format-specifier mismatch
in us_pcsa_process.cpp.

Fixes ehb54/ultrascan-tickets#912


  Commit: 8ebc45097882afa73f22a184410e310658fca0de
      https://github.com/ehb54/ultrascan3/commit/8ebc45097882afa73f22a184410e310658fca0de
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: 733d3f549696b0efe49cd26d0840bdf6ab37d5e7
      https://github.com/ehb54/ultrascan3/commit/733d3f549696b0efe49cd26d0840bdf6ab37d5e7
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge pull request #445 from ehb54/bump-to-v4.1.0

Bump to v4.1.0


  Commit: 951770eef3cf63893454a5402ccb79e4a64062db
      https://github.com/ehb54/ultrascan3/commit/951770eef3cf63893454a5402ccb79e4a64062db
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-911


  Commit: d981490e29291aa7d6124604cc0ea33dcc753df3
      https://github.com/ehb54/ultrascan3/commit/d981490e29291aa7d6124604cc0ea33dcc753df3
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Merge pull request #452 from ehb54/ehb54-issue-911

Fix CodeQL build-target detection (sh != bash, == in [ ])


  Commit: cb2753416846b0e812f495ef4a5f2161dd35280c
      https://github.com/ehb54/ultrascan3/commit/cb2753416846b0e812f495ef4a5f2161dd35280c
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-912


  Commit: e3b3099b8aaebbe3c4fc5ddb2e7acb7186893133
      https://github.com/ehb54/ultrascan3/commit/e3b3099b8aaebbe3c4fc5ddb2e7acb7186893133
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  Merge pull request #453 from ehb54/ehb54-issue-912

Fix remaining CodeQL security alerts (multiplication overflow + format arg)


  Commit: d689ce8f674d78d26e7bff34f3928a4950f933af
      https://github.com/ehb54/ultrascan3/commit/d689ce8f674d78d26e7bff34f3928a4950f933af
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Robustly detect sphinx-build/python3 for DOMAN doc build on RHEL8

RHEL8 variants ship a too-old default python3 (3.6) plus optional
python3.11/python3.12 packages with no sphinx-build shim on PATH,
so the existing "which sphinx-build" check frequently misses a
working installation. Search candidate interpreters newest-first,
self-install Sphinx via ensurepip/pip if needed, and shim a scoped
python3 symlink on PATH only for the doc make step when the chosen
interpreter isn't named python3.

Fixes ultrascan-tickets#925


  Commit: f41aa3fd5b8d0ec601363a640f3b964ba85b1e51
      https://github.com/ehb54/ultrascan3/commit/f41aa3fd5b8d0ec601363a640f3b964ba85b1e51
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Reject Python interpreters too old for conf.py in DOMAN detection

doc/manual/source/conf.py uses Python >=3.9 syntax (PEP 585 builtin
generics, e.g. "list[str]"). The find_doc_python() search only checked
"import sphinx" succeeding, so a too-old default python3 (e.g. RHEL's
3.6) with a stale manually pip-installed Sphinx from before this
script existed got picked over a usable python3.11/python3.12 on the
same host, and the build then crashed in conf.py with "TypeError:
'type' object is not subscriptable". Add an explicit version check
that rejects any candidate interpreter below 3.9 before checking for
or installing Sphinx.

ehb54/ultrascan-tickets#925


  Commit: 18e656c09220a8883e1755f461737db76d91c710
      https://github.com/ehb54/ultrascan3/commit/18e656c09220a8883e1755f461737db76d91c710
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Drop --upgrade from ensurepip call in DOMAN detection

"ensurepip --upgrade" bootstraps pip from the bundled wheel and then
has pip upgrade itself from PyPI, which fails outright on
network-restricted hosts. Plain "ensurepip" only installs the bundled
wheel (fully offline) and is all that's needed to get a working pip
module before installing doc/manual/source/requirements.txt.

ehb54/ultrascan-tickets#925


  Commit: 25987d47541a67eb9c6168d741326e47ede154b9
      https://github.com/ehb54/ultrascan3/commit/25987d47541a67eb9c6168d741326e47ede154b9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Fix DOMAN fast path to check python3, not sphinx-build

doc/manual/Makefile invokes the interpreter as plain "python3"
(SPHINXBUILD ?= python3 -m sphinx), not "sphinx-build". The previous
fast path checked "sphinx-build --version" and returned immediately on
success, but an unrelated sphinx-build entry-point script tied to some
other (possibly too-old) interpreter can be on PATH and "work" -- since
--version never touches conf.py -- while "python3 -m sphinx" still
fails. This bypassed the version-gated python3.X search entirely and
explains why the previous DOMAN fixes had no effect on a host with a
stale sphinx-build shim left over from a manual "pip install --user"
under python3.6. Check bare python3 directly instead.

ehb54/ultrascan-tickets#925


  Commit: c71f3b106e12d2e2c40ee77a9695bee1793ff680
      https://github.com/ehb54/ultrascan3/commit/c71f3b106e12d2e2c40ee77a9695bee1793ff680
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Merge pull request #457 from ehb54/ehb54-issue-925

makeall.sh: robust sphinx/python3 detection for DOMAN on RHEL8 variants


  Commit: 6d06a0c1b49dfa1141dc8625e75bc03918635a40
      https://github.com/ehb54/ultrascan3/commit/6d06a0c1b49dfa1141dc8625e75bc03918635a40
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Include LICENSE.txt in Linux release packages

The Linux tar.xz packaging script never copied LICENSE.txt into the
package, unlike the Windows packaging script which does. Add the same
copy step so Linux packages ship a license file too.

Fixes ehb54/ultrascan-tickets#868


  Commit: c67d82488c7f281c78458954341098446e6baea0
      https://github.com/ehb54/ultrascan3/commit/c67d82488c7f281c78458954341098446e6baea0
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge pull request #458 from ehb54/ehb54-issue-868

Include LICENSE.txt in Linux release packages


  Commit: e47a1e408f3d0ac6a7db58fdf0cab65ab3b30a6f
      https://github.com/ehb54/ultrascan3/commit/e47a1e408f3d0ac6a7db58fdf0cab65ab3b30a6f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP-dataDisk: 1. EXP: 5. Solutions -- exclude (unspecified) item in all solution cahnnels for uploaded form disk data...


  Commit: 8a9c0cc6be7aaf9304035a342cbaeaba80e24135
      https://github.com/ehb54/ultrascan3/commit/8a9c0cc6be7aaf9304035a342cbaeaba80e24135
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #459 from ehb54/alexey-dev-issue929

GMP-dataDisk: 1. EXP: 5. Solutions -- exclude (unspecified) item in all solution cahnnels for uploaded form disk data...


  Commit: ed7f5a0cdf313c3337076a886caebe0f469d88a7
      https://github.com/ehb54/ultrascan3/commit/ed7f5a0cdf313c3337076a886caebe0f469d88a7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: 888dfa5cada04313f4e905ecab395a6080a7ad24
      https://github.com/ehb54/ultrascan3/commit/888dfa5cada04313f4e905ecab395a6080a7ad24
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  [edited mesage]Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: edda3c63be4e85f9fde90d971bf72dd1e184c1aa
      https://github.com/ehb54/ultrascan3/commit/edda3c63be4e85f9fde90d971bf72dd1e184c1aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge pull request #460 from ehb54/alexey-dev-issue928

Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: b9470a9bb9ca3b1859b7f798fa5f5e76a33a99ab
      https://github.com/ehb54/ultrascan3/commit/b9470a9bb9ca3b1859b7f798fa5f5e76a33a99ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: f0244186bf701788c6e7bc3915a4cca84aabe865
      https://github.com/ehb54/ultrascan3/commit/f0244186bf701788c6e7bc3915a4cca84aabe865
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue932


  Commit: 16b34f7a8252e4af4fbca5ebbd01f38bbb376beb
      https://github.com/ehb54/ultrascan3/commit/16b34f7a8252e4af4fbca5ebbd01f38bbb376beb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  [add connection check when attemting to Save]Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: 9c0f94c5d0a9f09a78152c7c5862b7f2e9a8bf6b
      https://github.com/ehb54/ultrascan3/commit/9c0f94c5d0a9f09a78152c7c5862b7f2e9a8bf6b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge branch 'alexey-dev-issue932' of github.com:ehb54/ultrascan3 into alexey-dev-issue932


  Commit: fb0e0bd78e483abe98e103bc0093440b38c5c669
      https://github.com/ehb54/ultrascan3/commit/fb0e0bd78e483abe98e103bc0093440b38c5c669
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  [[1]add connection check when attemting to Save]Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: 5732996f335aec054f71c4e536a044841eb385b5
      https://github.com/ehb54/ultrascan3/commit/5732996f335aec054f71c4e536a044841eb385b5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Merge pull request #461 from ehb54/alexey-dev-issue932

Preferences: Database -> Change: enable Save Entry button for any existing or new entries only after Test Connection is successful.


  Commit: 0d4d8870eb492684324b6bc7a5a39ca6b12c1c63
      https://github.com/ehb54/ultrascan3/commit/0d4d8870eb492684324b6bc7a5a39ca6b12c1c63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  US: hide "GMP" menu item for MacOS only...


  Commit: 1dd7a098a12171044289211cd22079f8b12f527d
      https://github.com/ehb54/ultrascan3/commit/1dd7a098a12171044289211cd22079f8b12f527d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  US: hide "Utilitoes->Data Acqusition" menu item for MacOS only...


  Commit: 37dfa3e81496bc5667af8082527f5ea1065c8133
      https://github.com/ehb54/ultrascan3/commit/37dfa3e81496bc5667af8082527f5ea1065c8133
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Merge pull request #462 from ehb54/alexey-dev-issue935

US: hide "GMP" menu item for MacOS only...


  Commit: 7eb866b9fcef86510463852edf2b6db9c2010dce
      https://github.com/ehb54/ultrascan3/commit/7eb866b9fcef86510463852edf2b6db9c2010dce
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-27 (Sat, 27 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix: restrict Sphinx dirty-check to source files to match revision.sh

The conf.py generate_version_metadata() was running git diff against all
tracked files with no path filter. On a macOS release build, a non-source
file (doc, script, etc.) was modified, causing conf.py to mark the build
dirty and embed ? in the Qt Help namespace/version string ? even though
revision.sh (splash screen) correctly showed no dirty flag because it
already restricts to *.h *.cpp *.ui *.qrc.

Fix: add the same -- *.h *.cpp *.ui *.qrc pathspec filter to both git diff
calls in conf.py so the dirty indicator is consistent with revision.sh.

Closes #936

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 52636d73ba151811a714c312eaae23119fbc3e22
      https://github.com/ehb54/ultrascan3/commit/52636d73ba151811a714c312eaae23119fbc3e22
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Merge pull request #464 from ehb54/issue-936

fix: restrict Sphinx dirty-check to source files (issue #936)


  Commit: 9153af9e9169c5ea50ab39f1e8b9a6c1cd6859bc
      https://github.com/ehb54/ultrascan3/commit/9153af9e9169c5ea50ab39f1e8b9a6c1cd6859bc
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix: change qthelp namespace from org.sphinx to com.aucsolutions

Closes ehb54/ultrascan-tickets#939

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: cc6eed0f49f97edb31642145d1c9757b4d7f5a53
      https://github.com/ehb54/ultrascan3/commit/cc6eed0f49f97edb31642145d1c9757b4d7f5a53
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into issue-939


  Commit: a22f52e0935d5bb7994769ffb9401e352f5bb3cf
      https://github.com/ehb54/ultrascan3/commit/a22f52e0935d5bb7994769ffb9401e352f5bb3cf
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Merge pull request #466 from ehb54/issue-939

fix: change qthelp namespace from org.sphinx to com.aucsolutions


  Commit: 6fc2e4866baf59178b492f7e345fb36de180ebd8
      https://github.com/ehb54/ultrascan3/commit/6fc2e4866baf59178b492f7e345fb36de180ebd8
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    A .github/gtest-us.json
    A .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    A VERSION
    M admin/cmake/FindQwt.cmake
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A admin/cmake/triplets/x64-mingw-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    M admin/release/linux.pl
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
    R doc/manual/buffer_new.body
    R doc/manual/buffer_select.body
    R doc/manual/buffer_settings.body
    R doc/manual/cfa_viewer.body
    R doc/manual/colorgradient.body
    R doc/manual/combine_models.body
    R doc/manual/components.body
    R doc/manual/config.body
    R doc/manual/config2.body
    R doc/manual/convert-experiment.body
    R doc/manual/convert-seltrip.body
    R doc/manual/convert.body
    R doc/manual/data_loader.body
    R doc/manual/database_config.body
    R doc/manual/ddist_combine.body
    R doc/manual/dens_match.body
    R doc/manual/dens_match_mparam.body
    R doc/manual/dens_match_rmvmods.body
    R doc/manual/experiment/experiment_cells.body
    R doc/manual/experiment/experiment_general.body
    R doc/manual/experiment/experiment_photomult.body
    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
    R doc/manual/fe_match/fe_match_lddat.body
    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
    R doc/manual/ga_initialize.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
    R doc/manual/images/color-1.png
    R doc/manual/images/color-2.png
    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
    R doc/manual/images/colorgrad1.png
    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
    R doc/manual/images/combine_models.png
    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
    R doc/manual/images/config2.png
    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
    R doc/manual/images/densmatch_mpars_empty.png
    R doc/manual/images/densmatch_rmvmodels.png
    R doc/manual/images/eq1-mean.png
    R doc/manual/images/eq2-skew.png
    R doc/manual/images/eq3-kurtosis.png
    R doc/manual/images/eq4-moments.png
    R doc/manual/images/eq5-variance.png
    R doc/manual/images/eq6-stddev.png
    R doc/manual/images/eq7-probsigma.png
    R doc/manual/images/eq8-confidence.png
    R doc/manual/images/experiment_cells.png
    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
    R doc/manual/images/fe_match_adv.png
    R doc/manual/images/fe_match_lddat1.png
    R doc/manual/images/fe_match_lddat2.png
    R doc/manual/images/fe_match_lddat3.png
    R doc/manual/images/fe_match_lddat4.png
    R doc/manual/images/fe_match_ra.png
    R doc/manual/images/fe_match_resplot.png
    R doc/manual/images/fe_match_sim1.png
    R doc/manual/images/fe_match_sim2.png
    R doc/manual/images/fe_match_sim3_1b.png
    R doc/manual/images/fe_match_sim3_1p.png
    R doc/manual/images/fe_match_sim3_2b.png
    R doc/manual/images/fe_match_sim3_2p.png
    R doc/manual/images/fe_match_sim3_3b.png
    R doc/manual/images/fe_match_sim3_4b.png
    R doc/manual/images/fe_match_sim3_5b.png
    R doc/manual/images/fe_match_sim3_5p.png
    R doc/manual/images/fe_match_sim3_6b.png
    R doc/manual/images/fe_match_sim3_7b.png
    R doc/manual/images/fe_match_sim3_8b.png
    R doc/manual/images/fe_match_sim4.png
    R doc/manual/images/fe_match_sim5.png
    R doc/manual/images/fe_match_sim6.png
    R doc/manual/images/fe_match_sim7.png
    R doc/manual/images/fit_men-editupd.png
    R doc/manual/images/fit_men-load.png
    R doc/manual/images/fit_meniscus.png
    R doc/manual/images/ga_initialize.png
    R doc/manual/images/gmp/audit_trail/gmp_audit_trail_01.png
    R doc/manual/images/gmp/audit_trail/gmp_audit_trail_02.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_01.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_02.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_03.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_04.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_05.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_06.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_07.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_08.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_09.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_10.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_11.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_12.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_13.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_14.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_15.png
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    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    R qwtplot3d/lingua_de.ts
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_defines.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_experiment.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #469 from ehb54/main

Merge main into somo-qt6


Compare: https://github.com/ehb54/ultrascan3/compare/8886d756072f...6fc2e4866baf

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From noreply at github.com  Wed Jul  1 07:58:58 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 06:58:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 02d921: Address PR #335 review
 feedback from doluk
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/68f716-02d921@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 02d921b6bfd9c82aab4bd08018955fb1f0dfdb26
      https://github.com/ehb54/ultrascan3/commit/02d921b6bfd9c82aab4bd08018955fb1f0dfdb26
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp

  Log Message:
  -----------
  Address PR #335 review feedback from doluk

- Qt::WFlags -> Qt::WindowFlags (lightingdlgbase.h)
- inline the const-wrapper save_svg overload (us3i_gui_util.cpp)
- drop dead Qt3/4 QT_VERSION include guard (us_config.cpp)
- hoist repeated regex construction to static const in
  fileNameCheck (us_hydrodyn.cpp), anaflex txt-extension checks
  (us_hydrodyn_anaflex_core.cpp), and the leading-'=' strip in
  US_Hydrodyn_Best::load (us_hydrodyn_best.cpp)
- move QRegularExpression include next to other Qt includes and
  simplify rx_spaces construction (us_hydrodyn_addresidue.cpp)
- remove duplicate QRegularExpression include (us_hydrodyn_bd_core.cpp)
- combine QRegularExpression rx construction with its pattern and
  drop the now-redundant setPattern call (us_hydrodyn_beads_load.cpp)



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From noreply at github.com  Wed Jul  1 07:58:58 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 06:58:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 005210: Address PR #335 review
 feedback from doluk
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/6fc2e4-005210@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 005210ec1222cf2098477fef7cbc62cdfdb1c08b
      https://github.com/ehb54/ultrascan3/commit/005210ec1222cf2098477fef7cbc62cdfdb1c08b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp

  Log Message:
  -----------
  Address PR #335 review feedback from doluk

- Qt::WFlags -> Qt::WindowFlags (lightingdlgbase.h)
- inline the const-wrapper save_svg overload (us3i_gui_util.cpp)
- drop dead Qt3/4 QT_VERSION include guard (us_config.cpp)
- hoist repeated regex construction to static const in
  fileNameCheck (us_hydrodyn.cpp), anaflex txt-extension checks
  (us_hydrodyn_anaflex_core.cpp), and the leading-'=' strip in
  US_Hydrodyn_Best::load (us_hydrodyn_best.cpp)
- move QRegularExpression include next to other Qt includes and
  simplify rx_spaces construction (us_hydrodyn_addresidue.cpp)
- remove duplicate QRegularExpression include (us_hydrodyn_bd_core.cpp)
- combine QRegularExpression rx construction with its pattern and
  drop the now-redundant setPattern call (us_hydrodyn_beads_load.cpp)



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From noreply at github.com  Wed Jul  1 08:34:08 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 07:34:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] eb825d: Skip explicit cipher list
 on MSYS2/64 Windows buil...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/a22f52-dd1a79@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: eb825d66df4c5c3e0841f6cd6a56571b29889a3c
      https://github.com/ehb54/ultrascan3/commit/eb825d66df4c5c3e0841f6cd6a56571b29889a3c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Skip explicit cipher list on MSYS2/64 Windows builds (#940)

MSYS2/64 (MINGW64) Windows builds link a Schannel-backed libmariadb,
which fails to match any suite from the OpenSSL-style CIPHER list:
"TLS/SSL error: no cipher match Error 0x80090331
(SEC_E_ALGORITHM_MISMATCH)".

Rather than imposing a substitute OpenSSL-style cipher string that
Schannel may or may not understand, skip calling
mysql_options(MYSQL_OPT_SSL_CIPHER, ...) entirely on __MINGW64__ and
let the backend negotiate its own default cipher suite set. This is a
workaround pending the real fix of linking an OpenSSL-backed MariaDB
Connector/C on Windows.

MSVC/vcpkg builds and Linux/macOS builds are unaffected (__MINGW64__
is not defined there).

Fixes ehb54/ultrascan-tickets#940

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: dd1a79e3b1c92c841119387bd1da9de25d53ade4
      https://github.com/ehb54/ultrascan3/commit/dd1a79e3b1c92c841119387bd1da9de25d53ade4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge pull request #467 from ehb54/ehb54-issue-940

Fix Schannel TLS cipher mismatch on MSYS2/64 Windows builds


Compare: https://github.com/ehb54/ultrascan3/compare/a22f52e0935d...dd1a79e3b1c9

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From noreply at github.com  Wed Jul  1 08:34:13 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 07:34:13 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-940/eb825d-000000@github.com>

  Branch: refs/heads/ehb54-issue-940
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Jul  1 08:39:36 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 07:39:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] eb825d: Skip explicit cipher list
 on MSYS2/64 Windows buil...
Message-ID: <ehb54/ultrascan3/push/refs/heads/issue-941/d099a4-73d10e@github.com>

  Branch: refs/heads/issue-941
  Home:   https://github.com/ehb54/ultrascan3
  Commit: eb825d66df4c5c3e0841f6cd6a56571b29889a3c
      https://github.com/ehb54/ultrascan3/commit/eb825d66df4c5c3e0841f6cd6a56571b29889a3c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Skip explicit cipher list on MSYS2/64 Windows builds (#940)

MSYS2/64 (MINGW64) Windows builds link a Schannel-backed libmariadb,
which fails to match any suite from the OpenSSL-style CIPHER list:
"TLS/SSL error: no cipher match Error 0x80090331
(SEC_E_ALGORITHM_MISMATCH)".

Rather than imposing a substitute OpenSSL-style cipher string that
Schannel may or may not understand, skip calling
mysql_options(MYSQL_OPT_SSL_CIPHER, ...) entirely on __MINGW64__ and
let the backend negotiate its own default cipher suite set. This is a
workaround pending the real fix of linking an OpenSSL-backed MariaDB
Connector/C on Windows.

MSVC/vcpkg builds and Linux/macOS builds are unaffected (__MINGW64__
is not defined there).

Fixes ehb54/ultrascan-tickets#940

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: dd1a79e3b1c92c841119387bd1da9de25d53ade4
      https://github.com/ehb54/ultrascan3/commit/dd1a79e3b1c92c841119387bd1da9de25d53ade4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge pull request #467 from ehb54/ehb54-issue-940

Fix Schannel TLS cipher mismatch on MSYS2/64 Windows builds


  Commit: 73d10e1ac2511df9f115150909f8efa4e15e2aa9
      https://github.com/ehb54/ultrascan3/commit/73d10e1ac2511df9f115150909f8efa4e15e2aa9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


Compare: https://github.com/ehb54/ultrascan3/compare/d099a4448e73...73d10e1ac251

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From noreply at github.com  Wed Jul  1 08:40:07 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 07:40:07 -0700
Subject: [us-commits] [ehb54/ultrascan3] eb825d: Skip explicit cipher list
 on MSYS2/64 Windows buil...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/005210-4dd383@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: eb825d66df4c5c3e0841f6cd6a56571b29889a3c
      https://github.com/ehb54/ultrascan3/commit/eb825d66df4c5c3e0841f6cd6a56571b29889a3c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Skip explicit cipher list on MSYS2/64 Windows builds (#940)

MSYS2/64 (MINGW64) Windows builds link a Schannel-backed libmariadb,
which fails to match any suite from the OpenSSL-style CIPHER list:
"TLS/SSL error: no cipher match Error 0x80090331
(SEC_E_ALGORITHM_MISMATCH)".

Rather than imposing a substitute OpenSSL-style cipher string that
Schannel may or may not understand, skip calling
mysql_options(MYSQL_OPT_SSL_CIPHER, ...) entirely on __MINGW64__ and
let the backend negotiate its own default cipher suite set. This is a
workaround pending the real fix of linking an OpenSSL-backed MariaDB
Connector/C on Windows.

MSVC/vcpkg builds and Linux/macOS builds are unaffected (__MINGW64__
is not defined there).

Fixes ehb54/ultrascan-tickets#940

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: dd1a79e3b1c92c841119387bd1da9de25d53ade4
      https://github.com/ehb54/ultrascan3/commit/dd1a79e3b1c92c841119387bd1da9de25d53ade4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge pull request #467 from ehb54/ehb54-issue-940

Fix Schannel TLS cipher mismatch on MSYS2/64 Windows builds


  Commit: 4dd383414126596486f0a9d7f4a2594aa26cbbb2
      https://github.com/ehb54/ultrascan3/commit/4dd383414126596486f0a9d7f4a2594aa26cbbb2
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


Compare: https://github.com/ehb54/ultrascan3/compare/005210ec1222...4dd383414126

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From noreply at github.com  Wed Jul  1 08:43:12 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 07:43:12 -0700
Subject: [us-commits] [ehb54/ultrascan3] 768ca9: Roll out per-amplitude
 Gaussian minimum to dad/mal...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/02d921-768ca9@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 768ca91ff963992cfbb912f512740052402f1fac
      https://github.com/ehb54/ultrascan3/commit/768ca91ff963992cfbb912f512740052402f1fac
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_dad_fit.h
    M us_somo/develop/include/us_hydrodyn_dad_options.h
    M us_somo/develop/include/us_hydrodyn_mals_fit.h
    M us_somo/develop/include/us_hydrodyn_mals_options.h
    M us_somo/develop/include/us_hydrodyn_mals_saxs_fit.h
    M us_somo/develop/include/us_hydrodyn_mals_saxs_options.h
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp

  Log Message:
  -----------
  Roll out per-amplitude Gaussian minimum to dad/mals/mals_saxs fit modules

HPLC's Gaussian fit split its single amplitude-and-width floor
(hplc_ampl_width_min) into two independent minimums: the pre-existing
one continues to bound width, while the new hplc_ampl_min bounds
amplitude. The sibling dad/mals/mals_saxs SAXS fit modules were never
updated to match, so their amplitude clamp (in setup_run and
lock_zeros) still reuses the combined width_min value.

Add the same ampl_min gparam, options-dialog widget, and fit-module
member to dad, mals, and mals_saxs, and repoint their amplitude clamp
logic at it, mirroring hplc_fit.cpp/hplc_options.cpp/hplc.cpp exactly.



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From noreply at github.com  Wed Jul  1 20:43:42 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 19:43:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] 37703a: somo qt6 branch - initial
 commit from somo-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/dd1a79-67350c@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
      https://github.com/ehb54/ultrascan3/commit/37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 9cc80a805f0c89d30fd663cffa4e544bdccfddd6
      https://github.com/ehb54/ultrascan3/commit/9cc80a805f0c89d30fd663cffa4e544bdccfddd6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql debug info


  Commit: 8f49d1cadd471936ba76ad95fe0001436a3685a7
      https://github.com/ehb54/ultrascan3/commit/8f49d1cadd471936ba76ad95fe0001436a3685a7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M us_somo/develop/libus_somo.pro

  Log Message:
  -----------
  remove us_color from libus_somo


  Commit: 642330d0e7562d863f6471b57e528cdf5aec013c
      https://github.com/ehb54/ultrascan3/commit/642330d0e7562d863f6471b57e528cdf5aec013c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
      https://github.com/ehb54/ultrascan3/commit/fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 1a808d5061ef553acf0aa97a83c04af9d82970bc
      https://github.com/ehb54/ultrascan3/commit/1a808d5061ef553acf0aa97a83c04af9d82970bc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 24783d42d61d7132dd5622e8027c9f6f59de5608
      https://github.com/ehb54/ultrascan3/commit/24783d42d61d7132dd5622e8027c9f6f59de5608
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  restore deprecations


  Commit: c37b59afbb01c067585c5da09c200e295282decc
      https://github.com/ehb54/ultrascan3/commit/c37b59afbb01c067585c5da09c200e295282decc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 59ba4be5192bd4024037ed7173a13061a59c41ce
      https://github.com/ehb54/ultrascan3/commit/59ba4be5192bd4024037ed7173a13061a59c41ce
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql fix


  Commit: cfd59439653a91b6cdcfd88d8a348ccb934a6cba
      https://github.com/ehb54/ultrascan3/commit/cfd59439653a91b6cdcfd88d8a348ccb934a6cba
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 46434a20d02da7dd7cb8edb14455747838aae8e4
      https://github.com/ehb54/ultrascan3/commit/46434a20d02da7dd7cb8edb14455747838aae8e4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  relax somo error for test


  Commit: 4bafd3f55ff93229f51bcd4cd0ece35195af707c
      https://github.com/ehb54/ultrascan3/commit/4bafd3f55ff93229f51bcd4cd0ece35195af707c
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Update compiler flags and defines in local.pri.somo


  Commit: a7e3fd4276bf018f3e37d73c4e11598037b8d409
      https://github.com/ehb54/ultrascan3/commit/a7e3fd4276bf018f3e37d73c4e11598037b8d409
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo datetime dirhist fix


  Commit: 34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
      https://github.com/ehb54/ultrascan3/commit/34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Clean up deprecated warning flags in local.pri.somo

Removed deprecated warning definitions for Qt.


  Commit: 87377fece32656c6472a465a06493b17084169fe
      https://github.com/ehb54/ultrascan3/commit/87377fece32656c6472a465a06493b17084169fe
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 8886d756072fc33f5d8db65458bae9bd00574c52
      https://github.com/ehb54/ultrascan3/commit/8886d756072fc33f5d8db65458bae9bd00574c52
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-01-19 (Mon, 19 Jan 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp

  Log Message:
  -----------
  somo qt6 compat regex bugfix


  Commit: 6fc2e4866baf59178b492f7e345fb36de180ebd8
      https://github.com/ehb54/ultrascan3/commit/6fc2e4866baf59178b492f7e345fb36de180ebd8
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    A .github/gtest-us.json
    A .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    A VERSION
    M admin/cmake/FindQwt.cmake
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A admin/cmake/triplets/x64-mingw-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    M admin/release/linux.pl
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
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    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
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    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
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    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
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    R doc/manual/2dsa/2dsa_advan.body
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    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
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    R doc/manual/cfa_viewer.body
    R doc/manual/colorgradient.body
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    R doc/manual/components.body
    R doc/manual/config.body
    R doc/manual/config2.body
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    R doc/manual/convert.body
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    R doc/manual/database_config.body
    R doc/manual/ddist_combine.body
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    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
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    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
    R doc/manual/ga_initialize.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
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    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
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    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
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    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
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    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
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    R doc/manual/images/densmatch_rmvmodels.png
    R doc/manual/images/eq1-mean.png
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    R doc/manual/images/eq4-moments.png
    R doc/manual/images/eq5-variance.png
    R doc/manual/images/eq6-stddev.png
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    R doc/manual/images/eq8-confidence.png
    R doc/manual/images/experiment_cells.png
    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
    R doc/manual/images/fe_match_adv.png
    R doc/manual/images/fe_match_lddat1.png
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    R doc/manual/images/fe_match_lddat4.png
    R doc/manual/images/fe_match_ra.png
    R doc/manual/images/fe_match_resplot.png
    R doc/manual/images/fe_match_sim1.png
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    R doc/manual/images/fit_men-editupd.png
    R doc/manual/images/fit_men-load.png
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    R doc/manual/images/ga_initialize.png
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    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    R qwtplot3d/lingua_de.ts
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_defines.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_experiment.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #469 from ehb54/main

Merge main into somo-qt6


  Commit: 005210ec1222cf2098477fef7cbc62cdfdb1c08b
      https://github.com/ehb54/ultrascan3/commit/005210ec1222cf2098477fef7cbc62cdfdb1c08b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp

  Log Message:
  -----------
  Address PR #335 review feedback from doluk

- Qt::WFlags -> Qt::WindowFlags (lightingdlgbase.h)
- inline the const-wrapper save_svg overload (us3i_gui_util.cpp)
- drop dead Qt3/4 QT_VERSION include guard (us_config.cpp)
- hoist repeated regex construction to static const in
  fileNameCheck (us_hydrodyn.cpp), anaflex txt-extension checks
  (us_hydrodyn_anaflex_core.cpp), and the leading-'=' strip in
  US_Hydrodyn_Best::load (us_hydrodyn_best.cpp)
- move QRegularExpression include next to other Qt includes and
  simplify rx_spaces construction (us_hydrodyn_addresidue.cpp)
- remove duplicate QRegularExpression include (us_hydrodyn_bd_core.cpp)
- combine QRegularExpression rx construction with its pattern and
  drop the now-redundant setPattern call (us_hydrodyn_beads_load.cpp)


  Commit: 4dd383414126596486f0a9d7f4a2594aa26cbbb2
      https://github.com/ehb54/ultrascan3/commit/4dd383414126596486f0a9d7f4a2594aa26cbbb2
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 67350cbc9b652fe2183c4a6889631191739a5cdb
      https://github.com/ehb54/ultrascan3/commit/67350cbc9b652fe2183c4a6889631191739a5cdb
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #335 from ehb54/somo-qt6

somo qt6 branch - initial commit from somo-dev


Compare: https://github.com/ehb54/ultrascan3/compare/dd1a79e3b1c9...67350cbc9b65

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From noreply at github.com  Wed Jul  1 20:43:46 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 19:43:46 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/4dd383-000000@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Jul  1 20:44:48 2026
From: noreply at github.com (emre brookes)
Date: Wed, 01 Jul 2026 19:44:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] 37703a: somo qt6 branch - initial
 commit from somo-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/issue-941/73d10e-5924b0@github.com>

  Branch: refs/heads/issue-941
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
      https://github.com/ehb54/ultrascan3/commit/37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 9cc80a805f0c89d30fd663cffa4e544bdccfddd6
      https://github.com/ehb54/ultrascan3/commit/9cc80a805f0c89d30fd663cffa4e544bdccfddd6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql debug info


  Commit: 8f49d1cadd471936ba76ad95fe0001436a3685a7
      https://github.com/ehb54/ultrascan3/commit/8f49d1cadd471936ba76ad95fe0001436a3685a7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M us_somo/develop/libus_somo.pro

  Log Message:
  -----------
  remove us_color from libus_somo


  Commit: 642330d0e7562d863f6471b57e528cdf5aec013c
      https://github.com/ehb54/ultrascan3/commit/642330d0e7562d863f6471b57e528cdf5aec013c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
      https://github.com/ehb54/ultrascan3/commit/fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 1a808d5061ef553acf0aa97a83c04af9d82970bc
      https://github.com/ehb54/ultrascan3/commit/1a808d5061ef553acf0aa97a83c04af9d82970bc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 24783d42d61d7132dd5622e8027c9f6f59de5608
      https://github.com/ehb54/ultrascan3/commit/24783d42d61d7132dd5622e8027c9f6f59de5608
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  restore deprecations


  Commit: c37b59afbb01c067585c5da09c200e295282decc
      https://github.com/ehb54/ultrascan3/commit/c37b59afbb01c067585c5da09c200e295282decc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 59ba4be5192bd4024037ed7173a13061a59c41ce
      https://github.com/ehb54/ultrascan3/commit/59ba4be5192bd4024037ed7173a13061a59c41ce
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql fix


  Commit: cfd59439653a91b6cdcfd88d8a348ccb934a6cba
      https://github.com/ehb54/ultrascan3/commit/cfd59439653a91b6cdcfd88d8a348ccb934a6cba
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 46434a20d02da7dd7cb8edb14455747838aae8e4
      https://github.com/ehb54/ultrascan3/commit/46434a20d02da7dd7cb8edb14455747838aae8e4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  relax somo error for test


  Commit: 4bafd3f55ff93229f51bcd4cd0ece35195af707c
      https://github.com/ehb54/ultrascan3/commit/4bafd3f55ff93229f51bcd4cd0ece35195af707c
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Update compiler flags and defines in local.pri.somo


  Commit: a7e3fd4276bf018f3e37d73c4e11598037b8d409
      https://github.com/ehb54/ultrascan3/commit/a7e3fd4276bf018f3e37d73c4e11598037b8d409
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo datetime dirhist fix


  Commit: 34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
      https://github.com/ehb54/ultrascan3/commit/34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Clean up deprecated warning flags in local.pri.somo

Removed deprecated warning definitions for Qt.


  Commit: 87377fece32656c6472a465a06493b17084169fe
      https://github.com/ehb54/ultrascan3/commit/87377fece32656c6472a465a06493b17084169fe
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 8886d756072fc33f5d8db65458bae9bd00574c52
      https://github.com/ehb54/ultrascan3/commit/8886d756072fc33f5d8db65458bae9bd00574c52
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-01-19 (Mon, 19 Jan 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp

  Log Message:
  -----------
  somo qt6 compat regex bugfix


  Commit: 6fc2e4866baf59178b492f7e345fb36de180ebd8
      https://github.com/ehb54/ultrascan3/commit/6fc2e4866baf59178b492f7e345fb36de180ebd8
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    A .github/gtest-us.json
    A .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    A VERSION
    M admin/cmake/FindQwt.cmake
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A admin/cmake/triplets/x64-mingw-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    M admin/release/linux.pl
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
    R doc/manual/buffer_new.body
    R doc/manual/buffer_select.body
    R doc/manual/buffer_settings.body
    R doc/manual/cfa_viewer.body
    R doc/manual/colorgradient.body
    R doc/manual/combine_models.body
    R doc/manual/components.body
    R doc/manual/config.body
    R doc/manual/config2.body
    R doc/manual/convert-experiment.body
    R doc/manual/convert-seltrip.body
    R doc/manual/convert.body
    R doc/manual/data_loader.body
    R doc/manual/database_config.body
    R doc/manual/ddist_combine.body
    R doc/manual/dens_match.body
    R doc/manual/dens_match_mparam.body
    R doc/manual/dens_match_rmvmods.body
    R doc/manual/experiment/experiment_cells.body
    R doc/manual/experiment/experiment_general.body
    R doc/manual/experiment/experiment_photomult.body
    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
    R doc/manual/fe_match/fe_match_lddat.body
    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
    R doc/manual/ga_initialize.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
    R doc/manual/images/color-1.png
    R doc/manual/images/color-2.png
    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
    R doc/manual/images/colorgrad1.png
    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
    R doc/manual/images/combine_models.png
    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
    R doc/manual/images/config2.png
    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
    R doc/manual/images/densmatch_mpars_empty.png
    R doc/manual/images/densmatch_rmvmodels.png
    R doc/manual/images/eq1-mean.png
    R doc/manual/images/eq2-skew.png
    R doc/manual/images/eq3-kurtosis.png
    R doc/manual/images/eq4-moments.png
    R doc/manual/images/eq5-variance.png
    R doc/manual/images/eq6-stddev.png
    R doc/manual/images/eq7-probsigma.png
    R doc/manual/images/eq8-confidence.png
    R doc/manual/images/experiment_cells.png
    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
    R doc/manual/images/fe_match_adv.png
    R doc/manual/images/fe_match_lddat1.png
    R doc/manual/images/fe_match_lddat2.png
    R doc/manual/images/fe_match_lddat3.png
    R doc/manual/images/fe_match_lddat4.png
    R doc/manual/images/fe_match_ra.png
    R doc/manual/images/fe_match_resplot.png
    R doc/manual/images/fe_match_sim1.png
    R doc/manual/images/fe_match_sim2.png
    R doc/manual/images/fe_match_sim3_1b.png
    R doc/manual/images/fe_match_sim3_1p.png
    R doc/manual/images/fe_match_sim3_2b.png
    R doc/manual/images/fe_match_sim3_2p.png
    R doc/manual/images/fe_match_sim3_3b.png
    R doc/manual/images/fe_match_sim3_4b.png
    R doc/manual/images/fe_match_sim3_5b.png
    R doc/manual/images/fe_match_sim3_5p.png
    R doc/manual/images/fe_match_sim3_6b.png
    R doc/manual/images/fe_match_sim3_7b.png
    R doc/manual/images/fe_match_sim3_8b.png
    R doc/manual/images/fe_match_sim4.png
    R doc/manual/images/fe_match_sim5.png
    R doc/manual/images/fe_match_sim6.png
    R doc/manual/images/fe_match_sim7.png
    R doc/manual/images/fit_men-editupd.png
    R doc/manual/images/fit_men-load.png
    R doc/manual/images/fit_meniscus.png
    R doc/manual/images/ga_initialize.png
    R doc/manual/images/gmp/audit_trail/gmp_audit_trail_01.png
    R doc/manual/images/gmp/audit_trail/gmp_audit_trail_02.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_01.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_02.png
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    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
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    M programs/us_density_match/us_density_match.cpp
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    M programs/us_dmga_init/us_dmga_init.cpp
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    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
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    M programs/us_experiment/us_proto_ranges.cpp
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    M programs/us_fematch/CMakeLists.txt
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    M programs/us_ga_init/us_ga_init.cpp
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    M programs/us_integral/us_delete_models.h
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    M programs/us_mpi_analysis/2dsa_worker.cpp
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    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    R qwtplot3d/lingua_de.ts
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_defines.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_experiment.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #469 from ehb54/main

Merge main into somo-qt6


  Commit: 005210ec1222cf2098477fef7cbc62cdfdb1c08b
      https://github.com/ehb54/ultrascan3/commit/005210ec1222cf2098477fef7cbc62cdfdb1c08b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp

  Log Message:
  -----------
  Address PR #335 review feedback from doluk

- Qt::WFlags -> Qt::WindowFlags (lightingdlgbase.h)
- inline the const-wrapper save_svg overload (us3i_gui_util.cpp)
- drop dead Qt3/4 QT_VERSION include guard (us_config.cpp)
- hoist repeated regex construction to static const in
  fileNameCheck (us_hydrodyn.cpp), anaflex txt-extension checks
  (us_hydrodyn_anaflex_core.cpp), and the leading-'=' strip in
  US_Hydrodyn_Best::load (us_hydrodyn_best.cpp)
- move QRegularExpression include next to other Qt includes and
  simplify rx_spaces construction (us_hydrodyn_addresidue.cpp)
- remove duplicate QRegularExpression include (us_hydrodyn_bd_core.cpp)
- combine QRegularExpression rx construction with its pattern and
  drop the now-redundant setPattern call (us_hydrodyn_beads_load.cpp)


  Commit: 4dd383414126596486f0a9d7f4a2594aa26cbbb2
      https://github.com/ehb54/ultrascan3/commit/4dd383414126596486f0a9d7f4a2594aa26cbbb2
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 67350cbc9b652fe2183c4a6889631191739a5cdb
      https://github.com/ehb54/ultrascan3/commit/67350cbc9b652fe2183c4a6889631191739a5cdb
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #335 from ehb54/somo-qt6

somo qt6 branch - initial commit from somo-dev


  Commit: 5924b0fe87a290c4e598e447b28d84cdc4780865
      https://github.com/ehb54/ultrascan3/commit/5924b0fe87a290c4e598e447b28d84cdc4780865
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


Compare: https://github.com/ehb54/ultrascan3/compare/73d10e1ac251...5924b0fe87a2

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From noreply at github.com  Thu Jul  2 08:54:49 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 07:54:49 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6986a9: Update qwt to 6.3.0 in
 release Dockerfiles
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-qwt-6.3.0-dockerfiles/000000-6986a9@github.com>

  Branch: refs/heads/ehb54-qwt-6.3.0-dockerfiles
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6986a9417f6347a587094bb50bb7e84ff4e199fd
      https://github.com/ehb54/ultrascan3/commit/6986a9417f6347a587094bb50bb7e84ff4e199fd
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  Update qwt to 6.3.0 in release Dockerfiles

Bump qwt_version from 6.1.6 to 6.3.0 in the ubuntu and redhat release
Dockerfiles. The download URL already uses downloads.sourceforge.net
(not a hardcoded mirror), and qwt-6.3.0.tar.bz2 is confirmed present
at that path.



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From noreply at github.com  Thu Jul  2 08:58:33 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 07:58:33 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-qwt-6.3.0-dockerfiles/6986a9-000000@github.com>

  Branch: refs/heads/ehb54-qwt-6.3.0-dockerfiles
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Jul  2 08:58:31 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 07:58:31 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6986a9: Update qwt to 6.3.0 in
 release Dockerfiles
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/721dbb-f82e19@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6986a9417f6347a587094bb50bb7e84ff4e199fd
      https://github.com/ehb54/ultrascan3/commit/6986a9417f6347a587094bb50bb7e84ff4e199fd
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  Update qwt to 6.3.0 in release Dockerfiles

Bump qwt_version from 6.1.6 to 6.3.0 in the ubuntu and redhat release
Dockerfiles. The download URL already uses downloads.sourceforge.net
(not a hardcoded mirror), and qwt-6.3.0.tar.bz2 is confirmed present
at that path.


  Commit: f82e19a707168b5425b295b5aa067add2225ba99
      https://github.com/ehb54/ultrascan3/commit/f82e19a707168b5425b295b5aa067add2225ba99
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  Merge pull request #470 from ehb54/ehb54-qwt-6.3.0-dockerfiles

Update qwt to 6.3.0 in release Dockerfiles


Compare: https://github.com/ehb54/ultrascan3/compare/721dbb00c966...f82e19a70716

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From noreply at github.com  Thu Jul  2 11:36:20 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 10:36:20 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0b8a38: SOMO: add CMake build
 skeleton (us_somo)
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/000000-0b8a38@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0b8a387a66c03657734e707cf3e3c77bc2b6f59a
      https://github.com/ehb54/ultrascan3/commit/0b8a387a66c03657734e707cf3e3c77bc2b6f59a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    A us_somo/CMakeLists.txt
    A us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: add CMake build skeleton (us_somo)

Initial, not-yet-buildable CMake scaffolding for the SOMO suite, to be
iterated on (likely on a Linux/remote build host).

- us_somo/CMakeLists.txt: thin forwarder -> add_subdirectory(develop),
  matching the root's existing `# add_subdirectory(us_somo)` hook.
- us_somo/develop/CMakeLists.txt: standalone-capable build defining the
  self-contained libus_somo (SONAME .10, vendored utils fork, no us_utils
  link) plus thin apps us3_somo/us_admin/us3_config/us_saxs_cmds_t, with
  SOMO_ENABLE_MPI/CUDA/ADOLC options (default OFF).

Known TODOs (see in-file comments): src/ source partitioning (main()-bearing
/ app-specific TUs), 3dplot vs root qwtplot3d, and redirecting revision.sh
output out of the source tree.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul  2 11:40:55 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 10:40:55 -0700
Subject: [us-commits] [ehb54/ultrascan3] dd47c9: SOMO: use libus_somo.pro
 source list instead of glob
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/0b8a38-dd47c9@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: dd47c9c61b0705301d4f2ede1dcba49d7a4aeecb
      https://github.com/ehb54/ultrascan3/commit/dd47c9c61b0705301d4f2ede1dcba49d7a4aeecb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt
    A us_somo/develop/somo_lib_sources.cmake

  Log Message:
  -----------
  SOMO: use libus_somo.pro source list instead of glob

Replace the file(GLOB src/*.cpp) placeholder with the authoritative
SOURCES/HEADERS extracted from libus_somo.pro into somo_lib_sources.cmake
(347 sources, 235 headers).

- Globbing was wrong: several src/ TUs are app-specific and excluded from
  the lib, and the lib additionally pulls in shd_mpi/shs_use.cpp.
- src/us_saxs_util_cuda.cpp is a lib member per the .pro (not per-app);
  drop the CUDA source special-casing from the lib and from us_saxs_cmds_t.
- Omit generated include/us_revision.h from compiled sources.

Refs ehb54/ultrascan-tickets#943

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From noreply at github.com  Thu Jul  2 11:50:33 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 10:50:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5ba820: SOMO: extract per-app
 sources from .pro; split GUI...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/dd47c9-5ba820@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5ba8208849583b50493cd6ca5a4d707928ded295
      https://github.com/ehb54/ultrascan3/commit/5ba8208849583b50493cd6ca5a4d707928ded295
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt
    A us_somo/develop/somo_app_sources.cmake

  Log Message:
  -----------
  SOMO: extract per-app sources from .pro; split GUI vs standalone tools

Apps fall into two classes (verified against .pro files and ldd of deployed
binaries), so a uniform lib-linking model was wrong:

- GUI apps (generic.pri): single main.cpp linking libus_somo (+ qwt).
  us3_somo / us_admin / us3_config -> somo_add_gui_app().
- Standalone tools (cmdline.pri): main.cpp + a curated ../src subset compiled
  directly into the exe; do NOT link libus_somo and do NOT link qwt (ldd of
  us_saxs_cmds_t confirms neither). us_saxs_cmds_t, us_cluster_server_t, and
  the optional MPI/CUDA variants -> somo_add_tool().

Per-tool source subsets extracted from each tool's own .pro into
somo_app_sources.cmake (us_saxs_cmds_t 63, us_saxs_cmds_mpi 66,
us_saxs_cmds_mpi_cuda 56, us_cluster_server_t 1 source; +headers).

Both generated list files validated with `cmake -P`.

Refs ehb54/ultrascan-tickets#943

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From noreply at github.com  Thu Jul  2 11:59:35 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 10:59:35 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3b58b0: SOMO: add minimal
 standalone vcpkg manifest for us...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/5ba820-3b58b0@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3b58b0b2e420e5a5a87f0b1fad01839a5efdd011
      https://github.com/ehb54/ultrascan3/commit/3b58b0b2e420e5a5a87f0b1fad01839a5efdd011
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt
    A us_somo/develop/vcpkg-configuration.json
    A us_somo/develop/vcpkg.json

  Log Message:
  -----------
  SOMO: add minimal standalone vcpkg manifest for us_somo/develop

Enables standalone `cmake -S us_somo/develop` builds (manifest mode reads
vcpkg.json from the configured source dir). Minimal by design ? only the deps
the SOMO CMakeLists actually find_package()s:

- zlib, openssl, qt5-base, qt5-svg, qt5-multimedia, qwt-6-1-6,
  qwtplot3d-qwt-6-1-6-qt5
- no DB (SOMO is NO_DB) and no qt5-datavis3d (SOMO uses its own 3dplot).

vcpkg-configuration.json reuses the repo-root overlay-ports
(../../buildsys/vcpkg/overlay-ports) for the custom qwt/qwtplot3d/multimedia
ports; builtin-baseline matches the root manifest to stay in lockstep.

When built from the root instead (US3_BUILD_SOMO), this manifest is ignored and
the root qt5-app feature supplies everything.

Refs ehb54/ultrascan-tickets#943

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From noreply at github.com  Thu Jul  2 12:03:22 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 11:03:22 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9a2286: SOMO: standalone manifest
 uses qwt 6.3.0 (matches ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/3b58b0-9a2286@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9a2286e10f2b024bfafdc9c7429fb7cf8fd5df1a
      https://github.com/ehb54/ultrascan3/commit/9a2286e10f2b024bfafdc9c7429fb7cf8fd5df1a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M us_somo/develop/vcpkg.json

  Log Message:
  -----------
  SOMO: standalone manifest uses qwt 6.3.0 (matches main as of PR #335)

Switch qwt-6-1-6 / qwtplot3d-qwt-6-1-6-qt5 -> qwt-6-3-0-qt5 /
qwtplot3d-qwt-6-3-0-qt5 (Qt5 + Qwt 6.3.0, matching the root qt5-qwt630-app
feature). Overlay ports already present in buildsys/vcpkg/overlay-ports.

Refs ehb54/ultrascan-tickets#943

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From noreply at github.com  Thu Jul  2 12:16:04 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 11:16:04 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3a3efd: SOMO: support both Qt5 and
 Qt6 (PR #335 made SOMO ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/9a2286-3a3efd@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3a3efdb03a7cb094776b2a0f6c7d45d4d55a5d29
      https://github.com/ehb54/ultrascan3/commit/3a3efdb03a7cb094776b2a0f6c7d45d4d55a5d29
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt
    M us_somo/develop/vcpkg.json

  Log Message:
  -----------
  SOMO: support both Qt5 and Qt6 (PR #335 made SOMO Qt5/Qt6 compatible)

CMakeLists: use the version-agnostic idiom
    find_package(QT NAMES Qt6 Qt5 REQUIRED COMPONENTS Core)
    find_package(Qt${QT_VERSION_MAJOR} REQUIRED COMPONENTS ...)
and link Qt${QT_VERSION_MAJOR}::... so SOMO follows whichever Qt the build
selects (Qt5 today, Qt6 for the next release). CI/CodeQL exercise both.

Standalone vcpkg.json: replace the flat Qt5 dep list with qt5 (default) and
qt6 features (qtbase/qtsvg/qtmultimedia + qwt-6-3-0-qt6/qwtplot3d-qwt-6-3-0-qt6);
select Qt6 via --x-feature=qt6. Overlay ports already present.

TODO(Qt6): QtOpenGL split ? add OpenGLWidgets component if the code uses
QOpenGLWidget under Qt6.

Refs ehb54/ultrascan-tickets#943

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From noreply at github.com  Thu Jul  2 13:36:38 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Jul 2026 12:36:38 -0700
Subject: [us-commits] [ehb54/ultrascan3] 55e94a: fix: update browser
 settings handling for MacOS an...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/67350c-c31386@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 55e94a0e3813f79d50549bd166d3cf26934208c0
      https://github.com/ehb54/ultrascan3/commit/55e94a0e3813f79d50549bd166d3cf26934208c0
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M gui/us_help.cpp
    M utils/us_settings.cpp

  Log Message:
  -----------
  fix: update browser settings handling for MacOS and Windows


  Commit: d099a4448e73330af2c3bd0fc9ec64a435bf7d2a
      https://github.com/ehb54/ultrascan3/commit/d099a4448e73330af2c3bd0fc9ec64a435bf7d2a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_settings.cpp

  Log Message:
  -----------
  fix: initialize status variable to zero in us_settings.cpp


  Commit: 73d10e1ac2511df9f115150909f8efa4e15e2aa9
      https://github.com/ehb54/ultrascan3/commit/73d10e1ac2511df9f115150909f8efa4e15e2aa9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


  Commit: 5924b0fe87a290c4e598e447b28d84cdc4780865
      https://github.com/ehb54/ultrascan3/commit/5924b0fe87a290c4e598e447b28d84cdc4780865
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


  Commit: c31386b4ac5c903cb5949ed662b915274aed6658
      https://github.com/ehb54/ultrascan3/commit/c31386b4ac5c903cb5949ed662b915274aed6658
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M gui/us_help.cpp
    M utils/us_settings.cpp

  Log Message:
  -----------
  Merge pull request #468 from ehb54/issue-941

fix: update browser settings handling for MacOS and Windows


Compare: https://github.com/ehb54/ultrascan3/compare/67350cbc9b65...c31386b4ac5c

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From noreply at github.com  Thu Jul  2 13:41:02 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 12:41:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1b589d: SOMO: add minimal docker
 cmake/vcpkg build env; ge...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/3a3efd-1b589d@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1b589df12e222a28fd783e302fc358d5ce53c14b
      https://github.com/ehb54/ultrascan3/commit/1b589df12e222a28fd783e302fc358d5ce53c14b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M .gitignore
    M us_somo/develop/CMakeLists.txt
    A us_somo/develop/docker/Dockerfile
    A us_somo/develop/docker/README.md
    A us_somo/develop/docker/build.sh

  Log Message:
  -----------
  SOMO: add minimal docker cmake/vcpkg build env; generate both version headers

- us_somo/develop/docker/{Dockerfile,build.sh,README.md}: minimal Linux build
  environment (toolchain + vcpkg + Qt's system build-deps only; vcpkg builds
  Qt/qwt/qwtplot3d from source). build.sh bind-mounts the repo, picks a dynamic
  triplet by arch, caches vcpkg binaries in a volume, builds qt5 (default)/qt6.
- CMakeLists: us_somo_genheaders runs BOTH main-style scripts ? version.sh
  (us_version.h; run by makesomo.sh in the qmake build, needs $us3) and
  revision.sh (us_revision.h; run by qmake's revision target, needs $ULTRASCAN)
  with the repo root wired in. us_config.cpp needs us_version.h, which the prior
  revision-only target never produced.
- .gitignore: add the generated /us_somo/develop/include/us_revision.h (matching
  the existing us_version.h entry) and the /us_somo/develop/build-docker/ tree.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul  2 13:44:07 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 12:44:07 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1725fa: SOMO docker: release-only
 dynamic Linux triplets (...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/1b589d-1725fa@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1725fa634faf6b9cc8546fe3ec5324f3a1d0b8bc
      https://github.com/ehb54/ultrascan3/commit/1725fa634faf6b9cc8546fe3ec5324f3a1d0b8bc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M us_somo/develop/docker/build.sh
    A us_somo/develop/docker/triplets/arm64-linux-dynamic.cmake
    A us_somo/develop/docker/triplets/x64-linux-dynamic.cmake

  Log Message:
  -----------
  SOMO docker: release-only dynamic Linux triplets (skip debug Qt)

vcpkg was building both debug and release Qt (~2x time). Add release-only,
dynamic x64/arm64 Linux overlay triplets (mirroring admin/cmake/triplets/
arm64-linux.cmake: VCPKG_LIBRARY_LINKAGE dynamic + VCPKG_BUILD_TYPE release) and
point build.sh at them via VCPKG_OVERLAY_TRIPLETS. Dynamic because SOMO needs
shared Qt.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul  2 16:28:13 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 15:28:13 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/release-2026-Q2/000000-c31386@github.com>

  Branch: refs/heads/release-2026-Q2
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Date: Thu, 02 Jul 2026 15:29:00 -0700
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/release-2026-Q2/000000-bf3122@github.com>

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Subject: [us-commits] [ehb54/us3lims_gridctl]
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/release-2026-Q2/000000-5d00d5@github.com>

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Date: Thu, 02 Jul 2026 15:30:09 -0700
Subject: [us-commits] [ehb54/us3lims_dbinst]
Message-ID: <ehb54/us3lims_dbinst/push/refs/heads/release-2026-Q2/000000-45595d@github.com>

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Date: Thu, 02 Jul 2026 15:31:00 -0700
Subject: [us-commits] [ehb54/us3lims_common]
Message-ID: <ehb54/us3lims_common/push/refs/heads/release-2026-Q2/000000-2a60c1@github.com>

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Date: Thu, 02 Jul 2026 15:32:03 -0700
Subject: [us-commits] [ehb54/us3lims_newinst]
Message-ID: <ehb54/us3lims_newinst/push/refs/heads/release-2026-Q2/000000-6cdc72@github.com>

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Date: Thu, 02 Jul 2026 15:33:57 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo]
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/release-2026-Q2/000000-f13d5c@github.com>

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Date: Thu, 02 Jul 2026 15:43:16 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/tags/v4.1.0/000000-dde188@github.com>

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Date: Thu, 02 Jul 2026 15:43:22 -0700
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/tags/v4.1.0/000000-7dbd65@github.com>

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Subject: [us-commits] [ehb54/us3lims_gridctl]
Message-ID: <ehb54/us3lims_gridctl/push/refs/tags/v4.1.0/000000-d91484@github.com>

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Subject: [us-commits] [ehb54/us3lims_dbinst]
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Date: Thu, 02 Jul 2026 15:43:45 -0700
Subject: [us-commits] [ehb54/us3lims_common]
Message-ID: <ehb54/us3lims_common/push/refs/tags/v4.1.0/000000-a25568@github.com>

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Subject: [us-commits] [ehb54/us3lims_webinfo]
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From noreply at github.com  Thu Jul  2 16:44:59 2026
From: noreply at github.com (emre brookes)
Date: Thu, 02 Jul 2026 15:44:59 -0700
Subject: [us-commits] [ehb54/us3lims_newinst]
Message-ID: <ehb54/us3lims_newinst/push/refs/tags/v4.1.0/000000-4ea219@github.com>

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From noreply at github.com  Thu Jul  2 17:58:46 2026
From: noreply at github.com (github-actions[bot])
Date: Thu, 02 Jul 2026 16:58:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 435b89: Bump version to 4.2.0-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/bump-to-v4.2.0-dev/000000-435b89@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 435b89afe6c30e42df5aba726ea83b875be9a649
      https://github.com/ehb54/ultrascan3/commit/435b89afe6c30e42df5aba726ea83b875be9a649
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Bump version to 4.2.0-dev



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From noreply at github.com  Thu Jul  2 17:59:14 2026
From: noreply at github.com (github-actions[bot])
Date: Thu, 02 Jul 2026 16:59:14 -0700
Subject: [us-commits] [ehb54/us3_sql] 7b42af: Bump version to 4.2.0-dev
Message-ID: <ehb54/us3_sql/push/refs/heads/bump-to-v4.2.0-dev/000000-7b42af@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/us3_sql
  Commit: 7b42af6d2443bf50f1f69b825c33af1dda544fae
      https://github.com/ehb54/us3_sql/commit/7b42af6d2443bf50f1f69b825c33af1dda544fae
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev



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From noreply at github.com  Thu Jul  2 17:59:42 2026
From: noreply at github.com (github-actions[bot])
Date: Thu, 02 Jul 2026 16:59:42 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl] 9cb265: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/bump-to-v4.2.0-dev/000000-9cb265@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: 9cb26506131078dc3676ef1d4f163f6853e1a892
      https://github.com/ehb54/us3lims_gridctl/commit/9cb26506131078dc3676ef1d4f163f6853e1a892
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev



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From noreply at github.com  Thu Jul  2 18:00:05 2026
From: noreply at github.com (github-actions[bot])
Date: Thu, 02 Jul 2026 17:00:05 -0700
Subject: [us-commits] [ehb54/us3lims_dbinst] 072a2f: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_dbinst/push/refs/heads/bump-to-v4.2.0-dev/000000-072a2f@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/us3lims_dbinst
  Commit: 072a2fecc57c897ae7c54bd86e0f7340cf95ae40
      https://github.com/ehb54/us3lims_dbinst/commit/072a2fecc57c897ae7c54bd86e0f7340cf95ae40
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev



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From noreply at github.com  Thu Jul  2 18:00:31 2026
From: noreply at github.com (github-actions[bot])
Date: Thu, 02 Jul 2026 17:00:31 -0700
Subject: [us-commits] [ehb54/us3lims_common] ded16d: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_common/push/refs/heads/bump-to-v4.2.0-dev/000000-ded16d@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/us3lims_common
  Commit: ded16d851d2f1334891c40665ef8ed01a005d92d
      https://github.com/ehb54/us3lims_common/commit/ded16d851d2f1334891c40665ef8ed01a005d92d
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev



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From noreply at github.com  Thu Jul  2 18:02:33 2026
From: noreply at github.com (github-actions[bot])
Date: Thu, 02 Jul 2026 17:02:33 -0700
Subject: [us-commits] [ehb54/us3lims_newinst] 185503: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_newinst/push/refs/heads/bump-to-v4.2.0-dev/000000-185503@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/us3lims_newinst
  Commit: 185503dcb97912d4bfb3a3cc5c1bb3036f2f6fe8
      https://github.com/ehb54/us3lims_newinst/commit/185503dcb97912d4bfb3a3cc5c1bb3036f2f6fe8
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev



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From noreply at github.com  Thu Jul  2 18:03:13 2026
From: noreply at github.com (github-actions[bot])
Date: Thu, 02 Jul 2026 17:03:13 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo] b62c50: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/bump-to-v4.2.0-dev/000000-b62c50@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/us3lims_webinfo
  Commit: b62c5001f42bf9268b4d06951d0e8e85a8238587
      https://github.com/ehb54/us3lims_webinfo/commit/b62c5001f42bf9268b4d06951d0e8e85a8238587
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev



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From noreply at github.com  Thu Jul  2 18:55:00 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Jul 2026 17:55:00 -0700
Subject: [us-commits] [ehb54/us3lims_dbinst] 072a2f: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_dbinst/push/refs/heads/main/45595d-d4ddd0@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_dbinst
  Commit: 072a2fecc57c897ae7c54bd86e0f7340cf95ae40
      https://github.com/ehb54/us3lims_dbinst/commit/072a2fecc57c897ae7c54bd86e0f7340cf95ae40
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: d4ddd03e0c925cdad8eb680bab52c0dfa2cc7269
      https://github.com/ehb54/us3lims_dbinst/commit/d4ddd03e0c925cdad8eb680bab52c0dfa2cc7269
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #62 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


Compare: https://github.com/ehb54/us3lims_dbinst/compare/45595d10d644...d4ddd03e0c92

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From noreply at github.com  Thu Jul  2 18:55:20 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Jul 2026 17:55:20 -0700
Subject: [us-commits] [ehb54/us3lims_newinst] 185503: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_newinst/push/refs/heads/main/6cdc72-75f41a@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_newinst
  Commit: 185503dcb97912d4bfb3a3cc5c1bb3036f2f6fe8
      https://github.com/ehb54/us3lims_newinst/commit/185503dcb97912d4bfb3a3cc5c1bb3036f2f6fe8
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: 75f41acb55cf78e00a68ec2ebdc2ac934bf59cf0
      https://github.com/ehb54/us3lims_newinst/commit/75f41acb55cf78e00a68ec2ebdc2ac934bf59cf0
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #19 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


Compare: https://github.com/ehb54/us3lims_newinst/compare/6cdc72cd3ed9...75f41acb55cf

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From noreply at github.com  Thu Jul  2 18:57:29 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Jul 2026 17:57:29 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo] b62c50: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/main/f13d5c-23bcdf@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_webinfo
  Commit: b62c5001f42bf9268b4d06951d0e8e85a8238587
      https://github.com/ehb54/us3lims_webinfo/commit/b62c5001f42bf9268b4d06951d0e8e85a8238587
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: 23bcdf82907976a5f8b0ab251535ecac91e63395
      https://github.com/ehb54/us3lims_webinfo/commit/23bcdf82907976a5f8b0ab251535ecac91e63395
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #13 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


Compare: https://github.com/ehb54/us3lims_webinfo/compare/f13d5c7a8415...23bcdf829079

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From noreply at github.com  Thu Jul  2 18:58:10 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Jul 2026 17:58:10 -0700
Subject: [us-commits] [ehb54/us3lims_common] ded16d: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_common/push/refs/heads/main/2a60c1-4e25de@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_common
  Commit: ded16d851d2f1334891c40665ef8ed01a005d92d
      https://github.com/ehb54/us3lims_common/commit/ded16d851d2f1334891c40665ef8ed01a005d92d
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: 4e25de4a189a80e74e25cde0e799e908ba9c0abf
      https://github.com/ehb54/us3lims_common/commit/4e25de4a189a80e74e25cde0e799e908ba9c0abf
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #23 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


Compare: https://github.com/ehb54/us3lims_common/compare/2a60c1339566...4e25de4a189a

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From noreply at github.com  Thu Jul  2 18:58:41 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Jul 2026 17:58:41 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl] 9cb265: Bump version to
 4.2.0-dev
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/main/5d00d5-b0acd2@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: 9cb26506131078dc3676ef1d4f163f6853e1a892
      https://github.com/ehb54/us3lims_gridctl/commit/9cb26506131078dc3676ef1d4f163f6853e1a892
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: b0acd2f3bb3a3897b2534094cccc427450087213
      https://github.com/ehb54/us3lims_gridctl/commit/b0acd2f3bb3a3897b2534094cccc427450087213
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #29 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


Compare: https://github.com/ehb54/us3lims_gridctl/compare/5d00d5db8381...b0acd2f3bb3a

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From noreply at github.com  Thu Jul  2 18:59:03 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Jul 2026 17:59:03 -0700
Subject: [us-commits] [ehb54/us3_sql] 7b42af: Bump version to 4.2.0-dev
Message-ID: <ehb54/us3_sql/push/refs/heads/main/bf3122-9fdadd@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3_sql
  Commit: 7b42af6d2443bf50f1f69b825c33af1dda544fae
      https://github.com/ehb54/us3_sql/commit/7b42af6d2443bf50f1f69b825c33af1dda544fae
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: 9fdadd7d5bf1de8708116654a327531d2ece0726
      https://github.com/ehb54/us3_sql/commit/9fdadd7d5bf1de8708116654a327531d2ece0726
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #37 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


Compare: https://github.com/ehb54/us3_sql/compare/bf3122bde8d4...9fdadd7d5bf1

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From noreply at github.com  Sat Jul  4 08:27:06 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 07:27:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] f985cf: SOMO docker: add
 autotools/gettext/ltdl deps for v...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/1725fa-f985cf@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f985cfef9c2bf90e432e56fca3ab8aac9621d4db
      https://github.com/ehb54/ultrascan3/commit/f985cfef9c2bf90e432e56fca3ab8aac9621d4db
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/docker/Dockerfile

  Log Message:
  -----------
  SOMO docker: add autotools/gettext/ltdl deps for vcpkg autoreconf ports

First vcpkg build failed building libxcrypt:x64-linux in vcpkg_run_autoreconf.
Minimal Ubuntu lacked the macros/tools autotools ports need. Add libtool-bin,
libltdl-dev (the port explicitly asks for ltdl dev files), gettext, autopoint,
and perl.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 08:35:52 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 07:35:52 -0700
Subject: [us-commits] [ehb54/ultrascan3] b8c1b4: SOMO docker: add
 python3-venv/pip + gperf for libs...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/f985cf-b8c1b4@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b8c1b4b3fe5bb908ae84f1b4cbf657039812ea05
      https://github.com/ehb54/ultrascan3/commit/b8c1b4b3fe5bb908ae84f1b4cbf657039812ea05
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/docker/Dockerfile

  Log Message:
  -----------
  SOMO docker: add python3-venv/pip + gperf for libsystemd/Qt

libsystemd (pulled transitively via dbus->Qt) failed at `python3 -m venv`
because the minimal image had python3 but not python3-venv. Add python3-venv,
python3-pip, and gperf (needed by systemd/Qt builds).

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 14:58:23 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 13:58:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9adf30: SOMO docker: add
 libsm/ice/xcb-xinput for Qt6 qtba...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/b8c1b4-9adf30@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9adf30b29a5b43752e23a6f5db463dd73d0e9596
      https://github.com/ehb54/ultrascan3/commit/9adf30b29a5b43752e23a6f5db463dd73d0e9596
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/docker/Dockerfile

  Log Message:
  -----------
  SOMO docker: add libsm/ice/xcb-xinput for Qt6 qtbase host tool

The qt5 build pulls a Qt6 qtbase as a HOST build tool (qwt-6-3-0-qt5 ->
vcpkg-qmake -> qtbase). qtbase's vcpkg feature set forces xcb-sm and
xcb-xinput ON, which need X11 session-management (libSM/libICE) and
libxcb-xinput dev libs that the minimal image lacked. SOMO target stays Qt5.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 15:50:37 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 14:50:37 -0700
Subject: [us-commits] [ehb54/ultrascan3] c444eb: SOMO: fix genheaders custom
 command quoting (two C...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/9adf30-c444eb@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c444eb2f94d517a68c6b7c0ce57995e426de0d55
      https://github.com/ehb54/ultrascan3/commit/c444eb2f94d517a68c6b7c0ce57995e426de0d55
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: fix genheaders custom command quoting (two COMMANDs, not sh -c)

The inline `sh -c "cd ... && sh version.sh && sh revision.sh"` got mangled by
Ninja's escaping (`sh version.sh: not found`). Use two separate COMMANDs with
WORKING_DIRECTORY instead.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 15:54:01 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 14:54:01 -0700
Subject: [us-commits] [ehb54/ultrascan3] f79ce3: SOMO: give standalone tools
 the Qwt include path (...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/c444eb-f79ce3@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f79ce34dca4c27f5db5924439775d505e30fbfdb
      https://github.com/ehb54/ultrascan3/commit/f79ce34dca4c27f5db5924439775d505e30fbfdb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: give standalone tools the Qwt include path (headers, not link)

Tool sources compile SOMO headers that #include <qwt_*.h> (us_hydrodyn_asa.h
etc.). The qwt code paths are compiled out under -DCMDLINE so no qwt LINK is
needed (matches the deployed ldd), but the headers must be on the include path.
Add Qwt::Qwt's INTERFACE_INCLUDE_DIRECTORIES to somo_add_tool targets.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 15:56:56 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 14:56:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] cf1d26: SOMO: add qwt header dir
 (vcpkg nests under includ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/f79ce3-cf1d26@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cf1d265200c36a99ec607f362a95d1a4fec1e98a
      https://github.com/ehb54/ultrascan3/commit/cf1d265200c36a99ec607f362a95d1a4fec1e98a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: add qwt header dir (vcpkg nests under include/qwt); drop Qt3 cluster tool

- vcpkg installs qwt headers under include/qwt/, but SOMO does #include
  <qwt_counter.h> (flat). find_path(SOMO_QWT_INCLUDE_DIR NAMES qwt_counter.h
  PATH_SUFFIXES qwt) and add it to the lib (PUBLIC) and the standalone tools.
- Drop us_cluster_server_t: its us_cluster_server_global.h includes <q3socket.h>
  (Qt3Support), removed since Qt5 ? cannot build on Qt5/Qt6.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 16:09:26 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 15:09:26 -0700
Subject: [us-commits] [ehb54/ultrascan3] 034d89: SOMO: unique include guards
 for copy-pasted Q_OBJE...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/cf1d26-034d89@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 034d89c8f9dcd3d15bdd4d0aa67018583b5a6eb7
      https://github.com/ehb54/ultrascan3/commit/034d89c8f9dcd3d15bdd4d0aa67018583b5a6eb7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us3i_util.h
    M us_somo/develop/include/us_hydrodyn_dad_conc_csv_frames.h
    M us_somo/develop/include/us_hydrodyn_mals_conc_csv_frames.h
    M us_somo/develop/include/us_hydrodyn_mals_saxs_conc_csv_frames.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_conc_csv_frames.h

  Log Message:
  -----------
  SOMO: unique include guards for copy-pasted Q_OBJECT headers

Under AUTOMOC all moc outputs compile in one combined TU (mocs_compilation.cpp),
so duplicate include guards make later headers vanish -> "class has not been
declared" for their moc. (qmake hid this: each moc was its own TU.)

Fix the Q_OBJECT collisions:
- us_hydrodyn_{dad,mals,mals_saxs,saxs_hplc}_conc_csv_frames.h all shared
  US_HYDRODYN_SAXS_CONC_CSV_FRAMES_H -> give each a filename-derived guard.
- us3i_util.h shared US_UTIL_H with us_util.h (Q_OBJECT) -> US3I_UTIL_H.

Non-Q_OBJECT guard collisions (X.h/X_hydro.h, us3i_*/us_* pairs) don't affect
the moc TU and are left for now.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 16:14:57 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 15:14:57 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3fdb6c: SOMO: guard duplicated
 uhshs_data struct; dedup qw...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/034d89-3fdb6c@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3fdb6c2bf2ec623d2a0fbc7dbef7ac3ee8800f05
      https://github.com/ehb54/ultrascan3/commit/3fdb6c2bf2ec623d2a0fbc7dbef7ac3ee8800f05
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt
    M us_somo/develop/include/us_hydrodyn_dad_simulate.h
    M us_somo/develop/include/us_hydrodyn_mals_saxs_simulate.h
    M us_somo/develop/include/us_hydrodyn_mals_simulate.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_simulate.h

  Log Message:
  -----------
  SOMO: guard duplicated uhshs_data struct; dedup qwt scrollbar/zoomer moc

- struct uhshs_data is copy-pasted (byte-identical) into four *_simulate.h
  headers; the combined AUTOMOC TU includes several at once -> redefinition.
  Wrap each with #ifndef UHSHS_DATA_STRUCT_DEFINED.
- scrollbar/scrollzoomer exist in both src/qwt/ and include/qwt/ (identical);
  AUTOMOC mocs both (listed include/qwt header + src/qwt adjacency to the .cpp)
  -> duplicate moc symbols. SKIP_AUTOMOC on the src/qwt/*.cpp keeps one moc.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 16:25:55 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 15:25:55 -0700
Subject: [us-commits] [ehb54/ultrascan3] fe255e: SOMO: define PLATFORM/TITLE
 (us_register.cpp), mat...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/3fdb6c-fe255e@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fe255eed85937d236965da2b18da3fadf1bcdf23
      https://github.com/ehb54/ultrascan3/commit/fe255eed85937d236965da2b18da3fadf1bcdf23
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: define PLATFORM/TITLE (us_register.cpp), matching root us3

us_register.cpp reads PLATFORM/TITLE but only #defines them under arch macros
(INTEL/OPTERON/MAC/...), none set on x86_64 Linux -> undefined at use. The root
us3 build defines them directly via -D; mirror with a directory-wide definition.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 16:49:18 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 15:49:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5e4a68: SOMO: define INTEL arch
 macro for us_register.cpp ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/fe255e-5e4a68@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5e4a68fa385013a186b9a45b48e36e43e864a355
      https://github.com/ehb54/ultrascan3/commit/5e4a68fa385013a186b9a45b48e36e43e864a355
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: define INTEL arch macro for us_register.cpp (Linux)

Defining PLATFORM/TITLE via -D string literals didn't survive quote-escaping.
us_register.cpp already sets PLATFORM/TITLE from an arch macro (#if defined(INTEL)
||WIN32), so just define INTEL on Linux and let the file define the strings
itself. APPLE handled by MAC, Windows by WIN32.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 17:16:30 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 16:16:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] 42764d: SOMO docker: separate
 vcpkg_installed per Qt feature
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/5e4a68-42764d@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 42764de9d74233a75f9b1a70715f371b8c7ab6f3
      https://github.com/ehb54/ultrascan3/commit/42764de9d74233a75f9b1a70715f371b8c7ab6f3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/docker/build.sh

  Log Message:
  -----------
  SOMO docker: separate vcpkg_installed per Qt feature

qt5 and qt6 builds shared one VCPKG_INSTALLED_DIR, so switching features
clobbered the other's installed Qt (e.g. a qt6 build removes qt5-base),
breaking coexisting runnable artifacts. Use vcpkg_installed-$FEATURE.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 20:53:14 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 19:53:14 -0700
Subject: [us-commits] [ehb54/ultrascan3] 02454a: SOMO docker: add nasm for
 Qt6 ffmpeg (qtmultimedia...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/42764d-02454a@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 02454ae6715f4321b38cad3a5e26cdd9a09ee912
      https://github.com/ehb54/ultrascan3/commit/02454ae6715f4321b38cad3a5e26cdd9a09ee912
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/docker/Dockerfile

  Log Message:
  -----------
  SOMO docker: add nasm for Qt6 ffmpeg (qtmultimedia backend)

Qt6 qtmultimedia pulls ffmpeg, which needs nasm to build its assembly.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 21:52:40 2026
From: noreply at github.com (emre brookes)
Date: Sat, 04 Jul 2026 20:52:40 -0700
Subject: [us-commits] [ehb54/ultrascan3] 227538: SOMO: cast vector<bool>
 element for QString::arg (...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/02454a-227538@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2275387bc411645b32c8aea397106c307aadceec
      https://github.com/ehb54/ultrascan3/commit/2275387bc411645b32c8aea397106c307aadceec
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-04 (Sat, 04 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp

  Log Message:
  -----------
  SOMO: cast vector<bool> element for QString::arg (Qt6)

use_chi2s is vector<vector<bool>>; QString("%1").arg(use_chi2s[i][j]) passes a
std::vector<bool>::reference proxy, which Qt6's stricter arg() template rejects
(Qt5 promoted it to int). Add an explicit (int) cast ? portable across Qt5/Qt6.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul  4 23:45:01 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 04 Jul 2026 22:45:01 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo]
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/793-request-remove-from-lims-webmaster-partners/3fb7ac-000000@github.com>

  Branch: refs/heads/793-request-remove-from-lims-webmaster-partners
  Home:   https://github.com/ehb54/us3lims_webinfo

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From noreply at github.com  Sat Jul  4 23:45:03 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 04 Jul 2026 22:45:03 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo]
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/904-update-bump-pr-sha-us3lims_webinfo/661159-000000@github.com>

  Branch: refs/heads/904-update-bump-pr-sha-us3lims_webinfo
  Home:   https://github.com/ehb54/us3lims_webinfo

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From noreply at github.com  Sat Jul  4 23:45:18 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 04 Jul 2026 22:45:18 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo]
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/bump-to-v4.2.0-dev/b62c50-000000@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/us3lims_webinfo

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From noreply at github.com  Sat Jul  4 23:45:22 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 04 Jul 2026 22:45:22 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo]
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/bump-to-v4.1.0/e38fbd-000000@github.com>

  Branch: refs/heads/bump-to-v4.1.0
  Home:   https://github.com/ehb54/us3lims_webinfo

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From noreply at github.com  Mon Jul  6 06:28:43 2026
From: noreply at github.com (Lukas Dobler)
Date: Mon, 06 Jul 2026 05:28:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] 37703a: somo qt6 branch - initial
 commit from somo-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_branch_python_venv/e992b5-72beec@github.com>

  Branch: refs/heads/lukas/us_branch_python_venv
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
      https://github.com/ehb54/ultrascan3/commit/37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 9cc80a805f0c89d30fd663cffa4e544bdccfddd6
      https://github.com/ehb54/ultrascan3/commit/9cc80a805f0c89d30fd663cffa4e544bdccfddd6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql debug info


  Commit: 8f49d1cadd471936ba76ad95fe0001436a3685a7
      https://github.com/ehb54/ultrascan3/commit/8f49d1cadd471936ba76ad95fe0001436a3685a7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M us_somo/develop/libus_somo.pro

  Log Message:
  -----------
  remove us_color from libus_somo


  Commit: 642330d0e7562d863f6471b57e528cdf5aec013c
      https://github.com/ehb54/ultrascan3/commit/642330d0e7562d863f6471b57e528cdf5aec013c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
      https://github.com/ehb54/ultrascan3/commit/fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 1a808d5061ef553acf0aa97a83c04af9d82970bc
      https://github.com/ehb54/ultrascan3/commit/1a808d5061ef553acf0aa97a83c04af9d82970bc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 24783d42d61d7132dd5622e8027c9f6f59de5608
      https://github.com/ehb54/ultrascan3/commit/24783d42d61d7132dd5622e8027c9f6f59de5608
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  restore deprecations


  Commit: c37b59afbb01c067585c5da09c200e295282decc
      https://github.com/ehb54/ultrascan3/commit/c37b59afbb01c067585c5da09c200e295282decc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 59ba4be5192bd4024037ed7173a13061a59c41ce
      https://github.com/ehb54/ultrascan3/commit/59ba4be5192bd4024037ed7173a13061a59c41ce
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql fix


  Commit: cfd59439653a91b6cdcfd88d8a348ccb934a6cba
      https://github.com/ehb54/ultrascan3/commit/cfd59439653a91b6cdcfd88d8a348ccb934a6cba
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 46434a20d02da7dd7cb8edb14455747838aae8e4
      https://github.com/ehb54/ultrascan3/commit/46434a20d02da7dd7cb8edb14455747838aae8e4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  relax somo error for test


  Commit: 4bafd3f55ff93229f51bcd4cd0ece35195af707c
      https://github.com/ehb54/ultrascan3/commit/4bafd3f55ff93229f51bcd4cd0ece35195af707c
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Update compiler flags and defines in local.pri.somo


  Commit: a7e3fd4276bf018f3e37d73c4e11598037b8d409
      https://github.com/ehb54/ultrascan3/commit/a7e3fd4276bf018f3e37d73c4e11598037b8d409
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo datetime dirhist fix


  Commit: 34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
      https://github.com/ehb54/ultrascan3/commit/34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Clean up deprecated warning flags in local.pri.somo

Removed deprecated warning definitions for Qt.


  Commit: 87377fece32656c6472a465a06493b17084169fe
      https://github.com/ehb54/ultrascan3/commit/87377fece32656c6472a465a06493b17084169fe
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 8886d756072fc33f5d8db65458bae9bd00574c52
      https://github.com/ehb54/ultrascan3/commit/8886d756072fc33f5d8db65458bae9bd00574c52
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-01-19 (Mon, 19 Jan 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp

  Log Message:
  -----------
  somo qt6 compat regex bugfix


  Commit: 000572b4470833c4cd55dc8c07bfe30eadfb08f0
      https://github.com/ehb54/ultrascan3/commit/000572b4470833c4cd55dc8c07bfe30eadfb08f0
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-01-24 (Sat, 24 Jan 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Bump version to 4.1.0


  Commit: 63ddc08f86dd138595c248e3ec8653b3e4640132
      https://github.com/ehb54/ultrascan3/commit/63ddc08f86dd138595c248e3ec8653b3e4640132
  Author: ehb <ehb at ehbs-MacBook-Pro.local>
  Date:   2026-02-25 (Wed, 25 Feb 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  restore macx:LIBS, expected for OSX package pipeline


  Commit: 42f2fd0ef0f999defd30ec52c17df8d7acf8ccef
      https://github.com/ehb54/ultrascan3/commit/42f2fd0ef0f999defd30ec52c17df8d7acf8ccef
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-02-25 (Wed, 25 Feb 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  add VER to qwtplot3d


  Commit: 11572ca66d369080b73f5925c9b46c3b7200c538
      https://github.com/ehb54/ultrascan3/commit/11572ca66d369080b73f5925c9b46c3b7200c538
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/source/index.rst

  Log Message:
  -----------
  Update Sphinx build system: include `auto_index.py`, link PDF manual in HTML, and clean PDF on `make clean`.


  Commit: e2fbf48c659f3fad2922c9067a43f1b3bdc0ec5e
      https://github.com/ehb54/ultrascan3/commit/e2fbf48c659f3fad2922c9067a43f1b3bdc0ec5e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Update LaTeX configuration: set `latex_use_xindy` to False and redefine font settings for better Unicode handling and compatibility.


  Commit: 78d927e26195be17b4a8ff09959676a6247bcb34
      https://github.com/ehb54/ultrascan3/commit/78d927e26195be17b4a8ff09959676a6247bcb34
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Ensure zoom stack initialization on zoom button press


  Commit: dcc8ccbdac5394275563aeee0c8c523a6df45589
      https://github.com/ehb54/ultrascan3/commit/dcc8ccbdac5394275563aeee0c8c523a6df45589
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-06 (Mon, 06 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Refactor zoom logic to handle null plots and absolute values


  Commit: f7169d62eaece4fd69dd8f88ab06432a8bb390f0
      https://github.com/ehb54/ultrascan3/commit/f7169d62eaece4fd69dd8f88ab06432a8bb390f0
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h
    A test/utils/test_us_help_pages.cpp

  Log Message:
  -----------
  Add unit test for validating existence of help pages and refactor zoom stack initialization for improved consistency.


  Commit: a542b58b077c8629e05993705eb0967c8e2ed720
      https://github.com/ehb54/ultrascan3/commit/a542b58b077c8629e05993705eb0967c8e2ed720
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Update .gitignore to exclude `doc/manual/build`


  Commit: 3841b3da9b269c931e61bd8332217ea7edafa5ce
      https://github.com/ehb54/ultrascan3/commit/3841b3da9b269c931e61bd8332217ea7edafa5ce
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M utils/CMakeLists.txt
    M utils/us_extern.h

  Log Message:
  -----------
  Add static library support: define `US_UTIL_STATIC` and conditionally update `us_extern.h`.


  Commit: 8bd5bb513393dabe50c036ffbfe60f96a6b3ca21
      https://github.com/ehb54/ultrascan3/commit/8bd5bb513393dabe50c036ffbfe60f96a6b3ca21
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M utils/us_buffer.h

  Log Message:
  -----------
  Initialize `grad_form` flag to `false` in `us_buffer.h`.


  Commit: 923260944deb1b79e310ceb98a16effa5b5090ca
      https://github.com/ehb54/ultrascan3/commit/923260944deb1b79e310ceb98a16effa5b5090ca
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_get_run.h
    M gui/us_load_auc.h
    M gui/us_model_loader.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h

  Log Message:
  -----------
  Update help file paths for improved documentation consistency and organization.


  Commit: 78e6d90c9756f558dd3c67e03ec447dbaa996a8a
      https://github.com/ehb54/ultrascan3/commit/78e6d90c9756f558dd3c67e03ec447dbaa996a8a
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  Let github action only build the documnetaion with the qthelp builder, because latex dependencies are currently missing


  Commit: 05eb1370b6158124bcafd398fef77466e66be0aa
      https://github.com/ehb54/ultrascan3/commit/05eb1370b6158124bcafd398fef77466e66be0aa
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Remove feature commit in wrong branch


  Commit: 18c02644a764f585fd585e1af1c21e4d5790b60c
      https://github.com/ehb54/ultrascan3/commit/18c02644a764f585fd585e1af1c21e4d5790b60c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Merge pull request #406 from ehb54/lukas/us_plot_zoom_qwt616

Ensure zoom stack initialization on zoom button press


  Commit: 3c1312a39ac562248315fb410c301c9d8eab79f5
      https://github.com/ehb54/ultrascan3/commit/3c1312a39ac562248315fb410c301c9d8eab79f5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M gui/us_plot.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/manual_test/make


  Commit: 99fc3a66c861b6275cedd397bfd03e34e85d9435
      https://github.com/ehb54/ultrascan3/commit/99fc3a66c861b6275cedd397bfd03e34e85d9435
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    A .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Add GitHub Actions workflow for Sphinx documentation build


  Commit: 5fa677c2afd3175fa29a37165561f4125a867c5d
      https://github.com/ehb54/ultrascan3/commit/5fa677c2afd3175fa29a37165561f4125a867c5d
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Refactor Sphinx GitHub Actions workflow: replace deprecated problem matcher usage, streamline build commands, and add error handling.


  Commit: b91a5ae2fecdc63970efdf031426e000eff8cc6e
      https://github.com/ehb54/ultrascan3/commit/b91a5ae2fecdc63970efdf031426e000eff8cc6e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    A .github/sphinx-matcher.json

  Log Message:
  -----------
  Add Sphinx problem matcher configuration for GitHub Actions


  Commit: 45da34200ce91a23a4f1f8d168e7a1ee612b03b5
      https://github.com/ehb54/ultrascan3/commit/45da34200ce91a23a4f1f8d168e7a1ee612b03b5
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Annotate Sphinx build warnings in GitHub Actions workflow and update qthelp build step for improved error handling.


  Commit: f3750319ef93a4a4b5f925ffaa38acd1ebb8f6f5
      https://github.com/ehb54/ultrascan3/commit/f3750319ef93a4a4b5f925ffaa38acd1ebb8f6f5
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M .github/workflows/sphinx-doc-build.yml

  Log Message:
  -----------
  Replace custom Sphinx warning annotation script with `sphinx-doc/github-problem-matcher` for streamlined GitHub Actions workflow.


  Commit: bc2b74fbb9b5698c8269f2d6b060ce420ab6697a
      https://github.com/ehb54/ultrascan3/commit/bc2b74fbb9b5698c8269f2d6b060ce420ab6697a
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    R .github/sphinx-matcher.json

  Log Message:
  -----------
  Remove obsolete Sphinx problem matcher configuration from GitHub Actions.


  Commit: 715a3fd86ec9bdb692b3e1fa0ce393a86548c213
      https://github.com/ehb54/ultrascan3/commit/715a3fd86ec9bdb692b3e1fa0ce393a86548c213
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
  -----------
  Fix triplicates to triples


  Commit: f1b1aba77a1f2da432e6262d842221eb275d2dd0
      https://github.com/ehb54/ultrascan3/commit/f1b1aba77a1f2da432e6262d842221eb275d2dd0
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    A doc/manual/source/_static/images/dmga-save.png
    A doc/manual/source/_static/images/dmga.png
    A doc/manual/source/_static/images/dmga_constr.png
    A doc/manual/source/_static/images/fe_dmga_adv.png
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  update to latest


  Commit: ff98f3a480b918b42a59334bc0506f87b59b5a37
      https://github.com/ehb54/ultrascan3/commit/ff98f3a480b918b42a59334bc0506f87b59b5a37
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    M programs/us_integral/us_delete_models.h

  Log Message:
  -----------
  first link change -  integral


  Commit: 584135021b461a9f753c2ac63b2f37df4cd85b0b
      https://github.com/ehb54/ultrascan3/commit/584135021b461a9f753c2ac63b2f37df4cd85b0b
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-07 (Tue, 07 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/delseltrip.png
    M doc/manual/source/common_dialogs.rst
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.h

  Log Message:
  -----------
  update us_experiment show.help


  Commit: 8e3da82ae6b7563f455e97718bb1f335a1c9bfcc
      https://github.com/ehb54/ultrascan3/commit/8e3da82ae6b7563f455e97718bb1f335a1c9bfcc
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  Standardize terminology: replace "Triplicates" with "Triples" across documentation for clarity and consistency.


  Commit: 7128a07267ee0a0fd7913ea221c2cd891b7099a8
      https://github.com/ehb54/ultrascan3/commit/7128a07267ee0a0fd7913ea221c2cd891b7099a8
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    M test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp

  Log Message:
  -----------
  Improve test failure messages: use `ADD_FAILURE_AT` for precise file/line annotation and enhance regex and help file error clarity


  Commit: 9cf710938424ec4c02179f22bb8da50b226085c6
      https://github.com/ehb54/ultrascan3/commit/9cf710938424ec4c02179f22bb8da50b226085c6
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Add GoogleTest problem matcher to GitHub Actions workflows for enhanced test failure annotation


  Commit: d849477c413c4de8c709970000b9beed563952aa
      https://github.com/ehb54/ultrascan3/commit/d849477c413c4de8c709970000b9beed563952aa
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    M programs/us_2dsa/us_2dsa.h
    M programs/us_config/us_color.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h

  Log Message:
  -----------
  unit test link updates


  Commit: ba9907ccbb59086289b70ee897744f22b939a693
      https://github.com/ehb54/ultrascan3/commit/ba9907ccbb59086289b70ee897744f22b939a693
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-08 (Wed, 08 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/select_prefilt.png
    M doc/manual/source/common_dialogs.rst
    M gui/us_select_edits.h
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_font.cpp

  Log Message:
  -----------
  unit tests help link update


  Commit: 9a107befce5878fa969190700c2a2f6ef48ce068
      https://github.com/ehb54/ultrascan3/commit/9a107befce5878fa969190700c2a2f6ef48ce068
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A doc/manual/source/analysprof_general.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/convert.rst
    A doc/manual/source/ramp_data.rst
    A doc/manual/source/us_administrator.rst
    M doc/manual/source/us_edit.rst
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_config/us_advanced.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_ramp/us_experiment_gui_ra.h

  Log Message:
  -----------
  updates


  Commit: 6fe43510daa8d32555c611669eaa32ab11da07ff
      https://github.com/ehb54/ultrascan3/commit/6fe43510daa8d32555c611669eaa32ab11da07ff
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/edit_exclude_scan.png
    A doc/manual/source/_static/images/edit_scan.png

  Log Message:
  -----------
  images


  Commit: 290b3ed2436ce1c133fb54567579f869c3e2ea70
      https://github.com/ehb54/ultrascan3/commit/290b3ed2436ce1c133fb54567579f869c3e2ea70
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M doc/manual/source/dens_match.rst
    M programs/us_density_match/us_model_params.h

  Log Message:
  -----------
  update link


  Commit: 6242d49b69ff170e32c1fd9ada173147b3744e39
      https://github.com/ehb54/ultrascan3/commit/6242d49b69ff170e32c1fd9ada173147b3744e39
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A doc/manual/source/global_equil.rst
    M doc/manual/source/us_edit.rst

  Log Message:
  -----------
  update


  Commit: 0924fcb4af9a8403c404ace536fffa1cf6209b6f
      https://github.com/ehb54/ultrascan3/commit/0924fcb4af9a8403c404ace536fffa1cf6209b6f
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/index.rst
    M doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_pcsa/us_mlplot.h

  Log Message:
  -----------
  unit test


  Commit: c8515e182cb1cddab6d51258efd8a99f97c8c667
      https://github.com/ehb54/ultrascan3/commit/c8515e182cb1cddab6d51258efd8a99f97c8c667
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M .github/gtest-us.json

  Log Message:
  -----------
  Fix matcher


  Commit: ff35eb4d37eed1d9a2fdd2200d69a00adfcdb41c
      https://github.com/ehb54/ultrascan3/commit/ff35eb4d37eed1d9a2fdd2200d69a00adfcdb41c
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/index.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_select.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/components.rst
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dens_match.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/experiment/cells.rst
    M doc/manual/source/experiment/optics.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/submit.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/model_editor.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_adv.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/rotor.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/vhw_enhanced.rst
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_pcsa/us_mrecs_loader.h

  Log Message:
  -----------
  sphynx links


  Commit: 287fbcbd18bec2e702fabfb4298a69a0b62ee537
      https://github.com/ehb54/ultrascan3/commit/287fbcbd18bec2e702fabfb4298a69a0b62ee537
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M .gitignore
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/_static/images/delseltrip.png
    A doc/manual/source/_static/images/dmga-save.png
    A doc/manual/source/_static/images/dmga.png
    A doc/manual/source/_static/images/dmga_constr.png
    A doc/manual/source/_static/images/edit_exclude_scan.png
    A doc/manual/source/_static/images/edit_scan.png
    A doc/manual/source/_static/images/fe_dmga_adv.png
    A doc/manual/source/_static/images/select_prefilt.png
    A doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_select.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/components.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dens_match.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/cells.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/optics.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/submit.rst
    M doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    A doc/manual/source/global_equil.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/model_editor.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_adv.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    A doc/manual/source/ramp_data.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/rotor.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    A doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_get_run.h
    M gui/us_load_auc.h
    M gui/us_model_loader.h
    M gui/us_select_edits.h
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.h
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    A test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp
    M utils/CMakeLists.txt
    M utils/us_buffer.h
    M utils/us_extern.h

  Log Message:
  -----------
  Merge pull request #408 from ehb54/lukas/manual_test/make

Enhance documentation build system and improve Unicode handling


  Commit: 29678f933d80ecac003838e4bde2c37a65512482
      https://github.com/ehb54/ultrascan3/commit/29678f933d80ecac003838e4bde2c37a65512482
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-09 (Thu, 09 Apr 2026)

  Changed paths:
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  GMP  -- additional check for the protocol internals equality before submitting GMP run: check for operator (and revs & approvers)...


  Commit: 77adb01c3a9c4133da796314b1007c031f6dd089
      https://github.com/ehb54/ultrascan3/commit/77adb01c3a9c4133da796314b1007c031f6dd089
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-10 (Fri, 10 Apr 2026)

  Changed paths:
    M doc/manual/source/config.rst

  Log Message:
  -----------
  check new branch


  Commit: 0a0e0eca8a8da8aa4db25e74431e3d89b5808edb
      https://github.com/ehb54/ultrascan3/commit/0a0e0eca8a8da8aa4db25e74431e3d89b5808edb
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-10 (Fri, 10 Apr 2026)

  Changed paths:

  Log Message:
  -----------
  Merge pull request #410 from ehb54/main

Merge pull request #408 from ehb54/lukas/manual_test/make


  Commit: d2c99821961553c3153b8d32337f97b7511bcf81
      https://github.com/ehb54/ultrascan3/commit/d2c99821961553c3153b8d32337f97b7511bcf81
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/rotor_calibration.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  triplicates


  Commit: 6b12d783265172c421a37e224b8adad3f695e245
      https://github.com/ehb54/ultrascan3/commit/6b12d783265172c421a37e224b8adad3f695e245
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst

  Log Message:
  -----------
  minor missplacing


  Commit: c1845c6f4b9734df2f812c0b62d782d4f2609c9a
      https://github.com/ehb54/ultrascan3/commit/c1845c6f4b9734df2f812c0b62d782d4f2609c9a
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst

  Log Message:
  -----------
  minor


  Commit: 999f5967cfac93e336d82d6d37f650a584730945
      https://github.com/ehb54/ultrascan3/commit/999f5967cfac93e336d82d6d37f650a584730945
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/vhw_combine.rst

  Log Message:
  -----------
  ref and doc updates


  Commit: 5442f4062fa7bdbd225d10d4108a9913de662afe
      https://github.com/ehb54/ultrascan3/commit/5442f4062fa7bdbd225d10d4108a9913de662afe
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/_static/images/load_us3.png
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
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  referencing


  Commit: 5d940737536ba92999909c398bc2c791d46ffd4d
      https://github.com/ehb54/ultrascan3/commit/5d940737536ba92999909c398bc2c791d46ffd4d
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  referencing update


  Commit: 792ea02cbd0b900f1898086c35fa6b3c11e54201
      https://github.com/ehb54/ultrascan3/commit/792ea02cbd0b900f1898086c35fa6b3c11e54201
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-13 (Mon, 13 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/config.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  reference update 2


  Commit: 54a049bf6cfd4facaa834f4e91979253d3aa6b86
      https://github.com/ehb54/ultrascan3/commit/54a049bf6cfd4facaa834f4e91979253d3aa6b86
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    A doc/manual/source/_static/images/cmenu_help.png
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/rmsd_query.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
  -----------
  sphinx-build -M linkcheck /source /build -q --keep-going  + DMGA protocol


  Commit: 5ec1de61dba0f60ca68a98e66e6f8098e0d70384
      https://github.com/ehb54/ultrascan3/commit/5ec1de61dba0f60ca68a98e66e6f8098e0d70384
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  manual name change


  Commit: 73e408bbda42ba6961f01111ffb11b59c8976fce
      https://github.com/ehb54/ultrascan3/commit/73e408bbda42ba6961f01111ffb11b59c8976fce
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/index.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst

  Log Message:
  -----------
  minor updates


  Commit: aadeecb1340fbe3c58273b592171ad822dbd05dd
      https://github.com/ehb54/ultrascan3/commit/aadeecb1340fbe3c58273b592171ad822dbd05dd
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/index.rst

  Log Message:
  -----------
  minor updates in Index


  Commit: 26b3afbb4f6320ad269fb86433af8187d3a79256
      https://github.com/ehb54/ultrascan3/commit/26b3afbb4f6320ad269fb86433af8187d3a79256
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/reporter_comrep.png
    M doc/manual/source/index.rst
    M doc/manual/source/reporter.rst

  Log Message:
  -----------
  These MINOR changes are killing me


  Commit: c35c8a4a2d552e064e5d40205f75deef685d0d6e
      https://github.com/ehb54/ultrascan3/commit/c35c8a4a2d552e064e5d40205f75deef685d0d6e
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-14 (Tue, 14 Apr 2026)

  Changed paths:
    M doc/manual/source/fe_match/index.rst

  Log Message:
  -----------
  Minoooor


  Commit: abf6f6f3682a1676d7d1e8f7dd0f02419fb1954f
      https://github.com/ehb54/ultrascan3/commit/abf6f6f3682a1676d7d1e8f7dd0f02419fb1954f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-15 (Wed, 15 Apr 2026)

  Changed paths:
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge pull request #409 from ehb54/alexey-dev-issue814

GMP  -- additional check for the protocol internals equality before submitting GMP runs: operator(s)


  Commit: 79bb847a03d6a66112ac96beede10610bbba2246
      https://github.com/ehb54/ultrascan3/commit/79bb847a03d6a66112ac96beede10610bbba2246
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Ensure zoom check considers spectrogram items in `us_plot.cpp`


  Commit: 0d3c4779cd3d7e85fc5bc4ad7e449a6afcaf99ff
      https://github.com/ehb54/ultrascan3/commit/0d3c4779cd3d7e85fc5bc4ad7e449a6afcaf99ff
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Refactor signal-slot connections in `us_pseudo3d_combine.cpp` to use modern `&QButtonGroup::idReleased` syntax.


  Commit: e3131079c98204bcde4f43e59bc6114c81d4d6bd
      https://github.com/ehb54/ultrascan3/commit/e3131079c98204bcde4f43e59bc6114c81d4d6bd
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Refactor signal-slot connections in `us_pseudo3d_combine.cpp` to use modern syntax for improved readability and maintainability.


  Commit: c85594c8e6e1edab8b7adae963da46ffe5913fc6
      https://github.com/ehb54/ultrascan3/commit/c85594c8e6e1edab8b7adae963da46ffe5913fc6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-04-16 (Thu, 16 Apr 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h

  Log Message:
  -----------
  Model Selector  -- allow Accept for GMP-generated models...


  Commit: 6bcf83da27c47886d434f95cb5c8b5b393efcc79
      https://github.com/ehb54/ultrascan3/commit/6bcf83da27c47886d434f95cb5c8b5b393efcc79
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-20 (Mon, 20 Apr 2026)

  Changed paths:
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_spectrum.rst

  Log Message:
  -----------
  us_buoyancy introduction, Us_spectrum introduction,images and application updated.


  Commit: b5159ec368c6454947e70949aaffbdde6b41c221
      https://github.com/ehb54/ultrascan3/commit/b5159ec368c6454947e70949aaffbdde6b41c221
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-20 (Mon, 20 Apr 2026)

  Changed paths:
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge branch 'main' into haben/docs-crosslinking


  Commit: 0d231234973612a639bab8cf3fc26fb81c88717f
      https://github.com/ehb54/ultrascan3/commit/0d231234973612a639bab8cf3fc26fb81c88717f
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-20 (Mon, 20 Apr 2026)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
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    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  Merge pull request #412 from ehb54/haben/docs-crosslinking

Document cross linking, manual help buttons and new pages added.


  Commit: 47638222ab16a5ea91b3b1574d03c5038374b2a4
      https://github.com/ehb54/ultrascan3/commit/47638222ab16a5ea91b3b1574d03c5038374b2a4
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2026-04-21 (Tue, 21 Apr 2026)

  Changed paths:
    M doc/manual/source/start_page-mw.rst

  Log Message:
  -----------
  replaced old image in doc


  Commit: 1fece8e1783a00b7b4b2d53c0d3fb24784b20678
      https://github.com/ehb54/ultrascan3/commit/1fece8e1783a00b7b4b2d53c0d3fb24784b20678
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-21 (Tue, 21 Apr 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into haben/docs-crosslinking


  Commit: c0dbe2538c5177518ec31c51efdbe5540a5df70d
      https://github.com/ehb54/ultrascan3/commit/c0dbe2538c5177518ec31c51efdbe5540a5df70d
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2026-04-21 (Tue, 21 Apr 2026)

  Changed paths:
    M doc/manual/source/start_page-mw.rst

  Log Message:
  -----------
  Merge pull request #415 from ehb54/haben/docs-crosslinking

replaced old image in doc


  Commit: 0d1643338fa17f6186a4ad8679ba4cccf89fd394
      https://github.com/ehb54/ultrascan3/commit/0d1643338fa17f6186a4ad8679ba4cccf89fd394
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_pseudo3d_combine


  Commit: eca543a22ebb2991eb0b445f72e347063fbc8c72
      https://github.com/ehb54/ultrascan3/commit/eca543a22ebb2991eb0b445f72e347063fbc8c72
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  standardize reference section formatting in start_page.rst and start_page-mw.rst


  Commit: a4f1f53d77b4eb249b8afb6b09bf96f052e25542
      https://github.com/ehb54/ultrascan3/commit/a4f1f53d77b4eb249b8afb6b09bf96f052e25542
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix VERSION file path, change default version from unknown to 4.1.0-dev, refactor release construction


  Commit: db21d0c5a194f41886b613e65623c07d2bc40f9d
      https://github.com/ehb54/ultrascan3/commit/db21d0c5a194f41886b613e65623c07d2bc40f9d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M utils/us_defines.h

  Log Message:
  -----------
  add conditional definitions for US_Version and US_Description in us_defines.h


  Commit: 9cbcea1782add3926f1f936aa6696c0e418a0a33
      https://github.com/ehb54/ultrascan3/commit/9cbcea1782add3926f1f936aa6696c0e418a0a33
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  add __pycache__ to .gitignore


  Commit: 102b83ab79cfa7cf1af1b528d6422565dd8b4bba
      https://github.com/ehb54/ultrascan3/commit/102b83ab79cfa7cf1af1b528d6422565dd8b4bba
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix spacing for no local changes


  Commit: ffce8c0558eef867b786192bfa509ba0b615e715
      https://github.com/ehb54/ultrascan3/commit/ffce8c0558eef867b786192bfa509ba0b615e715
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M utils/us_defines.h

  Log Message:
  -----------
  Remove version and description guards in us_defines.h


  Commit: 36dc1785d98214993d36bfc9d3b4d8274ddf93ba
      https://github.com/ehb54/ultrascan3/commit/36dc1785d98214993d36bfc9d3b4d8274ddf93ba
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Update path comment for VERSION file location


  Commit: 8cf8988f671379dcf266a35155e091020469e547
      https://github.com/ehb54/ultrascan3/commit/8cf8988f671379dcf266a35155e091020469e547
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp

  Log Message:
  -----------
  Refactor signal-slot connections across multiple modules to use modern syntax for improved readability and maintainability.


  Commit: e55fdb6a821372263be14ebfd0bd4debd621c904
      https://github.com/ehb54/ultrascan3/commit/e55fdb6a821372263be14ebfd0bd4debd621c904
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Ensure axis checks account for spectrogram items in `us_plot.cpp`


  Commit: 33967fac5d6dd4415b67c2e8bc928de7aad9504b
      https://github.com/ehb54/ultrascan3/commit/33967fac5d6dd4415b67c2e8bc928de7aad9504b
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M programs/us_pcsa/us_analysis_control_pc.cpp

  Log Message:
  -----------
  Refactor signal-slot connections in `us_analysis_control_pc.cpp` to use modern syntax for improved readability and maintainability.


  Commit: 3c2f9d3ede41ffdcd79d070e45afb8a238e729fb
      https://github.com/ehb54/ultrascan3/commit/3c2f9d3ede41ffdcd79d070e45afb8a238e729fb
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Simplify lambda expressions in `us_pseudo3d_combine.cpp` by removing redundant `&` capture.


  Commit: c20633e9c5e7406950dbc174cae33f60cb8c2d17
      https://github.com/ehb54/ultrascan3/commit/c20633e9c5e7406950dbc174cae33f60cb8c2d17
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Remove future annotations import

Removed future annotations import from conf.py.


  Commit: 60491d8fe675ed9c20c175e16153aa1a2f594186
      https://github.com/ehb54/ultrascan3/commit/60491d8fe675ed9c20c175e16153aa1a2f594186
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Add __pycache__ to .gitignore


  Commit: 2cb09af8870f32c9aa5e3463851c91e6741e0bdd
      https://github.com/ehb54/ultrascan3/commit/2cb09af8870f32c9aa5e3463851c91e6741e0bdd
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/source/conf.py
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  Merge pull request #416 from ehb54/lukas/manual_versioning

Standardize formatting and update versioning in manual


  Commit: eba2b0e533d5a81cad63c0edd5319256ba404cdd
      https://github.com/ehb54/ultrascan3/commit/eba2b0e533d5a81cad63c0edd5319256ba404cdd
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/source/conf.py
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_pseudo3d_combine


  Commit: 46ff46e5434d882cb83343ffd5b854bf6f41f7d1
      https://github.com/ehb54/ultrascan3/commit/46ff46e5434d882cb83343ffd5b854bf6f41f7d1
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue819


  Commit: bf1f52b701e7d998a5d22f3fb3cfac685fe25b11
      https://github.com/ehb54/ultrascan3/commit/bf1f52b701e7d998a5d22f3fb3cfac685fe25b11
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-04-25 (Sat, 25 Apr 2026)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge pull request #413 from ehb54/lukas/us_pseudo3d_combine

Lukas/us pseudo3d combine


  Commit: 409fa95fadf7055d7f1a80221d9570136a3c74ea
      https://github.com/ehb54/ultrascan3/commit/409fa95fadf7055d7f1a80221d9570136a3c74ea
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-22 (Fri, 22 May 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-dataDisk: 1.EXP.: 4. Cells --  Fix logic for changing centerpieces only for cells uploaded from data-from-diks; depending on rotor choice, if uploaded data contains counter-balancing cell, then mirror centerpieces; if no counter-balancing cell exists, do not trigger mirroring, keep cell disabled...


  Commit: c2f09171367a1f7251e1b6c2f115e67a2ec2aa7e
      https://github.com/ehb54/ultrascan3/commit/c2f09171367a1f7251e1b6c2f115e67a2ec2aa7e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-23 (Sat, 23 May 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M scripts/build.sh

  Log Message:
  -----------
  Fix: MariaDB Connector/C auth plugin packaging for Windows and Linux desktop deploys


  Commit: 955a18e6afbf33a71fb3cb653635e8a1fdcba309
      https://github.com/ehb54/ultrascan3/commit/955a18e6afbf33a71fb3cb653635e8a1fdcba309
  Author: Saeed <github.com/samo38>
  Date:   2026-05-25 (Mon, 25 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  us_extinction_gui: load multiple files to the target list in the us_extinction


  Commit: 8ffe17a2ff45c1bd98abb4f443c8e85a44607408
      https://github.com/ehb54/ultrascan3/commit/8ffe17a2ff45c1bd98abb4f443c8e85a44607408
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-25 (Mon, 25 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected...


  Commit: d65cc7b90bd9cfd09a504b97d1e991b5e9709798
      https://github.com/ehb54/ultrascan3/commit/d65cc7b90bd9cfd09a504b97d1e991b5e9709798
  Author: Saeed <github.com/samo38>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  fix the ct_plt range for D values


  Commit: 70c051b3319c22d073aec3e7963574dd431d374b
      https://github.com/ehb54/ultrascan3/commit/70c051b3319c22d073aec3e7963574dd431d374b
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge pull request #421 from samo38/ticket_821

ticket 821: load multiple files in the Spectra Fitter


  Commit: 47568edd1c571d37f6d337dac8403bf2b63355a7
      https://github.com/ehb54/ultrascan3/commit/47568edd1c571d37f6d337dac8403bf2b63355a7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue847


  Commit: 9caa64325023045f92d621ea29c7c24238abe010
      https://github.com/ehb54/ultrascan3/commit/9caa64325023045f92d621ea29c7c24238abe010
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue845


  Commit: 3f5b75b4f2c1f0e13c26e4f5200970f1a849ccce
      https://github.com/ehb54/ultrascan3/commit/3f5b75b4f2c1f0e13c26e4f5200970f1a849ccce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  [Warning message edited]Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected...


  Commit: 8b4bb030d983d019042fbafc5db11ecddb4cef59
      https://github.com/ehb54/ultrascan3/commit/8b4bb030d983d019042fbafc5db11ecddb4cef59
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  [Warning message edited]Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected...


  Commit: 4c2a5827c767a8efdf04d90f65582b75aa7b8f7b
      https://github.com/ehb54/ultrascan3/commit/4c2a5827c767a8efdf04d90f65582b75aa7b8f7b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp

  Log Message:
  -----------
  Merge branch 'alexey-dev-issue845' of github.com:ehb54/ultrascan3 into alexey-dev-issue845


  Commit: e41650e2a92988aaf178bb235f6fd635ae7732a5
      https://github.com/ehb54/ultrascan3/commit/e41650e2a92988aaf178bb235f6fd635ae7732a5
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-05-27 (Wed, 27 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  Merge pull request #422 from ehb54/alexey-dev-issue845

Database:Manage Models & US_Astfem: -- preclude segfault when clicking Edit Current Analyte in properties when no analyte uploaded and selected.


  Commit: 3c4763f65a21b749bfe07dc42e2128122b695384
      https://github.com/ehb54/ultrascan3/commit/3c4763f65a21b749bfe07dc42e2128122b695384
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-05-27 (Wed, 27 May 2026)

  Changed paths:
    M gui/us_properties.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue847


  Commit: 2d6c96d3534c682e0f41a653e60626ac9ca3cda5
      https://github.com/ehb54/ultrascan3/commit/2d6c96d3534c682e0f41a653e60626ac9ca3cda5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-27 (Wed, 27 May 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  1. EXP. setup for: GMP | R&D | Protocol Dev. -- (1) Previous Panel: disable when 1st tab index; (2) Next Panel: disable when last tab index; Enable both buttons otherwise...


  Commit: 336ecdb767221596e40fe03b4109ae958a244155
      https://github.com/ehb54/ultrascan3/commit/336ecdb767221596e40fe03b4109ae958a244155
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge pull request #420 from ehb54/alexey-dev-issue847

GMP-dataDisk: 1.EXP.: 4. Cells --  Fix logic for changing centerpiece?


  Commit: 4271414177534df7efc4fa581c55c7156f3ddabd
      https://github.com/ehb54/ultrascan3/commit/4271414177534df7efc4fa581c55c7156f3ddabd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue855


  Commit: 128150af07823bd4765583981c14e72a886ececb
      https://github.com/ehb54/ultrascan3/commit/128150af07823bd4765583981c14e72a886ececb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_plot.cpp
    M gui/us_properties.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue819


  Commit: ac4b2e251a870242701d557b0f9fb1bde83f1ba1
      https://github.com/ehb54/ultrascan3/commit/ac4b2e251a870242701d557b0f9fb1bde83f1ba1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-28 (Thu, 28 May 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge pull request #424 from ehb54/alexey-dev-issue855

1. EXP. setup for: GMP | R&D | Protocol Dev. -- Previous Panel & Next Panel buttons


  Commit: 4d55ef620df76f15f779937d88eae46dc5476934
      https://github.com/ehb54/ultrascan3/commit/4d55ef620df76f15f779937d88eae46dc5476934
  Author: Saeed <github.com/samo38>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  us_pseudo3d_combine.cpp: update ct range


  Commit: bfbbceba435317993ba1177f8d6ed0a5810550da
      https://github.com/ehb54/ultrascan3/commit/bfbbceba435317993ba1177f8d6ed0a5810550da
  Author: Saeed <github.com/samo38>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  update ct range


  Commit: 3650572bd17f9308587dfbf1d1410498922d61fc
      https://github.com/ehb54/ultrascan3/commit/3650572bd17f9308587dfbf1d1410498922d61fc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP: 2. Rotor/Labs  : in a non-typical situation where oper. or revs. or appr, lists are empty, disable Add to List button...


  Commit: fada6882842c5ae682cd424efd87744e75cace23
      https://github.com/ehb54/ultrascan3/commit/fada6882842c5ae682cd424efd87744e75cace23
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge pull request #426 from ehb54/alexey-dev-issue857

GMP: 2. Rotor/Labs  tab: Add to List bttns


  Commit: a2adfa71f41c800e6f524a3cc455920214b68843
      https://github.com/ehb54/ultrascan3/commit/a2adfa71f41c800e6f524a3cc455920214b68843
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue819


  Commit: 7d69bb500e80be10d428dd0e6858038dfd36f238
      https://github.com/ehb54/ultrascan3/commit/7d69bb500e80be10d428dd0e6858038dfd36f238
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h

  Log Message:
  -----------
  Merge pull request #414 from ehb54/alexey-dev-issue819

Model Selector  -- allow Accept for GMP-generated models...


  Commit: 081a9573c4b25b4a1160d69485efb294378d580d
      https://github.com/ehb54/ultrascan3/commit/081a9573c4b25b4a1160d69485efb294378d580d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge branch 'main' into t842_gaplot


  Commit: 3e9d2e13ca1148add7cf8287085ba3db3a5863c2
      https://github.com/ehb54/ultrascan3/commit/3e9d2e13ca1148add7cf8287085ba3db3a5863c2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Refactor default database selection process

Refactor database selection logic to avoid redundant calls and improve clarity.


  Commit: c4f9c771e1b24dc0e93e5dca2db4cdb010f1dc9e
      https://github.com/ehb54/ultrascan3/commit/c4f9c771e1b24dc0e93e5dca2db4cdb010f1dc9e
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Update database selection logic for default DB


  Commit: 88b1ac951023136e21e2f1ab0c2fd000ad06eac8
      https://github.com/ehb54/ultrascan3/commit/88b1ac951023136e21e2f1ab0c2fd000ad06eac8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Delete .github/workflows/unit-tests.yml


  Commit: 59261739cdcce7bb342cec6d0eca84439819b56d
      https://github.com/ehb54/ultrascan3/commit/59261739cdcce7bb342cec6d0eca84439819b56d
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt

  Log Message:
  -----------
  Fix: Copy MariaDB auth plugins to build directory for development


  Commit: 8b547ef902833338a45d98fe066ac0c767fdf626
      https://github.com/ehb54/ultrascan3/commit/8b547ef902833338a45d98fe066ac0c767fdf626
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Fix: Add US3 version string to Linux deployment CMake configuration


  Commit: 845441e33ec92b9dc3657f2b7871f2183122a73b
      https://github.com/ehb54/ultrascan3/commit/845441e33ec92b9dc3657f2b7871f2183122a73b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M scripts/build.ps1

  Log Message:
  -----------
  Fix: Enhance Windows deployment process for Qt tools in CMake and PowerShell scripts


  Commit: cae5416d082d2ffb9ce37e3299da1d6ba4818688
      https://github.com/ehb54/ultrascan3/commit/cae5416d082d2ffb9ce37e3299da1d6ba4818688
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/toolchain.cmake
    M scripts/build.ps1

  Log Message:
  -----------
  Fix: Improve windeployqt handling for Windows ARM64 and x64 builds in CMake


  Commit: ffe103a9cda3bf0765d63babc1383b5b73c60f00
      https://github.com/ehb54/ultrascan3/commit/ffe103a9cda3bf0765d63babc1383b5b73c60f00
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Merge pull request #429 from ehb54/lukas/unit_test_v1_removal

Delete .github/workflows/unit-tests.yml


  Commit: ba2e69f89d211b977e99532f5a2ee4f5635fe241
      https://github.com/ehb54/ultrascan3/commit/ba2e69f89d211b977e99532f5a2ee4f5635fe241
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    M scripts/build.ps1

  Log Message:
  -----------
  Fix: Enhance build script for Windows by adding build type handling and ensuring full build before packaging


  Commit: 07ebae5c1a9fb79e304cf43ad4969948dbf53c1f
      https://github.com/ehb54/ultrascan3/commit/07ebae5c1a9fb79e304cf43ad4969948dbf53c1f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    M CMakeLists.txt
    M programs/us/us.cpp

  Log Message:
  -----------
  Fix: Copy MariaDB auth plugins to build directory for Windows development


  Commit: 4d0251f74bed05cb83787a04885731d3b152f4b5
      https://github.com/ehb54/ultrascan3/commit/4d0251f74bed05cb83787a04885731d3b152f4b5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-01 (Mon, 01 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M gui/us_extinction_gui.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_properties.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into 840-bug-cmake-build---mariadb-plugin-missing-macos


  Commit: ce276826700547ec7106f9d689b8d998e2001315
      https://github.com/ehb54/ultrascan3/commit/ce276826700547ec7106f9d689b8d998e2001315
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot at users.noreply.github.com>


  Commit: 48619c5707bd21b1fca1d26626f0d42608ec56a7
      https://github.com/ehb54/ultrascan3/commit/48619c5707bd21b1fca1d26626f0d42608ec56a7
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot at users.noreply.github.com>


  Commit: 7c437d150e86857f0f355ba642049e8298aa2967
      https://github.com/ehb54/ultrascan3/commit/7c437d150e86857f0f355ba642049e8298aa2967
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  Merge pull request #428 from ehb54/840-bug-cmake-build---mariadb-plugin-missing

Fix: MariaDB Connector/C auth plugin packaging for Windows and Linux ?


  Commit: c9483a2b187a96210afec12c05ea37f140d27c77
      https://github.com/ehb54/ultrascan3/commit/c9483a2b187a96210afec12c05ea37f140d27c77
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_config_db


  Commit: 77b0d98c96b9428b9058a18a1cde8a5234fd77de
      https://github.com/ehb54/ultrascan3/commit/77b0d98c96b9428b9058a18a1cde8a5234fd77de
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-06-03 (Wed, 03 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Merge pull request #427 from ehb54/lukas/us_config_db

Refactor default database selection process


  Commit: 8109d2d1f8a808b98af3173590fdf0a1bd470a4a
      https://github.com/ehb54/ultrascan3/commit/8109d2d1f8a808b98af3173590fdf0a1bd470a4a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-03 (Wed, 03 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  GMP, Prot_devel, utils/xpn_data : remove unused function, ensure xpn (optima) host is configured during xpn->connect...


  Commit: 25fa9df5a94aabc9a5a53be7d6e15d767a17c238
      https://github.com/ehb54/ultrascan3/commit/25fa9df5a94aabc9a5a53be7d6e15d767a17c238
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-04 (Thu, 04 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #430 from ehb54/alexey-dev-issue872

GMP, Prot_devel, utils/xpn_data : remove unused function, ensure xpn host is configured?


  Commit: 6cf1e2de27f3dc7a74383050c085f36898bb156b
      https://github.com/ehb54/ultrascan3/commit/6cf1e2de27f3dc7a74383050c085f36898bb156b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  GMP, R&D -- correct interplay between scan counts, scan interval, minimum scan interval in 3. Sppeds and 7. Ranges ...


  Commit: 5ce35ace4e6f0bd6eb3de4111d93a0c754c613e8
      https://github.com/ehb54/ultrascan3/commit/5ce35ace4e6f0bd6eb3de4111d93a0c754c613e8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  GMP, R&D -- The first sentence after Attention should not have started with a period. Line should have started with "Please..."....


  Commit: 439bf47d73c1de196a1c091f8629403731ac42e6
      https://github.com/ehb54/ultrascan3/commit/439bf47d73c1de196a1c091f8629403731ac42e6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  Merge pull request #432 from ehb54/alexey-dev-issue873

GMP, R&D -- The first sentence after Attention should not have started with a period. Line should have started with "Please..."....


  Commit: c70b0809570e8451264f061bfddbf0d90ed7d45b
      https://github.com/ehb54/ultrascan3/commit/c70b0809570e8451264f061bfddbf0d90ed7d45b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue874


  Commit: ab4e29f258a4a76852473bb029a8d05af5101e3b
      https://github.com/ehb54/ultrascan3/commit/ab4e29f258a4a76852473bb029a8d05af5101e3b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-07 (Sun, 07 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge pull request #431 from ehb54/alexey-dev-issue874

GMP, R&D -- correct interplay between scan counts, scan interval, min. scan interval


  Commit: b3e1c3148e849dfa0bb3115413e07983b919844e
      https://github.com/ehb54/ultrascan3/commit/b3e1c3148e849dfa0bb3115413e07983b919844e
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  add a label to show the buffer manual state


  Commit: f9dc1123f5d504527a1a5a5f98992c035cda5368
      https://github.com/ehb54/ultrascan3/commit/f9dc1123f5d504527a1a5a5f98992c035cda5368
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 372d4a9b863855920c8f9fcc63e1e874250bcdae
      https://github.com/ehb54/ultrascan3/commit/372d4a9b863855920c8f9fcc63e1e874250bcdae
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  auto scale xy after selecting a new parameter


  Commit: c00094277c02fa9f1bbf1ea45e6c392960605b9e
      https://github.com/ehb54/ultrascan3/commit/c00094277c02fa9f1bbf1ea45e6c392960605b9e
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M gui/us_extinction_gui.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_properties.cpp
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: f28a5e62b10d404ecce483e3109f42b1623253c4
      https://github.com/ehb54/ultrascan3/commit/f28a5e62b10d404ecce483e3109f42b1623253c4
  Author: Saeed <github.com/samo38>
  Date:   2026-06-09 (Tue, 09 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  fixed type cast warnings in us_mpi_analysis.cpp, ga_worker.cpp


  Commit: f3611e7f434e44d3d1c61e7d0e945a94035388f9
      https://github.com/ehb54/ultrascan3/commit/f3611e7f434e44d3d1c61e7d0e945a94035388f9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge pull request #435 from samo38/t861_security_warn

clean security warnings


  Commit: f80b73498a4973369419673e90274f59d9b598b3
      https://github.com/ehb54/ultrascan3/commit/f80b73498a4973369419673e90274f59d9b598b3
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 3dddb9117fd90c1f6e1fdeec16f309bcc7b74a10
      https://github.com/ehb54/ultrascan3/commit/3dddb9117fd90c1f6e1fdeec16f309bcc7b74a10
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: bde95ecaf2c093c38c510529ade5c772aeb0d058
      https://github.com/ehb54/ultrascan3/commit/bde95ecaf2c093c38c510529ade5c772aeb0d058
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 5be7ae9df7ec29fa88487a9dc72834ca6c3ab515
      https://github.com/ehb54/ultrascan3/commit/5be7ae9df7ec29fa88487a9dc72834ca6c3ab515
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_config/us_newxpnhost_db.cpp

  Log Message:
  -----------
  US_Config:Intruments -- incorporate test_Connectivity into Save routing, remove extra connectivity check step...


  Commit: 32473b578707e256cf293eb356d873413dd769b6
      https://github.com/ehb54/ultrascan3/commit/32473b578707e256cf293eb356d873413dd769b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_config/us_newxpnhost_db.cpp

  Log Message:
  -----------
  Merge pull request #436 from ehb54/alexey-dev-issue882

US_Config:Intruments -- incorporate test_Connectivity into Save routing


  Commit: 4aec245df7e6c8b1e030e812298d6cba7cab845e
      https://github.com/ehb54/ultrascan3/commit/4aec245df7e6c8b1e030e812298d6cba7cab845e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  GMP: 2. LIVE_UPDATE -- spelling error fixed...


  Commit: 12f71524c0445a97e2b0b1aaf3d53f6736ea6301
      https://github.com/ehb54/ultrascan3/commit/12f71524c0445a97e2b0b1aaf3d53f6736ea6301
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  GMP: -- modify message for marking run as FAILED/NPT FAILED...


  Commit: 3c7169cde650dedca3d3402f744d3253f88868d5
      https://github.com/ehb54/ultrascan3/commit/3c7169cde650dedca3d3402f744d3253f88868d5
  Author: Saeed <github.com/samo38>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 1be10ca817665f8309bb3df08852200424397547
      https://github.com/ehb54/ultrascan3/commit/1be10ca817665f8309bb3df08852200424397547
  Author: Saeed <github.com/samo38>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/t842_gaplot' into t842_gaplot


  Commit: 6a2abeacf5fcb63c4355bea33d0a8665ebf1aea3
      https://github.com/ehb54/ultrascan3/commit/6a2abeacf5fcb63c4355bea33d0a8665ebf1aea3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  GMP main window -- modify text in the upper textarea...


  Commit: 3fbee9fcc1783c2c585c16e2fe0cdb6c22982a61
      https://github.com/ehb54/ultrascan3/commit/3fbee9fcc1783c2c585c16e2fe0cdb6c22982a61
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  [1]GMP main window -- modify text in the upper textarea...


  Commit: 290881f0fb957f5129113ca6c0d363cda44d453e
      https://github.com/ehb54/ultrascan3/commit/290881f0fb957f5129113ca6c0d363cda44d453e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge pull request #437 from ehb54/alexey-dev-issue885

GMP: 2. LIVE_UPDATE -- spelling error fixed...


  Commit: 51eac7bb6878f0d5e5b586795486cea3043d3d0c
      https://github.com/ehb54/ultrascan3/commit/51eac7bb6878f0d5e5b586795486cea3043d3d0c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue887


  Commit: 27153f63f856b1d20b1465999a14d3e3281e707a
      https://github.com/ehb54/ultrascan3/commit/27153f63f856b1d20b1465999a14d3e3281e707a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue886


  Commit: 4241a57028574e3cd23f3c3291191974fc72a7f5
      https://github.com/ehb54/ultrascan3/commit/4241a57028574e3cd23f3c3291191974fc72a7f5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge pull request #438 from ehb54/alexey-dev-issue887

GMP: -- modify message for marking run as FAILED/NOT FAILED...


  Commit: 5b1e1e57275a9d2d7788c8c73c68af8bffc728aa
      https://github.com/ehb54/ultrascan3/commit/5b1e1e57275a9d2d7788c8c73c68af8bffc728aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue886


  Commit: 1b9d32c8d947abd0215b70dbe7495fc98759a47b
      https://github.com/ehb54/ultrascan3/commit/1b9d32c8d947abd0215b70dbe7495fc98759a47b
  Author: Saeed <github.com/samo38>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  update the ct range by data


  Commit: 1f2dea5900a814f27165ae2bc9b401c3dfee187c
      https://github.com/ehb54/ultrascan3/commit/1f2dea5900a814f27165ae2bc9b401c3dfee187c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge pull request #439 from ehb54/alexey-dev-issue886

GMP main window -- modify text in the upper textarea...


  Commit: 5e1874151de9b54802972297c327c677ea4ed1c9
      https://github.com/ehb54/ultrascan3/commit/5e1874151de9b54802972297c327c677ea4ed1c9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: cbb216d0d629fbbe7c3294431c08f61989b2e7a2
      https://github.com/ehb54/ultrascan3/commit/cbb216d0d629fbbe7c3294431c08f61989b2e7a2
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  upadte ct x and y in the set_limits()


  Commit: 67a4d242dabc14876d9354b93434c818b5baf7ec
      https://github.com/ehb54/ultrascan3/commit/67a4d242dabc14876d9354b93434c818b5baf7ec
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M gui/us_spectrodata.cpp

  Log Message:
  -----------
  in the setRaster function, if xrng becomes 0, xinc becomes INF. The same approach for xrng is applied here.


  Commit: 6f904c41c021e36595b930817137f19ef8ccce19
      https://github.com/ehb54/ultrascan3/commit/6f904c41c021e36595b930817137f19ef8ccce19
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  connect the replot_data function to the pb_refresh


  Commit: c24e05faa744af2d76beb4c61148bc79fa771670
      https://github.com/ehb54/ultrascan3/commit/c24e05faa744af2d76beb4c61148bc79fa771670
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  fixed the issue with draw bins manually


  Commit: 959da46aacd3efb25d3f0a0009e3da52819f733b
      https://github.com/ehb54/ultrascan3/commit/959da46aacd3efb25d3f0a0009e3da52819f733b
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: 32feaefb494d632b390d9acb54c6daefdd47089b
      https://github.com/ehb54/ultrascan3/commit/32feaefb494d632b390d9acb54c6daefdd47089b
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  set range of ct by data


  Commit: 9c70967b72e22425120bb3e0971e49e2cab828a2
      https://github.com/ehb54/ultrascan3/commit/9c70967b72e22425120bb3e0971e49e2cab828a2
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 0678091c6b8ea3a347d8bda5c1f8887a6d3ee65b
      https://github.com/ehb54/ultrascan3/commit/0678091c6b8ea3a347d8bda5c1f8887a6d3ee65b
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Merge pull request #433 from samo38/t870_buffer

Add buffer manual state to the Buffer and Solution GUI


  Commit: 075459dfc9537700e37aba51b3f8a5bb57c3c1c6
      https://github.com/ehb54/ultrascan3/commit/075459dfc9537700e37aba51b3f8a5bb57c3c1c6
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_select_item.cpp
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 16547f24596d6f1a1c6e10976383ed8bc2b74819
      https://github.com/ehb54/ultrascan3/commit/16547f24596d6f1a1c6e10976383ed8bc2b74819
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  Merge pull request #425 from samo38/t842_gaplot

ticket 842: GA plot range issue


  Commit: a7cbce78277c83da3570ae8b311270ecf88d59a5
      https://github.com/ehb54/ultrascan3/commit/a7cbce78277c83da3570ae8b311270ecf88d59a5
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: c7efd6ac8d78505ee8782507280e4a224fd9e858
      https://github.com/ehb54/ultrascan3/commit/c7efd6ac8d78505ee8782507280e4a224fd9e858
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge pull request #423 from samo38/ticket_822_pseudo3d_plot

ticket_822: us_pseudo3d_combine manually diffusion plotting issue


  Commit: 1eb5f81fa55c76e1991446dfaaafd472f62ff46f
      https://github.com/ehb54/ultrascan3/commit/1eb5f81fa55c76e1991446dfaaafd472f62ff46f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: 8285d5c355b2c8730c274762fd27522a30d3cd18
      https://github.com/ehb54/ultrascan3/commit/8285d5c355b2c8730c274762fd27522a30d3cd18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [2: select Project, do not enable tabs]GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: 245d4309e28c9db90cffbef3cb981c97b69a9b4a
      https://github.com/ehb54/ultrascan3/commit/245d4309e28c9db90cffbef3cb981c97b69a9b4a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue891


  Commit: 7870bc0e407e502ff7e3dac5490ba89f35c0a24b
      https://github.com/ehb54/ultrascan3/commit/7870bc0e407e502ff7e3dac5490ba89f35c0a24b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge pull request #440 from ehb54/alexey-dev-issue891

GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk selected to prevent user-filled protocol creation


  Commit: 04bc610b180db0057d777dd09625732e535d15d1
      https://github.com/ehb54/ultrascan3/commit/04bc610b180db0057d777dd09625732e535d15d1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Protocol-Developer: remove v.0,1 from the window title ...


  Commit: aabf6395ab17f75fe98ee8a1856d0df8163ac5a0
      https://github.com/ehb54/ultrascan3/commit/aabf6395ab17f75fe98ee8a1856d0df8163ac5a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge pull request #442 from ehb54/alexey-dev-issue890

Protocol-Developer: remove v.0,1 from the window title ...


  Commit: c01e1313f848d52ba4e9f5c91129eac8c54f2b4d
      https://github.com/ehb54/ultrascan3/commit/c01e1313f848d52ba4e9f5c91129eac8c54f2b4d
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  fix: Update bump PR commit SHA in workflow configuration


  Commit: 52cc7dc3a6bb04f611fd929cf3e9a34d8ff69e1c
      https://github.com/ehb54/ultrascan3/commit/52cc7dc3a6bb04f611fd929cf3e9a34d8ff69e1c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #444 from ehb54/898-update-bump-pr-commit-sha-ultrascan3

Update workflow configuration for commit SHA bump


  Commit: bbe49a767b0802c2c444243ec79fb5dbeeaf2d14
      https://github.com/ehb54/ultrascan3/commit/bbe49a767b0802c2c444243ec79fb5dbeeaf2d14
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/bump-version.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    M admin/cmake/GenerateVersion.cmake
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    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
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    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
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    A doc/manual/source/astfem_sim.rst
    A doc/manual/source/auto_index.py
    A doc/manual/source/beckman_openauc.rst
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    A doc/manual/source/buoyancy_editor.rst
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    A doc/manual/source/combine_models.rst
    A doc/manual/source/common_dialogs.rst
    A doc/manual/source/components.rst
    A doc/manual/source/conf.py
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    A doc/manual/source/convert.rst
    A doc/manual/source/ddist_combine.rst
    A doc/manual/source/dens_match.rst
    A doc/manual/source/dmga_init.rst
    A doc/manual/source/dmga_init_constr.rst
    A doc/manual/source/experiment/cells.rst
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    A doc/manual/source/experiment/rotor.rst
    A doc/manual/source/experiment/solutions.rst
    A doc/manual/source/experiment/speeds.rst
    A doc/manual/source/experiment/submit.rst
    A doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    A doc/manual/source/fe_match/fe_match_adv.rst
    A doc/manual/source/fe_match/fe_match_main.rst
    A doc/manual/source/fe_match/fe_match_simulate.rst
    A doc/manual/source/fe_match/index.rst
    A doc/manual/source/fit_meniscus.rst
    A doc/manual/source/ga_initialize.rst
    A doc/manual/source/global_equil.rst
    A doc/manual/source/gmp/gmp.rst
    A doc/manual/source/gmp/gmp_audit_trail.rst
    A doc/manual/source/gmp/gmp_automation.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    A doc/manual/source/gmp/gmp_data_acquisition/index.rst
    A doc/manual/source/gmp/gmp_protocol_development.rst
    A doc/manual/source/gmp/gmp_report_generator.rst
    A doc/manual/source/gmp/gmp_signature.rst
    A doc/manual/source/gmp/index.rst
    A doc/manual/source/grid_editor.rst
    A doc/manual/source/idist_combine.rst
    A doc/manual/source/index.rst
    A doc/manual/source/manage_data.rst
    A doc/manual/source/model_editor.rst
    A doc/manual/source/multi-wavelength/index.rst
    A doc/manual/source/multi-wavelength/mwl_species_fit.rst
    A doc/manual/source/multi-wavelength/mwl_species_sim.rst
    A doc/manual/source/multi-wavelength/mwl_spectra.rst
    A doc/manual/source/multi-wavelength/mwlr_viewer.rst
    A doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    A doc/manual/source/pcsa/pcsa.rst
    A doc/manual/source/pcsa/pcsa_adv.rst
    A doc/manual/source/pcsa/pcsa_analys.rst
    A doc/manual/source/pcsa/pcsa_mlines.rst
    A doc/manual/source/pcsa/pcsa_results.rst
    A doc/manual/source/pcsa/pcsa_rpscan.rst
    A doc/manual/source/predict1.rst
    A doc/manual/source/predict2.rst
    A doc/manual/source/pseudo3d.rst
    A doc/manual/source/ramp_data.rst
    A doc/manual/source/register.rst
    A doc/manual/source/reporter.rst
    A doc/manual/source/requirements.txt
    A doc/manual/source/rmsd_query.rst
    A doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    A doc/manual/source/run_details.rst
    A doc/manual/source/sassoc.rst
    A doc/manual/source/second_moment.rst
    A doc/manual/source/simparams.rst
    A doc/manual/source/solutions/index.rst
    A doc/manual/source/solutions/solution_edit.rst
    A doc/manual/source/solutions/solution_new.rst
    A doc/manual/source/solutions/solution_select.rst
    A doc/manual/source/solutions/solution_settings.rst
    A doc/manual/source/start_page-abde.rst
    A doc/manual/source/start_page-dm.rst
    A doc/manual/source/start_page-int.rst
    A doc/manual/source/start_page-mw.rst
    A doc/manual/source/start_page-new.rst
    A doc/manual/source/start_page-rpt.rst
    A doc/manual/source/start_page.rst
    A doc/manual/source/time_derivative.rst
    A doc/manual/source/tmst_viewer.rst
    A doc/manual/source/us_administrator.rst
    A doc/manual/source/us_buoyancy.rst
    A doc/manual/source/us_edit.rst
    A doc/manual/source/us_equiltime.rst
    A doc/manual/source/us_extinction.rst
    A doc/manual/source/us_fds_filemanager.rst
    A doc/manual/source/us_investigator.rst
    A doc/manual/source/us_modelmetrics.rst
    A doc/manual/source/us_project.rst
    A doc/manual/source/us_spectrum.rst
    A doc/manual/source/vhw_combine.rst
    A doc/manual/source/vhw_distrib_plot.rst
    A doc/manual/source/vhw_enhanced.rst
    A doc/manual/source/xpn_viewer.rst
    R doc/manual/template.img.body
    R doc/manual/tidy.conf
    R doc/manual/time_derivative.body
    R doc/manual/ultrascan3.txt
    R doc/manual/us_buffer.body
    R doc/manual/us_edit.body
    R doc/manual/us_edit_mwl.body
    R doc/manual/us_equiltime.body
    R doc/manual/us_fds_filemanager.body
    R doc/manual/us_investigator.body
    R doc/manual/us_modelmetrics.body
    R doc/manual/us_project.body
    R doc/manual/us_solution.body
    R doc/manual/uscol.body
    R doc/manual/uscolor2.body
    R doc/manual/usfont.body
    R doc/manual/usfont2.body
    R doc/manual/vhw_combine.body
    R doc/manual/vhw_distrib_plot.body
    R doc/manual/vhw_enhanced.body
    R doc/manual/wrapped-images.lst
    M etc/etc_belongs_list.txt
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/libus_gui.pro
    M gui/us_abstractrotor_gui.h
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_get_run.h
    M gui/us_help.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.cpp
    M gui/us_model_loader.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_rotor_gui.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    R qwtplot3d/lingua_de.ts
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_extern.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_memory.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_solve_sim.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: e7fc39e0ded8d0a6cfe774a4c39f42f3e26ec5c2
      https://github.com/ehb54/ultrascan3/commit/e7fc39e0ded8d0a6cfe774a4c39f42f3e26ec5c2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro
    M local.pri.template

  Log Message:
  -----------
  Fix macx build: guard -lqwtplot3d self-link and add -lus_utils to libus_gui

local.pri.template: split -lqwtplot3d onto a guarded line so that
when qwtplot3d itself is being built it does not try to link against
its own not-yet-existing library (ld: library not found for -lqwtplot3d).

gui/libus_gui.pro: add macx LIBS += -lus_utils so that the symbols
moved into libus_gui in Nov 2025 (us_csv_loader, us_convert_gui,
us_extinction_gui, etc.) can resolve against libus_utils at link time.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: c81d8b70460860507d201fd8243784999eddf69b
      https://github.com/ehb54/ultrascan3/commit/c81d8b70460860507d201fd8243784999eddf69b
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-907


  Commit: 36f036553bd505b52b7b696575355f3d715ab159
      https://github.com/ehb54/ultrascan3/commit/36f036553bd505b52b7b696575355f3d715ab159
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro
    M local.pri.template

  Log Message:
  -----------
  Merge pull request #446 from ehb54/ehb54-issue-907

Fix macx build: guard -lqwtplot3d self-link and add -lus_utils to libus_gui


  Commit: c7fe1d915db484906fa21f7fdb059dd46ca14e3d
      https://github.com/ehb54/ultrascan3/commit/c7fe1d915db484906fa21f7fdb059dd46ca14e3d
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Delete doc/manual/source/__pycache__/auto_index.cpython-39.pyc


  Commit: 8ed782c9a9b80ae3e81e35cfb88056da7f66986b
      https://github.com/ehb54/ultrascan3/commit/8ed782c9a9b80ae3e81e35cfb88056da7f66986b
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Add Python bytecode files to .gitignore


  Commit: 02b1998e8c4e4190087e112ea223ffc452d892c1
      https://github.com/ehb54/ultrascan3/commit/02b1998e8c4e4190087e112ea223ffc452d892c1
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Merge pull request #447 from ehb54/ehb54-issue-908

Remove Python bytecode files and update .gitignore


  Commit: 2b7ce8e951545aceafde79228ff691ba4b5b2961
      https://github.com/ehb54/ultrascan3/commit/2b7ce8e951545aceafde79228ff691ba4b5b2961
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  revision.sh: limit ? marker to source code file changes only

Previously git diff checked all tracked files, causing the LOCAL_CHANGES
? symbol to appear whenever build scripts, .pri files, or other non-source
files differed from upstream ? including during normal packaging builds.

Restrict the check to file types that produce compiled output:
*.h, *.cpp, *.ui (Qt Designer), *.qrc (Qt resources).

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: a1bf5d7f2eb4649cd5167b42db38d5c6e4aa4d0d
      https://github.com/ehb54/ultrascan3/commit/a1bf5d7f2eb4649cd5167b42db38d5c6e4aa4d0d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  revision.sh: fix pathspec scope for source-file delta check

git diff pathspecs with bare globs (*.h) only match within the current
directory, not repo-wide. Since the script cd's to programs/us/, the
check was missing changes in gui/, utils/, etc.

Fix by running git -C from the repo root so all subdirectories are covered.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 325d0cbff2d496aaf6a42add91e63d096b0e9d26
      https://github.com/ehb54/ultrascan3/commit/325d0cbff2d496aaf6a42add91e63d096b0e9d26
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-909


  Commit: c4a785babca12aa43bf7f624928fa31cf97da1f4
      https://github.com/ehb54/ultrascan3/commit/c4a785babca12aa43bf7f624928fa31cf97da1f4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  Merge pull request #448 from ehb54/ehb54-issue-909

revision.sh: limit ? marker to source code file changes only


  Commit: 45ef026ad65a694d99671bd358216a9d7f7330d3
      https://github.com/ehb54/ultrascan3/commit/45ef026ad65a694d99671bd358216a9d7f7330d3
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
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    M .github/workflows/bump-version.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M admin/cmake/toolchain.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
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    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
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    R doc/manual/gmp/gmp_signature.body
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    R doc/manual/header.us3
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    R doc/manual/images/analytes.png
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    R doc/manual/images/buffer_edit.png
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    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
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    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
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    R doc/manual/images/convert-mwl.png
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    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
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    R doc/manual/images/data_loader-edits.png
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    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
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    R doc/manual/images/densmatch_main.png
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    R doc/manual/images/experiment_cells.png
    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
    R doc/manual/images/fe_match_adv.png
    R doc/manual/images/fe_match_lddat1.png
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    A doc/manual/source/_static/images/us_convert_definedscans.png
    A doc/manual/source/_static/images/us_convert_definesubset.png
    A doc/manual/source/_static/images/us_edit.png
    A doc/manual/source/_static/images/us_edit_mwl.png
    A doc/manual/source/_static/images/us_equiltime.png
    A doc/manual/source/_static/images/us_extinction-0.png
    A doc/manual/source/_static/images/us_extinction-00.png
    A doc/manual/source/_static/images/us_extinction-000.png
    A doc/manual/source/_static/images/us_extinction-1.png
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    A doc/manual/source/_static/images/us_extinction-3.png
    A doc/manual/source/_static/images/us_fds_filemanager-0.png
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    A doc/manual/source/_static/images/us_fds_filemanager-4.png
    A doc/manual/source/_static/images/us_investigator-2.png
    A doc/manual/source/_static/images/us_investigator.png
    A doc/manual/source/_static/images/us_modelmetrics-0.png
    A doc/manual/source/_static/images/us_modmet_report.png
    A doc/manual/source/_static/images/us_project.png
    A doc/manual/source/_static/images/us_project1.png
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    A doc/manual/source/_static/images/us_project_add-supdata.png
    A doc/manual/source/_static/images/us_project_edit-supdata.png
    A doc/manual/source/_static/images/us_project_web.png
    A doc/manual/source/_static/images/us_project_webed.png
    A doc/manual/source/_static/images/us_solution1.png
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    A doc/manual/source/_static/images/us_spectrum-load.png
    A doc/manual/source/_static/images/usfont-1.png
    A doc/manual/source/_static/images/usfont-2.png
    A doc/manual/source/_static/images/vhw_combine-combo.png
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    A doc/manual/source/_static/images/vhw_distribution.png
    A doc/manual/source/_static/images/vhw_enh_groups.png
    A doc/manual/source/_static/images/vhw_enh_groups.png6-33-11.png
    A doc/manual/source/_static/images/vhw_enh_groups_res.png
    A doc/manual/source/_static/images/vhw_enhanced.png
    A doc/manual/source/_static/images/vhw_histogram.png
    A doc/manual/source/_static/images/xpn_report1.png
    A doc/manual/source/_static/images/xpn_report2.png
    A doc/manual/source/_static/images/xpn_viewer-loaded.png
    A doc/manual/source/_static/images/xpn_viewer-saved.png
    A doc/manual/source/_static/images/xpn_viewer.png
    A doc/manual/source/_static/images/zvalue_eq.png
    A doc/manual/source/_static/js/language_data.js
    A doc/manual/source/_static/js/sphinx_highlight.js
    A doc/manual/source/_static/language_data.js
    A doc/manual/source/_static/qthelp.css
    A doc/manual/source/_static/sphinx_highlight.js
    A doc/manual/source/analysprof_general.rst
    A doc/manual/source/analyte/analyte_edit.rst
    A doc/manual/source/analyte/analyte_new.rst
    A doc/manual/source/analyte/analyte_select.rst
    A doc/manual/source/analyte/analyte_settings.rst
    A doc/manual/source/analyte/index.rst
    A doc/manual/source/associations.rst
    A doc/manual/source/astfem_sim.rst
    A doc/manual/source/auto_index.py
    A doc/manual/source/beckman_openauc.rst
    A doc/manual/source/buffer/buffer_edit.rst
    A doc/manual/source/buffer/buffer_new.rst
    A doc/manual/source/buffer/buffer_select.rst
    A doc/manual/source/buffer/buffer_settings.rst
    A doc/manual/source/buffer/index.rst
    A doc/manual/source/buoyancy_editor.rst
    A doc/manual/source/colorgradient.rst
    A doc/manual/source/combine_models.rst
    A doc/manual/source/common_dialogs.rst
    A doc/manual/source/components.rst
    A doc/manual/source/conf.py
    A doc/manual/source/config.rst
    A doc/manual/source/convert.rst
    A doc/manual/source/ddist_combine.rst
    A doc/manual/source/dens_match.rst
    A doc/manual/source/dmga_init.rst
    A doc/manual/source/dmga_init_constr.rst
    A doc/manual/source/experiment/cells.rst
    A doc/manual/source/experiment/general.rst
    A doc/manual/source/experiment/import.rst
    A doc/manual/source/experiment/index.rst
    A doc/manual/source/experiment/liveupdate.rst
    A doc/manual/source/experiment/optics.rst
    A doc/manual/source/experiment/range.rst
    A doc/manual/source/experiment/rotor.rst
    A doc/manual/source/experiment/solutions.rst
    A doc/manual/source/experiment/speeds.rst
    A doc/manual/source/experiment/submit.rst
    A doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    A doc/manual/source/fe_match/fe_match_adv.rst
    A doc/manual/source/fe_match/fe_match_main.rst
    A doc/manual/source/fe_match/fe_match_simulate.rst
    A doc/manual/source/fe_match/index.rst
    A doc/manual/source/fit_meniscus.rst
    A doc/manual/source/ga_initialize.rst
    A doc/manual/source/global_equil.rst
    A doc/manual/source/gmp/gmp.rst
    A doc/manual/source/gmp/gmp_audit_trail.rst
    A doc/manual/source/gmp/gmp_automation.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    A doc/manual/source/gmp/gmp_data_acquisition/index.rst
    A doc/manual/source/gmp/gmp_protocol_development.rst
    A doc/manual/source/gmp/gmp_report_generator.rst
    A doc/manual/source/gmp/gmp_signature.rst
    A doc/manual/source/gmp/index.rst
    A doc/manual/source/grid_editor.rst
    A doc/manual/source/idist_combine.rst
    A doc/manual/source/index.rst
    A doc/manual/source/manage_data.rst
    A doc/manual/source/model_editor.rst
    A doc/manual/source/multi-wavelength/index.rst
    A doc/manual/source/multi-wavelength/mwl_species_fit.rst
    A doc/manual/source/multi-wavelength/mwl_species_sim.rst
    A doc/manual/source/multi-wavelength/mwl_spectra.rst
    A doc/manual/source/multi-wavelength/mwlr_viewer.rst
    A doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    A doc/manual/source/pcsa/pcsa.rst
    A doc/manual/source/pcsa/pcsa_adv.rst
    A doc/manual/source/pcsa/pcsa_analys.rst
    A doc/manual/source/pcsa/pcsa_mlines.rst
    A doc/manual/source/pcsa/pcsa_results.rst
    A doc/manual/source/pcsa/pcsa_rpscan.rst
    A doc/manual/source/predict1.rst
    A doc/manual/source/predict2.rst
    A doc/manual/source/pseudo3d.rst
    A doc/manual/source/ramp_data.rst
    A doc/manual/source/register.rst
    A doc/manual/source/reporter.rst
    A doc/manual/source/requirements.txt
    A doc/manual/source/rmsd_query.rst
    A doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    A doc/manual/source/run_details.rst
    A doc/manual/source/sassoc.rst
    A doc/manual/source/second_moment.rst
    A doc/manual/source/simparams.rst
    A doc/manual/source/solutions/index.rst
    A doc/manual/source/solutions/solution_edit.rst
    A doc/manual/source/solutions/solution_new.rst
    A doc/manual/source/solutions/solution_select.rst
    A doc/manual/source/solutions/solution_settings.rst
    A doc/manual/source/start_page-abde.rst
    A doc/manual/source/start_page-dm.rst
    A doc/manual/source/start_page-int.rst
    A doc/manual/source/start_page-mw.rst
    A doc/manual/source/start_page-new.rst
    A doc/manual/source/start_page-rpt.rst
    A doc/manual/source/start_page.rst
    A doc/manual/source/time_derivative.rst
    A doc/manual/source/tmst_viewer.rst
    A doc/manual/source/us_administrator.rst
    A doc/manual/source/us_buoyancy.rst
    A doc/manual/source/us_edit.rst
    A doc/manual/source/us_equiltime.rst
    A doc/manual/source/us_extinction.rst
    A doc/manual/source/us_fds_filemanager.rst
    A doc/manual/source/us_investigator.rst
    A doc/manual/source/us_modelmetrics.rst
    A doc/manual/source/us_project.rst
    A doc/manual/source/us_spectrum.rst
    A doc/manual/source/vhw_combine.rst
    A doc/manual/source/vhw_distrib_plot.rst
    A doc/manual/source/vhw_enhanced.rst
    A doc/manual/source/xpn_viewer.rst
    R doc/manual/template.img.body
    R doc/manual/tidy.conf
    R doc/manual/time_derivative.body
    R doc/manual/ultrascan3.txt
    R doc/manual/us_buffer.body
    R doc/manual/us_edit.body
    R doc/manual/us_edit_mwl.body
    R doc/manual/us_equiltime.body
    R doc/manual/us_fds_filemanager.body
    R doc/manual/us_investigator.body
    R doc/manual/us_modelmetrics.body
    R doc/manual/us_project.body
    R doc/manual/us_solution.body
    R doc/manual/uscol.body
    R doc/manual/uscolor2.body
    R doc/manual/usfont.body
    R doc/manual/usfont2.body
    R doc/manual/vhw_combine.body
    R doc/manual/vhw_distrib_plot.body
    R doc/manual/vhw_enhanced.body
    R doc/manual/wrapped-images.lst
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_get_run.h
    M gui/us_help.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_properties.cpp
    M gui/us_rotor_gui.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M local.pri.template
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    R qwtplot3d/lingua_de.ts
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    M scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_extern.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_memory.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_solve_sim.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-766


  Commit: 3ba8a99c404673869fe12bb20bdfd05fc1cbb9e9
      https://github.com/ehb54/ultrascan3/commit/3ba8a99c404673869fe12bb20bdfd05fc1cbb9e9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  remove redundant macx{} block in libus_gui.pro

The single-line macx: LIBS already covers this; the block added in
the prior commit was duplicate.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 5b846ae2ba06a1fe8922ca5463989738b9ac9388
      https://github.com/ehb54/ultrascan3/commit/5b846ae2ba06a1fe8922ca5463989738b9ac9388
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  Merge pull request #375 from ehb54/ehb54-issue-766

fix win32 gui link: add version suffix to -lqwtplot3d


  Commit: e42355993bdf8df5f59068aae970ffe9d7447c95
      https://github.com/ehb54/ultrascan3/commit/e42355993bdf8df5f59068aae970ffe9d7447c95
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    M gui/libus_gui.pro
    M local.pri.template
    M programs/us/revision.sh

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: 4102be089f9a53763e66d2b41a5d7ff0a81baee9
      https://github.com/ehb54/ultrascan3/commit/4102be089f9a53763e66d2b41a5d7ff0a81baee9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Fix linux.pl package name generation for new version/revision header format

us_revision.h no longer has a single REVISION field; it now has separate
BUILDNUM/GIT_REVISION/REVISION_DATE/LOCAL_CHANGES fields. The old
"grep REVISION" matched both GIT_REVISION and REVISION_DATE, producing a
multi-line value that broke the generated package directory name and the
shell commands built from it (used by both the redhat and ubuntu release
Dockerfiles). Build the package name from US_Version (utils/us_defines.h)
and BUILDNUM instead.

Fixes ehb54/ultrascan-tickets#910


  Commit: 22905927a67f8bb8637ed325009771296c5b9052
      https://github.com/ehb54/ultrascan3/commit/22905927a67f8bb8637ed325009771296c5b9052
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge pull request #451 from ehb54/ehb54-issue-910

Fix linux.pl package name generation for new version/revision header format


  Commit: 3c4a6a12de6f56ab3ccb0e05512fe01538445686
      https://github.com/ehb54/ultrascan3/commit/3c4a6a12de6f56ab3ccb0e05512fe01538445686
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Fix CodeQL build-target detection: == is not valid in POSIX sh [ ]

The "Calculate Build Targets" step runs under sh (dash), where [ ] only
supports = not ==. Every [ "$X" == "true" ] test errored as "unexpected
operator" and was treated as false, so the full-rebuild branch never ran
even on a push to main with FORCE_ALL=true. This meant CodeQL's analysis
database only ever contained whichever programs happened to be touched
by a given push's diff, causing already-open alerts in untouched files
(e.g. us_spectrum.cpp) to flap between Fixed/Reappeared across unrelated
PRs without the underlying code ever changing.

Fixes ehb54/ultrascan-tickets#911


  Commit: 2bb70f296f3ecc8f762152da20c145583f3d4fc1
      https://github.com/ehb54/ultrascan3/commit/2bb70f296f3ecc8f762152da20c145583f3d4fc1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  Fix remaining CodeQL security alerts: int-multiplication overflow + format arg

Same pattern as PR #435: cast one multiplication operand to qsizetype
before sizing a QVector, so the multiply itself doesn't happen in (32-bit)
int before widening. Also fixes a %d/qsizetype format-specifier mismatch
in us_pcsa_process.cpp.

Fixes ehb54/ultrascan-tickets#912


  Commit: 8ebc45097882afa73f22a184410e310658fca0de
      https://github.com/ehb54/ultrascan3/commit/8ebc45097882afa73f22a184410e310658fca0de
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: 733d3f549696b0efe49cd26d0840bdf6ab37d5e7
      https://github.com/ehb54/ultrascan3/commit/733d3f549696b0efe49cd26d0840bdf6ab37d5e7
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge pull request #445 from ehb54/bump-to-v4.1.0

Bump to v4.1.0


  Commit: 951770eef3cf63893454a5402ccb79e4a64062db
      https://github.com/ehb54/ultrascan3/commit/951770eef3cf63893454a5402ccb79e4a64062db
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-911


  Commit: d981490e29291aa7d6124604cc0ea33dcc753df3
      https://github.com/ehb54/ultrascan3/commit/d981490e29291aa7d6124604cc0ea33dcc753df3
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Merge pull request #452 from ehb54/ehb54-issue-911

Fix CodeQL build-target detection (sh != bash, == in [ ])


  Commit: cb2753416846b0e812f495ef4a5f2161dd35280c
      https://github.com/ehb54/ultrascan3/commit/cb2753416846b0e812f495ef4a5f2161dd35280c
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-912


  Commit: e3b3099b8aaebbe3c4fc5ddb2e7acb7186893133
      https://github.com/ehb54/ultrascan3/commit/e3b3099b8aaebbe3c4fc5ddb2e7acb7186893133
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  Merge pull request #453 from ehb54/ehb54-issue-912

Fix remaining CodeQL security alerts (multiplication overflow + format arg)


  Commit: d689ce8f674d78d26e7bff34f3928a4950f933af
      https://github.com/ehb54/ultrascan3/commit/d689ce8f674d78d26e7bff34f3928a4950f933af
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Robustly detect sphinx-build/python3 for DOMAN doc build on RHEL8

RHEL8 variants ship a too-old default python3 (3.6) plus optional
python3.11/python3.12 packages with no sphinx-build shim on PATH,
so the existing "which sphinx-build" check frequently misses a
working installation. Search candidate interpreters newest-first,
self-install Sphinx via ensurepip/pip if needed, and shim a scoped
python3 symlink on PATH only for the doc make step when the chosen
interpreter isn't named python3.

Fixes ultrascan-tickets#925


  Commit: f41aa3fd5b8d0ec601363a640f3b964ba85b1e51
      https://github.com/ehb54/ultrascan3/commit/f41aa3fd5b8d0ec601363a640f3b964ba85b1e51
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Reject Python interpreters too old for conf.py in DOMAN detection

doc/manual/source/conf.py uses Python >=3.9 syntax (PEP 585 builtin
generics, e.g. "list[str]"). The find_doc_python() search only checked
"import sphinx" succeeding, so a too-old default python3 (e.g. RHEL's
3.6) with a stale manually pip-installed Sphinx from before this
script existed got picked over a usable python3.11/python3.12 on the
same host, and the build then crashed in conf.py with "TypeError:
'type' object is not subscriptable". Add an explicit version check
that rejects any candidate interpreter below 3.9 before checking for
or installing Sphinx.

ehb54/ultrascan-tickets#925


  Commit: 18e656c09220a8883e1755f461737db76d91c710
      https://github.com/ehb54/ultrascan3/commit/18e656c09220a8883e1755f461737db76d91c710
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Drop --upgrade from ensurepip call in DOMAN detection

"ensurepip --upgrade" bootstraps pip from the bundled wheel and then
has pip upgrade itself from PyPI, which fails outright on
network-restricted hosts. Plain "ensurepip" only installs the bundled
wheel (fully offline) and is all that's needed to get a working pip
module before installing doc/manual/source/requirements.txt.

ehb54/ultrascan-tickets#925


  Commit: 25987d47541a67eb9c6168d741326e47ede154b9
      https://github.com/ehb54/ultrascan3/commit/25987d47541a67eb9c6168d741326e47ede154b9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Fix DOMAN fast path to check python3, not sphinx-build

doc/manual/Makefile invokes the interpreter as plain "python3"
(SPHINXBUILD ?= python3 -m sphinx), not "sphinx-build". The previous
fast path checked "sphinx-build --version" and returned immediately on
success, but an unrelated sphinx-build entry-point script tied to some
other (possibly too-old) interpreter can be on PATH and "work" -- since
--version never touches conf.py -- while "python3 -m sphinx" still
fails. This bypassed the version-gated python3.X search entirely and
explains why the previous DOMAN fixes had no effect on a host with a
stale sphinx-build shim left over from a manual "pip install --user"
under python3.6. Check bare python3 directly instead.

ehb54/ultrascan-tickets#925


  Commit: c71f3b106e12d2e2c40ee77a9695bee1793ff680
      https://github.com/ehb54/ultrascan3/commit/c71f3b106e12d2e2c40ee77a9695bee1793ff680
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Merge pull request #457 from ehb54/ehb54-issue-925

makeall.sh: robust sphinx/python3 detection for DOMAN on RHEL8 variants


  Commit: 6d06a0c1b49dfa1141dc8625e75bc03918635a40
      https://github.com/ehb54/ultrascan3/commit/6d06a0c1b49dfa1141dc8625e75bc03918635a40
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Include LICENSE.txt in Linux release packages

The Linux tar.xz packaging script never copied LICENSE.txt into the
package, unlike the Windows packaging script which does. Add the same
copy step so Linux packages ship a license file too.

Fixes ehb54/ultrascan-tickets#868


  Commit: c67d82488c7f281c78458954341098446e6baea0
      https://github.com/ehb54/ultrascan3/commit/c67d82488c7f281c78458954341098446e6baea0
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge pull request #458 from ehb54/ehb54-issue-868

Include LICENSE.txt in Linux release packages


  Commit: e47a1e408f3d0ac6a7db58fdf0cab65ab3b30a6f
      https://github.com/ehb54/ultrascan3/commit/e47a1e408f3d0ac6a7db58fdf0cab65ab3b30a6f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP-dataDisk: 1. EXP: 5. Solutions -- exclude (unspecified) item in all solution cahnnels for uploaded form disk data...


  Commit: 8a9c0cc6be7aaf9304035a342cbaeaba80e24135
      https://github.com/ehb54/ultrascan3/commit/8a9c0cc6be7aaf9304035a342cbaeaba80e24135
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #459 from ehb54/alexey-dev-issue929

GMP-dataDisk: 1. EXP: 5. Solutions -- exclude (unspecified) item in all solution cahnnels for uploaded form disk data...


  Commit: ed7f5a0cdf313c3337076a886caebe0f469d88a7
      https://github.com/ehb54/ultrascan3/commit/ed7f5a0cdf313c3337076a886caebe0f469d88a7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: 888dfa5cada04313f4e905ecab395a6080a7ad24
      https://github.com/ehb54/ultrascan3/commit/888dfa5cada04313f4e905ecab395a6080a7ad24
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  [edited mesage]Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: edda3c63be4e85f9fde90d971bf72dd1e184c1aa
      https://github.com/ehb54/ultrascan3/commit/edda3c63be4e85f9fde90d971bf72dd1e184c1aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge pull request #460 from ehb54/alexey-dev-issue928

Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: b9470a9bb9ca3b1859b7f798fa5f5e76a33a99ab
      https://github.com/ehb54/ultrascan3/commit/b9470a9bb9ca3b1859b7f798fa5f5e76a33a99ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: f0244186bf701788c6e7bc3915a4cca84aabe865
      https://github.com/ehb54/ultrascan3/commit/f0244186bf701788c6e7bc3915a4cca84aabe865
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue932


  Commit: 16b34f7a8252e4af4fbca5ebbd01f38bbb376beb
      https://github.com/ehb54/ultrascan3/commit/16b34f7a8252e4af4fbca5ebbd01f38bbb376beb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  [add connection check when attemting to Save]Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: 9c0f94c5d0a9f09a78152c7c5862b7f2e9a8bf6b
      https://github.com/ehb54/ultrascan3/commit/9c0f94c5d0a9f09a78152c7c5862b7f2e9a8bf6b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge branch 'alexey-dev-issue932' of github.com:ehb54/ultrascan3 into alexey-dev-issue932


  Commit: fb0e0bd78e483abe98e103bc0093440b38c5c669
      https://github.com/ehb54/ultrascan3/commit/fb0e0bd78e483abe98e103bc0093440b38c5c669
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  [[1]add connection check when attemting to Save]Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: 5732996f335aec054f71c4e536a044841eb385b5
      https://github.com/ehb54/ultrascan3/commit/5732996f335aec054f71c4e536a044841eb385b5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Merge pull request #461 from ehb54/alexey-dev-issue932

Preferences: Database -> Change: enable Save Entry button for any existing or new entries only after Test Connection is successful.


  Commit: 0d4d8870eb492684324b6bc7a5a39ca6b12c1c63
      https://github.com/ehb54/ultrascan3/commit/0d4d8870eb492684324b6bc7a5a39ca6b12c1c63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  US: hide "GMP" menu item for MacOS only...


  Commit: 1dd7a098a12171044289211cd22079f8b12f527d
      https://github.com/ehb54/ultrascan3/commit/1dd7a098a12171044289211cd22079f8b12f527d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  US: hide "Utilitoes->Data Acqusition" menu item for MacOS only...


  Commit: 37dfa3e81496bc5667af8082527f5ea1065c8133
      https://github.com/ehb54/ultrascan3/commit/37dfa3e81496bc5667af8082527f5ea1065c8133
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Merge pull request #462 from ehb54/alexey-dev-issue935

US: hide "GMP" menu item for MacOS only...


  Commit: 7eb866b9fcef86510463852edf2b6db9c2010dce
      https://github.com/ehb54/ultrascan3/commit/7eb866b9fcef86510463852edf2b6db9c2010dce
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-27 (Sat, 27 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix: restrict Sphinx dirty-check to source files to match revision.sh

The conf.py generate_version_metadata() was running git diff against all
tracked files with no path filter. On a macOS release build, a non-source
file (doc, script, etc.) was modified, causing conf.py to mark the build
dirty and embed ? in the Qt Help namespace/version string ? even though
revision.sh (splash screen) correctly showed no dirty flag because it
already restricts to *.h *.cpp *.ui *.qrc.

Fix: add the same -- *.h *.cpp *.ui *.qrc pathspec filter to both git diff
calls in conf.py so the dirty indicator is consistent with revision.sh.

Closes #936

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 52636d73ba151811a714c312eaae23119fbc3e22
      https://github.com/ehb54/ultrascan3/commit/52636d73ba151811a714c312eaae23119fbc3e22
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Merge pull request #464 from ehb54/issue-936

fix: restrict Sphinx dirty-check to source files (issue #936)


  Commit: 9153af9e9169c5ea50ab39f1e8b9a6c1cd6859bc
      https://github.com/ehb54/ultrascan3/commit/9153af9e9169c5ea50ab39f1e8b9a6c1cd6859bc
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix: change qthelp namespace from org.sphinx to com.aucsolutions

Closes ehb54/ultrascan-tickets#939

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: cc6eed0f49f97edb31642145d1c9757b4d7f5a53
      https://github.com/ehb54/ultrascan3/commit/cc6eed0f49f97edb31642145d1c9757b4d7f5a53
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into issue-939


  Commit: a22f52e0935d5bb7994769ffb9401e352f5bb3cf
      https://github.com/ehb54/ultrascan3/commit/a22f52e0935d5bb7994769ffb9401e352f5bb3cf
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Merge pull request #466 from ehb54/issue-939

fix: change qthelp namespace from org.sphinx to com.aucsolutions


  Commit: eb825d66df4c5c3e0841f6cd6a56571b29889a3c
      https://github.com/ehb54/ultrascan3/commit/eb825d66df4c5c3e0841f6cd6a56571b29889a3c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Skip explicit cipher list on MSYS2/64 Windows builds (#940)

MSYS2/64 (MINGW64) Windows builds link a Schannel-backed libmariadb,
which fails to match any suite from the OpenSSL-style CIPHER list:
"TLS/SSL error: no cipher match Error 0x80090331
(SEC_E_ALGORITHM_MISMATCH)".

Rather than imposing a substitute OpenSSL-style cipher string that
Schannel may or may not understand, skip calling
mysql_options(MYSQL_OPT_SSL_CIPHER, ...) entirely on __MINGW64__ and
let the backend negotiate its own default cipher suite set. This is a
workaround pending the real fix of linking an OpenSSL-backed MariaDB
Connector/C on Windows.

MSVC/vcpkg builds and Linux/macOS builds are unaffected (__MINGW64__
is not defined there).

Fixes ehb54/ultrascan-tickets#940

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 55e94a0e3813f79d50549bd166d3cf26934208c0
      https://github.com/ehb54/ultrascan3/commit/55e94a0e3813f79d50549bd166d3cf26934208c0
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M gui/us_help.cpp
    M utils/us_settings.cpp

  Log Message:
  -----------
  fix: update browser settings handling for MacOS and Windows


  Commit: d099a4448e73330af2c3bd0fc9ec64a435bf7d2a
      https://github.com/ehb54/ultrascan3/commit/d099a4448e73330af2c3bd0fc9ec64a435bf7d2a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_settings.cpp

  Log Message:
  -----------
  fix: initialize status variable to zero in us_settings.cpp


  Commit: 6fc2e4866baf59178b492f7e345fb36de180ebd8
      https://github.com/ehb54/ultrascan3/commit/6fc2e4866baf59178b492f7e345fb36de180ebd8
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    A .github/gtest-us.json
    A .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    A VERSION
    M admin/cmake/FindQwt.cmake
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    A admin/cmake/triplets/x64-mingw-dynamic.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    M admin/release/linux.pl
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/drop-wmf-plugin.patch
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-multimedia/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-pkgconfig-qt5uiplugin-not-found.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/fix-spawnvp-argv.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/libclang.patch
    A buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qt5-tools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/config.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/fix_dll_install.patch
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt5/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
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    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
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    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
    R doc/manual/ga_initialize.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
    R doc/manual/images/color-1.png
    R doc/manual/images/color-2.png
    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
    R doc/manual/images/colorgrad1.png
    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
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    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
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    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
    R doc/manual/images/densmatch_mpars_empty.png
    R doc/manual/images/densmatch_rmvmodels.png
    R doc/manual/images/eq1-mean.png
    R doc/manual/images/eq2-skew.png
    R doc/manual/images/eq3-kurtosis.png
    R doc/manual/images/eq4-moments.png
    R doc/manual/images/eq5-variance.png
    R doc/manual/images/eq6-stddev.png
    R doc/manual/images/eq7-probsigma.png
    R doc/manual/images/eq8-confidence.png
    R doc/manual/images/experiment_cells.png
    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
    R doc/manual/images/fe_match_adv.png
    R doc/manual/images/fe_match_lddat1.png
    R doc/manual/images/fe_match_lddat2.png
    R doc/manual/images/fe_match_lddat3.png
    R doc/manual/images/fe_match_lddat4.png
    R doc/manual/images/fe_match_ra.png
    R doc/manual/images/fe_match_resplot.png
    R doc/manual/images/fe_match_sim1.png
    R doc/manual/images/fe_match_sim2.png
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    R doc/manual/images/fit_men-editupd.png
    R doc/manual/images/fit_men-load.png
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    R doc/manual/images/ga_initialize.png
    R doc/manual/images/gmp/audit_trail/gmp_audit_trail_01.png
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    M etc/etc_belongs_list.txt
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    M gui/us_extinctfitter_gui.cpp
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    M gui/us_get_run.cpp
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    M gui/us_images.cpp
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    M gui/us_investigator.cpp
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    M gui/us_load_auc.h
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    M gui/us_model_loader.cpp
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    M gui/us_mwl_data.cpp
    M gui/us_new_spectrum.cpp
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    M gui/us_passwd.cpp
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    M gui/us_select_edits.h
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    M gui/us_select_triples.h
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    M gui/us_solution_gui.cpp
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    M gui/us_spectrodata.cpp
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    M local.pri.template
    M makeall.sh
    A pkg/macos/README.md
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    M programs/CMakeLists.txt
    M programs/main1.inc
    M programs/us/CMakeLists.txt
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    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
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    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    R qwtplot3d/lingua_de.ts
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_defines.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_experiment.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #469 from ehb54/main

Merge main into somo-qt6


  Commit: 005210ec1222cf2098477fef7cbc62cdfdb1c08b
      https://github.com/ehb54/ultrascan3/commit/005210ec1222cf2098477fef7cbc62cdfdb1c08b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp

  Log Message:
  -----------
  Address PR #335 review feedback from doluk

- Qt::WFlags -> Qt::WindowFlags (lightingdlgbase.h)
- inline the const-wrapper save_svg overload (us3i_gui_util.cpp)
- drop dead Qt3/4 QT_VERSION include guard (us_config.cpp)
- hoist repeated regex construction to static const in
  fileNameCheck (us_hydrodyn.cpp), anaflex txt-extension checks
  (us_hydrodyn_anaflex_core.cpp), and the leading-'=' strip in
  US_Hydrodyn_Best::load (us_hydrodyn_best.cpp)
- move QRegularExpression include next to other Qt includes and
  simplify rx_spaces construction (us_hydrodyn_addresidue.cpp)
- remove duplicate QRegularExpression include (us_hydrodyn_bd_core.cpp)
- combine QRegularExpression rx construction with its pattern and
  drop the now-redundant setPattern call (us_hydrodyn_beads_load.cpp)


  Commit: dd1a79e3b1c92c841119387bd1da9de25d53ade4
      https://github.com/ehb54/ultrascan3/commit/dd1a79e3b1c92c841119387bd1da9de25d53ade4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge pull request #467 from ehb54/ehb54-issue-940

Fix Schannel TLS cipher mismatch on MSYS2/64 Windows builds


  Commit: 73d10e1ac2511df9f115150909f8efa4e15e2aa9
      https://github.com/ehb54/ultrascan3/commit/73d10e1ac2511df9f115150909f8efa4e15e2aa9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


  Commit: 4dd383414126596486f0a9d7f4a2594aa26cbbb2
      https://github.com/ehb54/ultrascan3/commit/4dd383414126596486f0a9d7f4a2594aa26cbbb2
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 67350cbc9b652fe2183c4a6889631191739a5cdb
      https://github.com/ehb54/ultrascan3/commit/67350cbc9b652fe2183c4a6889631191739a5cdb
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #335 from ehb54/somo-qt6

somo qt6 branch - initial commit from somo-dev


  Commit: 5924b0fe87a290c4e598e447b28d84cdc4780865
      https://github.com/ehb54/ultrascan3/commit/5924b0fe87a290c4e598e447b28d84cdc4780865
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


  Commit: c31386b4ac5c903cb5949ed662b915274aed6658
      https://github.com/ehb54/ultrascan3/commit/c31386b4ac5c903cb5949ed662b915274aed6658
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M gui/us_help.cpp
    M utils/us_settings.cpp

  Log Message:
  -----------
  Merge pull request #468 from ehb54/issue-941

fix: update browser settings handling for MacOS and Windows


  Commit: 72beec81ceb5c976e3987b559b8914bad2d88a06
      https://github.com/ehb54/ultrascan3/commit/72beec81ceb5c976e3987b559b8914bad2d88a06
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-06 (Mon, 06 Jul 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    A VERSION
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M admin/codeql/docker/local.pri.somo
    M admin/release/linux.pl
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/delseltrip.png
    A doc/manual/source/_static/images/dmga-save.png
    A doc/manual/source/_static/images/dmga.png
    A doc/manual/source/_static/images/dmga_constr.png
    A doc/manual/source/_static/images/edit_exclude_scan.png
    A doc/manual/source/_static/images/edit_scan.png
    A doc/manual/source/_static/images/fe_dmga_adv.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/select_prefilt.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    A doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_select.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/components.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dens_match.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/cells.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/optics.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/experiment/submit.rst
    M doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    A doc/manual/source/global_equil.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/model_editor.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_adv.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    A doc/manual/source/ramp_data.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    A doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/libus_gui.pro
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_get_run.h
    M gui/us_help.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_properties.cpp
    M gui/us_rotor_gui.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M local.pri.template
    M makeall.sh
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    A test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M utils/CMakeLists.txt
    M utils/us_buffer.h
    M utils/us_db2.cpp
    M utils/us_defines.h
    M utils/us_extern.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_run_protocol.cpp
    M utils/us_settings.cpp
    M utils/us_solve_sim.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/us_branch_python_venv


Compare: https://github.com/ehb54/ultrascan3/compare/e992b5f9eb5f...72beec81ceb5

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From noreply at github.com  Mon Jul  6 10:06:58 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 06 Jul 2026 09:06:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 37703a: somo qt6 branch - initial
 commit from somo-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/800-enhancement-nightly-build-using-vcpkg/32aff3-0e41a2@github.com>

  Branch: refs/heads/800-enhancement-nightly-build-using-vcpkg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
      https://github.com/ehb54/ultrascan3/commit/37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 9cc80a805f0c89d30fd663cffa4e544bdccfddd6
      https://github.com/ehb54/ultrascan3/commit/9cc80a805f0c89d30fd663cffa4e544bdccfddd6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql debug info


  Commit: 8f49d1cadd471936ba76ad95fe0001436a3685a7
      https://github.com/ehb54/ultrascan3/commit/8f49d1cadd471936ba76ad95fe0001436a3685a7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M us_somo/develop/libus_somo.pro

  Log Message:
  -----------
  remove us_color from libus_somo


  Commit: 642330d0e7562d863f6471b57e528cdf5aec013c
      https://github.com/ehb54/ultrascan3/commit/642330d0e7562d863f6471b57e528cdf5aec013c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
      https://github.com/ehb54/ultrascan3/commit/fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 1a808d5061ef553acf0aa97a83c04af9d82970bc
      https://github.com/ehb54/ultrascan3/commit/1a808d5061ef553acf0aa97a83c04af9d82970bc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  additional debugs, temp relax deprecations


  Commit: 24783d42d61d7132dd5622e8027c9f6f59de5608
      https://github.com/ehb54/ultrascan3/commit/24783d42d61d7132dd5622e8027c9f6f59de5608
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  restore deprecations


  Commit: c37b59afbb01c067585c5da09c200e295282decc
      https://github.com/ehb54/ultrascan3/commit/c37b59afbb01c067585c5da09c200e295282decc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 59ba4be5192bd4024037ed7173a13061a59c41ce
      https://github.com/ehb54/ultrascan3/commit/59ba4be5192bd4024037ed7173a13061a59c41ce
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  codeql fix


  Commit: cfd59439653a91b6cdcfd88d8a348ccb934a6cba
      https://github.com/ehb54/ultrascan3/commit/cfd59439653a91b6cdcfd88d8a348ccb934a6cba
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


  Commit: 46434a20d02da7dd7cb8edb14455747838aae8e4
      https://github.com/ehb54/ultrascan3/commit/46434a20d02da7dd7cb8edb14455747838aae8e4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  relax somo error for test


  Commit: 4bafd3f55ff93229f51bcd4cd0ece35195af707c
      https://github.com/ehb54/ultrascan3/commit/4bafd3f55ff93229f51bcd4cd0ece35195af707c
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Update compiler flags and defines in local.pri.somo


  Commit: a7e3fd4276bf018f3e37d73c4e11598037b8d409
      https://github.com/ehb54/ultrascan3/commit/a7e3fd4276bf018f3e37d73c4e11598037b8d409
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo datetime dirhist fix


  Commit: 34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
      https://github.com/ehb54/ultrascan3/commit/34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Clean up deprecated warning flags in local.pri.somo

Removed deprecated warning definitions for Qt.


  Commit: 87377fece32656c6472a465a06493b17084169fe
      https://github.com/ehb54/ultrascan3/commit/87377fece32656c6472a465a06493b17084169fe
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 8886d756072fc33f5d8db65458bae9bd00574c52
      https://github.com/ehb54/ultrascan3/commit/8886d756072fc33f5d8db65458bae9bd00574c52
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-01-19 (Mon, 19 Jan 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp

  Log Message:
  -----------
  somo qt6 compat regex bugfix


  Commit: 000572b4470833c4cd55dc8c07bfe30eadfb08f0
      https://github.com/ehb54/ultrascan3/commit/000572b4470833c4cd55dc8c07bfe30eadfb08f0
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-01-24 (Sat, 24 Jan 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Bump version to 4.1.0


  Commit: 63ddc08f86dd138595c248e3ec8653b3e4640132
      https://github.com/ehb54/ultrascan3/commit/63ddc08f86dd138595c248e3ec8653b3e4640132
  Author: ehb <ehb at ehbs-MacBook-Pro.local>
  Date:   2026-02-25 (Wed, 25 Feb 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  restore macx:LIBS, expected for OSX package pipeline


  Commit: 42f2fd0ef0f999defd30ec52c17df8d7acf8ccef
      https://github.com/ehb54/ultrascan3/commit/42f2fd0ef0f999defd30ec52c17df8d7acf8ccef
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-02-25 (Wed, 25 Feb 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  add VER to qwtplot3d


  Commit: d65cc7b90bd9cfd09a504b97d1e991b5e9709798
      https://github.com/ehb54/ultrascan3/commit/d65cc7b90bd9cfd09a504b97d1e991b5e9709798
  Author: Saeed <github.com/samo38>
  Date:   2026-05-26 (Tue, 26 May 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  fix the ct_plt range for D values


  Commit: 4d55ef620df76f15f779937d88eae46dc5476934
      https://github.com/ehb54/ultrascan3/commit/4d55ef620df76f15f779937d88eae46dc5476934
  Author: Saeed <github.com/samo38>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  us_pseudo3d_combine.cpp: update ct range


  Commit: bfbbceba435317993ba1177f8d6ed0a5810550da
      https://github.com/ehb54/ultrascan3/commit/bfbbceba435317993ba1177f8d6ed0a5810550da
  Author: Saeed <github.com/samo38>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  update ct range


  Commit: 081a9573c4b25b4a1160d69485efb294378d580d
      https://github.com/ehb54/ultrascan3/commit/081a9573c4b25b4a1160d69485efb294378d580d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge branch 'main' into t842_gaplot


  Commit: 6cf1e2de27f3dc7a74383050c085f36898bb156b
      https://github.com/ehb54/ultrascan3/commit/6cf1e2de27f3dc7a74383050c085f36898bb156b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  GMP, R&D -- correct interplay between scan counts, scan interval, minimum scan interval in 3. Sppeds and 7. Ranges ...


  Commit: 5ce35ace4e6f0bd6eb3de4111d93a0c754c613e8
      https://github.com/ehb54/ultrascan3/commit/5ce35ace4e6f0bd6eb3de4111d93a0c754c613e8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  GMP, R&D -- The first sentence after Attention should not have started with a period. Line should have started with "Please..."....


  Commit: 439bf47d73c1de196a1c091f8629403731ac42e6
      https://github.com/ehb54/ultrascan3/commit/439bf47d73c1de196a1c091f8629403731ac42e6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  Merge pull request #432 from ehb54/alexey-dev-issue873

GMP, R&D -- The first sentence after Attention should not have started with a period. Line should have started with "Please..."....


  Commit: c70b0809570e8451264f061bfddbf0d90ed7d45b
      https://github.com/ehb54/ultrascan3/commit/c70b0809570e8451264f061bfddbf0d90ed7d45b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-05 (Fri, 05 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue874


  Commit: ab4e29f258a4a76852473bb029a8d05af5101e3b
      https://github.com/ehb54/ultrascan3/commit/ab4e29f258a4a76852473bb029a8d05af5101e3b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-07 (Sun, 07 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge pull request #431 from ehb54/alexey-dev-issue874

GMP, R&D -- correct interplay between scan counts, scan interval, min. scan interval


  Commit: b3e1c3148e849dfa0bb3115413e07983b919844e
      https://github.com/ehb54/ultrascan3/commit/b3e1c3148e849dfa0bb3115413e07983b919844e
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  add a label to show the buffer manual state


  Commit: f9dc1123f5d504527a1a5a5f98992c035cda5368
      https://github.com/ehb54/ultrascan3/commit/f9dc1123f5d504527a1a5a5f98992c035cda5368
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 372d4a9b863855920c8f9fcc63e1e874250bcdae
      https://github.com/ehb54/ultrascan3/commit/372d4a9b863855920c8f9fcc63e1e874250bcdae
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  auto scale xy after selecting a new parameter


  Commit: c00094277c02fa9f1bbf1ea45e6c392960605b9e
      https://github.com/ehb54/ultrascan3/commit/c00094277c02fa9f1bbf1ea45e6c392960605b9e
  Author: Saeed <github.com/samo38>
  Date:   2026-06-08 (Mon, 08 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M gui/us_extinction_gui.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_properties.cpp
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: f28a5e62b10d404ecce483e3109f42b1623253c4
      https://github.com/ehb54/ultrascan3/commit/f28a5e62b10d404ecce483e3109f42b1623253c4
  Author: Saeed <github.com/samo38>
  Date:   2026-06-09 (Tue, 09 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  fixed type cast warnings in us_mpi_analysis.cpp, ga_worker.cpp


  Commit: f3611e7f434e44d3d1c61e7d0e945a94035388f9
      https://github.com/ehb54/ultrascan3/commit/f3611e7f434e44d3d1c61e7d0e945a94035388f9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge pull request #435 from samo38/t861_security_warn

clean security warnings


  Commit: f80b73498a4973369419673e90274f59d9b598b3
      https://github.com/ehb54/ultrascan3/commit/f80b73498a4973369419673e90274f59d9b598b3
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 3dddb9117fd90c1f6e1fdeec16f309bcc7b74a10
      https://github.com/ehb54/ultrascan3/commit/3dddb9117fd90c1f6e1fdeec16f309bcc7b74a10
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: bde95ecaf2c093c38c510529ade5c772aeb0d058
      https://github.com/ehb54/ultrascan3/commit/bde95ecaf2c093c38c510529ade5c772aeb0d058
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 5be7ae9df7ec29fa88487a9dc72834ca6c3ab515
      https://github.com/ehb54/ultrascan3/commit/5be7ae9df7ec29fa88487a9dc72834ca6c3ab515
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_config/us_newxpnhost_db.cpp

  Log Message:
  -----------
  US_Config:Intruments -- incorporate test_Connectivity into Save routing, remove extra connectivity check step...


  Commit: 32473b578707e256cf293eb356d873413dd769b6
      https://github.com/ehb54/ultrascan3/commit/32473b578707e256cf293eb356d873413dd769b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_config/us_newxpnhost_db.cpp

  Log Message:
  -----------
  Merge pull request #436 from ehb54/alexey-dev-issue882

US_Config:Intruments -- incorporate test_Connectivity into Save routing


  Commit: 4aec245df7e6c8b1e030e812298d6cba7cab845e
      https://github.com/ehb54/ultrascan3/commit/4aec245df7e6c8b1e030e812298d6cba7cab845e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  GMP: 2. LIVE_UPDATE -- spelling error fixed...


  Commit: 12f71524c0445a97e2b0b1aaf3d53f6736ea6301
      https://github.com/ehb54/ultrascan3/commit/12f71524c0445a97e2b0b1aaf3d53f6736ea6301
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-10 (Wed, 10 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  GMP: -- modify message for marking run as FAILED/NPT FAILED...


  Commit: 3c7169cde650dedca3d3402f744d3253f88868d5
      https://github.com/ehb54/ultrascan3/commit/3c7169cde650dedca3d3402f744d3253f88868d5
  Author: Saeed <github.com/samo38>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M scripts/build.ps1
    M scripts/build.sh
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_solve_sim.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 1be10ca817665f8309bb3df08852200424397547
      https://github.com/ehb54/ultrascan3/commit/1be10ca817665f8309bb3df08852200424397547
  Author: Saeed <github.com/samo38>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/t842_gaplot' into t842_gaplot


  Commit: 6a2abeacf5fcb63c4355bea33d0a8665ebf1aea3
      https://github.com/ehb54/ultrascan3/commit/6a2abeacf5fcb63c4355bea33d0a8665ebf1aea3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  GMP main window -- modify text in the upper textarea...


  Commit: 3fbee9fcc1783c2c585c16e2fe0cdb6c22982a61
      https://github.com/ehb54/ultrascan3/commit/3fbee9fcc1783c2c585c16e2fe0cdb6c22982a61
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  [1]GMP main window -- modify text in the upper textarea...


  Commit: 290881f0fb957f5129113ca6c0d363cda44d453e
      https://github.com/ehb54/ultrascan3/commit/290881f0fb957f5129113ca6c0d363cda44d453e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge pull request #437 from ehb54/alexey-dev-issue885

GMP: 2. LIVE_UPDATE -- spelling error fixed...


  Commit: 51eac7bb6878f0d5e5b586795486cea3043d3d0c
      https://github.com/ehb54/ultrascan3/commit/51eac7bb6878f0d5e5b586795486cea3043d3d0c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue887


  Commit: 27153f63f856b1d20b1465999a14d3e3281e707a
      https://github.com/ehb54/ultrascan3/commit/27153f63f856b1d20b1465999a14d3e3281e707a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-11 (Thu, 11 Jun 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue886


  Commit: 4241a57028574e3cd23f3c3291191974fc72a7f5
      https://github.com/ehb54/ultrascan3/commit/4241a57028574e3cd23f3c3291191974fc72a7f5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge pull request #438 from ehb54/alexey-dev-issue887

GMP: -- modify message for marking run as FAILED/NOT FAILED...


  Commit: 5b1e1e57275a9d2d7788c8c73c68af8bffc728aa
      https://github.com/ehb54/ultrascan3/commit/5b1e1e57275a9d2d7788c8c73c68af8bffc728aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue886


  Commit: 1b9d32c8d947abd0215b70dbe7495fc98759a47b
      https://github.com/ehb54/ultrascan3/commit/1b9d32c8d947abd0215b70dbe7495fc98759a47b
  Author: Saeed <github.com/samo38>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  update the ct range by data


  Commit: 1f2dea5900a814f27165ae2bc9b401c3dfee187c
      https://github.com/ehb54/ultrascan3/commit/1f2dea5900a814f27165ae2bc9b401c3dfee187c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp

  Log Message:
  -----------
  Merge pull request #439 from ehb54/alexey-dev-issue886

GMP main window -- modify text in the upper textarea...


  Commit: 5e1874151de9b54802972297c327c677ea4ed1c9
      https://github.com/ehb54/ultrascan3/commit/5e1874151de9b54802972297c327c677ea4ed1c9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-12 (Fri, 12 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: cbb216d0d629fbbe7c3294431c08f61989b2e7a2
      https://github.com/ehb54/ultrascan3/commit/cbb216d0d629fbbe7c3294431c08f61989b2e7a2
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  upadte ct x and y in the set_limits()


  Commit: 67a4d242dabc14876d9354b93434c818b5baf7ec
      https://github.com/ehb54/ultrascan3/commit/67a4d242dabc14876d9354b93434c818b5baf7ec
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M gui/us_spectrodata.cpp

  Log Message:
  -----------
  in the setRaster function, if xrng becomes 0, xinc becomes INF. The same approach for xrng is applied here.


  Commit: 6f904c41c021e36595b930817137f19ef8ccce19
      https://github.com/ehb54/ultrascan3/commit/6f904c41c021e36595b930817137f19ef8ccce19
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  connect the replot_data function to the pb_refresh


  Commit: c24e05faa744af2d76beb4c61148bc79fa771670
      https://github.com/ehb54/ultrascan3/commit/c24e05faa744af2d76beb4c61148bc79fa771670
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  fixed the issue with draw bins manually


  Commit: 959da46aacd3efb25d3f0a0009e3da52819f733b
      https://github.com/ehb54/ultrascan3/commit/959da46aacd3efb25d3f0a0009e3da52819f733b
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: 32feaefb494d632b390d9acb54c6daefdd47089b
      https://github.com/ehb54/ultrascan3/commit/32feaefb494d632b390d9acb54c6daefdd47089b
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-13 (Sat, 13 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  set range of ct by data


  Commit: 9c70967b72e22425120bb3e0971e49e2cab828a2
      https://github.com/ehb54/ultrascan3/commit/9c70967b72e22425120bb3e0971e49e2cab828a2
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t870_buffer


  Commit: 0678091c6b8ea3a347d8bda5c1f8887a6d3ee65b
      https://github.com/ehb54/ultrascan3/commit/0678091c6b8ea3a347d8bda5c1f8887a6d3ee65b
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h

  Log Message:
  -----------
  Merge pull request #433 from samo38/t870_buffer

Add buffer manual state to the Buffer and Solution GUI


  Commit: 075459dfc9537700e37aba51b3f8a5bb57c3c1c6
      https://github.com/ehb54/ultrascan3/commit/075459dfc9537700e37aba51b3f8a5bb57c3c1c6
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_select_item.cpp
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into t842_gaplot


  Commit: 16547f24596d6f1a1c6e10976383ed8bc2b74819
      https://github.com/ehb54/ultrascan3/commit/16547f24596d6f1a1c6e10976383ed8bc2b74819
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  Merge pull request #425 from samo38/t842_gaplot

ticket 842: GA plot range issue


  Commit: a7cbce78277c83da3570ae8b311270ecf88d59a5
      https://github.com/ehb54/ultrascan3/commit/a7cbce78277c83da3570ae8b311270ecf88d59a5
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/main' into ticket_822_pseudo3d_plot


  Commit: c7efd6ac8d78505ee8782507280e4a224fd9e858
      https://github.com/ehb54/ultrascan3/commit/c7efd6ac8d78505ee8782507280e4a224fd9e858
  Author: Saeed Mortezazadeh <49119048+samo38 at users.noreply.github.com>
  Date:   2026-06-14 (Sun, 14 Jun 2026)

  Changed paths:
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge pull request #423 from samo38/ticket_822_pseudo3d_plot

ticket_822: us_pseudo3d_combine manually diffusion plotting issue


  Commit: 1eb5f81fa55c76e1991446dfaaafd472f62ff46f
      https://github.com/ehb54/ultrascan3/commit/1eb5f81fa55c76e1991446dfaaafd472f62ff46f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: 8285d5c355b2c8730c274762fd27522a30d3cd18
      https://github.com/ehb54/ultrascan3/commit/8285d5c355b2c8730c274762fd27522a30d3cd18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [2: select Project, do not enable tabs]GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk option clicked; unlock only when valid .auc data-from-disk uploaded & downstream protocol parameters are generated; correct behavior for Next/Previous lower buttons: disable Next when at 2. Lab/Rotor tab, enable when back to 1. General; disable when back to 2. Lab/Rorot ...


  Commit: 245d4309e28c9db90cffbef3cb981c97b69a9b4a
      https://github.com/ehb54/ultrascan3/commit/245d4309e28c9db90cffbef3cb981c97b69a9b4a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue891


  Commit: 7870bc0e407e502ff7e3dac5490ba89f35c0a24b
      https://github.com/ehb54/ultrascan3/commit/7870bc0e407e502ff7e3dac5490ba89f35c0a24b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-15 (Mon, 15 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge pull request #440 from ehb54/alexey-dev-issue891

GMP: dataDisk -- disable all upcoming tabs in 1. EXP settings when dataDisk selected to prevent user-filled protocol creation


  Commit: 04bc610b180db0057d777dd09625732e535d15d1
      https://github.com/ehb54/ultrascan3/commit/04bc610b180db0057d777dd09625732e535d15d1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Protocol-Developer: remove v.0,1 from the window title ...


  Commit: aabf6395ab17f75fe98ee8a1856d0df8163ac5a0
      https://github.com/ehb54/ultrascan3/commit/aabf6395ab17f75fe98ee8a1856d0df8163ac5a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge pull request #442 from ehb54/alexey-dev-issue890

Protocol-Developer: remove v.0,1 from the window title ...


  Commit: c01e1313f848d52ba4e9f5c91129eac8c54f2b4d
      https://github.com/ehb54/ultrascan3/commit/c01e1313f848d52ba4e9f5c91129eac8c54f2b4d
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  fix: Update bump PR commit SHA in workflow configuration


  Commit: 52cc7dc3a6bb04f611fd929cf3e9a34d8ff69e1c
      https://github.com/ehb54/ultrascan3/commit/52cc7dc3a6bb04f611fd929cf3e9a34d8ff69e1c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #444 from ehb54/898-update-bump-pr-commit-sha-ultrascan3

Update workflow configuration for commit SHA bump


  Commit: bbe49a767b0802c2c444243ec79fb5dbeeaf2d14
      https://github.com/ehb54/ultrascan3/commit/bbe49a767b0802c2c444243ec79fb5dbeeaf2d14
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/bump-version.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/arm64-osx-dynamic.cmake
    A admin/cmake/triplets/arm64-windows.cmake
    M admin/cmake/triplets/x64-osx-dynamic.cmake
    R alpha/srcdevel
    R alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
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    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
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    A doc/manual/source/_static/images/us_solution1.png
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    A doc/manual/source/_static/images/usfont-1.png
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    A doc/manual/source/_static/images/vhw_combine-combo.png
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    A doc/manual/source/_static/images/vhw_enh_groups_res.png
    A doc/manual/source/_static/images/vhw_enhanced.png
    A doc/manual/source/_static/images/vhw_histogram.png
    A doc/manual/source/_static/images/xpn_report1.png
    A doc/manual/source/_static/images/xpn_report2.png
    A doc/manual/source/_static/images/xpn_viewer-loaded.png
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    A doc/manual/source/_static/images/zvalue_eq.png
    A doc/manual/source/_static/js/language_data.js
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    A doc/manual/source/_static/qthelp.css
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    A doc/manual/source/analysprof_general.rst
    A doc/manual/source/analyte/analyte_edit.rst
    A doc/manual/source/analyte/analyte_new.rst
    A doc/manual/source/analyte/analyte_select.rst
    A doc/manual/source/analyte/analyte_settings.rst
    A doc/manual/source/analyte/index.rst
    A doc/manual/source/associations.rst
    A doc/manual/source/astfem_sim.rst
    A doc/manual/source/auto_index.py
    A doc/manual/source/beckman_openauc.rst
    A doc/manual/source/buffer/buffer_edit.rst
    A doc/manual/source/buffer/buffer_new.rst
    A doc/manual/source/buffer/buffer_select.rst
    A doc/manual/source/buffer/buffer_settings.rst
    A doc/manual/source/buffer/index.rst
    A doc/manual/source/buoyancy_editor.rst
    A doc/manual/source/colorgradient.rst
    A doc/manual/source/combine_models.rst
    A doc/manual/source/common_dialogs.rst
    A doc/manual/source/components.rst
    A doc/manual/source/conf.py
    A doc/manual/source/config.rst
    A doc/manual/source/convert.rst
    A doc/manual/source/ddist_combine.rst
    A doc/manual/source/dens_match.rst
    A doc/manual/source/dmga_init.rst
    A doc/manual/source/dmga_init_constr.rst
    A doc/manual/source/experiment/cells.rst
    A doc/manual/source/experiment/general.rst
    A doc/manual/source/experiment/import.rst
    A doc/manual/source/experiment/index.rst
    A doc/manual/source/experiment/liveupdate.rst
    A doc/manual/source/experiment/optics.rst
    A doc/manual/source/experiment/range.rst
    A doc/manual/source/experiment/rotor.rst
    A doc/manual/source/experiment/solutions.rst
    A doc/manual/source/experiment/speeds.rst
    A doc/manual/source/experiment/submit.rst
    A doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    A doc/manual/source/fe_match/fe_match_adv.rst
    A doc/manual/source/fe_match/fe_match_main.rst
    A doc/manual/source/fe_match/fe_match_simulate.rst
    A doc/manual/source/fe_match/index.rst
    A doc/manual/source/fit_meniscus.rst
    A doc/manual/source/ga_initialize.rst
    A doc/manual/source/global_equil.rst
    A doc/manual/source/gmp/gmp.rst
    A doc/manual/source/gmp/gmp_audit_trail.rst
    A doc/manual/source/gmp/gmp_automation.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    A doc/manual/source/gmp/gmp_data_acquisition/index.rst
    A doc/manual/source/gmp/gmp_protocol_development.rst
    A doc/manual/source/gmp/gmp_report_generator.rst
    A doc/manual/source/gmp/gmp_signature.rst
    A doc/manual/source/gmp/index.rst
    A doc/manual/source/grid_editor.rst
    A doc/manual/source/idist_combine.rst
    A doc/manual/source/index.rst
    A doc/manual/source/manage_data.rst
    A doc/manual/source/model_editor.rst
    A doc/manual/source/multi-wavelength/index.rst
    A doc/manual/source/multi-wavelength/mwl_species_fit.rst
    A doc/manual/source/multi-wavelength/mwl_species_sim.rst
    A doc/manual/source/multi-wavelength/mwl_spectra.rst
    A doc/manual/source/multi-wavelength/mwlr_viewer.rst
    A doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    A doc/manual/source/pcsa/pcsa.rst
    A doc/manual/source/pcsa/pcsa_adv.rst
    A doc/manual/source/pcsa/pcsa_analys.rst
    A doc/manual/source/pcsa/pcsa_mlines.rst
    A doc/manual/source/pcsa/pcsa_results.rst
    A doc/manual/source/pcsa/pcsa_rpscan.rst
    A doc/manual/source/predict1.rst
    A doc/manual/source/predict2.rst
    A doc/manual/source/pseudo3d.rst
    A doc/manual/source/ramp_data.rst
    A doc/manual/source/register.rst
    A doc/manual/source/reporter.rst
    A doc/manual/source/requirements.txt
    A doc/manual/source/rmsd_query.rst
    A doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    A doc/manual/source/run_details.rst
    A doc/manual/source/sassoc.rst
    A doc/manual/source/second_moment.rst
    A doc/manual/source/simparams.rst
    A doc/manual/source/solutions/index.rst
    A doc/manual/source/solutions/solution_edit.rst
    A doc/manual/source/solutions/solution_new.rst
    A doc/manual/source/solutions/solution_select.rst
    A doc/manual/source/solutions/solution_settings.rst
    A doc/manual/source/start_page-abde.rst
    A doc/manual/source/start_page-dm.rst
    A doc/manual/source/start_page-int.rst
    A doc/manual/source/start_page-mw.rst
    A doc/manual/source/start_page-new.rst
    A doc/manual/source/start_page-rpt.rst
    A doc/manual/source/start_page.rst
    A doc/manual/source/time_derivative.rst
    A doc/manual/source/tmst_viewer.rst
    A doc/manual/source/us_administrator.rst
    A doc/manual/source/us_buoyancy.rst
    A doc/manual/source/us_edit.rst
    A doc/manual/source/us_equiltime.rst
    A doc/manual/source/us_extinction.rst
    A doc/manual/source/us_fds_filemanager.rst
    A doc/manual/source/us_investigator.rst
    A doc/manual/source/us_modelmetrics.rst
    A doc/manual/source/us_project.rst
    A doc/manual/source/us_spectrum.rst
    A doc/manual/source/vhw_combine.rst
    A doc/manual/source/vhw_distrib_plot.rst
    A doc/manual/source/vhw_enhanced.rst
    A doc/manual/source/xpn_viewer.rst
    R doc/manual/template.img.body
    R doc/manual/tidy.conf
    R doc/manual/time_derivative.body
    R doc/manual/ultrascan3.txt
    R doc/manual/us_buffer.body
    R doc/manual/us_edit.body
    R doc/manual/us_edit_mwl.body
    R doc/manual/us_equiltime.body
    R doc/manual/us_fds_filemanager.body
    R doc/manual/us_investigator.body
    R doc/manual/us_modelmetrics.body
    R doc/manual/us_project.body
    R doc/manual/us_solution.body
    R doc/manual/uscol.body
    R doc/manual/uscolor2.body
    R doc/manual/usfont.body
    R doc/manual/usfont2.body
    R doc/manual/vhw_combine.body
    R doc/manual/vhw_distrib_plot.body
    R doc/manual/vhw_enhanced.body
    R doc/manual/wrapped-images.lst
    M etc/etc_belongs_list.txt
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon.icns
    M gui/CMakeLists.txt
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/libus_gui.pro
    M gui/us_abstractrotor_gui.h
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_get_run.h
    M gui/us_help.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.cpp
    M gui/us_model_loader.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_rotor_gui.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    R qwtplot3d/lingua_de.ts
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_extern.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_memory.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_solve_sim.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: e7fc39e0ded8d0a6cfe774a4c39f42f3e26ec5c2
      https://github.com/ehb54/ultrascan3/commit/e7fc39e0ded8d0a6cfe774a4c39f42f3e26ec5c2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro
    M local.pri.template

  Log Message:
  -----------
  Fix macx build: guard -lqwtplot3d self-link and add -lus_utils to libus_gui

local.pri.template: split -lqwtplot3d onto a guarded line so that
when qwtplot3d itself is being built it does not try to link against
its own not-yet-existing library (ld: library not found for -lqwtplot3d).

gui/libus_gui.pro: add macx LIBS += -lus_utils so that the symbols
moved into libus_gui in Nov 2025 (us_csv_loader, us_convert_gui,
us_extinction_gui, etc.) can resolve against libus_utils at link time.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: c81d8b70460860507d201fd8243784999eddf69b
      https://github.com/ehb54/ultrascan3/commit/c81d8b70460860507d201fd8243784999eddf69b
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-907


  Commit: 36f036553bd505b52b7b696575355f3d715ab159
      https://github.com/ehb54/ultrascan3/commit/36f036553bd505b52b7b696575355f3d715ab159
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro
    M local.pri.template

  Log Message:
  -----------
  Merge pull request #446 from ehb54/ehb54-issue-907

Fix macx build: guard -lqwtplot3d self-link and add -lus_utils to libus_gui


  Commit: c7fe1d915db484906fa21f7fdb059dd46ca14e3d
      https://github.com/ehb54/ultrascan3/commit/c7fe1d915db484906fa21f7fdb059dd46ca14e3d
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Delete doc/manual/source/__pycache__/auto_index.cpython-39.pyc


  Commit: 8ed782c9a9b80ae3e81e35cfb88056da7f66986b
      https://github.com/ehb54/ultrascan3/commit/8ed782c9a9b80ae3e81e35cfb88056da7f66986b
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  Add Python bytecode files to .gitignore


  Commit: 02b1998e8c4e4190087e112ea223ffc452d892c1
      https://github.com/ehb54/ultrascan3/commit/02b1998e8c4e4190087e112ea223ffc452d892c1
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Merge pull request #447 from ehb54/ehb54-issue-908

Remove Python bytecode files and update .gitignore


  Commit: 2b7ce8e951545aceafde79228ff691ba4b5b2961
      https://github.com/ehb54/ultrascan3/commit/2b7ce8e951545aceafde79228ff691ba4b5b2961
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  revision.sh: limit ? marker to source code file changes only

Previously git diff checked all tracked files, causing the LOCAL_CHANGES
? symbol to appear whenever build scripts, .pri files, or other non-source
files differed from upstream ? including during normal packaging builds.

Restrict the check to file types that produce compiled output:
*.h, *.cpp, *.ui (Qt Designer), *.qrc (Qt resources).

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: a1bf5d7f2eb4649cd5167b42db38d5c6e4aa4d0d
      https://github.com/ehb54/ultrascan3/commit/a1bf5d7f2eb4649cd5167b42db38d5c6e4aa4d0d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  revision.sh: fix pathspec scope for source-file delta check

git diff pathspecs with bare globs (*.h) only match within the current
directory, not repo-wide. Since the script cd's to programs/us/, the
check was missing changes in gui/, utils/, etc.

Fix by running git -C from the repo root so all subdirectories are covered.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 325d0cbff2d496aaf6a42add91e63d096b0e9d26
      https://github.com/ehb54/ultrascan3/commit/325d0cbff2d496aaf6a42add91e63d096b0e9d26
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-909


  Commit: c4a785babca12aa43bf7f624928fa31cf97da1f4
      https://github.com/ehb54/ultrascan3/commit/c4a785babca12aa43bf7f624928fa31cf97da1f4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M programs/us/revision.sh

  Log Message:
  -----------
  Merge pull request #448 from ehb54/ehb54-issue-909

revision.sh: limit ? marker to source code file changes only


  Commit: 45ef026ad65a694d99671bd358216a9d7f7330d3
      https://github.com/ehb54/ultrascan3/commit/45ef026ad65a694d99671bd358216a9d7f7330d3
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    A .github/gtest-us.json
    M .github/workflows/bump-version.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    A admin/cmake/packaging/linux/LinuxPkg.cmake
    A admin/cmake/packaging/macos/MacDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcDeploy.cmake
    A admin/cmake/packaging/macos/MacHpcPkg.cmake
    A admin/cmake/packaging/macos/MacOsDeployQtAssistant.cmake
    A admin/cmake/packaging/macos/MacOsPkg.cmake
    A admin/cmake/packaging/macos/StageAssistantDev.cmake
    A admin/cmake/packaging/windows/WinDeploy.cmake
    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    M admin/cmake/toolchain.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/fix-arm64-no-fpu-neon64.patch
    A buildsys/vcpkg/overlay-ports/mpg123/have-fpu.diff
    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
    M buildsys/vcpkg/overlay-ports/qt5-tools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
    A buildsys/vcpkg/overlay-ports/qttools/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    M buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/portfile.cmake
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    M doc/manual/CMakeLists.txt
    M doc/manual/Makefile
    M doc/manual/README.md
    R doc/manual/advanced_config.body
    R doc/manual/analytes.body
    R doc/manual/associations.body
    R doc/manual/astfem_sim.body
    R doc/manual/buffer_edit.body
    R doc/manual/buffer_new.body
    R doc/manual/buffer_select.body
    R doc/manual/buffer_settings.body
    R doc/manual/cfa_viewer.body
    R doc/manual/colorgradient.body
    R doc/manual/combine_models.body
    R doc/manual/components.body
    R doc/manual/config.body
    R doc/manual/config2.body
    R doc/manual/convert-experiment.body
    R doc/manual/convert-seltrip.body
    R doc/manual/convert.body
    R doc/manual/data_loader.body
    R doc/manual/database_config.body
    R doc/manual/ddist_combine.body
    R doc/manual/dens_match.body
    R doc/manual/dens_match_mparam.body
    R doc/manual/dens_match_rmvmods.body
    R doc/manual/experiment/experiment_cells.body
    R doc/manual/experiment/experiment_general.body
    R doc/manual/experiment/experiment_photomult.body
    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/export_legacy.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
    R doc/manual/fe_match/fe_match_lddat.body
    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fit_meniscus.body
    R doc/manual/footer.us3
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    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/grid_editor.body
    R doc/manual/header.us3
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
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    R doc/manual/images/color-a.png
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    R doc/manual/images/colorgrad.png
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    R doc/manual/images/combine_models-save.png
    R doc/manual/images/combine_models.png
    R doc/manual/images/components.png
    R doc/manual/images/config.png
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    R doc/manual/images/convert-RIdata.png
    R doc/manual/images/convert-exclude.png
    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
    R doc/manual/images/convert-subset.png
    R doc/manual/images/convert-tolerance.png
    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
    R doc/manual/images/data_loader-trips.png
    R doc/manual/images/data_loader.png
    R doc/manual/images/database.png
    R doc/manual/images/ddist_combine-selrun.png
    R doc/manual/images/ddist_combine.png
    R doc/manual/images/densmatch_main.png
    R doc/manual/images/densmatch_mpars_completed.png
    R doc/manual/images/densmatch_mpars_empty.png
    R doc/manual/images/densmatch_rmvmodels.png
    R doc/manual/images/eq1-mean.png
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    R doc/manual/images/eq7-probsigma.png
    R doc/manual/images/eq8-confidence.png
    R doc/manual/images/experiment_cells.png
    R doc/manual/images/experiment_general.png
    R doc/manual/images/experiment_photomult.png
    R doc/manual/images/experiment_rotor.png
    R doc/manual/images/experiment_solutions.png
    R doc/manual/images/experiment_speeds.png
    R doc/manual/images/experiment_upload.png
    R doc/manual/images/export_legacy.png
    R doc/manual/images/fe_match.png
    R doc/manual/images/fe_match_3dplot.png
    R doc/manual/images/fe_match_adv.png
    R doc/manual/images/fe_match_lddat1.png
    R doc/manual/images/fe_match_lddat2.png
    R doc/manual/images/fe_match_lddat3.png
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    R doc/manual/images/fe_match_ra.png
    R doc/manual/images/fe_match_resplot.png
    R doc/manual/images/fe_match_sim1.png
    R doc/manual/images/fe_match_sim2.png
    R doc/manual/images/fe_match_sim3_1b.png
    R doc/manual/images/fe_match_sim3_1p.png
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    R doc/manual/images/fe_match_sim7.png
    R doc/manual/images/fit_men-editupd.png
    R doc/manual/images/fit_men-load.png
    R doc/manual/images/fit_meniscus.png
    R doc/manual/images/ga_initialize.png
    R doc/manual/images/gmp/audit_trail/gmp_audit_trail_01.png
    R doc/manual/images/gmp/audit_trail/gmp_audit_trail_02.png
    R doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_01.png
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    A doc/manual/source/_static/images/us_convert_definedscans.png
    A doc/manual/source/_static/images/us_convert_definesubset.png
    A doc/manual/source/_static/images/us_edit.png
    A doc/manual/source/_static/images/us_edit_mwl.png
    A doc/manual/source/_static/images/us_equiltime.png
    A doc/manual/source/_static/images/us_extinction-0.png
    A doc/manual/source/_static/images/us_extinction-00.png
    A doc/manual/source/_static/images/us_extinction-000.png
    A doc/manual/source/_static/images/us_extinction-1.png
    A doc/manual/source/_static/images/us_extinction-2.png
    A doc/manual/source/_static/images/us_extinction-3.png
    A doc/manual/source/_static/images/us_fds_filemanager-0.png
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    A doc/manual/source/_static/images/us_fds_filemanager-2.png
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    A doc/manual/source/_static/images/us_fds_filemanager-4.png
    A doc/manual/source/_static/images/us_investigator-2.png
    A doc/manual/source/_static/images/us_investigator.png
    A doc/manual/source/_static/images/us_modelmetrics-0.png
    A doc/manual/source/_static/images/us_modmet_report.png
    A doc/manual/source/_static/images/us_project.png
    A doc/manual/source/_static/images/us_project1.png
    A doc/manual/source/_static/images/us_project2.png
    A doc/manual/source/_static/images/us_project3.png
    A doc/manual/source/_static/images/us_project_add-supdata.png
    A doc/manual/source/_static/images/us_project_edit-supdata.png
    A doc/manual/source/_static/images/us_project_web.png
    A doc/manual/source/_static/images/us_project_webed.png
    A doc/manual/source/_static/images/us_solution1.png
    A doc/manual/source/_static/images/us_solution2.png
    A doc/manual/source/_static/images/us_solution3.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    A doc/manual/source/_static/images/us_spectrum-0.png
    A doc/manual/source/_static/images/us_spectrum-1.png
    A doc/manual/source/_static/images/us_spectrum-load.png
    A doc/manual/source/_static/images/usfont-1.png
    A doc/manual/source/_static/images/usfont-2.png
    A doc/manual/source/_static/images/vhw_combine-combo.png
    A doc/manual/source/_static/images/vhw_combine-envel.png
    A doc/manual/source/_static/images/vhw_combine-selrun.png
    A doc/manual/source/_static/images/vhw_combine.png
    A doc/manual/source/_static/images/vhw_distribution.png
    A doc/manual/source/_static/images/vhw_enh_groups.png
    A doc/manual/source/_static/images/vhw_enh_groups.png6-33-11.png
    A doc/manual/source/_static/images/vhw_enh_groups_res.png
    A doc/manual/source/_static/images/vhw_enhanced.png
    A doc/manual/source/_static/images/vhw_histogram.png
    A doc/manual/source/_static/images/xpn_report1.png
    A doc/manual/source/_static/images/xpn_report2.png
    A doc/manual/source/_static/images/xpn_viewer-loaded.png
    A doc/manual/source/_static/images/xpn_viewer-saved.png
    A doc/manual/source/_static/images/xpn_viewer.png
    A doc/manual/source/_static/images/zvalue_eq.png
    A doc/manual/source/_static/js/language_data.js
    A doc/manual/source/_static/js/sphinx_highlight.js
    A doc/manual/source/_static/language_data.js
    A doc/manual/source/_static/qthelp.css
    A doc/manual/source/_static/sphinx_highlight.js
    A doc/manual/source/analysprof_general.rst
    A doc/manual/source/analyte/analyte_edit.rst
    A doc/manual/source/analyte/analyte_new.rst
    A doc/manual/source/analyte/analyte_select.rst
    A doc/manual/source/analyte/analyte_settings.rst
    A doc/manual/source/analyte/index.rst
    A doc/manual/source/associations.rst
    A doc/manual/source/astfem_sim.rst
    A doc/manual/source/auto_index.py
    A doc/manual/source/beckman_openauc.rst
    A doc/manual/source/buffer/buffer_edit.rst
    A doc/manual/source/buffer/buffer_new.rst
    A doc/manual/source/buffer/buffer_select.rst
    A doc/manual/source/buffer/buffer_settings.rst
    A doc/manual/source/buffer/index.rst
    A doc/manual/source/buoyancy_editor.rst
    A doc/manual/source/colorgradient.rst
    A doc/manual/source/combine_models.rst
    A doc/manual/source/common_dialogs.rst
    A doc/manual/source/components.rst
    A doc/manual/source/conf.py
    A doc/manual/source/config.rst
    A doc/manual/source/convert.rst
    A doc/manual/source/ddist_combine.rst
    A doc/manual/source/dens_match.rst
    A doc/manual/source/dmga_init.rst
    A doc/manual/source/dmga_init_constr.rst
    A doc/manual/source/experiment/cells.rst
    A doc/manual/source/experiment/general.rst
    A doc/manual/source/experiment/import.rst
    A doc/manual/source/experiment/index.rst
    A doc/manual/source/experiment/liveupdate.rst
    A doc/manual/source/experiment/optics.rst
    A doc/manual/source/experiment/range.rst
    A doc/manual/source/experiment/rotor.rst
    A doc/manual/source/experiment/solutions.rst
    A doc/manual/source/experiment/speeds.rst
    A doc/manual/source/experiment/submit.rst
    A doc/manual/source/export_legacy.rst
    A doc/manual/source/fe_match/fe_dmga_adv.rst
    A doc/manual/source/fe_match/fe_match_adv.rst
    A doc/manual/source/fe_match/fe_match_main.rst
    A doc/manual/source/fe_match/fe_match_simulate.rst
    A doc/manual/source/fe_match/index.rst
    A doc/manual/source/fit_meniscus.rst
    A doc/manual/source/ga_initialize.rst
    A doc/manual/source/global_equil.rst
    A doc/manual/source/gmp/gmp.rst
    A doc/manual/source/gmp/gmp_audit_trail.rst
    A doc/manual/source/gmp/gmp_automation.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    A doc/manual/source/gmp/gmp_data_acquisition/index.rst
    A doc/manual/source/gmp/gmp_protocol_development.rst
    A doc/manual/source/gmp/gmp_report_generator.rst
    A doc/manual/source/gmp/gmp_signature.rst
    A doc/manual/source/gmp/index.rst
    A doc/manual/source/grid_editor.rst
    A doc/manual/source/idist_combine.rst
    A doc/manual/source/index.rst
    A doc/manual/source/manage_data.rst
    A doc/manual/source/model_editor.rst
    A doc/manual/source/multi-wavelength/index.rst
    A doc/manual/source/multi-wavelength/mwl_species_fit.rst
    A doc/manual/source/multi-wavelength/mwl_species_sim.rst
    A doc/manual/source/multi-wavelength/mwl_spectra.rst
    A doc/manual/source/multi-wavelength/mwlr_viewer.rst
    A doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/load_modelrecs.rst
    A doc/manual/source/pcsa/pcsa.rst
    A doc/manual/source/pcsa/pcsa_adv.rst
    A doc/manual/source/pcsa/pcsa_analys.rst
    A doc/manual/source/pcsa/pcsa_mlines.rst
    A doc/manual/source/pcsa/pcsa_results.rst
    A doc/manual/source/pcsa/pcsa_rpscan.rst
    A doc/manual/source/predict1.rst
    A doc/manual/source/predict2.rst
    A doc/manual/source/pseudo3d.rst
    A doc/manual/source/ramp_data.rst
    A doc/manual/source/register.rst
    A doc/manual/source/reporter.rst
    A doc/manual/source/requirements.txt
    A doc/manual/source/rmsd_query.rst
    A doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    A doc/manual/source/run_details.rst
    A doc/manual/source/sassoc.rst
    A doc/manual/source/second_moment.rst
    A doc/manual/source/simparams.rst
    A doc/manual/source/solutions/index.rst
    A doc/manual/source/solutions/solution_edit.rst
    A doc/manual/source/solutions/solution_new.rst
    A doc/manual/source/solutions/solution_select.rst
    A doc/manual/source/solutions/solution_settings.rst
    A doc/manual/source/start_page-abde.rst
    A doc/manual/source/start_page-dm.rst
    A doc/manual/source/start_page-int.rst
    A doc/manual/source/start_page-mw.rst
    A doc/manual/source/start_page-new.rst
    A doc/manual/source/start_page-rpt.rst
    A doc/manual/source/start_page.rst
    A doc/manual/source/time_derivative.rst
    A doc/manual/source/tmst_viewer.rst
    A doc/manual/source/us_administrator.rst
    A doc/manual/source/us_buoyancy.rst
    A doc/manual/source/us_edit.rst
    A doc/manual/source/us_equiltime.rst
    A doc/manual/source/us_extinction.rst
    A doc/manual/source/us_fds_filemanager.rst
    A doc/manual/source/us_investigator.rst
    A doc/manual/source/us_modelmetrics.rst
    A doc/manual/source/us_project.rst
    A doc/manual/source/us_spectrum.rst
    A doc/manual/source/vhw_combine.rst
    A doc/manual/source/vhw_distrib_plot.rst
    A doc/manual/source/vhw_enhanced.rst
    A doc/manual/source/xpn_viewer.rst
    R doc/manual/template.img.body
    R doc/manual/tidy.conf
    R doc/manual/time_derivative.body
    R doc/manual/ultrascan3.txt
    R doc/manual/us_buffer.body
    R doc/manual/us_edit.body
    R doc/manual/us_edit_mwl.body
    R doc/manual/us_equiltime.body
    R doc/manual/us_fds_filemanager.body
    R doc/manual/us_investigator.body
    R doc/manual/us_modelmetrics.body
    R doc/manual/us_project.body
    R doc/manual/us_solution.body
    R doc/manual/uscol.body
    R doc/manual/uscolor2.body
    R doc/manual/usfont.body
    R doc/manual/usfont2.body
    R doc/manual/vhw_combine.body
    R doc/manual/vhw_distrib_plot.body
    R doc/manual/vhw_enhanced.body
    R doc/manual/wrapped-images.lst
    M etc/etc_belongs_list.txt
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    R etc/us3-GMP-icon-128x128.xpm
    R etc/us3-GMP-icon-32x32.ico
    R etc/us3-GMP-icon-32x32.png
    R etc/us3-GMP-icon-32x32.xpm
    R etc/us3-GMP-icon-48x48.ico
    R etc/us3-GMP-icon-48x48.png
    R etc/us3-GMP-icon-48x48.xpm
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_abstractrotor_gui.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_get_run.h
    M gui/us_help.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_properties.cpp
    M gui/us_rotor_gui.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M local.pri.template
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    R qwtplot3d/lingua_de.ts
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    M scripts/build.bat
    M scripts/build.ps1
    M scripts/build.sh
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    M test/utils/test_us_regex.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_extern.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_memory.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_solve_sim.cpp
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-766


  Commit: 3ba8a99c404673869fe12bb20bdfd05fc1cbb9e9
      https://github.com/ehb54/ultrascan3/commit/3ba8a99c404673869fe12bb20bdfd05fc1cbb9e9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  remove redundant macx{} block in libus_gui.pro

The single-line macx: LIBS already covers this; the block added in
the prior commit was duplicate.

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 5b846ae2ba06a1fe8922ca5463989738b9ac9388
      https://github.com/ehb54/ultrascan3/commit/5b846ae2ba06a1fe8922ca5463989738b9ac9388
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-18 (Thu, 18 Jun 2026)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  Merge pull request #375 from ehb54/ehb54-issue-766

fix win32 gui link: add version suffix to -lqwtplot3d


  Commit: e42355993bdf8df5f59068aae970ffe9d7447c95
      https://github.com/ehb54/ultrascan3/commit/e42355993bdf8df5f59068aae970ffe9d7447c95
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .gitignore
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    M gui/libus_gui.pro
    M local.pri.template
    M programs/us/revision.sh

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: 4102be089f9a53763e66d2b41a5d7ff0a81baee9
      https://github.com/ehb54/ultrascan3/commit/4102be089f9a53763e66d2b41a5d7ff0a81baee9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Fix linux.pl package name generation for new version/revision header format

us_revision.h no longer has a single REVISION field; it now has separate
BUILDNUM/GIT_REVISION/REVISION_DATE/LOCAL_CHANGES fields. The old
"grep REVISION" matched both GIT_REVISION and REVISION_DATE, producing a
multi-line value that broke the generated package directory name and the
shell commands built from it (used by both the redhat and ubuntu release
Dockerfiles). Build the package name from US_Version (utils/us_defines.h)
and BUILDNUM instead.

Fixes ehb54/ultrascan-tickets#910


  Commit: 22905927a67f8bb8637ed325009771296c5b9052
      https://github.com/ehb54/ultrascan3/commit/22905927a67f8bb8637ed325009771296c5b9052
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge pull request #451 from ehb54/ehb54-issue-910

Fix linux.pl package name generation for new version/revision header format


  Commit: 3c4a6a12de6f56ab3ccb0e05512fe01538445686
      https://github.com/ehb54/ultrascan3/commit/3c4a6a12de6f56ab3ccb0e05512fe01538445686
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Fix CodeQL build-target detection: == is not valid in POSIX sh [ ]

The "Calculate Build Targets" step runs under sh (dash), where [ ] only
supports = not ==. Every [ "$X" == "true" ] test errored as "unexpected
operator" and was treated as false, so the full-rebuild branch never ran
even on a push to main with FORCE_ALL=true. This meant CodeQL's analysis
database only ever contained whichever programs happened to be touched
by a given push's diff, causing already-open alerts in untouched files
(e.g. us_spectrum.cpp) to flap between Fixed/Reappeared across unrelated
PRs without the underlying code ever changing.

Fixes ehb54/ultrascan-tickets#911


  Commit: 2bb70f296f3ecc8f762152da20c145583f3d4fc1
      https://github.com/ehb54/ultrascan3/commit/2bb70f296f3ecc8f762152da20c145583f3d4fc1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  Fix remaining CodeQL security alerts: int-multiplication overflow + format arg

Same pattern as PR #435: cast one multiplication operand to qsizetype
before sizing a QVector, so the multiply itself doesn't happen in (32-bit)
int before widening. Also fixes a %d/qsizetype format-specifier mismatch
in us_pcsa_process.cpp.

Fixes ehb54/ultrascan-tickets#912


  Commit: 8ebc45097882afa73f22a184410e310658fca0de
      https://github.com/ehb54/ultrascan3/commit/8ebc45097882afa73f22a184410e310658fca0de
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.1.0


  Commit: 733d3f549696b0efe49cd26d0840bdf6ab37d5e7
      https://github.com/ehb54/ultrascan3/commit/733d3f549696b0efe49cd26d0840bdf6ab37d5e7
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge pull request #445 from ehb54/bump-to-v4.1.0

Bump to v4.1.0


  Commit: 951770eef3cf63893454a5402ccb79e4a64062db
      https://github.com/ehb54/ultrascan3/commit/951770eef3cf63893454a5402ccb79e4a64062db
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-911


  Commit: d981490e29291aa7d6124604cc0ea33dcc753df3
      https://github.com/ehb54/ultrascan3/commit/d981490e29291aa7d6124604cc0ea33dcc753df3
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Merge pull request #452 from ehb54/ehb54-issue-911

Fix CodeQL build-target detection (sh != bash, == in [ ])


  Commit: cb2753416846b0e812f495ef4a5f2161dd35280c
      https://github.com/ehb54/ultrascan3/commit/cb2753416846b0e812f495ef4a5f2161dd35280c
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-912


  Commit: e3b3099b8aaebbe3c4fc5ddb2e7acb7186893133
      https://github.com/ehb54/ultrascan3/commit/e3b3099b8aaebbe3c4fc5ddb2e7acb7186893133
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  Merge pull request #453 from ehb54/ehb54-issue-912

Fix remaining CodeQL security alerts (multiplication overflow + format arg)


  Commit: d689ce8f674d78d26e7bff34f3928a4950f933af
      https://github.com/ehb54/ultrascan3/commit/d689ce8f674d78d26e7bff34f3928a4950f933af
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Robustly detect sphinx-build/python3 for DOMAN doc build on RHEL8

RHEL8 variants ship a too-old default python3 (3.6) plus optional
python3.11/python3.12 packages with no sphinx-build shim on PATH,
so the existing "which sphinx-build" check frequently misses a
working installation. Search candidate interpreters newest-first,
self-install Sphinx via ensurepip/pip if needed, and shim a scoped
python3 symlink on PATH only for the doc make step when the chosen
interpreter isn't named python3.

Fixes ultrascan-tickets#925


  Commit: f41aa3fd5b8d0ec601363a640f3b964ba85b1e51
      https://github.com/ehb54/ultrascan3/commit/f41aa3fd5b8d0ec601363a640f3b964ba85b1e51
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Reject Python interpreters too old for conf.py in DOMAN detection

doc/manual/source/conf.py uses Python >=3.9 syntax (PEP 585 builtin
generics, e.g. "list[str]"). The find_doc_python() search only checked
"import sphinx" succeeding, so a too-old default python3 (e.g. RHEL's
3.6) with a stale manually pip-installed Sphinx from before this
script existed got picked over a usable python3.11/python3.12 on the
same host, and the build then crashed in conf.py with "TypeError:
'type' object is not subscriptable". Add an explicit version check
that rejects any candidate interpreter below 3.9 before checking for
or installing Sphinx.

ehb54/ultrascan-tickets#925


  Commit: 18e656c09220a8883e1755f461737db76d91c710
      https://github.com/ehb54/ultrascan3/commit/18e656c09220a8883e1755f461737db76d91c710
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Drop --upgrade from ensurepip call in DOMAN detection

"ensurepip --upgrade" bootstraps pip from the bundled wheel and then
has pip upgrade itself from PyPI, which fails outright on
network-restricted hosts. Plain "ensurepip" only installs the bundled
wheel (fully offline) and is all that's needed to get a working pip
module before installing doc/manual/source/requirements.txt.

ehb54/ultrascan-tickets#925


  Commit: 25987d47541a67eb9c6168d741326e47ede154b9
      https://github.com/ehb54/ultrascan3/commit/25987d47541a67eb9c6168d741326e47ede154b9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Fix DOMAN fast path to check python3, not sphinx-build

doc/manual/Makefile invokes the interpreter as plain "python3"
(SPHINXBUILD ?= python3 -m sphinx), not "sphinx-build". The previous
fast path checked "sphinx-build --version" and returned immediately on
success, but an unrelated sphinx-build entry-point script tied to some
other (possibly too-old) interpreter can be on PATH and "work" -- since
--version never touches conf.py -- while "python3 -m sphinx" still
fails. This bypassed the version-gated python3.X search entirely and
explains why the previous DOMAN fixes had no effect on a host with a
stale sphinx-build shim left over from a manual "pip install --user"
under python3.6. Check bare python3 directly instead.

ehb54/ultrascan-tickets#925


  Commit: c71f3b106e12d2e2c40ee77a9695bee1793ff680
      https://github.com/ehb54/ultrascan3/commit/c71f3b106e12d2e2c40ee77a9695bee1793ff680
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M makeall.sh

  Log Message:
  -----------
  Merge pull request #457 from ehb54/ehb54-issue-925

makeall.sh: robust sphinx/python3 detection for DOMAN on RHEL8 variants


  Commit: 6d06a0c1b49dfa1141dc8625e75bc03918635a40
      https://github.com/ehb54/ultrascan3/commit/6d06a0c1b49dfa1141dc8625e75bc03918635a40
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Include LICENSE.txt in Linux release packages

The Linux tar.xz packaging script never copied LICENSE.txt into the
package, unlike the Windows packaging script which does. Add the same
copy step so Linux packages ship a license file too.

Fixes ehb54/ultrascan-tickets#868


  Commit: c67d82488c7f281c78458954341098446e6baea0
      https://github.com/ehb54/ultrascan3/commit/c67d82488c7f281c78458954341098446e6baea0
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-23 (Tue, 23 Jun 2026)

  Changed paths:
    M admin/release/linux.pl

  Log Message:
  -----------
  Merge pull request #458 from ehb54/ehb54-issue-868

Include LICENSE.txt in Linux release packages


  Commit: e47a1e408f3d0ac6a7db58fdf0cab65ab3b30a6f
      https://github.com/ehb54/ultrascan3/commit/e47a1e408f3d0ac6a7db58fdf0cab65ab3b30a6f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP-dataDisk: 1. EXP: 5. Solutions -- exclude (unspecified) item in all solution cahnnels for uploaded form disk data...


  Commit: 8a9c0cc6be7aaf9304035a342cbaeaba80e24135
      https://github.com/ehb54/ultrascan3/commit/8a9c0cc6be7aaf9304035a342cbaeaba80e24135
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #459 from ehb54/alexey-dev-issue929

GMP-dataDisk: 1. EXP: 5. Solutions -- exclude (unspecified) item in all solution cahnnels for uploaded form disk data...


  Commit: ed7f5a0cdf313c3337076a886caebe0f469d88a7
      https://github.com/ehb54/ultrascan3/commit/ed7f5a0cdf313c3337076a886caebe0f469d88a7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: 888dfa5cada04313f4e905ecab395a6080a7ad24
      https://github.com/ehb54/ultrascan3/commit/888dfa5cada04313f4e905ecab395a6080a7ad24
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  [edited mesage]Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: edda3c63be4e85f9fde90d971bf72dd1e184c1aa
      https://github.com/ehb54/ultrascan3/commit/edda3c63be4e85f9fde90d971bf72dd1e184c1aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge pull request #460 from ehb54/alexey-dev-issue928

Database: Manage Data: if there is no DB conenction, inform the user and close the program instead of proceeding and crashing...


  Commit: b9470a9bb9ca3b1859b7f798fa5f5e76a33a99ab
      https://github.com/ehb54/ultrascan3/commit/b9470a9bb9ca3b1859b7f798fa5f5e76a33a99ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: f0244186bf701788c6e7bc3915a4cca84aabe865
      https://github.com/ehb54/ultrascan3/commit/f0244186bf701788c6e7bc3915a4cca84aabe865
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue932


  Commit: 16b34f7a8252e4af4fbca5ebbd01f38bbb376beb
      https://github.com/ehb54/ultrascan3/commit/16b34f7a8252e4af4fbca5ebbd01f38bbb376beb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  [add connection check when attemting to Save]Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: 9c0f94c5d0a9f09a78152c7c5862b7f2e9a8bf6b
      https://github.com/ehb54/ultrascan3/commit/9c0f94c5d0a9f09a78152c7c5862b7f2e9a8bf6b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_manage_data/us_manage_data.cpp

  Log Message:
  -----------
  Merge branch 'alexey-dev-issue932' of github.com:ehb54/ultrascan3 into alexey-dev-issue932


  Commit: fb0e0bd78e483abe98e103bc0093440b38c5c669
      https://github.com/ehb54/ultrascan3/commit/fb0e0bd78e483abe98e103bc0093440b38c5c669
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  [[1]add connection check when attemting to Save]Preferences: Database -> Change: enable Save Entry button for any existing or new entry only after Test Connetction is successful...


  Commit: 5732996f335aec054f71c4e536a044841eb385b5
      https://github.com/ehb54/ultrascan3/commit/5732996f335aec054f71c4e536a044841eb385b5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-25 (Thu, 25 Jun 2026)

  Changed paths:
    M programs/us_config/us_database.cpp

  Log Message:
  -----------
  Merge pull request #461 from ehb54/alexey-dev-issue932

Preferences: Database -> Change: enable Save Entry button for any existing or new entries only after Test Connection is successful.


  Commit: 0d4d8870eb492684324b6bc7a5a39ca6b12c1c63
      https://github.com/ehb54/ultrascan3/commit/0d4d8870eb492684324b6bc7a5a39ca6b12c1c63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  US: hide "GMP" menu item for MacOS only...


  Commit: 1dd7a098a12171044289211cd22079f8b12f527d
      https://github.com/ehb54/ultrascan3/commit/1dd7a098a12171044289211cd22079f8b12f527d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  US: hide "Utilitoes->Data Acqusition" menu item for MacOS only...


  Commit: 37dfa3e81496bc5667af8082527f5ea1065c8133
      https://github.com/ehb54/ultrascan3/commit/37dfa3e81496bc5667af8082527f5ea1065c8133
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-06-26 (Fri, 26 Jun 2026)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Merge pull request #462 from ehb54/alexey-dev-issue935

US: hide "GMP" menu item for MacOS only...


  Commit: 7eb866b9fcef86510463852edf2b6db9c2010dce
      https://github.com/ehb54/ultrascan3/commit/7eb866b9fcef86510463852edf2b6db9c2010dce
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-27 (Sat, 27 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix: restrict Sphinx dirty-check to source files to match revision.sh

The conf.py generate_version_metadata() was running git diff against all
tracked files with no path filter. On a macOS release build, a non-source
file (doc, script, etc.) was modified, causing conf.py to mark the build
dirty and embed ? in the Qt Help namespace/version string ? even though
revision.sh (splash screen) correctly showed no dirty flag because it
already restricts to *.h *.cpp *.ui *.qrc.

Fix: add the same -- *.h *.cpp *.ui *.qrc pathspec filter to both git diff
calls in conf.py so the dirty indicator is consistent with revision.sh.

Closes #936

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 52636d73ba151811a714c312eaae23119fbc3e22
      https://github.com/ehb54/ultrascan3/commit/52636d73ba151811a714c312eaae23119fbc3e22
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Merge pull request #464 from ehb54/issue-936

fix: restrict Sphinx dirty-check to source files (issue #936)


  Commit: 9153af9e9169c5ea50ab39f1e8b9a6c1cd6859bc
      https://github.com/ehb54/ultrascan3/commit/9153af9e9169c5ea50ab39f1e8b9a6c1cd6859bc
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  fix: change qthelp namespace from org.sphinx to com.aucsolutions

Closes ehb54/ultrascan-tickets#939

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: cc6eed0f49f97edb31642145d1c9757b4d7f5a53
      https://github.com/ehb54/ultrascan3/commit/cc6eed0f49f97edb31642145d1c9757b4d7f5a53
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch 'main' into issue-939


  Commit: a22f52e0935d5bb7994769ffb9401e352f5bb3cf
      https://github.com/ehb54/ultrascan3/commit/a22f52e0935d5bb7994769ffb9401e352f5bb3cf
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-29 (Mon, 29 Jun 2026)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  Merge pull request #466 from ehb54/issue-939

fix: change qthelp namespace from org.sphinx to com.aucsolutions


  Commit: eb825d66df4c5c3e0841f6cd6a56571b29889a3c
      https://github.com/ehb54/ultrascan3/commit/eb825d66df4c5c3e0841f6cd6a56571b29889a3c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Skip explicit cipher list on MSYS2/64 Windows builds (#940)

MSYS2/64 (MINGW64) Windows builds link a Schannel-backed libmariadb,
which fails to match any suite from the OpenSSL-style CIPHER list:
"TLS/SSL error: no cipher match Error 0x80090331
(SEC_E_ALGORITHM_MISMATCH)".

Rather than imposing a substitute OpenSSL-style cipher string that
Schannel may or may not understand, skip calling
mysql_options(MYSQL_OPT_SSL_CIPHER, ...) entirely on __MINGW64__ and
let the backend negotiate its own default cipher suite set. This is a
workaround pending the real fix of linking an OpenSSL-backed MariaDB
Connector/C on Windows.

MSVC/vcpkg builds and Linux/macOS builds are unaffected (__MINGW64__
is not defined there).

Fixes ehb54/ultrascan-tickets#940

Co-Authored-By: Claude Sonnet 4.6 <noreply at anthropic.com>


  Commit: 55e94a0e3813f79d50549bd166d3cf26934208c0
      https://github.com/ehb54/ultrascan3/commit/55e94a0e3813f79d50549bd166d3cf26934208c0
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M gui/us_help.cpp
    M utils/us_settings.cpp

  Log Message:
  -----------
  fix: update browser settings handling for MacOS and Windows


  Commit: d099a4448e73330af2c3bd0fc9ec64a435bf7d2a
      https://github.com/ehb54/ultrascan3/commit/d099a4448e73330af2c3bd0fc9ec64a435bf7d2a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-30 (Tue, 30 Jun 2026)

  Changed paths:
    M utils/us_settings.cpp

  Log Message:
  -----------
  fix: initialize status variable to zero in us_settings.cpp


  Commit: 6fc2e4866baf59178b492f7e345fb36de180ebd8
      https://github.com/ehb54/ultrascan3/commit/6fc2e4866baf59178b492f7e345fb36de180ebd8
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    A .github/gtest-us.json
    A .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/sphinx-doc-build.yml
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    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M LICENSE.txt
    R README.linguist
    M README.manual
    A VERSION
    M admin/cmake/FindQwt.cmake
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/README.md
    A admin/cmake/packaging/README.md
    A admin/cmake/packaging/linux/LinuxDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    A admin/cmake/packaging/linux/LinuxHpcPkg.cmake
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    A admin/cmake/packaging/windows/WinPkg.cmake
    A admin/cmake/packaging/windows/WindowsDeployQtAssistant.cmake
    A admin/cmake/toolchain.cmake
    A admin/cmake/triplets/arm64-linux.cmake
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    M admin/cmake/triplets/x64-osx-dynamic.cmake
    M admin/release/linux.pl
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    R alpha/us.cpp
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    A buildsys/vcpkg/overlay-ports/mpg123/pkgconfig.diff
    A buildsys/vcpkg/overlay-ports/mpg123/portfile.cmake
    A buildsys/vcpkg/overlay-ports/mpg123/vcpkg.json
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    A buildsys/vcpkg/overlay-ports/qttools/devendor-litehtml.patch
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    A buildsys/vcpkg/overlay-ports/qttools/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qttools/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qttools/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
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    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/config.patch
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    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt5/unofficial-qwt-config.cmake
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    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/unofficial-qwt-config.cmake
    A buildsys/vcpkg/overlay-ports/qwt-6-3-0-qt6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
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    R doc/manual/template.img.body
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    R doc/manual/wrapped-images.lst
    M etc/etc_belongs_list.txt
    A etc/icons/make-icons.sh
    A etc/icons/us3-icon-master-512.png
    R etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
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    M gui.pri
    M gui/CMakeLists.txt
    M gui/fix-mac-make.sh
    R gui/images.qrc
    M gui/images/us3-icon-128x128.png
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    M gui/libus_gui.pro
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    M gui/us_abstractrotor_gui.h
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_data_loader.h
    M gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_get_run.cpp
    M gui/us_get_run.h
    M gui/us_gui_util.cpp
    M gui/us_help.cpp
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.cpp
    M gui/us_load_auc.h
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_model_loader.cpp
    M gui/us_model_loader.h
    M gui/us_mwl_data.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_new_spectrum.h
    M gui/us_passwd.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_project_gui.h
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_rotor_gui.h
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.h
    M gui/us_select_triples.h
    M gui/us_selectbox.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.h
    M local.pri.template
    M makeall.sh
    A pkg/macos/README.md
    A pkg/macos/component.plist
    A pkg/macos/distribution.xml.in
    A pkg/macos/launcher/UltraScan3.app/Contents/Info.plist
    A pkg/macos/launcher/UltraScan3.app/Contents/MacOS/UltraScan3
    A pkg/macos/postinstall
    A pkg/macos/preinstall
    A pkg/macos/resources/Welcome.txt.in
    A pkg/macos/resources/background.png
    A pkg/macos/ultrascan_sysctl.plist
    A pkg/macos/uninstall.sh
    M programs/CMakeLists.txt
    M programs/main1.inc
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    R programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_advanced.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_config.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.h
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_select_lambdas.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_globalequil/us_model_adpars.h
    M programs/us_globalequil/us_model_select.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_worker.cpp
    M programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_worker.cpp
    M programs/us_mpi_analysis/revision.sh
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.h
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    R propignore
    R proppng
    R proptext
    M qmakeall.sh
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    R qwtplot3d/lingua_de.ts
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    A scripts/bootstrap-linux.sh
    A scripts/bootstrap-macos.sh
    A scripts/bootstrap-windows.ps1
    A scripts/bootstrap.bat
    A scripts/build.bat
    A scripts/build.ps1
    M scripts/build.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_crypto.cpp
    A test/utils/test_us_help_pages.cpp
    A test/utils/test_us_regex.cpp
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_time_state.cpp
    A us-build
    M utils/CMakeLists.txt
    M utils/ius_db2.h
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.cpp
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_convert.cpp
    M utils/us_convert.h
    M utils/us_convertio.cpp
    M utils/us_convertio.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_defines.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_experiment.cpp
    M utils/us_experiment.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h
    R vcpkg
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #469 from ehb54/main

Merge main into somo-qt6


  Commit: 005210ec1222cf2098477fef7cbc62cdfdb1c08b
      https://github.com/ehb54/ultrascan3/commit/005210ec1222cf2098477fef7cbc62cdfdb1c08b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp

  Log Message:
  -----------
  Address PR #335 review feedback from doluk

- Qt::WFlags -> Qt::WindowFlags (lightingdlgbase.h)
- inline the const-wrapper save_svg overload (us3i_gui_util.cpp)
- drop dead Qt3/4 QT_VERSION include guard (us_config.cpp)
- hoist repeated regex construction to static const in
  fileNameCheck (us_hydrodyn.cpp), anaflex txt-extension checks
  (us_hydrodyn_anaflex_core.cpp), and the leading-'=' strip in
  US_Hydrodyn_Best::load (us_hydrodyn_best.cpp)
- move QRegularExpression include next to other Qt includes and
  simplify rx_spaces construction (us_hydrodyn_addresidue.cpp)
- remove duplicate QRegularExpression include (us_hydrodyn_bd_core.cpp)
- combine QRegularExpression rx construction with its pattern and
  drop the now-redundant setPattern call (us_hydrodyn_beads_load.cpp)


  Commit: dd1a79e3b1c92c841119387bd1da9de25d53ade4
      https://github.com/ehb54/ultrascan3/commit/dd1a79e3b1c92c841119387bd1da9de25d53ade4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge pull request #467 from ehb54/ehb54-issue-940

Fix Schannel TLS cipher mismatch on MSYS2/64 Windows builds


  Commit: 73d10e1ac2511df9f115150909f8efa4e15e2aa9
      https://github.com/ehb54/ultrascan3/commit/73d10e1ac2511df9f115150909f8efa4e15e2aa9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


  Commit: 4dd383414126596486f0a9d7f4a2594aa26cbbb2
      https://github.com/ehb54/ultrascan3/commit/4dd383414126596486f0a9d7f4a2594aa26cbbb2
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


  Commit: 67350cbc9b652fe2183c4a6889631191739a5cdb
      https://github.com/ehb54/ultrascan3/commit/67350cbc9b652fe2183c4a6889631191739a5cdb
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #335 from ehb54/somo-qt6

somo qt6 branch - initial commit from somo-dev


  Commit: 5924b0fe87a290c4e598e447b28d84cdc4780865
      https://github.com/ehb54/ultrascan3/commit/5924b0fe87a290c4e598e447b28d84cdc4780865
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-01 (Wed, 01 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into issue-941


  Commit: c31386b4ac5c903cb5949ed662b915274aed6658
      https://github.com/ehb54/ultrascan3/commit/c31386b4ac5c903cb5949ed662b915274aed6658
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M gui/us_help.cpp
    M utils/us_settings.cpp

  Log Message:
  -----------
  Merge pull request #468 from ehb54/issue-941

fix: update browser settings handling for MacOS and Windows


  Commit: 0e41a20a321c39a27e8379902ef769bd1c537011
      https://github.com/ehb54/ultrascan3/commit/0e41a20a321c39a27e8379902ef769bd1c537011
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-06 (Mon, 06 Jul 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .gitignore
    A VERSION
    M admin/codeql/docker/local.pri.somo
    M admin/release/linux.pl
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    M doc/manual/source/conf.py
    M gui/libus_gui.pro
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_help.cpp
    M gui/us_select_item.cpp
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M local.pri.template
    M makeall.sh
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_settings.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


Compare: https://github.com/ehb54/ultrascan3/compare/32aff34ae237...0e41a20a321c

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From noreply at github.com  Mon Jul  6 10:39:48 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 06 Jul 2026 09:39:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] 56ac62: add: nightly build
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/c31386-dc00ac@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 56ac62aee0f30eb92b6ba1c4fb11e0b3a4be919c
      https://github.com/ehb54/ultrascan3/commit/56ac62aee0f30eb92b6ba1c4fb11e0b3a4be919c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    A .github/workflows/nightly-builds.yml
    A .github/workflows/nightly-macos-arm.yml
    A .github/workflows/nightly-macos-intel.yml
    A .github/workflows/nightly-oraclelinux8.yml
    A .github/workflows/nightly-ubuntu.yml
    A .github/workflows/nightly-windows.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    M programs/us/CMakeLists.txt
    M scripts/bootstrap-linux.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M vcpkg.json

  Log Message:
  -----------
  add: nightly build


  Commit: 2d14470510d03383cc580dc728ceaf34b28a9111
      https://github.com/ehb54/ultrascan3/commit/2d14470510d03383cc580dc728ceaf34b28a9111
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: ce0e7bc73c888397b643b77a02254123918c717f
      https://github.com/ehb54/ultrascan3/commit/ce0e7bc73c888397b643b77a02254123918c717f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: b61ed7ce96981f2cb26951cc5d14ba599e34ae18
      https://github.com/ehb54/ultrascan3/commit/b61ed7ce96981f2cb26951cc5d14ba599e34ae18
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch '800-enhancement-nightly-build-using-vcpkg' of github.com:ehb54/ultrascan3 into 800-enhancement-nightly-build-using-vcpkg


  Commit: 438ca1c0535b533e30d747dbfaaea341f80130df
      https://github.com/ehb54/ultrascan3/commit/438ca1c0535b533e30d747dbfaaea341f80130df
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  mod: rollback to match main


  Commit: 97bcfb0c7e017363e4cad1a6b8cf95a30bed82be
      https://github.com/ehb54/ultrascan3/commit/97bcfb0c7e017363e4cad1a6b8cf95a30bed82be
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-01 (Fri, 01 May 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  fix: resolve warning


  Commit: 2964bb347925c13d2a1dcfe7b03f3ce469c6190a
      https://github.com/ehb54/ultrascan3/commit/2964bb347925c13d2a1dcfe7b03f3ce469c6190a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-02 (Sat, 02 May 2026)

  Changed paths:
    M .github/workflows/nightly-builds.yml
    M .github/workflows/nightly-oraclelinux8.yml
    M .github/workflows/nightly-ubuntu.yml
    M .github/workflows/release.yml
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M scripts/build.sh

  Log Message:
  -----------
  mod: standard naming and xz used


  Commit: a7f952b2fbd09af29abbe74039f4d006e6662f42
      https://github.com/ehb54/ultrascan3/commit/a7f952b2fbd09af29abbe74039f4d006e6662f42
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-18 (Mon, 18 May 2026)

  Changed paths:
    M .github/workflows/nightly-builds.yml
    M .github/workflows/nightly-macos-arm.yml
    M .github/workflows/nightly-macos-intel.yml
    M .github/workflows/nightly-oraclelinux8.yml
    M .github/workflows/nightly-ubuntu.yml
    M .github/workflows/nightly-windows.yml
    M .github/workflows/release.yml
    M scripts/bootstrap-linux.sh
    M us-build

  Log Message:
  -----------
  fix(ci): nightly gate logic, bootstrap improvements, SHA bump to d40ab4b6


  Commit: 3aca19dec6d034a4606e10eee12ebc053f6bcbd7
      https://github.com/ehb54/ultrascan3/commit/3aca19dec6d034a4606e10eee12ebc053f6bcbd7
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-05-18 (Mon, 18 May 2026)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 46622569dc9e5cae5f731a56d2200b57fc981db8
      https://github.com/ehb54/ultrascan3/commit/46622569dc9e5cae5f731a56d2200b57fc981db8
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-19 (Tue, 19 May 2026)

  Changed paths:
    M programs/us_analyte/CMakeLists.txt
    M programs/us_export_legacy/CMakeLists.txt

  Log Message:
  -----------
  fix: changed program names to match what us_win_data.cpp uses.


  Commit: 0b97fc731d6dc06bcc6f64ed95c91667a0f8a591
      https://github.com/ehb54/ultrascan3/commit/0b97fc731d6dc06bcc6f64ed95c91667a0f8a591
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-19 (Tue, 19 May 2026)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/800-enhancement-nightly-build-using-vcpkg' into 800-enhancement-nightly-build-using-vcpkg


  Commit: aa28f848f31dce5d87784af68a9ce96752fb6584
      https://github.com/ehb54/ultrascan3/commit/aa28f848f31dce5d87784af68a9ce96752fb6584
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  fix(cmake): find qhelpgenerator before add_subdirectory(doc/manual) so Qt help files are built on first configure


  Commit: ee3c66db7273692c74d982760682c646a13ed113
      https://github.com/ehb54/ultrascan3/commit/ee3c66db7273692c74d982760682c646a13ed113
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_properties.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 07f813016ff39565ddcf9e01ce3ca3a29ecc863a
      https://github.com/ehb54/ultrascan3/commit/07f813016ff39565ddcf9e01ce3ca3a29ecc863a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    A .github/workflows/nightly-build.yml
    R .github/workflows/nightly-builds.yml
    R .github/workflows/nightly-macos-arm.yml
    R .github/workflows/nightly-macos-intel.yml
    R .github/workflows/nightly-oraclelinux8.yml
    R .github/workflows/nightly-ubuntu.yml
    R .github/workflows/nightly-windows.yml
    M .github/workflows/on-demand-build.yml
    M .github/workflows/release.yml

  Log Message:
  -----------
  refactor: rename nightly build workflow files and update references for consistency


  Commit: 8ee0408d863d9af9868a15ba00610567482b5d1d
      https://github.com/ehb54/ultrascan3/commit/8ee0408d863d9af9868a15ba00610567482b5d1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 74a065b515b243ce83392ca76022b87d3d4dcb6c
      https://github.com/ehb54/ultrascan3/commit/74a065b515b243ce83392ca76022b87d3d4dcb6c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 32aff34ae2377dd1854ab45ea784dcac5a4731d0
      https://github.com/ehb54/ultrascan3/commit/32aff34ae2377dd1854ab45ea784dcac5a4731d0
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-04 (Thu, 04 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 0e41a20a321c39a27e8379902ef769bd1c537011
      https://github.com/ehb54/ultrascan3/commit/0e41a20a321c39a27e8379902ef769bd1c537011
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-06 (Mon, 06 Jul 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .gitignore
    A VERSION
    M admin/codeql/docker/local.pri.somo
    M admin/release/linux.pl
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    M doc/manual/source/conf.py
    M gui/libus_gui.pro
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_help.cpp
    M gui/us_select_item.cpp
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M local.pri.template
    M makeall.sh
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_settings.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: dc00acf48dd3b8ab26645b2b104a19d152e81d4a
      https://github.com/ehb54/ultrascan3/commit/dc00acf48dd3b8ab26645b2b104a19d152e81d4a
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-06 (Mon, 06 Jul 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    A .github/workflows/nightly-build.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    M programs/us/CMakeLists.txt
    M programs/us_analyte/CMakeLists.txt
    M programs/us_export_legacy/CMakeLists.txt
    M scripts/bootstrap-linux.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M us-build
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #417 from ehb54/800-enhancement-nightly-build-using-vcpkg

Add nightly build configuration


Compare: https://github.com/ehb54/ultrascan3/compare/c31386b4ac5c...dc00acf48dd3

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From noreply at github.com  Mon Jul  6 10:40:00 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 06 Jul 2026 09:40:00 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/800-enhancement-nightly-build-using-vcpkg/0e41a2-000000@github.com>

  Branch: refs/heads/800-enhancement-nightly-build-using-vcpkg
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Jul  7 14:15:02 2026
From: noreply at github.com (emre brookes)
Date: Tue, 07 Jul 2026 13:15:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 819778: Root: add US3_BUILD_SOMO
 option + add_subdirectory...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/227538-819778@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 819778c98085cee0706495af6bde9551f5bd0d6c
      https://github.com/ehb54/ultrascan3/commit/819778c98085cee0706495af6bde9551f5bd0d6c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-07 (Tue, 07 Jul 2026)

  Changed paths:
    M CMakeLists.txt
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  Root: add US3_BUILD_SOMO option + add_subdirectory(us_somo); harden SOMO for in-root build

- Root CMakeLists: option(US3_BUILD_SOMO OFF) and a guarded add_subdirectory(us_somo)
  (skipped in HPC ? SOMO is a Qt-GUI suite), replacing the commented placeholder.
- SOMO develop CMakeLists, for correctness when included via add_subdirectory:
  * pin CMAKE_CXX_STANDARD 17 in both modes (root sets a lower global standard);
  * only add_compile_definitions(INTEL) in standalone ? a root build already
    defines PLATFORM/TITLE globally, so INTEL would clash on TITLE.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul  7 15:02:16 2026
From: noreply at github.com (emre brookes)
Date: Tue, 07 Jul 2026 14:02:16 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9c1223: SOMO: define INTEL in root
 builds too (string -DPL...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/819778-9c1223@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9c12233a9772838baf81b604d861587c6eaeaaef
      https://github.com/ehb54/ultrascan3/commit/9c12233a9772838baf81b604d861587c6eaeaaef
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-07 (Tue, 07 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: define INTEL in root builds too (string -DPLATFORM/-DTITLE don't survive)

The root defines PLATFORM/TITLE via add_compile_definitions(PLATFORM="intel"),
but the string value doesn't survive CMake's quote-escaping into a usable macro
(same symptom as standalone: us_register.cpp sees PLATFORM "not declared").
Drop the standalone-only guard on INTEL ? the bareword arch macro works in both
modes and the parent's non-functional PLATFORM/TITLE cause no clash.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul  7 15:14:08 2026
From: noreply at github.com (emre brookes)
Date: Tue, 07 Jul 2026 14:14:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] be6537: SOMO: disable LTO for the
 subtree (root enables it...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/9c1223-be6537@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: be65378efe0fb20067e8352464442b4374b736e1
      https://github.com/ehb54/ultrascan3/commit/be65378efe0fb20067e8352464442b4374b736e1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-07 (Tue, 07 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: disable LTO for the subtree (root enables it globally)

The root build turns on CMAKE_INTERPROCEDURAL_OPTIMIZATION_RELEASE. LTO on the
shared libus_somo drops symbols the GUI apps link against (undefined references
to US_Register/US_Config/us_tr...). SOMO builds cleanly without LTO (standalone,
and its qmake build never used it), so disable it for this subtree only.

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul  7 15:29:25 2026
From: noreply at github.com (emre brookes)
Date: Tue, 07 Jul 2026 14:29:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 59b12e: SOMO: default symbol
 visibility in-subtree (root s...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-943/be6537-59b12e@github.com>

  Branch: refs/heads/ehb54-issue-943
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 59b12e5432131bef98078c9d1c06497d179791b3
      https://github.com/ehb54/ultrascan3/commit/59b12e5432131bef98078c9d1c06497d179791b3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-07 (Tue, 07 Jul 2026)

  Changed paths:
    M us_somo/develop/CMakeLists.txt

  Log Message:
  -----------
  SOMO: default symbol visibility in-subtree (root sets -fvisibility=hidden)

admin/cmake/platform-config.cmake adds -fvisibility=hidden globally. SOMO's
classes aren't export-annotated, so libus_somo.so ended up exporting NO symbols
and the GUI apps failed to link (undefined US_Register/US_Admin/US_Config/...).
Restore default visibility for the SOMO subtree (as standalone / qmake).

Refs ehb54/ultrascan-tickets#943

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Wed Jul  8 13:28:19 2026
From: noreply at github.com (github-actions[bot])
Date: Wed, 08 Jul 2026 12:28:19 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/tags/nightly/000000-dc00ac@github.com>

  Branch: refs/tags/nightly
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Jul  8 14:10:23 2026
From: noreply at github.com (alexsav815)
Date: Wed, 08 Jul 2026 13:10:23 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/000000-dc00ac@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Jul  8 17:14:55 2026
From: noreply at github.com (alexsav815)
Date: Wed, 08 Jul 2026 16:14:55 -0700
Subject: [us-commits] [ehb54/ultrascan3] 63750e: GMP:dataDisk - work towards
 extention of the uploa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/dc00ac-63750e@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
      https://github.com/ehb54/ultrascan3/commit/63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...



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From noreply at github.com  Wed Jul  8 22:01:33 2026
From: noreply at github.com (alexsav815)
Date: Wed, 08 Jul 2026 21:01:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] e1345a: [more Work on] GMP:dataDisk
 - work towards extenti...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/63750e-e1345a@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e1345a3206da2fc4942f218fc813fda1682f69cd
      https://github.com/ehb54/ultrascan3/commit/e1345a3206da2fc4942f218fc813fda1682f69cd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...



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From noreply at github.com  Wed Jul  8 23:39:10 2026
From: noreply at github.com (alexsav815)
Date: Wed, 08 Jul 2026 22:39:10 -0700
Subject: [us-commits] [ehb54/ultrascan3] f51e6b: [1more Work on]
 GMP:dataDisk - work towards extent...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/e1345a-f51e6b@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f51e6bac3a1d4943c3291b8db1525d9f18419844
      https://github.com/ehb54/ultrascan3/commit/f51e6bac3a1d4943c3291b8db1525d9f18419844
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...



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From noreply at github.com  Wed Jul  8 23:49:52 2026
From: noreply at github.com (alexsav815)
Date: Wed, 08 Jul 2026 22:49:52 -0700
Subject: [us-commits] [ehb54/ultrascan3] 044f72: [2more Work on]
 GMP:dataDisk - work towards extent...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/f51e6b-044f72@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 044f72440db40f7632169394d6ee0b593998562a
      https://github.com/ehb54/ultrascan3/commit/044f72440db40f7632169394d6ee0b593998562a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...



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From noreply at github.com  Thu Jul  9 01:13:47 2026
From: noreply at github.com (alexsav815)
Date: Thu, 09 Jul 2026 00:13:47 -0700
Subject: [us-commits] [ehb54/ultrascan3] 37a4a0: [33more Work on]
 GMP:dataDisk - work towards exten...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/044f72-37a4a0@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 37a4a06b5999bf9f3c243fbe38ede1a3fea379af
      https://github.com/ehb54/ultrascan3/commit/37a4a06b5999bf9f3c243fbe38ede1a3fea379af
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [33more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush



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From noreply at github.com  Thu Jul  9 08:09:03 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 09 Jul 2026 07:09:03 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute/000000-dc00ac@github.com>

  Branch: refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Jul  9 08:24:42 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 09 Jul 2026 07:24:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8567f6: Add missing execute
 permission to shell scripts in...
Message-ID: <ehb54/ultrascan3/push/refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute/dc00ac-a43e63@github.com>

  Branch: refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
      https://github.com/ehb54/ultrascan3/commit/8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Add missing execute permission to shell scripts in scripts/


  Commit: a43e638e495930eb941519ece5e33498e89fd1ec
      https://github.com/ehb54/ultrascan3/commit/a43e638e495930eb941519ece5e33498e89fd1ec
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: improve python3 version check and update-alternatives registration


Compare: https://github.com/ehb54/ultrascan3/compare/dc00acf48dd3...a43e638e4959

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From noreply at github.com  Thu Jul  9 08:59:01 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 09 Jul 2026 07:59:01 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7f15d5: mod: make executable
Message-ID: <ehb54/ultrascan3/push/refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute/a43e63-7f15d5@github.com>

  Branch: refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7f15d549465db31e042d59a5686dc8e2cd2b056a
      https://github.com/ehb54/ultrascan3/commit/7f15d549465db31e042d59a5686dc8e2cd2b056a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  mod: make executable



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From noreply at github.com  Thu Jul  9 10:40:39 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 09 Jul 2026 09:40:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] 36dd73: fix: conditionally include
 python39 packages based...
Message-ID: <ehb54/ultrascan3/push/refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute/7f15d5-36dd73@github.com>

  Branch: refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 36dd7367a1f0d64008dcf711a3c7265de78867f7
      https://github.com/ehb54/ultrascan3/commit/36dd7367a1f0d64008dcf711a3c7265de78867f7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  fix: conditionally include python39 packages based on python3 version



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From noreply at github.com  Thu Jul  9 18:03:53 2026
From: noreply at github.com (alexsav815)
Date: Thu, 09 Jul 2026 17:03:53 -0700
Subject: [us-commits] [ehb54/ultrascan3] f22ca7: [Back compatibility with a
 1-channel RA-sim. data]...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/37a4a0-f22ca7@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f22ca7ce48ab875427dac618f91e473b40d937ce
      https://github.com/ehb54/ultrascan3/commit/f22ca7ce48ab875427dac618f91e473b40d937ce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [Back compatibility with a 1-channel RA-sim. data] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush



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From noreply at github.com  Fri Jul 10 07:12:30 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 06:12:30 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/000000-dc00ac@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Jul 10 07:18:30 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 06:18:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] 20ccb4: fix: exclude GMP tools from
 macOS installer build
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/dc00ac-20ccb4@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 20ccb45b6967b8c3f581b968b80d854960bc3d13
      https://github.com/ehb54/ultrascan3/commit/20ccb45b6967b8c3f581b968b80d854960bc3d13
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  fix: exclude GMP tools from macOS installer build



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From noreply at github.com  Fri Jul 10 07:23:46 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 06:23:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 464018: fix: exclude academic GMP
 tools from macOS install...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/20ccb4-464018@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4640187c336491ae4198499a67942de773ff96e0
      https://github.com/ehb54/ultrascan3/commit/4640187c336491ae4198499a67942de773ff96e0
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  fix: exclude academic GMP tools from macOS installer build



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From noreply at github.com  Fri Jul 10 07:36:20 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 06:36:20 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/843-request-macintosh-style-is-deprecated/000000-dc00ac@github.com>

  Branch: refs/heads/843-request-macintosh-style-is-deprecated
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Jul 10 07:37:54 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 06:37:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 73a270: fix: update default GUI
 style for MacOS to 'macOS'...
Message-ID: <ehb54/ultrascan3/push/refs/heads/843-request-macintosh-style-is-deprecated/dc00ac-73a270@github.com>

  Branch: refs/heads/843-request-macintosh-style-is-deprecated
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 73a27078af4dfa87f2178651d2907835d3cf9b92
      https://github.com/ehb54/ultrascan3/commit/73a27078af4dfa87f2178651d2907835d3cf9b92
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  fix: update default GUI style for MacOS to 'macOS' in Qt 6



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From noreply at github.com  Fri Jul 10 08:04:49 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 07:04:49 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/758-bug-extra-logos/000000-dc00ac@github.com>

  Branch: refs/heads/758-bug-extra-logos
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Jul 10 09:03:00 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 08:03:00 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2cd235: GMP:IP+RI - prevent crush
 at 4. EDIT when IP loade...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/f22ca7-2cd235@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
      https://github.com/ehb54/ultrascan3/commit/2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP:IP+RI - prevent crush at 4. EDIT when IP loaded first due to leagcy protocol re-using and scan_nth set to 0...



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From noreply at github.com  Fri Jul 10 10:16:38 2026
From: noreply at github.com (emre brookes)
Date: Fri, 10 Jul 2026 09:16:38 -0700
Subject: [us-commits] [ehb54/ultrascan3] f087cb: Fix SIGSEGV in HPLC SAXS
 get_peak: use file, not w...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/768ca9-f087cb@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f087cb2f504871f6f79df846004b7ea6f0926d57
      https://github.com/ehb54/ultrascan3/commit/f087cb2f504871f6f79df846004b7ea6f0926d57
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp

  Log Message:
  -----------
  Fix SIGSEGV in HPLC SAXS get_peak: use file, not wheel_file, for end-range clamp

get_peak() operates on its `file` argument, but the gauss-fit-end range
clamp compared the typed value against f_qs[ wheel_file ].back() instead
of f_qs[ file ].back(). During Repeak, wheel_file is stale or empty (it is
never set in repeak()), so f_qs[ wheel_file ] default-inserts an empty
vector and .back() dereferences nullptr-8 (0xfffffffffffffff8), crashing.

The check is now symmetric with the start-range clamp above and with its
own body on the next line, both of which key on `file`.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 10 10:31:35 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 09:31:35 -0700
Subject: [us-commits] [ehb54/ultrascan3] 73a270: fix: update default GUI
 style for MacOS to 'macOS'...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/dc00ac-e69cf6@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 73a27078af4dfa87f2178651d2907835d3cf9b92
      https://github.com/ehb54/ultrascan3/commit/73a27078af4dfa87f2178651d2907835d3cf9b92
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  fix: update default GUI style for MacOS to 'macOS' in Qt 6


  Commit: e69cf69c249ce62533cd87f25c93dde746147ffa
      https://github.com/ehb54/ultrascan3/commit/e69cf69c249ce62533cd87f25c93dde746147ffa
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge pull request #474 from ehb54/843-request-macintosh-style-is-deprecated

Update default GUI style for macOS in Qt 6


Compare: https://github.com/ehb54/ultrascan3/compare/dc00acf48dd3...e69cf69c249c

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From noreply at github.com  Fri Jul 10 10:31:49 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 09:31:49 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/843-request-macintosh-style-is-deprecated/73a270-000000@github.com>

  Branch: refs/heads/843-request-macintosh-style-is-deprecated
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Jul 10 10:32:25 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 09:32:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 73a270: fix: update default GUI
 style for MacOS to 'macOS'...
Message-ID: <ehb54/ultrascan3/push/refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute/36dd73-aa00be@github.com>

  Branch: refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 73a27078af4dfa87f2178651d2907835d3cf9b92
      https://github.com/ehb54/ultrascan3/commit/73a27078af4dfa87f2178651d2907835d3cf9b92
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  fix: update default GUI style for MacOS to 'macOS' in Qt 6


  Commit: e69cf69c249ce62533cd87f25c93dde746147ffa
      https://github.com/ehb54/ultrascan3/commit/e69cf69c249ce62533cd87f25c93dde746147ffa
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge pull request #474 from ehb54/843-request-macintosh-style-is-deprecated

Update default GUI style for macOS in Qt 6


  Commit: aa00be99171275b2c91132092e04bce0f9cace1d
      https://github.com/ehb54/ultrascan3/commit/aa00be99171275b2c91132092e04bce0f9cace1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge branch 'main' into 955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute


Compare: https://github.com/ehb54/ultrascan3/compare/36dd7367a1f0...aa00be991712

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From noreply at github.com  Fri Jul 10 11:06:26 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 10:06:26 -0700
Subject: [us-commits] [ehb54/ultrascan3] a2f9d2: fix: remove unused logo
 handling from US_Reporter
Message-ID: <ehb54/ultrascan3/push/refs/heads/758-bug-extra-logos/dc00ac-a2f9d2@github.com>

  Branch: refs/heads/758-bug-extra-logos
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a2f9d27b561cba63475ff3dda2637d308c1654e9
      https://github.com/ehb54/ultrascan3/commit/a2f9d27b561cba63475ff3dda2637d308c1654e9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    R etc/beckman_logo.png
    M etc/etc_belongs_list.txt
    R etc/logo_hsc.png
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h

  Log Message:
  -----------
  fix: remove unused logo handling from US_Reporter



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From noreply at github.com  Fri Jul 10 11:07:00 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 10:07:00 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8567f6: Add missing execute
 permission to shell scripts in...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/e69cf6-833773@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
      https://github.com/ehb54/ultrascan3/commit/8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Add missing execute permission to shell scripts in scripts/


  Commit: a43e638e495930eb941519ece5e33498e89fd1ec
      https://github.com/ehb54/ultrascan3/commit/a43e638e495930eb941519ece5e33498e89fd1ec
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: improve python3 version check and update-alternatives registration


  Commit: 7f15d549465db31e042d59a5686dc8e2cd2b056a
      https://github.com/ehb54/ultrascan3/commit/7f15d549465db31e042d59a5686dc8e2cd2b056a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  mod: make executable


  Commit: 36dd7367a1f0d64008dcf711a3c7265de78867f7
      https://github.com/ehb54/ultrascan3/commit/36dd7367a1f0d64008dcf711a3c7265de78867f7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  fix: conditionally include python39 packages based on python3 version


  Commit: aa00be99171275b2c91132092e04bce0f9cace1d
      https://github.com/ehb54/ultrascan3/commit/aa00be99171275b2c91132092e04bce0f9cace1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge branch 'main' into 955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute


  Commit: 833773e788e0239ba91dae8b4fdd7110a147fb4b
      https://github.com/ehb54/ultrascan3/commit/833773e788e0239ba91dae8b4fdd7110a147fb4b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge pull request #472 from ehb54/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute

Add execute permission to shell scripts and improve version check


Compare: https://github.com/ehb54/ultrascan3/compare/e69cf69c249c...833773e788e0

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From noreply at github.com  Fri Jul 10 11:07:05 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 10:07:05 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute/aa00be-000000@github.com>

  Branch: refs/heads/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Jul 10 11:46:46 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 10:46:46 -0700
Subject: [us-commits] [ehb54/us3lims_common] d7e6bf: fix: sha commit update
Message-ID: <ehb54/us3lims_common/push/refs/heads/780-request-pbs-gfac-cleanup/cf287c-360369@github.com>

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_common
  Commit: d7e6bf08f525197b266920787c3d969398b09b10
      https://github.com/ehb54/us3lims_common/commit/d7e6bf08f525197b266920787c3d969398b09b10
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  fix: sha commit update


  Commit: 3f0fbf730f024188579702b09bc22cf574ca7248
      https://github.com/ehb54/us3lims_common/commit/3f0fbf730f024188579702b09bc22cf574ca7248
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #19 from ehb54/902-update-bump-pr-sha-us3lims_common

Fix SHA commit update


  Commit: b2febe50a398d26dd8aad44be9607bcec7e4f54a
      https://github.com/ehb54/us3lims_common/commit/b2febe50a398d26dd8aad44be9607bcec7e4f54a
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Bump version to 4.1.0


  Commit: 2257f349a7f87f57990c1a9e6fa79f25257682e3
      https://github.com/ehb54/us3lims_common/commit/2257f349a7f87f57990c1a9e6fa79f25257682e3
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Merge pull request #20 from ehb54/bump-to-v4.1.0

Bump to v4.1.0


  Commit: a6f9e2ef5a75d86857bb1a34acafa0e6573a7b62
      https://github.com/ehb54/us3lims_common/commit/a6f9e2ef5a75d86857bb1a34acafa0e6573a7b62
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php
    M global_config.php.template

  Log Message:
  -----------
  Validate sbatch submission status before recording a gfacID

submit_job() never checked the exit status of the sbatch/qsub exec()
call, and parsed the job ID positionally from the first output line
assuming it was always "Submitted batch job <N>". Under scheduler
load, sbatch can instead fail with e.g. "sbatch: error: Batch job
submission failed: Socket timed out on send/recv operation" - the
positional parse of that line happens to land on the literal word
"job", which then got stored as gfacID and tracked through the rest
of the pipeline as if a real job existed, eventually surfacing much
later and opaquely as "Failed data fetch" during cleanup.

Validate the sbatch output against /^Submitted batch job\s+(\d+)/
and check exec()'s exit status before accepting a job ID. Retry the
submission with exponential backoff on failure (configurable via
$global_sbatch_submit_retries / $global_sbatch_submit_retry_wait_seconds
in global_config.php, overridable per-cluster), since this class of
failure is transient and load-related. If all retries are exhausted,
update_db() now marks the request SUBMIT_TIMEOUT with the real error
instead of recording an empty/bogus gfacID and launching a jobmonitor
to watch a job that was never submitted.

Fixes ehb54/ultrascan-tickets#915


  Commit: 847e5742c9b159e56f1b3bbc82d72546fe9ec7a2
      https://github.com/ehb54/us3lims_common/commit/847e5742c9b159e56f1b3bbc82d72546fe9ec7a2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Extract mark_autoflow_submit_failed() to remove duplication

The submission-failure handling in update_db() inlined the same
connect/query/error/close pattern already used by the rest of the
function. Pull it into a small dedicated method instead.


  Commit: 65ff7461ff08cfb95bbb820e7270133bc9672a2a
      https://github.com/ehb54/us3lims_common/commit/65ff7461ff08cfb95bbb820e7270133bc9672a2a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Mark mark_autoflow_submit_failed() as private

Fixes the SonarCloud-flagged missing visibility modifier (php:S1784).


  Commit: 07777995aaccb65764ffb804c55ae5e29c8c6369
      https://github.com/ehb54/us3lims_common/commit/07777995aaccb65764ffb804c55ae5e29c8c6369
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:

  Log Message:
  -----------
  Retrigger SonarCloud analysis after fixing cpd.exclusions setting


  Commit: ed4504fe59fb16de017293bf2a1168bcc884dee1
      https://github.com/ehb54/us3lims_common/commit/ed4504fe59fb16de017293bf2a1168bcc884dee1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Reduce submit_job() cognitive complexity, fix method naming

Extract the sbatch/qsub retry loop and result-parsing logic out of
submit_job() into two small private helpers (attemptSubmit(),
parseSubmitResult()), addressing SonarCloud's flagged Cognitive
Complexity (29 vs 15 allowed). No behavior change, just relocated
code.

Also rename mark_autoflow_submit_failed() to markAutoflowSubmitFailed()
to satisfy the PHP method naming convention rule (php:S100).


  Commit: 367f2e89e377f413ebb2c4c5a3baef1074ee3646
      https://github.com/ehb54/us3lims_common/commit/367f2e89e377f413ebb2c4c5a3baef1074ee3646
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M class/submit_local.php
    M global_config.php.template

  Log Message:
  -----------
  Merge pull request #21 from ehb54/ehb54-issue-915

Validate sbatch submission status before recording a gfacID


  Commit: 651d220f49c593fb9a5d43d699e8ac1797b0818b
      https://github.com/ehb54/us3lims_common/commit/651d220f49c593fb9a5d43d699e8ac1797b0818b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Reset $output between sbatch retry attempts in attemptSubmit()

PHP's exec() appends to $output rather than replacing it. Since $output
was only initialized once before the retry loop added in PR #21,
parseSubmitResult()'s check of $output[0] (used to extract the slurm job
ID) stayed permanently stuck on the first attempt's output for the rest
of the retries, even after a later attempt genuinely succeeded.

Confirmed live via us3lims_dbutils' uslims_autoflow_test.php
--fake-sbatch fail-once: after a deliberately-failed first attempt,
attempts 2-4 each succeeded for real (three separate, duplicate jobs
submitted to the actual cluster) but were still misjudged as failures,
so the whole submission ended up reported FAILED with one of the
duplicate real jobs left running with no LIMS record of it.

Fixes ehb54/ultrascan-tickets#931


  Commit: 2a60c1339566ae809b747a57f9810040eaa2b306
      https://github.com/ehb54/us3lims_common/commit/2a60c1339566ae809b747a57f9810040eaa2b306
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-24 (Wed, 24 Jun 2026)

  Changed paths:
    M class/submit_local.php

  Log Message:
  -----------
  Merge pull request #22 from ehb54/ehb54-issue-931

Reset $output between sbatch retry attempts in attemptSubmit()


  Commit: ded16d851d2f1334891c40665ef8ed01a005d92d
      https://github.com/ehb54/us3lims_common/commit/ded16d851d2f1334891c40665ef8ed01a005d92d
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-03 (Fri, 03 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: 4e25de4a189a80e74e25cde0e799e908ba9c0abf
      https://github.com/ehb54/us3lims_common/commit/4e25de4a189a80e74e25cde0e799e908ba9c0abf
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #23 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


  Commit: a20741d7a949cc83a15dd33374cde79aad159779
      https://github.com/ehb54/us3lims_common/commit/a20741d7a949cc83a15dd33374cde79aad159779
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-05 (Sun, 05 Jul 2026)

  Changed paths:
    M class/submit_slurm.php
    M global_config.php.template

  Log Message:
  -----------
  Port sbatch retry/backoff and validation from submit_local.php (#915/#931)

submit_local.php is being removed in favor of submit_slurm.php's SSH+Slurm
path, but origin/main independently hardened submit_local.php's submit_job()
against transient sbatch failures (exit-status validation, --parsable
output validation, exponential-backoff retry, SUBMIT_TIMEOUT on exhausted
retries) to fix tickets #915 and #931. Port that behavior into
submit_slurm.php before it becomes the only submission path, via a new
runExec() seam so the retry logic is unit-testable without a real cluster.


  Commit: 8eabb9204c9029705ac2341cb980b3d2125a6407
      https://github.com/ehb54/us3lims_common/commit/8eabb9204c9029705ac2341cb980b3d2125a6407
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-05 (Sun, 05 Jul 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    A VERSION

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 780-request-pbs-gfac-cleanup

# Conflicts:
#	class/submit_local.php


  Commit: 360369d24f15b6773737d956e5618bd54f142160
      https://github.com/ehb54/us3lims_common/commit/360369d24f15b6773737d956e5618bd54f142160
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  fix: set max queue/run time to 0 so jobs aren't ended early.


Compare: https://github.com/ehb54/us3lims_common/compare/cf287c5a9797...360369d24f15

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From noreply at github.com  Fri Jul 10 12:03:40 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 10 Jul 2026 11:03:40 -0700
Subject: [us-commits] [ehb54/us3lims_common] 9c9f98: refactor: change
 function visibility to public in ...
Message-ID: <ehb54/us3lims_common/push/refs/heads/780-request-pbs-gfac-cleanup/360369-9c9f98@github.com>

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_common
  Commit: 9c9f98ccd4dd689284d56381be863fb775181240
      https://github.com/ehb54/us3lims_common/commit/9c9f98ccd4dd689284d56381be863fb775181240
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M class/submit_slurm.php

  Log Message:
  -----------
  refactor: change function visibility to public in submit_slurm.php



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From noreply at github.com  Fri Jul 10 13:20:12 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 12:20:12 -0700
Subject: [us-commits] [ehb54/ultrascan3] f4915d: GMP:3. IMPORT - test:
 capture message for disparat...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/2cd235-f4915d@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f4915d875bcf8965884d7059dab0011045ae16b8
      https://github.com/ehb54/ultrascan3/commit/f4915d875bcf8965884d7059dab0011045ae16b8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  GMP:3. IMPORT - test: capture message for disparate scans...



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From noreply at github.com  Fri Jul 10 13:29:14 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 12:29:14 -0700
Subject: [us-commits] [ehb54/ultrascan3] d81051: [1]GMP:3. IMPORT - test:
 capture message for dispa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/f4915d-d81051@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d81051ec6903d845918fcfa3b93d324988b84d52
      https://github.com/ehb54/ultrascan3/commit/d81051ec6903d845918fcfa3b93d324988b84d52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1]GMP:3. IMPORT - test: capture message for disparate scans...



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From noreply at github.com  Fri Jul 10 13:37:37 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 12:37:37 -0700
Subject: [us-commits] [ehb54/ultrascan3] f28932: [2]GMP:3. IMPORT - test:
 capture message for dispa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/d81051-f28932@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f289321afa9b9b656d8bde7b11a50b5e27b397a2
      https://github.com/ehb54/ultrascan3/commit/f289321afa9b9b656d8bde7b11a50b5e27b397a2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2]GMP:3. IMPORT - test: capture message for disparate scans...



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From noreply at github.com  Fri Jul 10 14:00:57 2026
From: noreply at github.com (emre brookes)
Date: Fri, 10 Jul 2026 13:00:57 -0700
Subject: [us-commits] [ehb54/ultrascan3] c48d22: HPLC/KIN Make I(q): clarify
 the top-% peak average...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-claude-avg-conc-docs/000000-c48d22@github.com>

  Branch: refs/heads/somo-dev-claude-avg-conc-docs
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c48d229f1006f0bd3360ff1fdf821482d198087d
      https://github.com/ehb54/ultrascan3/commit/c48d229f1006f0bd3360ff1fdf821482d198087d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_ciq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/somo/doc/manual/somo/saxs_hplc_ciq.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  HPLC/KIN Make I(q): clarify the top-% peak average retains concentration

Relabel the "average and normalize" checkbox to "average", add a tooltip,
and update the manual, to make explicit that the existing per-peak "_avg"
curve is scaled to the mean concentration of the averaged frames (the
concentration-scaled result, for Guinier/MW) while "_avg_n" is normalized
to concentration 1.0. No change to the averaging computation.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 10 14:08:18 2026
From: noreply at github.com (emre brookes)
Date: Fri, 10 Jul 2026 13:08:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] 36a225: Format Make I(q) average
 tooltip with HTML line br...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-claude-avg-conc-docs/c48d22-36a225@github.com>

  Branch: refs/heads/somo-dev-claude-avg-conc-docs
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 36a225651effc35e6944ed6c878c58c8ba575af1
      https://github.com/ehb54/ultrascan3/commit/36a225651effc35e6944ed6c878c58c8ba575af1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_ciq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp

  Log Message:
  -----------
  Format Make I(q) average tooltip with HTML line breaks

Qt renders the tooltip as rich text, so split the single run-on line into
per-suffix lines with <br> for readability.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 10 14:57:28 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 13:57:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] 857f3e: [And pass to 6.REPORT &&
 print it]GMP:3. IMPORT - ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/f28932-857f3e@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 857f3efd29534ce5ce6cf14c840be389eebd9b74
      https://github.com/ehb54/ultrascan3/commit/857f3efd29534ce5ce6cf14c840be389eebd9b74
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...



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From noreply at github.com  Fri Jul 10 16:54:43 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 15:54:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2a4da2: [[1]And pass to 6.REPORT &&
 print it]GMP:3. IMPORT...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/857f3e-2a4da2@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
      https://github.com/ehb54/ultrascan3/commit/2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [[1]And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...



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From noreply at github.com  Fri Jul 10 20:47:39 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 19:47:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] d56a96: [And for Audit Trail -- And
 pass to 6.REPORT && pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/2a4da2-d56a96@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d56a96153cae267abf3f0ab713d600e6c37a16ad
      https://github.com/ehb54/ultrascan3/commit/d56a96153cae267abf3f0ab713d600e6c37a16ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [And for Audit Trail -- And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...



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From noreply at github.com  Fri Jul 10 21:20:01 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 20:20:01 -0700
Subject: [us-commits] [ehb54/ultrascan3] e1a744: GMP:Audit Trail - add
 progress dialog for fetching...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/d56a96-e1a744@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e1a744a5b128a49750aed0f58d5b988527a78d00
      https://github.com/ehb54/ultrascan3/commit/e1a744a5b128a49750aed0f58d5b988527a78d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...



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From noreply at github.com  Fri Jul 10 21:24:39 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 20:24:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] beb102: [1]GMP:Audit Trail - add
 progress dialog for fetch...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/e1a744-beb102@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: beb1029bcdca1b2612f23cf65f739021388aac1f
      https://github.com/ehb54/ultrascan3/commit/beb1029bcdca1b2612f23cf65f739021388aac1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [1]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...



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From noreply at github.com  Fri Jul 10 21:29:19 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 20:29:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] 83fbef: [2]GMP:Audit Trail - add
 progress dialog for fetch...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/beb102-83fbef@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 83fbeffb53ca1d9a82583aa5a62cdc4527299f12
      https://github.com/ehb54/ultrascan3/commit/83fbeffb53ca1d9a82583aa5a62cdc4527299f12
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...



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From noreply at github.com  Fri Jul 10 21:37:55 2026
From: noreply at github.com (alexsav815)
Date: Fri, 10 Jul 2026 20:37:55 -0700
Subject: [us-commits] [ehb54/ultrascan3] 015742: [ the GMP run list is now
 cached for the life of t...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/83fbef-015742@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
      https://github.com/ehb54/ultrascan3/commit/01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [ the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...



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From noreply at github.com  Sat Jul 11 02:52:43 2026
From: noreply at github.com (alexsav815)
Date: Sat, 11 Jul 2026 01:52:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] 828342: [anf add Refresh list from
 inside GMP run list: t...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/015742-828342@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 828342afc1ebd1342fb402beb9010070781b07b7
      https://github.com/ehb54/ultrascan3/commit/828342afc1ebd1342fb402beb9010070781b07b7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  [anf add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...



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From noreply at github.com  Sat Jul 11 03:05:05 2026
From: noreply at github.com (alexsav815)
Date: Sat, 11 Jul 2026 02:05:05 -0700
Subject: [us-commits] [ehb54/ultrascan3] 10bd64: [[add option to Cancel scan,
 but not the first tim...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/828342-10bd64@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 10bd647e3ac0e99176196271ff1d6b97645cc030
      https://github.com/ehb54/ultrascan3/commit/10bd647e3ac0e99176196271ff1d6b97645cc030
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [[add option to Cancel scan, but not the first time]and add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...



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From noreply at github.com  Sat Jul 11 03:41:55 2026
From: noreply at github.com (alexsav815)
Date: Sat, 11 Jul 2026 02:41:55 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9d2438: GMP:eSignatures -- same
 user experience improvemen...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/10bd64-9d2438@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9d2438e1c6cec27070001ad1631548c32ccea3b4
      https://github.com/ehb54/ultrascan3/commit/9d2438e1c6cec27070001ad1631548c32ccea3b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...



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From noreply at github.com  Sat Jul 11 10:04:45 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 09:04:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] c48d22: HPLC/KIN Make I(q): clarify
 the top-% peak average...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/f087cb-df7f39@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c48d229f1006f0bd3360ff1fdf821482d198087d
      https://github.com/ehb54/ultrascan3/commit/c48d229f1006f0bd3360ff1fdf821482d198087d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_ciq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/somo/doc/manual/somo/saxs_hplc_ciq.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  HPLC/KIN Make I(q): clarify the top-% peak average retains concentration

Relabel the "average and normalize" checkbox to "average", add a tooltip,
and update the manual, to make explicit that the existing per-peak "_avg"
curve is scaled to the mean concentration of the averaged frames (the
concentration-scaled result, for Guinier/MW) while "_avg_n" is normalized
to concentration 1.0. No change to the averaging computation.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: 36a225651effc35e6944ed6c878c58c8ba575af1
      https://github.com/ehb54/ultrascan3/commit/36a225651effc35e6944ed6c878c58c8ba575af1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_ciq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp

  Log Message:
  -----------
  Format Make I(q) average tooltip with HTML line breaks

Qt renders the tooltip as rich text, so split the single run-on line into
per-suffix lines with <br> for readability.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: df7f39c0342f4f58c0aa899e350230f2b5b3e479
      https://github.com/ehb54/ultrascan3/commit/df7f39c0342f4f58c0aa899e350230f2b5b3e479
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_ciq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/somo/doc/manual/somo/saxs_hplc_ciq.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Merge pull request #476 from ehb54/somo-dev-claude-avg-conc-docs

HPLC/KIN Make I(q): document that the top-% peak average retains concentration (option A)


Compare: https://github.com/ehb54/ultrascan3/compare/f087cb2f5048...df7f39c0342f

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From noreply at github.com  Sat Jul 11 10:05:22 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 09:05:22 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-claude-avg-conc-docs/36a225-000000@github.com>

  Branch: refs/heads/somo-dev-claude-avg-conc-docs
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sat Jul 11 10:16:58 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 09:16:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] a0bd90: SAXS extrap-to-c0: add
 Zimm/Primus mode toggle
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/000000-a0bd90@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a0bd9077dbd128970d0b0235a106fc8cb14c33c4
      https://github.com/ehb54/ultrascan3/commit/a0bd9077dbd128970d0b0235a106fc8cb14c33c4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp

  Log Message:
  -----------
  SAXS extrap-to-c0: add Zimm/Primus mode toggle

The zero-concentration extrapolation previously always produced the
concentration-normalized I(q)/c intercept (Zimm-style, tagged Conc:1).
Comparing against ATSAS Primus/almerge output on real alpha-synuclein
data showed almerge instead reports absolute intensity on the
highest-concentration curve's scale.

Add a "Primus mode" checkbox to the concentration-assignment dialog.
When checked, do_extrap_c0:
  1. scales each curve onto the highest-concentration (reference) curve
     by a least-squares factor over the common q-grid,
  2. linearly extrapolates the scaled ABSOLUTE intensity vs c to c=0
     (not I/c), keeping the output on the reference's absolute scale,
  3. carries the reference curve's error bars into the output and tags
     it with the reference concentration instead of Conc:1.

Unchecked (default) preserves the existing Zimm behavior exactly.

Verified against ATSAS zc_001.dat: reproduces the result to ~1.5%
median at low q, with internal scale factors matching almerge's
printed factors.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 10:30:24 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 09:30:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] d57980: SAXS extrap-to-c0: drive
 extrapolation from select...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/a0bd90-d57980@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d579806535ad562d35e8b5173e1d728a478a9431
      https://github.com/ehb54/ultrascan3/commit/d579806535ad562d35e8b5173e1d728a478a9431
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp

  Log Message:
  -----------
  SAXS extrap-to-c0: drive extrapolation from selected rows

The concentration dialog now uses row selection (highlight) to choose
which curves are extrapolated:
  - whole-row multi-selection (ExtendedSelection); all rows selected by
    default, preserving the prior "extrapolate all" behavior,
  - the Extrapolate button is enabled only when >= 3 rows are selected
    and every selected row has a valid concentration,
  - the status line reports the selection/validity state,
  - only the selected curves' concentrations are returned; do_extrap_c0
    narrows its working set to the selected names.

Unselected rows no longer need a valid concentration to proceed.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 10:42:24 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 09:42:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] cc33f6: SAXS extrap-to-c0:
 method-tagged names, Help butto...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/d57980-cc33f6@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cc33f66d9056e834d6f144860d8b13a431cd6d56
      https://github.com/ehb54/ultrascan3/commit/cc33f66d9056e834d6f144860d8b13a431cd6d56
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    A us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: method-tagged names, Help button, manual page

- Output curve name now carries a method token so Zimm vs Primus results
  are distinguishable: <prefix>_extrap_c0_zimm / _extrap_c0_primus (the
  "zimm"/"primus" wording may change later).
- Added a Help button to the concentration/selection dialog, opening a
  new SOMO manual page.
- Added us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html documenting
  the module, both modes, curve selection, and output naming. Screenshot
  placeholders (somo_saxs_extrap_c0_launch/dialog/result.png) are marked
  with HTML comments pending images.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 11:02:15 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 10:02:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] 26e872: SAXS extrap-to-c0: handle
 already-normalized I*(q)...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/cc33f6-26e872@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 26e872e06367692095f323149f9f66f2f48ede60
      https://github.com/ehb54/ultrascan3/commit/26e872e06367692095f323149f9f66f2f48ede60
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: handle already-normalized I*(q) inputs

Curves named "*_Istarq_*" are already I*(q) (header units g/mol,
I(0)=MW): their intensity is already concentration-normalized even
though their Conc: header is non-unity. Previously the Zimm fit divided
every curve's intensity by its concentration, double-normalizing these.

Now:
  - Zimm mode uses an I*(q) curve's intensity as-is (no divide by c),
    while still using its real concentration as the regression x-axis.
  - A selection made entirely of I*(q) curves yields an already-
    normalized output, tagged Conc:1 in both modes (Primus no longer
    tags it with the reference concentration in that case).
  - Mixing I*(q) and raw-intensity curves in one extrapolation warns
    (different scales), without blocking.
  - Editor messages and the manual page document the behavior.

Primus mode never divides by c, so its intensity handling was already
correct; only its output concentration tag needed the all-I*(q) case.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 11:09:07 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 10:09:07 -0700
Subject: [us-commits] [ehb54/ultrascan3] 703b3c: SAXS extrap-to-c0 manual:
 add Zimm (1948) reference
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/26e872-703b3c@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 703b3cc15ca5307a034b4f701f1e76da69fe0e15
      https://github.com/ehb54/ultrascan3/commit/703b3cc15ca5307a034b4f701f1e76da69fe0e15
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0 manual: add Zimm (1948) reference

Cite Zimm, B. H. (1948) J. Chem. Phys. 16, 1093-1099 for the Zimm-mode
extrapolation, alongside the existing ATSAS reference for Primus mode.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 11:34:36 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 10:34:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] e4097b: Fix Crop Common dropping
 points due to 6-sig-fig q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-962/000000-e4097b@github.com>

  Branch: refs/heads/ehb54-issue-962
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e4097b6c1c59016b3be6e5cce40619c1bbbe0689
      https://github.com/ehb54/ultrascan3/commit/e4097b6c1c59016b3be6e5cce40619c1bbbe0689
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_vector.cpp
    M us_somo/somo/doc/manual/somo/somo_mals.html
    M us_somo/somo/doc/manual/somo/somo_mals_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html

  Log Message:
  -----------
  Fix Crop Common dropping points due to 6-sig-fig q rounding

Crop Common built the shared grid via US_Vector::intersection(), which
matches q values by exact double equality. Because .dat files store q to
6 significant figures, the same physical q point is rounded slightly
differently between files (e.g. 0.00547318 vs 0.00547317), so those
points missed the exact match and were dropped, leaving "holes" in the
common grid. On a set of 7 AlphaSyn HPLC curves this cut the common grid
from ~1053 points to 803.

Add US_Vector::canonical_map(), which clusters q values whose relative
gap is <= reltol (1e-4) and maps each to a canonical representative. A
cluster/tolerance merge (rather than fixed-grid rounding) is used so that
near-identical values never straddle a bin boundary. crop_common() snaps
the grids through this map before intersecting and uses the same map for
the per-curve filter; retained points keep their original q/I/sd values.

Applied to all five crop_common paths: SAXS HPLC/KIN, MALS, DAD (UV/Vis),
MALS-SAXS, and SAXS Buffer. Manual pages updated accordingly. On the 7
test curves the common grid is restored to 1045 points with no
over-merging (min real relative gap 8.3e-4, well above the 1e-4 tol).

Fixes ehb54/ultrascan-tickets#962

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 12:26:09 2026
From: noreply at github.com (alexsav815)
Date: Sat, 11 Jul 2026 11:26:09 -0700
Subject: [us-commits] [ehb54/ultrascan3] aea465: []GMP:eSignatures -- same
 user experience improvem...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/9d2438-aea465@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: aea46531df9dbdab71687e604f60e8047f1e66f1
      https://github.com/ehb54/ultrascan3/commit/aea46531df9dbdab71687e604f60e8047f1e66f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  []GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...



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From noreply at github.com  Sat Jul 11 12:50:21 2026
From: noreply at github.com (alexsav815)
Date: Sat, 11 Jul 2026 11:50:21 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8567f6: Add missing execute
 permission to shell scripts in...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/aea465-7981a6@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
      https://github.com/ehb54/ultrascan3/commit/8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Add missing execute permission to shell scripts in scripts/


  Commit: a43e638e495930eb941519ece5e33498e89fd1ec
      https://github.com/ehb54/ultrascan3/commit/a43e638e495930eb941519ece5e33498e89fd1ec
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: improve python3 version check and update-alternatives registration


  Commit: 7f15d549465db31e042d59a5686dc8e2cd2b056a
      https://github.com/ehb54/ultrascan3/commit/7f15d549465db31e042d59a5686dc8e2cd2b056a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  mod: make executable


  Commit: 36dd7367a1f0d64008dcf711a3c7265de78867f7
      https://github.com/ehb54/ultrascan3/commit/36dd7367a1f0d64008dcf711a3c7265de78867f7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  fix: conditionally include python39 packages based on python3 version


  Commit: 73a27078af4dfa87f2178651d2907835d3cf9b92
      https://github.com/ehb54/ultrascan3/commit/73a27078af4dfa87f2178651d2907835d3cf9b92
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  fix: update default GUI style for MacOS to 'macOS' in Qt 6


  Commit: e69cf69c249ce62533cd87f25c93dde746147ffa
      https://github.com/ehb54/ultrascan3/commit/e69cf69c249ce62533cd87f25c93dde746147ffa
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge pull request #474 from ehb54/843-request-macintosh-style-is-deprecated

Update default GUI style for macOS in Qt 6


  Commit: aa00be99171275b2c91132092e04bce0f9cace1d
      https://github.com/ehb54/ultrascan3/commit/aa00be99171275b2c91132092e04bce0f9cace1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge branch 'main' into 955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute


  Commit: 833773e788e0239ba91dae8b4fdd7110a147fb4b
      https://github.com/ehb54/ultrascan3/commit/833773e788e0239ba91dae8b4fdd7110a147fb4b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge pull request #472 from ehb54/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute

Add execute permission to shell scripts and improve version check


  Commit: 7981a62c68b5c180b08fd48e7452601700d341e1
      https://github.com/ehb54/ultrascan3/commit/7981a62c68b5c180b08fd48e7452601700d341e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M gui/us_gui_settings.cpp
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


Compare: https://github.com/ehb54/ultrascan3/compare/aea46531df9d...7981a62c68b5

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From noreply at github.com  Sat Jul 11 14:52:15 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 13:52:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] 841315: SAXS extrap-to-c0:
 scrollable per-q regression plo...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/703b3c-841315@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 84131551b71ed9b98a8a1bd83247706027101474
      https://github.com/ehb54/ultrascan3/commit/84131551b71ed9b98a8a1bd83247706027101474
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    A us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: scrollable per-q regression plot pop-up

Adds an opt-in viewer for the per-q linear regressions behind the
zero-concentration extrapolation, requested for inspecting the fits.

- New "Show per-q regression plots" checkbox in the concentration dialog
  (opt-in, off by default). When set, a pop-up opens after extrapolation.
- New US_Hydrodyn_Saxs_Iqq_Extrap_C0_Regplot (QFrame + US_Plot), modeled
  on the scale-trend popups: shows one q at a time -- each input curve as
  a point at its concentration WITH error bars, the fitted line, and the
  c=0 intercept (highlighted, with its error bar) at a dashed x=0 axis.
- A qwt_wheel (plus Prev/Next) scrolls q-by-q; the current q, intercept
  +/- error, and slope are shown below the plot.
- do_extrap_c0 now parses each curve's sd row and captures per-q
  (conc, y, y-error) points and the fit (intercept, slope, SE) to feed
  the viewer. Point y-errors follow the mode: sd/c (Zimm raw), sd (I*(q)),
  or scale*sd (Primus). Y-axis label matches the mode.
- Manual page documents the pop-up (image placeholder added).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 15:18:14 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 14:18:14 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2c58b4: SAXS extrap-to-c0: Primus
 mode = weighted merge, n...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/841315-2c58b4@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2c58b44034274c0cff1b5c5a19dd8db216b47a6a
      https://github.com/ehb54/ultrascan3/commit/2c58b44034274c0cff1b5c5a19dd8db216b47a6a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: Primus mode = weighted merge, not per-q extrapolation

Primus mode previously did a per-q linear fit of the scaled intensity vs
concentration and took the c=0 intercept. Once the curves are scaled onto
the reference their residual concentration dependence is negligible, so
that per-point fit mostly tracks noise -- it drove the high-q intensity
negative (25 negative points on the asyn test set), and since the error
column is the copied reference sd, those near-zero/negative points showed
enormous error bars on a log plot. This is what a colleague reported as
"Primus error bars too large vs ATSAS"; the sd column itself was already
byte-identical to the ATSAS reference.

Replace the per-q extrapolation with the inverse-variance weighted MERGE
of the scaled curves (matching ATSAS almerge). On the asyn data this
removes all 25 negative points (ATSAS has 0), eliminates all 37
huge-error-bar points, and matches the ATSAS zc_001.dat curve far better
(median rel. diff low/mid/high-q 0.008/0.032/0.104 vs 0.026/0.133/0.470).

The error column (reference sd), reference scaling, Conc tagging, and the
I*(q) handling are unchanged. The regression pop-up now draws a level
(slope 0) at the merged value. Zimm mode is untouched. Comments, editor
message, dialog tooltip, and manual page updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 15:30:00 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 14:30:00 -0700
Subject: [us-commits] [ehb54/ultrascan3] c3a78b: SAXS extrap-to-c0 regplot:
 real window, smooth whe...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/2c58b4-c3a78b@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c3a78b7e54531506109f8f9d5d786ff16aa50852
      https://github.com/ehb54/ultrascan3/commit/c3a78b7e54531506109f8f9d5d786ff16aa50852
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0 regplot: real window, smooth wheel, merge-aware labels

Fixes reported in first testing of the per-q regression pop-up:

- It rendered inside the SAS window instead of as its own window. It is a
  QFrame parented to the SAS window, which without a window flag is an
  embedded child. Set Qt::Window so it is a proper top-level window.

- The wheel snapped one step at a time (useless for scrolling) because the
  wheel-driven handler called set_index(), which reset the wheel value back
  to the integer index. Now dragging the wheel updates the plot to the
  nearest q WITHOUT snapping, so it scrolls smoothly; only Prev/Next snap
  the wheel and step by one q. Wheel given continuous fine steps, inertia
  (setMass(1.0)) so a flick keeps scrolling, and a minimum width.

- Primus mode is a weighted merge (slope 0), so "intercept at c=0" no longer
  fits. Added a merge_mode flag: the pop-up now labels the result "merged
  value", drops the c=0 vertical reference line, and drops the slope readout
  in Primus; Zimm is unchanged. Manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 16:32:13 2026
From: noreply at github.com (emre brookes)
Date: Sat, 11 Jul 2026 15:32:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] 711170: SAXS extrap-to-c0: faithful
 almerge hybrid (extrap...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/c3a78b-711170@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 71117052b048a7cb811e64ce91f1b73034a14eb3
      https://github.com/ehb54/ultrascan3/commit/71117052b048a7cb811e64ce91f1b73034a14eb3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: faithful almerge hybrid (extrapolate low-q + copy ref)

Primus mode now follows the actual ATSAS almerge algorithm (Petoukhov
2012 Eq 1; Franke 2017) rather than the prior "merge everywhere", which
was only coincidentally right for weakly-interacting data and lost the
structure-factor removal for strongly-interacting samples.

Algorithm:
- scale each curve to the reference (highest-conc) by c_ref/c_i;
- at each q, weighted-linear-fit the scaled intensity vs concentration
  -> c=0 intercept = infinite-dilution intensity;
- find the merging point where the extrapolation and the reference differ
  only by noise, via a CORMAP longest-run p-value test;
- below the merging point use the extrapolation, at/above it copy the
  reference curve (I and sd) verbatim.

A concentration scale (c_ref/c_i) is used rather than a data-driven
least-squares scale: on a simulated strong-concentration-dependence
series the LS scale is corrupted by the low-q structure factor and
recovers only ~85% of the known dilute limit, vs ~99% with c_ref/c_i.
The low-q extrapolation + high-q reference copy also eliminates the
negative-intensity / huge-error-bar artefact of the earlier per-q-all
extrapolation.

New: US_Saxs_Util::compute_p_value() -- pairwise CORMAP longest-run
p-value (numerically stable; matches saxsafold SAS::compute_p_value,
which was tested to match SOMO's cormap). Self-contained in us_saxs_util
so the SOMO-SAS module needs no HPLC/KIN window. Merge alpha is exposed
via the saxs_extrap_c0_pvalue_alpha gparam (default 0.01).

Regression pop-up: shows the per-q linear fit and, in Primus mode, marks
whether the current q's output is the extrapolated intercept or taken
from the reference. Manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 11 19:22:38 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 11 Jul 2026 18:22:38 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl] 8499f7: fix: correct
 HPCAnalysisResult column references f...
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/780-request-pbs-gfac-cleanup/ef1963-5afda2@github.com>

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: 8499f7ade0472e188218f9294d57dadaf5c87378
      https://github.com/ehb54/us3lims_gridctl/commit/8499f7ade0472e188218f9294d57dadaf5c87378
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gridctl.php
    M jobmonitor/cleanup_job.php
    M jobmonitor/gridctl.php
    M jobmonitor/jobmonitor.php
    M manage-us3-pipe.php
    M runID_info.php

  Log Message:
  -----------
  fix: correct HPCAnalysisResult column references from stale gfacID to backend_job_id and resolve jobmonitor's db_obj_result naming collision with listen-config.php

Co-Authored-By: Claude Sonnet 5 <noreply at anthropic.com>


  Commit: 05ebc898349beeb7a792fe7e5ae387ab48f3314f
      https://github.com/ehb54/us3lims_gridctl/commit/05ebc898349beeb7a792fe7e5ae387ab48f3314f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gridctl.php
    M jobmonitor/cleanup_job.php
    M jobmonitor/gridctl.php
    M manage-us3-pipe.php
    M runID_info.php

  Log Message:
  -----------
  fix: revert HPCAnalysisResult.gfacID references back from backend_job_id, since the rename was untracked local drift on one dev database rather than a real canonical schema change

Co-Authored-By: Claude Sonnet 5 <noreply at anthropic.com>


  Commit: 5afda25367d1fba4e304766caef11f3dfd1a60ba
      https://github.com/ehb54/us3lims_gridctl/commit/5afda25367d1fba4e304766caef11f3dfd1a60ba
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M submitone.php

  Log Message:
  -----------
  fix: restore analysisprofile XML attribute extraction and interactive-stage short-circuit in submitone.php, accidentally deleted by the prior Airavata/GFAC cleanup commit


Compare: https://github.com/ehb54/us3lims_gridctl/compare/ef1963ed749d...5afda25367d1

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From noreply at github.com  Sat Jul 11 23:39:29 2026
From: noreply at github.com (alexsav815)
Date: Sat, 11 Jul 2026 22:39:29 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue961/000000-833773@github.com>

  Branch: refs/heads/alexey-dev-issue961
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 12 00:13:47 2026
From: noreply at github.com (alexsav815)
Date: Sat, 11 Jul 2026 23:13:47 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8fbfd9: 2. LIVE_UPDATE stage: GMP
 vs R&D: pass flag for th...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue961/833773-8fbfd9@github.com>

  Branch: refs/heads/alexey-dev-issue961
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8fbfd948e503374ba161214696f34e1ec158228f
      https://github.com/ehb54/ultrascan3/commit/8fbfd948e503374ba161214696f34e1ec158228f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  2. LIVE_UPDATE stage: GMP vs R&D: pass flag for the program mode to the live update from the top-level us_comproject, to define different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...



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From noreply at github.com  Sun Jul 12 01:44:39 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 00:44:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3760c5: SAXS extrap-to-c0: Zimm
 fit-broadening (smooth con...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/711170-3760c5@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3760c59a96e15cedb87b5313e37db081afd4094f
      https://github.com/ehb54/ultrascan3/commit/3760c59a96e15cedb87b5313e37db081afd4094f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: Zimm fit-broadening (smooth concentration slope across q)

Adds an optional "Zimm fit broadening (q-window)" control to the
concentration dialog. The interparticle/interaction term (the per-q fit's
slope vs concentration) varies smoothly with q and dies off at high q, so
smoothing it across an N-point q-window and recomputing the intercept
(a = <I/c> - b_smoothed*<c>) removes extrapolation noise WITHOUT smearing
the form-factor detail carried by the intercept. Smoothing the output
curve directly (which would smear real features) is deliberately not done.

- 0 (default) = independent per-q fits, unchanged behavior.
- N > 1 = average the slope over an N-point window, then recompute each
  c=0 intercept. Validated against a known dilute-limit ground truth:
  N=5 improved accuracy (RMS 0.0089 vs 0.0139) and halved point-to-point
  noise on a simulated strong-interaction series.
- Zimm only; the field is disabled while Primus mode is checked.

The optional regression pop-up reflects it: reg_a/reg_b are updated so the
fit line uses the smoothed slope and its c=0 intercept, with a note above
the plot when broadening is active. Main plot uses the broadened curve.
Manual updated (Zimm section + regression-plot section).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 12 02:01:08 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 01:01:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0e667b: SAXS extrap-to-c0: guard
 Primus short-grid, doc/to...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/3760c5-0e667b@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0e667b5e04a2e1474e7e7def5db2c3f286654902
      https://github.com/ehb54/ultrascan3/commit/0e667b5e04a2e1474e7e7def5db2c3f286654902
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: guard Primus short-grid, doc/tooltip fixes

- Primus mode: the merge-point search used a fixed 50-pt CORMAP window
  guarded by "if (npts > 50)", leaving merge_idx = 0 for shorter curves.
  That made every output point copy the reference, so Primus silently
  returned the input curve with no extrapolation and no warning. Shrink
  the window for short grids, and when there are too few points to locate
  a merge, extrapolate the whole curve and warn. Curves with >= 51 points
  are unaffected.
- Update the Primus-mode checkbox tooltip: it still described the old
  "inverse-variance weighted merge"; it now matches the actual hybrid
  (scale to reference, extrapolate low q, copy reference above the merge).
- Manual: add the Petoukhov et al. 2012 almerge reference, cited in the
  body and code comments but missing from the References list.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 12 06:44:40 2026
From: noreply at github.com (alexsav815)
Date: Sun, 12 Jul 2026 05:44:40 -0700
Subject: [us-commits] [ehb54/ultrascan3] 69bb3f: [updated]2. LIVE_UPDATE
 stage: GMP vs R&D: differe...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue961/8fbfd9-69bb3f@github.com>

  Branch: refs/heads/alexey-dev-issue961
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 69bb3f83f418b000fce5d05520008f5be7e3c9d3
      https://github.com/ehb54/ultrascan3/commit/69bb3f83f418b000fce5d05520008f5be7e3c9d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  [updated]2. LIVE_UPDATE stage: GMP vs R&D: different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...



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From noreply at github.com  Sun Jul 12 07:11:34 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 06:11:34 -0700
Subject: [us-commits] [ehb54/ultrascan3] 014114: SAXS extrap-to-c0:
 penalized-slope fit with automa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/0e667b-014114@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 014114a65ecb55c7392bfb9870871141366c20ef
      https://github.com/ehb54/ultrascan3/commit/014114a65ecb55c7392bfb9870871141366c20ef
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: penalized-slope fit with automatic GCV regularization

Add a shared, physics-based extrapolation core used by both Zimm and
Primus modes. At each q the model is I_i = c_i*alpha(q) + Iex(q)
(inverse-variance weighted); a smoothness penalty is applied to ONLY the
concentration slope alpha(q) -- the interparticle/second-virial term,
smooth in q and decaying at high q -- leaving the intercept Iex(q) (the
form factor) untouched. The fit reduces to (diag(M)+lambda*D2'D2)alpha=R,
Iex=(Q-B*alpha)/C, solved via one symmetric eigendecomposition of the
whitened penalty (Eigen SelfAdjointEigenSolver); lambda is chosen
automatically by Generalized Cross-Validation (closed-form over the
eigenbasis). lambda=0 recovers the independent per-q weighted fit.

- New file-local helper us_extrap_c0_gcv_penalized(); guards degenerate
  and pathologically large (n>5000) grids by falling back to per-q OLS.
- Zimm: pre-pass feeds the penalized intercept/slope into the main loop
  (this also makes Zimm inverse-variance weighted). Primus: overwrites the
  noisy per-q Iex/slope before the merge test so both the crossover and
  the low-q output use the cleaner curve.
- Dialog: new "Automatic slope regularization (GCV) -- recommended"
  checkbox (default on, both modes); disables the manual boxcar q-window,
  which is kept for the classic GCV-off path.
- Manual updated.

Validated (Python prototype + exact re-implementation of this helper):
tracks the ground-truth-optimal lambda across simulated dilution series
(weak/strong, repulsive/attractive, 3-8 curves, uniform/log grids), and on
real asyn data gives a clean low-q Guinier (R^2=0.99, Rg=40.5 A) vs 0.44
for ATSAS almerge and 0.22 for per-q OLS. Review-only; not compiled here.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 12 07:18:55 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 06:18:55 -0700
Subject: [us-commits] [ehb54/ultrascan3] 800068: SAXS extrap-to-c0: Guinier
 QC, Primus error propag...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/014114-800068@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 80006862276e1b0ce576c4de2cdf4269fadaa81d
      https://github.com/ehb54/ultrascan3/commit/80006862276e1b0ce576c4de2cdf4269fadaa81d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp

  Log Message:
  -----------
  SAXS extrap-to-c0: Guinier QC, Primus error propagation, regplot GCV note

Three follow-ups to the GCV penalized-slope extrapolation:

- Guinier quality check: after producing the curve, fit ln I vs q^2 over
  the low-q region (refined so q_max*Rg <= 1.3) and report Rg, I(0) and the
  fit R^2 as a ground-truth-free QC signal (flagged dark-red if R^2 < 0.9).
  This was the decisive real-data test showing the GCV fit beats per-q OLS
  and almerge at low q; now surfaced to the user on every extrapolation.
- Primus error propagation: below the merge point (the extrapolated
  region) report the weighted-fit intercept standard error instead of the
  reference curve's sd, so the low-q extrapolation carries its own (with
  GCV, conservative/upper-bound) uncertainty; at/above the merge the output
  is the reference and keeps the reference sd.
- Regression viewer: annotate that automatic GCV slope regularization was
  in effect (effective slope dof), so it's clear the fit line reflects the
  globally-smoothed slope rather than the raw per-q intercept.

Verified (exact re-implementation of the new Guinier helper): on the real
GCV curve it gives Rg=39.2 A, R^2=0.998 over 59 points (q*Rg=1.25).
Review-only; not compiled here.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 12 07:24:13 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 06:24:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3d31c0: SAXS extrap-to-c0 manual:
 document GCV follow-ups, ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/800068-3d31c0@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3d31c07f5b021e931907956b0fbc58e4e34e7bda
      https://github.com/ehb54/ultrascan3/commit/3d31c07f5b021e931907956b0fbc58e4e34e7bda
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0 manual: document GCV follow-ups, fix stale Primus errors

- Correct the Primus error-bar description: the output now carries the
  reference curve's error only at/above the merging point, and the
  propagated intercept standard error below it (the extrapolated region).
- Document the Guinier quality check reported for every produced curve.
- Note the GCV annotation (effective slope dof) in the regression viewer.
- Bump the last-modified date.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 12 07:47:13 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 06:47:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] 98979b: SAXS extrap-to-c0:
 error-band Primus merge test (G...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/3d31c0-98979b@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 98979b73c555a8fed8a702b0a16cdef323cb85f6
      https://github.com/ehb54/ultrascan3/commit/98979b73c555a8fed8a702b0a16cdef323cb85f6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: error-band Primus merge test (GCV-robust)

The CORMAP sign-run merge test compares the GCV-smoothed extrapolation
against the noisy reference; a small consistent offset (the residual bias
of a nearly-linear regularized slope at high q) produces long same-sign
runs even when the curves agree to within noise, pushing the merge point
much too high (q~0.38 on the asyn data, so Primus extrapolated ~80% of the
curve and left a visible kink at the transition).

Replace it with an error-band test: the merge is the first q from which a
trailing window of the extrapolation agrees with the reference within the
reference's own errors -- reduced chi^2 of (Iex-Iref)/sd_ref <= threshold
(default 4 ~= 2 sigma; gparam saxs_extrap_c0_merge_chi2). On the asyn data
this moves the merge to the knee of the interaction (q~0.18) and copies the
reference over the biased high-q plateau, shrinking the kink. CORMAP is
kept as a fallback when the reference has no error column.

Manual updated. Review-only; not compiled here.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 12 08:10:13 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 07:10:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] e4097b: Fix Crop Common dropping
 points due to 6-sig-fig q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/df7f39-ba1b20@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e4097b6c1c59016b3be6e5cce40619c1bbbe0689
      https://github.com/ehb54/ultrascan3/commit/e4097b6c1c59016b3be6e5cce40619c1bbbe0689
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_vector.cpp
    M us_somo/somo/doc/manual/somo/somo_mals.html
    M us_somo/somo/doc/manual/somo/somo_mals_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html

  Log Message:
  -----------
  Fix Crop Common dropping points due to 6-sig-fig q rounding

Crop Common built the shared grid via US_Vector::intersection(), which
matches q values by exact double equality. Because .dat files store q to
6 significant figures, the same physical q point is rounded slightly
differently between files (e.g. 0.00547318 vs 0.00547317), so those
points missed the exact match and were dropped, leaving "holes" in the
common grid. On a set of 7 AlphaSyn HPLC curves this cut the common grid
from ~1053 points to 803.

Add US_Vector::canonical_map(), which clusters q values whose relative
gap is <= reltol (1e-4) and maps each to a canonical representative. A
cluster/tolerance merge (rather than fixed-grid rounding) is used so that
near-identical values never straddle a bin boundary. crop_common() snaps
the grids through this map before intersecting and uses the same map for
the per-curve filter; retained points keep their original q/I/sd values.

Applied to all five crop_common paths: SAXS HPLC/KIN, MALS, DAD (UV/Vis),
MALS-SAXS, and SAXS Buffer. Manual pages updated accordingly. On the 7
test curves the common grid is restored to 1045 points with no
over-merging (min real relative gap 8.3e-4, well above the 1e-4 tol).

Fixes ehb54/ultrascan-tickets#962

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: ba1b20cdef2d1c65d64073f42c0398864e14e4e9
      https://github.com/ehb54/ultrascan3/commit/ba1b20cdef2d1c65d64073f42c0398864e14e4e9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_vector.cpp
    M us_somo/somo/doc/manual/somo/somo_mals.html
    M us_somo/somo/doc/manual/somo/somo_mals_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html

  Log Message:
  -----------
  Merge pull request #478 from ehb54/ehb54-issue-962

Fix Crop Common dropping points from 6-sig-fig q rounding (holes)


Compare: https://github.com/ehb54/ultrascan3/compare/df7f39c0342f...ba1b20cdef2d

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From noreply at github.com  Sun Jul 12 08:10:16 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 07:10:16 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-962/e4097b-000000@github.com>

  Branch: refs/heads/ehb54-issue-962
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 12 08:11:59 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 07:11:59 -0700
Subject: [us-commits] [ehb54/ultrascan3] e4097b: Fix Crop Common dropping
 points due to 6-sig-fig q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/98979b-8e8a5a@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e4097b6c1c59016b3be6e5cce40619c1bbbe0689
      https://github.com/ehb54/ultrascan3/commit/e4097b6c1c59016b3be6e5cce40619c1bbbe0689
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_vector.cpp
    M us_somo/somo/doc/manual/somo/somo_mals.html
    M us_somo/somo/doc/manual/somo/somo_mals_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html

  Log Message:
  -----------
  Fix Crop Common dropping points due to 6-sig-fig q rounding

Crop Common built the shared grid via US_Vector::intersection(), which
matches q values by exact double equality. Because .dat files store q to
6 significant figures, the same physical q point is rounded slightly
differently between files (e.g. 0.00547318 vs 0.00547317), so those
points missed the exact match and were dropped, leaving "holes" in the
common grid. On a set of 7 AlphaSyn HPLC curves this cut the common grid
from ~1053 points to 803.

Add US_Vector::canonical_map(), which clusters q values whose relative
gap is <= reltol (1e-4) and maps each to a canonical representative. A
cluster/tolerance merge (rather than fixed-grid rounding) is used so that
near-identical values never straddle a bin boundary. crop_common() snaps
the grids through this map before intersecting and uses the same map for
the per-curve filter; retained points keep their original q/I/sd values.

Applied to all five crop_common paths: SAXS HPLC/KIN, MALS, DAD (UV/Vis),
MALS-SAXS, and SAXS Buffer. Manual pages updated accordingly. On the 7
test curves the common grid is restored to 1045 points with no
over-merging (min real relative gap 8.3e-4, well above the 1e-4 tol).

Fixes ehb54/ultrascan-tickets#962

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: ba1b20cdef2d1c65d64073f42c0398864e14e4e9
      https://github.com/ehb54/ultrascan3/commit/ba1b20cdef2d1c65d64073f42c0398864e14e4e9
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_vector.cpp
    M us_somo/somo/doc/manual/somo/somo_mals.html
    M us_somo/somo/doc/manual/somo/somo_mals_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html

  Log Message:
  -----------
  Merge pull request #478 from ehb54/ehb54-issue-962

Fix Crop Common dropping points from 6-sig-fig q rounding (holes)


  Commit: 8e8a5ab2a75bb06c5bf116bd8ea58878ed6ee289
      https://github.com/ehb54/ultrascan3/commit/8e8a5ab2a75bb06c5bf116bd8ea58878ed6ee289
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_vector.cpp
    M us_somo/somo/doc/manual/somo/somo_mals.html
    M us_somo/somo/doc/manual/somo/somo_mals_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html

  Log Message:
  -----------
  Merge pull request #482 from ehb54/somo-dev

Fix Crop Common point loss due to 6-sig-fig q rounding


Compare: https://github.com/ehb54/ultrascan3/compare/98979b73c555...8e8a5ab2a75b

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From noreply at github.com  Sun Jul 12 14:39:45 2026
From: noreply at github.com (emre brookes)
Date: Sun, 12 Jul 2026 13:39:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] bfefc5: SAXS extrap-to-c0: rename
 "Primus" mode to "Absolu...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/8e8a5a-bfefc5@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bfefc5e75a062e26e6025f2c422e8c6774de140c
      https://github.com/ehb54/ultrascan3/commit/bfefc5e75a062e26e6025f2c422e8c6774de140c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  SAXS extrap-to-c0: rename "Primus" mode to "Absolute-scale"

The old name signalled that we duplicate ATSAS's Primus/almerge algorithm
and leaned on their product names in the UI. Rename the mode to the neutral,
descriptive "Absolute-scale" (it outputs absolute intensity on the
reference scale, vs the Zimm mode's normalized I(q)/c).

- Output curve token _primus -> _absolute.
- Checkbox label, tooltip, editor messages, and the manual now say
  "Absolute-scale mode".
- Internal identifiers primus_mode/cb_primus/out_primus_mode ->
  absolute_mode/cb_absolute/out_absolute_mode.
- Scholarly citations to the ATSAS almerge algorithm (Petoukhov 2012,
  Franke 2017) are retained in the manual/comments as attribution -- only
  the mode's *name* changes, not the acknowledgement of prior art.

Review-only; not compiled here.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 12 16:44:15 2026
From: noreply at github.com (aaron-auc)
Date: Sun, 12 Jul 2026 15:44:15 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch/000000-833773@github.com>

  Branch: refs/heads/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 12 16:48:29 2026
From: noreply at github.com (aaron-auc)
Date: Sun, 12 Jul 2026 15:48:29 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3a329e: feat: add initial CMake
 configuration and vcpkg su...
Message-ID: <ehb54/ultrascan3/push/refs/heads/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch/833773-3a329e@github.com>

  Branch: refs/heads/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3a329e106454a1f26436acd02b7d43809c8fd0f6
      https://github.com/ehb54/ultrascan3/commit/3a329e106454a1f26436acd02b7d43809c8fd0f6
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  feat: add initial CMake configuration and vcpkg support for gumbo library



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From noreply at github.com  Sun Jul 12 22:57:10 2026
From: noreply at github.com (aaron-auc)
Date: Sun, 12 Jul 2026 21:57:10 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3a329e: feat: add initial CMake
 configuration and vcpkg su...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/833773-a6dc6e@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3a329e106454a1f26436acd02b7d43809c8fd0f6
      https://github.com/ehb54/ultrascan3/commit/3a329e106454a1f26436acd02b7d43809c8fd0f6
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  feat: add initial CMake configuration and vcpkg support for gumbo library


  Commit: a6dc6e628437424579410fe577bca9357bbb38cd
      https://github.com/ehb54/ultrascan3/commit/a6dc6e628437424579410fe577bca9357bbb38cd
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge pull request #483 from ehb54/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch

Add CMake configuration and vcpkg support for gumbo library


Compare: https://github.com/ehb54/ultrascan3/compare/833773e788e0...a6dc6e628437

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From noreply at github.com  Sun Jul 12 22:57:15 2026
From: noreply at github.com (aaron-auc)
Date: Sun, 12 Jul 2026 21:57:15 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch/3a329e-000000@github.com>

  Branch: refs/heads/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Jul 13 10:59:51 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 09:59:51 -0700
Subject: [us-commits] [ehb54/ultrascan3] 311ae9: extrap_c0: add reciprocal
 (c/I) and 2nd-order viri...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/bfefc5-311ae9@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 311ae95c2da467a90a09cc73f8fd444bc67346b4
      https://github.com/ehb54/ultrascan3/commit/311ae95c2da467a90a09cc73f8fd444bc67346b4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: add reciprocal (c/I) and 2nd-order virial concentration models

The additive Zimm fit (I/c vs c) reads I(0)/MW systematically low when
interparticle interactions are strong, because the second-virial structure
factor makes I(q,c)/c a saturating (convex) function of c. Add two
alternative concentration models, selectable per extrapolation:

  - reciprocal:  c/I = u + v*c,          I0 = 1/u   (linear in c; unbiased MW)
  - 2nd-virial:  c/I = u + v*c + w*c^2,   I0 = 1/u   (robust at strong interaction)

Reciprocal-1st reuses the existing GCV penalized-slope core (and per-q /
2-point fallbacks) by fitting the c/I axis and inverting the intercept, with
SE propagated as SE(u)/u^2. Virial-2 adds a per-q weighted quadratic (3x3
normal equations, needs >=4 concentrations). Additive remains the default and
its path is unchanged; absolute-scale mode is unaffected.

Validated against a physical Percus-Yevick hard-sphere ground truth: at
realistic suppression (~1.5x) reciprocal is within ~1% vs additive's ~3% low
and almerge's ~6% low; the 2nd-order virial holds to ~5% even at 5x
suppression where the 1st-order over-corrects.

GUI: a "Concentration model" drop-down in the concentration-assignment dialog
(default Additive). A power-user default may be preset via gparam
saxs_extrap_c0_model. Manual page updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 11:11:28 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 10:11:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0febd2: Add
 US_Saxs_Util::recompute_errors: standalone I(q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/000000-0febd2@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0febd2d9418b15f336c31d64e3a6dba485aa3bdb
      https://github.com/ehb54/ultrascan3/commit/0febd2d9418b15f336c31d64e3a6dba485aa3bdb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  Add US_Saxs_Util::recompute_errors: standalone I(q) error reassessment

Reproduces the spirit of BayesApp's error-assessment stage (Larsen &
Pedersen, J. Appl. Cryst. 2021) without a BIFT fit. A local weighted
quadratic smoother of I(q) supplies residuals and an effective DoF
(hat-trace); a reduced chi-square and two-sided chi-square p-value
(clean-room regularized incomplete gamma) drive the same significance +
>10% gate as bift.f. Rescales sigma in three modes: constant, non-constant
(per-bin, triangular-smoothed) and intensity-dependent.

Standalone approximation only: no p(r) model, no Ng, no Dmax. Documented
as such in the header.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 11:14:58 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 10:14:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] b35b1e: extrap_c0 regplot: fix
 reciprocal display, add fit...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/311ae9-b35b1e@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b35b1eb1794552dce22906c5116170db2b3b6e31
      https://github.com/ehb54/ultrascan3/commit/b35b1eb1794552dce22906c5116170db2b3b6e31
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp

  Log Message:
  -----------
  extrap_c0 regplot: fix reciprocal display, add fit stats, clearer intercept error bar

The per-q regression viewer previously plotted the reciprocal/virial fit in
the wrong axis: it drew the c/I data points but used the inverted output
intercept (I0 = 1/u) as the fit line, so line and points disagreed. Capture
the fit in its plotted axis instead -- additive in I/c, reciprocal/virial in
c/I -- and pass the model + quadratic coefficient to the viewer:

  - reciprocal/virial plots now show c/I vs c with the correct intercept u and,
    for the 2nd-order virial, the fitted parabola (sampled) rather than a line;
  - the results line reports u(c=0) and the derived I(0) = 1/u with propagated SE;
  - the y-axis is labelled c/I for the reciprocal models.

Also add a per-q goodness-of-fit readout (R^2, and reduced chi^2 when the data
carry error bars), and improve the extrapolated-point error bar visibility: the
c=0 reference line is now white (was red, hiding the red intercept error bar
drawn over it) and the intercept error bar is drawn a bit wider.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 11:19:05 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 10:19:05 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1a38f0: extrap_c0 manual: document
 regression-plot fit sta...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/b35b1e-1a38f0@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1a38f061f58448bfec54dc3ed3ca0b73dd9ee8db
      https://github.com/ehb54/ultrascan3/commit/1a38f061f58448bfec54dc3ed3ca0b73dd9ee8db
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 manual: document regression-plot fit stats and reciprocal c/I display

The per-q regression viewer now reports R^2 (and reduced chi^2 when errors are
present), plots the reciprocal/virial models on the c/I axis with I0 = 1/u, and
draws the 2nd-order virial parabola. Update the "Per-q regression plots" section
to match.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 11:35:00 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 10:35:00 -0700
Subject: [us-commits] [ehb54/ultrascan3] 63746d: extrap_c0: make reciprocal
 the default concentrati...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/1a38f0-63746d@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63746d648b7fcf291738a77b1e6b07c85e65db83
      https://github.com/ehb54/ultrascan3/commit/63746d648b7fcf291738a77b1e6b07c85e65db83
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: make reciprocal the default concentration model

The additive I/c fit reads MW low for interacting series; the reciprocal c/I
(true Zimm form) gives an unbiased MW and a fine profile, so it is the better
default. Additive is kept as an opt-in for work that wants the smoothest low-q
profile over MW accuracy (and is a candidate for later removal); the 2nd-order
virial stays for strongly interacting series. Dialog default, code default, and
manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:03:03 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:03:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] 17b638: Guard recompute_errors mode
 'I' against negative/z...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/0febd2-17b638@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 17b63846933b108cf79aa0781ecab9fe533859f5
      https://github.com/ehb54/ultrascan3/commit/17b63846933b108cf79aa0781ecab9fe533859f5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  Guard recompute_errors mode 'I' against negative/zero-crossing intensities

On background-subtracted or extrapolated curves I(q) crosses zero, and the
signed intensity term sigma+a*I could go negative, blowing up the a search
and emitting negative sigma (observed factors -13..1087 on real data). Use
sigma+a*|I| so the term is always >= sigma > 0. Add a general safety clamp
so no mode ever writes a non-positive or non-finite sigma (degenerate factor
falls back to 1). Modes C and N are unchanged.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:21:52 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:21:52 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1e0ed9: Add "SD rescale" button to
 HPLC/KIN s.d.util mode
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/17b638-1e0ed9@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1e0ed9e1faa70de51dffaff5c11c397b7fa02903
      https://github.com/ehb54/ultrascan3/commit/1e0ed9e1faa70de51dffaff5c11c397b7fa02903
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Add "SD rescale" button to HPLC/KIN s.d.util mode

Third button in the s.d.util row (alongside "SD eval."/"SD apply") that runs
US_Saxs_Util::recompute_errors on the selected curves. Prompts for the mode
(constant / non-constant / intensity-dependent) via US_Static::getItem (avoids
the OSX QInputDialog-in-slot bug), rescales each curve's SD in place, and logs
the verdict/chi2r/p per curve.

Undo: one full-restore crop_undo_data record per invocation, so the existing
"Crop undo" restores the original SDs. Enabled only for selected q-space curves
that already carry usable errors (all_selected_have_errors: count + matching
size + is_nonzero_vector). Curves lacking usable SDs are skipped with a message.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:24:42 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:24:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] ae748b: extrap_c0: decouple
 absolute mode into reference-s...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/63746d-ae748b@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ae748bc38c7f852ed6a7a937110a66c5439dacfc
      https://github.com/ehb54/ultrascan3/commit/ae748bc38c7f852ed6a7a937110a66c5439dacfc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp

  Log Message:
  -----------
  extrap_c0: decouple absolute mode into reference-scale + merge checkboxes

Replace the monolithic "Absolute-scale mode" with two orthogonal output
conventions, so any concentration model (additive / reciprocal / 2nd-order
virial) can drive either. The fit is now always the normalized concentration-
model fit; the reference (max-conc) curve is used only as a post-pass:

  - "Output on reference (absolute) scale": multiply the normalized fit by
    c_ref, tag with the reference concentration (else Conc:1).
  - "Splice reference curve at high q (almerge switchover)": above the
    auto-located merge point, copy the reference curve verbatim with its
    error bars (the "SDs from maximum" behavior, intrinsic to the splice).

This removes the separate reference-path fitter (scale*I fit + its own GCV):
absolute-below-merge is exactly normalized x c_ref, so it is computed by
scaling the normalized fit. Full-grid output index tracked (out_qidx) so the
merge splice covers q the fit skipped. All four checkbox combinations x three
fit forms are now valid; in particular the reference/absolute output finally
gets the unbiased reciprocal/virial MW (previously forced additive).

Regression viewer shows the normalized fit axis (c/I for reciprocal). Curve
tagging/naming and the editor summary describe the chosen fit + conventions.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:26:21 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:26:21 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5a7033: Relax SD rescale gate:
 accept curves with some zer...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/1e0ed9-5a7033@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5a703361099d4bb8304d7a5477af0bfbc32fb3d7
      https://github.com/ehb54/ultrascan3/commit/5a703361099d4bb8304d7a5477af0bfbc32fb3d7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Relax SD rescale gate: accept curves with some zero SDs

recompute_errors already excludes individual zero/negative points, so the
gate need only reject all-zero (placeholder) error vectors. Replace the strict
is_nonzero_vector (all non-zero) test with sd_has_usable_errors (at least one
positive value) in both the enable helper and the per-curve skip. Curves with
a few masked/zero-error points are now processed instead of skipped wholesale.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:42:43 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:42:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5e3b77: extrap_c0: encode fit model
 + output conventions i...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/ae748b-5e3b77@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5e3b77f13a10d92d0cfac0e518019f110c61e51c
      https://github.com/ehb54/ultrascan3/commit/5e3b77f13a10d92d0cfac0e518019f110c61e51c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp

  Log Message:
  -----------
  extrap_c0: encode fit model + output conventions in the curve name

The output name only carried a _zimm/_absolute token, so different fit models
or the reference-splice flag collided and were disambiguated by a meaningless
-1/-2 suffix. Encode all three choices instead:

  <prefix>_extrap_c0_<add|recip|virial2>[_abs][_merge]

so every distinct selection yields a distinct, self-describing name (additive
included). Collision suffixing still applies for genuine repeats.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:49:25 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:49:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 69bb9c: extrap_c0 manual: rewrite
 modes section for the tw...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/5e3b77-69bb9c@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 69bb9c6cbbb0c20ca5cb1bed2dc52ac1d8ca8ad4
      https://github.com/ehb54/ultrascan3/commit/69bb9c6cbbb0c20ca5cb1bed2dc52ac1d8ca8ad4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 manual: rewrite modes section for the two output-convention checkboxes

Replace the single "Absolute-scale mode" description with the two independent
checkboxes (output on reference scale; splice reference at high q), note they
combine freely with any concentration model into four behaviors, and update the
concentration-model, fit-broadening, regression-plot and output-naming sections
to match (including the new self-describing name tokens).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:54:09 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:54:09 -0700
Subject: [us-commits] [ehb54/ultrascan3] b29844: Show applied scale factor
 in SD rescale log
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/5a7033-b29844@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b29844fdcf97dde3af2de461f20571d1663441dc
      https://github.com/ehb54/ultrascan3/commit/b29844fdcf97dde3af2de461f20571d1663441dc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Show applied scale factor in SD rescale log

The per-curve log now reports the applied factor, not just reduced chi-square:
"factor X" for constant mode (X = sqrt(chi2r)), or "factor median X (min..max)"
for the per-point non-constant / intensity modes. Captures scale_factors from
recompute_errors for the summary.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 12:55:03 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 11:55:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7a16b4: Display SD rescale p-value
 as fixed-point (3 decim...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/b29844-7a16b4@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7a16b4d8ffd418112c7a52a607c5d2da07f36e88
      https://github.com/ehb54/ultrascan3/commit/7a16b4d8ffd418112c7a52a607c5d2da07f36e88
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Display SD rescale p-value as fixed-point (3 decimals)

Fixed-point 'f' with 3 decimals instead of 'g' scientific notation, so tiny
p-values read as 0.000 rather than e.g. 8.71e-31, while keeping the 0.003
significance threshold legible.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 13:07:53 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:07:53 -0700
Subject: [us-commits] [ehb54/ultrascan3] e2d0c3: extrap_c0: scale the
 spliced reference for a conti...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/69bb9c-e2d0c3@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e2d0c3b012a50fefb15cc2759bd2284830f4e185
      https://github.com/ehb54/ultrascan3/commit/e2d0c3b012a50fefb15cc2759bd2284830f4e185
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp

  Log Message:
  -----------
  extrap_c0: scale the spliced reference for a continuous merge cutover

The high-q reference splice copied the reference verbatim, but the dilute
extrapolation and the reference generally differ by a few percent at the merge
point (the extrapolation carries the true dilute-limit scale), leaving a visibly
bad step at the cutover (~5% on the alpha-syn test set, obvious near q=0.09).

Scale the spliced reference by the median ratio of the normalized extrapolation
to the normalized reference over a 25-point window just below the merge, so the
reference supplies clean high-q shape stitched smoothly onto the extrapolation
(the way almerge's scaled merge stays continuous). Removes the systematic step,
leaving only noise-level mismatch; the factor is reported in the editor.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 13:18:08 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:18:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] bd64fd: Document "SD rescale" in
 HPLC/KIN manual (S.D. Uti...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/7a16b4-bd64fd@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bd64fd69edefe841b82676a7f5e8fa1faa437d88
      https://github.com/ehb54/ultrascan3/commit/bd64fd69edefe841b82676a7f5e8fa1faa437d88
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Document "SD rescale" in HPLC/KIN manual (S.D. Util section)

Add a subsection to the S.D. Util documentation in somo_saxs_hplc.html
describing the new "SD rescale" button: purpose (assess/rescale existing
I(q) errors, vs the baseline-fluctuation SD estimation of eval/apply), the
BayesApp-based method and significance gate, the three modes (constant /
non-constant / intensity-dependent), verdict/factor reporting in Messages,
and undo. Updates the button count (two -> three) and cross-links the
SAS IFT / BayesApp module.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 13:20:46 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:20:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] a92ff4: Update last-edited dates on
 HPLC manual page
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/bd64fd-a92ff4@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a92ff44060c764135af406f73ec97b7635aaec33
      https://github.com/ehb54/ultrascan3/commit/a92ff44060c764135af406f73ec97b7635aaec33
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Update last-edited dates on HPLC manual page

Bump "Last updated" (header) and "Last modified" (footer) to July 2026 / July
13, 2026 to reflect the SD rescale documentation addition.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 13:26:18 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:26:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2771e3: extrap_c0: append the merge
 point q to the curve name
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/e2d0c3-2771e3@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2771e36432b805146894036fc6348ac7ebcc8231
      https://github.com/ehb54/ultrascan3/commit/2771e36432b805146894036fc6348ac7ebcc8231
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: append the merge point q to the curve name

When the reference is spliced, append the merge cutover q to the name (decimal
as underscore), e.g. Sub_..._extrap_c0_recip_abs_merge_q0_0898, so runs that cut
over at different q are distinguishable at a glance. Splice requested but no
cutover located (whole curve extrapolated) keeps a bare _merge. Manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 13:44:38 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:44:38 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0febd2: Add
 US_Saxs_Util::recompute_errors: standalone I(q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/ba1b20-d9d2b4@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0febd2d9418b15f336c31d64e3a6dba485aa3bdb
      https://github.com/ehb54/ultrascan3/commit/0febd2d9418b15f336c31d64e3a6dba485aa3bdb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  Add US_Saxs_Util::recompute_errors: standalone I(q) error reassessment

Reproduces the spirit of BayesApp's error-assessment stage (Larsen &
Pedersen, J. Appl. Cryst. 2021) without a BIFT fit. A local weighted
quadratic smoother of I(q) supplies residuals and an effective DoF
(hat-trace); a reduced chi-square and two-sided chi-square p-value
(clean-room regularized incomplete gamma) drive the same significance +
>10% gate as bift.f. Rescales sigma in three modes: constant, non-constant
(per-bin, triangular-smoothed) and intensity-dependent.

Standalone approximation only: no p(r) model, no Ng, no Dmax. Documented
as such in the header.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 17b63846933b108cf79aa0781ecab9fe533859f5
      https://github.com/ehb54/ultrascan3/commit/17b63846933b108cf79aa0781ecab9fe533859f5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  Guard recompute_errors mode 'I' against negative/zero-crossing intensities

On background-subtracted or extrapolated curves I(q) crosses zero, and the
signed intensity term sigma+a*I could go negative, blowing up the a search
and emitting negative sigma (observed factors -13..1087 on real data). Use
sigma+a*|I| so the term is always >= sigma > 0. Add a general safety clamp
so no mode ever writes a non-positive or non-finite sigma (degenerate factor
falls back to 1). Modes C and N are unchanged.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 1e0ed9e1faa70de51dffaff5c11c397b7fa02903
      https://github.com/ehb54/ultrascan3/commit/1e0ed9e1faa70de51dffaff5c11c397b7fa02903
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Add "SD rescale" button to HPLC/KIN s.d.util mode

Third button in the s.d.util row (alongside "SD eval."/"SD apply") that runs
US_Saxs_Util::recompute_errors on the selected curves. Prompts for the mode
(constant / non-constant / intensity-dependent) via US_Static::getItem (avoids
the OSX QInputDialog-in-slot bug), rescales each curve's SD in place, and logs
the verdict/chi2r/p per curve.

Undo: one full-restore crop_undo_data record per invocation, so the existing
"Crop undo" restores the original SDs. Enabled only for selected q-space curves
that already carry usable errors (all_selected_have_errors: count + matching
size + is_nonzero_vector). Curves lacking usable SDs are skipped with a message.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 5a703361099d4bb8304d7a5477af0bfbc32fb3d7
      https://github.com/ehb54/ultrascan3/commit/5a703361099d4bb8304d7a5477af0bfbc32fb3d7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Relax SD rescale gate: accept curves with some zero SDs

recompute_errors already excludes individual zero/negative points, so the
gate need only reject all-zero (placeholder) error vectors. Replace the strict
is_nonzero_vector (all non-zero) test with sd_has_usable_errors (at least one
positive value) in both the enable helper and the per-curve skip. Curves with
a few masked/zero-error points are now processed instead of skipped wholesale.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: b29844fdcf97dde3af2de461f20571d1663441dc
      https://github.com/ehb54/ultrascan3/commit/b29844fdcf97dde3af2de461f20571d1663441dc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Show applied scale factor in SD rescale log

The per-curve log now reports the applied factor, not just reduced chi-square:
"factor X" for constant mode (X = sqrt(chi2r)), or "factor median X (min..max)"
for the per-point non-constant / intensity modes. Captures scale_factors from
recompute_errors for the summary.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 7a16b4d8ffd418112c7a52a607c5d2da07f36e88
      https://github.com/ehb54/ultrascan3/commit/7a16b4d8ffd418112c7a52a607c5d2da07f36e88
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Display SD rescale p-value as fixed-point (3 decimals)

Fixed-point 'f' with 3 decimals instead of 'g' scientific notation, so tiny
p-values read as 0.000 rather than e.g. 8.71e-31, while keeping the 0.003
significance threshold legible.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: bd64fd69edefe841b82676a7f5e8fa1faa437d88
      https://github.com/ehb54/ultrascan3/commit/bd64fd69edefe841b82676a7f5e8fa1faa437d88
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Document "SD rescale" in HPLC/KIN manual (S.D. Util section)

Add a subsection to the S.D. Util documentation in somo_saxs_hplc.html
describing the new "SD rescale" button: purpose (assess/rescale existing
I(q) errors, vs the baseline-fluctuation SD estimation of eval/apply), the
BayesApp-based method and significance gate, the three modes (constant /
non-constant / intensity-dependent), verdict/factor reporting in Messages,
and undo. Updates the button count (two -> three) and cross-links the
SAS IFT / BayesApp module.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: a92ff44060c764135af406f73ec97b7635aaec33
      https://github.com/ehb54/ultrascan3/commit/a92ff44060c764135af406f73ec97b7635aaec33
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Update last-edited dates on HPLC manual page

Bump "Last updated" (header) and "Last modified" (footer) to July 2026 / July
13, 2026 to reflect the SD rescale documentation addition.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: d9d2b46041a54f808f8adc9f97e1b23947c165ae
      https://github.com/ehb54/ultrascan3/commit/d9d2b46041a54f808f8adc9f97e1b23947c165ae
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Merge pull request #484 from ehb54/ehb54-issue-966

SD rescale: standalone BayesApp-style error reassessment for I(q) (HPLC/KIN)


Compare: https://github.com/ehb54/ultrascan3/compare/ba1b20cdef2d...d9d2b46041a5

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From noreply at github.com  Mon Jul 13 13:44:42 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:44:42 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-966/a92ff4-000000@github.com>

  Branch: refs/heads/ehb54-issue-966
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Jul 13 13:46:36 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:46:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0febd2: Add
 US_Saxs_Util::recompute_errors: standalone I(q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/2771e3-1793c4@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0febd2d9418b15f336c31d64e3a6dba485aa3bdb
      https://github.com/ehb54/ultrascan3/commit/0febd2d9418b15f336c31d64e3a6dba485aa3bdb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  Add US_Saxs_Util::recompute_errors: standalone I(q) error reassessment

Reproduces the spirit of BayesApp's error-assessment stage (Larsen &
Pedersen, J. Appl. Cryst. 2021) without a BIFT fit. A local weighted
quadratic smoother of I(q) supplies residuals and an effective DoF
(hat-trace); a reduced chi-square and two-sided chi-square p-value
(clean-room regularized incomplete gamma) drive the same significance +
>10% gate as bift.f. Rescales sigma in three modes: constant, non-constant
(per-bin, triangular-smoothed) and intensity-dependent.

Standalone approximation only: no p(r) model, no Ng, no Dmax. Documented
as such in the header.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 17b63846933b108cf79aa0781ecab9fe533859f5
      https://github.com/ehb54/ultrascan3/commit/17b63846933b108cf79aa0781ecab9fe533859f5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  Guard recompute_errors mode 'I' against negative/zero-crossing intensities

On background-subtracted or extrapolated curves I(q) crosses zero, and the
signed intensity term sigma+a*I could go negative, blowing up the a search
and emitting negative sigma (observed factors -13..1087 on real data). Use
sigma+a*|I| so the term is always >= sigma > 0. Add a general safety clamp
so no mode ever writes a non-positive or non-finite sigma (degenerate factor
falls back to 1). Modes C and N are unchanged.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 1e0ed9e1faa70de51dffaff5c11c397b7fa02903
      https://github.com/ehb54/ultrascan3/commit/1e0ed9e1faa70de51dffaff5c11c397b7fa02903
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Add "SD rescale" button to HPLC/KIN s.d.util mode

Third button in the s.d.util row (alongside "SD eval."/"SD apply") that runs
US_Saxs_Util::recompute_errors on the selected curves. Prompts for the mode
(constant / non-constant / intensity-dependent) via US_Static::getItem (avoids
the OSX QInputDialog-in-slot bug), rescales each curve's SD in place, and logs
the verdict/chi2r/p per curve.

Undo: one full-restore crop_undo_data record per invocation, so the existing
"Crop undo" restores the original SDs. Enabled only for selected q-space curves
that already carry usable errors (all_selected_have_errors: count + matching
size + is_nonzero_vector). Curves lacking usable SDs are skipped with a message.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 5a703361099d4bb8304d7a5477af0bfbc32fb3d7
      https://github.com/ehb54/ultrascan3/commit/5a703361099d4bb8304d7a5477af0bfbc32fb3d7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Relax SD rescale gate: accept curves with some zero SDs

recompute_errors already excludes individual zero/negative points, so the
gate need only reject all-zero (placeholder) error vectors. Replace the strict
is_nonzero_vector (all non-zero) test with sd_has_usable_errors (at least one
positive value) in both the enable helper and the per-curve skip. Curves with
a few masked/zero-error points are now processed instead of skipped wholesale.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: b29844fdcf97dde3af2de461f20571d1663441dc
      https://github.com/ehb54/ultrascan3/commit/b29844fdcf97dde3af2de461f20571d1663441dc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Show applied scale factor in SD rescale log

The per-curve log now reports the applied factor, not just reduced chi-square:
"factor X" for constant mode (X = sqrt(chi2r)), or "factor median X (min..max)"
for the per-point non-constant / intensity modes. Captures scale_factors from
recompute_errors for the summary.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 7a16b4d8ffd418112c7a52a607c5d2da07f36e88
      https://github.com/ehb54/ultrascan3/commit/7a16b4d8ffd418112c7a52a607c5d2da07f36e88
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp

  Log Message:
  -----------
  Display SD rescale p-value as fixed-point (3 decimals)

Fixed-point 'f' with 3 decimals instead of 'g' scientific notation, so tiny
p-values read as 0.000 rather than e.g. 8.71e-31, while keeping the 0.003
significance threshold legible.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: bd64fd69edefe841b82676a7f5e8fa1faa437d88
      https://github.com/ehb54/ultrascan3/commit/bd64fd69edefe841b82676a7f5e8fa1faa437d88
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Document "SD rescale" in HPLC/KIN manual (S.D. Util section)

Add a subsection to the S.D. Util documentation in somo_saxs_hplc.html
describing the new "SD rescale" button: purpose (assess/rescale existing
I(q) errors, vs the baseline-fluctuation SD estimation of eval/apply), the
BayesApp-based method and significance gate, the three modes (constant /
non-constant / intensity-dependent), verdict/factor reporting in Messages,
and undo. Updates the button count (two -> three) and cross-links the
SAS IFT / BayesApp module.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: a92ff44060c764135af406f73ec97b7635aaec33
      https://github.com/ehb54/ultrascan3/commit/a92ff44060c764135af406f73ec97b7635aaec33
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Update last-edited dates on HPLC manual page

Bump "Last updated" (header) and "Last modified" (footer) to July 2026 / July
13, 2026 to reflect the SD rescale documentation addition.

Implements ehb54/ultrascan-tickets#966

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: d9d2b46041a54f808f8adc9f97e1b23947c165ae
      https://github.com/ehb54/ultrascan3/commit/d9d2b46041a54f808f8adc9f97e1b23947c165ae
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Merge pull request #484 from ehb54/ehb54-issue-966

SD rescale: standalone BayesApp-style error reassessment for I(q) (HPLC/KIN)


  Commit: 1793c4ba41a59efe738eb89faabe4b5d6e7ca81c
      https://github.com/ehb54/ultrascan3/commit/1793c4ba41a59efe738eb89faabe4b5d6e7ca81c
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html

  Log Message:
  -----------
  Merge pull request #485 from ehb54/somo-dev

Implement standalone I(q) error reassessment and SD rescale feature


Compare: https://github.com/ehb54/ultrascan3/compare/2771e36432b8...1793c4ba41a5

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From noreply at github.com  Mon Jul 13 13:50:34 2026
From: noreply at github.com (alexsav815)
Date: Mon, 13 Jul 2026 12:50:34 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3a329e: feat: add initial CMake
 configuration and vcpkg su...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue954/7981a6-89695a@github.com>

  Branch: refs/heads/alexey-dev-issue954
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3a329e106454a1f26436acd02b7d43809c8fd0f6
      https://github.com/ehb54/ultrascan3/commit/3a329e106454a1f26436acd02b7d43809c8fd0f6
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  feat: add initial CMake configuration and vcpkg support for gumbo library


  Commit: a6dc6e628437424579410fe577bca9357bbb38cd
      https://github.com/ehb54/ultrascan3/commit/a6dc6e628437424579410fe577bca9357bbb38cd
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge pull request #483 from ehb54/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch

Add CMake configuration and vcpkg support for gumbo library


  Commit: 89695a27c955ea41f1763c6af51d62064c11c7b3
      https://github.com/ehb54/ultrascan3/commit/89695a27c955ea41f1763c6af51d62064c11c7b3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


Compare: https://github.com/ehb54/ultrascan3/compare/7981a62c68b5...89695a27c955

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From noreply at github.com  Mon Jul 13 13:57:56 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 12:57:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8e3c1b: extrap_c0: optional
 post-fit SD reassessment of th...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/1793c4-8e3c1b@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8e3c1bee65b5781447da92afc9f81e9363b8000b
      https://github.com/ehb54/ultrascan3/commit/8e3c1bee65b5781447da92afc9f81e9363b8000b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: optional post-fit SD reassessment of the extrapolated curve

Add a "Recompute output SDs" drop-down to the extrapolation concentration
dialog (Off by default) that reassesses the extrapolated curve's error bars
after the fit, reusing the HPLC/KIN s.d.util "SD rescale" engine
(US_Saxs_Util::recompute_errors, BayesApp-style; Larsen & Pedersen 2021).

Modes: Constant (one factor for all q), Non-constant (per q-bin), and
Intensity-dependent (sd -> sd + a*|I|); Off keeps the propagated intercept
errors. The reassessment runs on the final output curve (out_I0/out_q/
out_I0_err), so when a reference tail is spliced in above the merge q it
spans the whole spliced curve. sigma is rescaled only when the fit warrants
it (poor fit and >10% off unity); the verdict, reduced chi^2 and p-value are
logged (p fixed-point, matching the s.d.util convention). Every recompute_errors
false-return path precedes any write to sd, so a skipped reassessment leaves
the propagated errors intact.

The chosen mode is encoded in the self-describing curve name
(_sdC / _sdN / _sdI). Manual updated (modes section + name tokens).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 14:15:15 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 13:15:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] de3635: extrap_c0: report the
 applied SD-reassessment fact...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/8e3c1b-de3635@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: de36353c181ca000db6fe7fe90e12cd1c694a234
      https://github.com/ehb54/ultrascan3/commit/de36353c181ca000db6fe7fe90e12cd1c694a234
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp

  Log Message:
  -----------
  extrap_c0: report the applied SD-reassessment factor in the log

The output SD-reassessment log gave the verdict and reduced chi^2 but not the
applied scale factor, so the constant mode (factor = sqrt(reduced chi^2), not
implied by chi^2 alone) showed no factor at all. Capture scale_factors from
recompute_errors and report "factor X" for constant or "factor median X
(min..max)" for the per-point non-constant / intensity modes, matching the
HPLC/KIN s.d.util "SD rescale" log format.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 15:18:42 2026
From: noreply at github.com (emre brookes)
Date: Mon, 13 Jul 2026 14:18:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] d46047: extrap_c0 manual: explain
 expected negative per-q ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/de3635-d46047@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d460470454f4b259675608a096197802f9c3ae0d
      https://github.com/ehb54/ultrascan3/commit/d460470454f4b259675608a096197802f9c3ae0d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 manual: explain expected negative per-q R^2 on the regplot

Document that a negative R^2 in the per-q regression viewer is expected and
benign, not an error: R^2 is measured about the plotted line, which under GCV
/ fit-broadening uses a slope borrowed from neighbouring q, so at noise-
dominated low q it can fit worse than a flat mean (R^2 < 0) -- the regularization
working as intended; also the fit is inverse-variance weighted while R^2 is
unweighted. Advise judging on reduced chi^2 and the Guinier QC too.

Also fix a stale "Absolute-scale mode" reference in the same section: the
reference/intercept title note appears when the reference is spliced (merge
checkbox), after that single mode was decoupled into ref_scale + merge_ref.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 13 23:02:17 2026
From: noreply at github.com (alexsav815)
Date: Mon, 13 Jul 2026 22:02:17 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue960/000000-a6dc6e@github.com>

  Branch: refs/heads/alexey-dev-issue960
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Jul 13 23:08:50 2026
From: noreply at github.com (alexsav815)
Date: Mon, 13 Jul 2026 22:08:50 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9f6e54: GMP | R&D: add debug for
 the optics...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue960/a6dc6e-9f6e54@github.com>

  Branch: refs/heads/alexey-dev-issue960
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9f6e54d9cabbb4430a65362bdad60f9ad953ade3
      https://github.com/ehb54/ultrascan3/commit/9f6e54d9cabbb4430a65362bdad60f9ad953ade3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP | R&D: add debug for the optics...



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From noreply at github.com  Mon Jul 13 23:14:08 2026
From: noreply at github.com (alexsav815)
Date: Mon, 13 Jul 2026 22:14:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] c02323: [and disable optics check
 for all cannels] GMP | R...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue960/9f6e54-c02323@github.com>

  Branch: refs/heads/alexey-dev-issue960
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c02323216374482944d9424afd2624f0f28264fb
      https://github.com/ehb54/ultrascan3/commit/c02323216374482944d9424afd2624f0f28264fb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [and disable optics check for all cannels] GMP | R&D: add debug for the optics...



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From noreply at github.com  Tue Jul 14 08:28:31 2026
From: noreply at github.com (emre brookes)
Date: Tue, 14 Jul 2026 07:28:31 -0700
Subject: [us-commits] [ehb54/ultrascan3] 041c52: extrap_c0: optional robust
 one-outlier-concentrati...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/d46047-041c52@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 041c52f2120cac4f100dbf8026f9c5771f27349f
      https://github.com/ehb54/ultrascan3/commit/041c52f2120cac4f100dbf8026f9c5771f27349f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_regplot.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_regplot.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: optional robust one-outlier-concentration QC

Add a "Automatically discard one outlier concentration (robust QC)" checkbox
(off by default) with two threshold fields to the extrapolation dialog. A curve
with a mis-entered concentration, a scaling error, or aggregation sits off the
concentration trend at essentially every q; because it is on the wrong x-axis
rather than merely noisy, inverse-variance weighting does not suppress it, so it
biases every per-q fit and can be picked as the high-q reference.

Detection is at the curve level (never per-q, which would overfit at 3-8 points
and stitch discontinuities into the output): file-scope us_extrap_c0_detect_outlier()
runs a cheap per-q weighted OLS on the model axis, takes each curve's median
standardized residual across q plus its one-sided fraction, and nominates the
worst. Gates: median residual >= sigma (field, default 3.0), one-sided >= 70%,
separation >= 2x the others, and pooled reduced chi^2 improved by >= the chi^2-gain
factor (field, default 1.5) if removed. Guarded so >= 3 curves remain (>= 4 for
2nd-order virial) with >= 3 distinct concentrations.

Removal happens before reference selection, so a bad curve cannot become the
reference. At most one curve is dropped. A strong outlier is always flagged in the
log even when auto-discard is off. The excluded curve is drawn as a red x
(QwtSymbol::XCross, the removed-Guinier-point convention) in the per-q regression
plots and noted there; the output name gains _qc1. Targets concentration/scale
outliers; aggregation stays the Guinier QC's job. Manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 14 08:59:00 2026
From: noreply at github.com (emre brookes)
Date: Tue, 14 Jul 2026 07:59:00 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5b3833: extrap_c0 outlier QC:
 mean|t|, always-report, drop...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/041c52-5b3833@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5b3833c24f987cfb6ca887d2bddcfdafb817e001
      https://github.com/ehb54/ultrascan3/commit/5b3833c24f987cfb6ca887d2bddcfdafb817e001
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 outlier QC: mean|t|, always-report, drop separation gate, fix sigma floor

Fixes from testing on the alpha-syn extrapolate2 set (the known-bad 1.818 curve
would not discard at any setting):

- The dialog silently floored both thresholds at 1.0 (validator + ok()), so a
  typed 0.5 fell back to the 3.0/1.5 defaults -- the entered value never applied.
  Sigma now accepts any value > 0 (it is a standardized-residual threshold, and
  mild outliers sit near 1-2); the chi^2 gain stays floored at 1.0 (a ratio < 1
  means removal worsens the fit, which is meaningless).

- Aggregate the per-curve residual as the MEAN |t| across q, not the median. A
  bad concentration/scale error is concentrated at low q (where it corrupts I(0));
  the median washed it out (1.06 for the 1.818 curve), the mean keeps it (1.62).

- Drop the hard separation >= 2x gate: it blocked genuine low-q outliers whose
  per-q spread overlaps the others (1.818 curve separation was 1.71x). Separation
  is still computed and reported, just not gated. Magnitude (sigma), systematic
  sign (>=70% one-sided) and global pooled-chi^2 gain remain the gates.

- Always report the evaluation when auto-discard is on: the most-outlying curve,
  its mean |t|, one-sided %, pooled chi^2 and gain, separation, the thresholds in
  effect, and the verdict (discarded, or kept with the failing gate named). A
  no-discard run is no longer silent -- the thresholds can now be tuned from the log.

On this set, sigma 1.5 with min chi^2 gain 1.2 now discards the 1.818 curve;
the conservative defaults (3.0/1.5) keep it and say why.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 14 09:23:31 2026
From: noreply at github.com (emre brookes)
Date: Tue, 14 Jul 2026 08:23:31 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2a9ff0: extrap_c0: add "Weight
 regression by curve errors ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/5b3833-2a9ff0@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2a9ff087427182a7eb9220032e4c8b41459ed907
      https://github.com/ehb54/ultrascan3/commit/2a9ff087427182a7eb9220032e4c8b41459ed907
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: add "Weight regression by curve errors (1/sigma^2)" toggle

New dialog checkbox (on by default) controlling whether the concentration
regressions use the curve SDs as inverse-variance weights.

- ON (default): all three fit paths (GCV precompute, 2nd-virial precompute, and
  the plain per-q linear fit) weight by 1/sigma^2 with sigma propagated onto the
  fit axis, and the intercept error bar is now taken from the WEIGHTED linear_fit
  overload. This fixes a prior inconsistency where the reported SE was always the
  unweighted OLS residual SE even on the (weighted) GCV path -- so default error
  bars change vs earlier builds (fit values on the default GCV path are unchanged;
  the non-default plain path changes both value and SE).

- OFF: ordinary least squares -- curve errors are still shown as regplot error
  bars but not used in the fit; the intercept error bar is the residual scatter.
  More robust when SDs are missing or mis-scaled (common in SAXS, and documented
  on this pipeline via recompute_errors). Output name gains _uw.

Scope: only the concentration regression, including the outlier detector, which
under OFF standardizes residuals by their per-q RMS instead of by sigma (so the
QC still works without trustworthy errors). The high-q reference merge test and
the post-fit SD reassessment are intrinsically error-based and unchanged.

Weighting uses the weighted linear_fit only when every point at a q has a usable
error (that overload divides by e^2 and only self-guards when ALL errors are
zero); q with any missing SD fall back to unweighted and the count is reported,
instead of silently mixing weighted and unweighted points.

Manual updated (weighting paragraph, scope boundary, _uw token, SE caveat).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 14 10:03:29 2026
From: noreply at github.com (emre brookes)
Date: Tue, 14 Jul 2026 09:03:29 -0700
Subject: [us-commits] [ehb54/ultrascan3] ba7adb: extrap_c0: optional
 transient recompute of input c...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/2a9ff0-ba7adb@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ba7adb784a08edc11aefce84b56bf0975c91d36d
      https://github.com/ehb54/ultrascan3/commit/ba7adb784a08edc11aefce84b56bf0975c91d36d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: optional transient recompute of input curve SDs before fitting

New dialog checkbox "Recompute input curve SDs before fitting (transient)"
(off by default) with a mode sub-option (Constant default / Non-constant /
Intensity-dependent). When on, each selected input curve's error bars are
reassessed from its own point-to-point scatter with US_Saxs_Util::recompute_errors
(the same BayesApp engine as the output SD reassessment and the s.d.util
"SD rescale" button) before anything else, so the reassessed errors feed the
outlier check, the 1/sigma^2 weights, and the reference merge test.

Transient: only the local name_to_err copy is updated; the loaded curves are
never modified (the s.d.util "SD rescale" button remains the way to apply
permanently). Per-curve verdict/factor and a summary are logged.

Also route the merge test's reference SD (ref_sd) from name_to_err instead of
re-parsing name_to_errors_map, so a transient recompute is reflected there too
(name_to_err is parsed identically and per-q aligned; raw map kept as fallback).

Output name gains _riC / _riN / _riI (placed before the _sd token, inputs
before output). Manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 14 20:52:32 2026
From: noreply at github.com (alexsav815)
Date: Tue, 14 Jul 2026 19:52:32 -0700
Subject: [us-commits] [ehb54/ultrascan3] 63750e: GMP:dataDisk - work towards
 extention of the uploa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/a6dc6e-1468dc@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
      https://github.com/ehb54/ultrascan3/commit/63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: e1345a3206da2fc4942f218fc813fda1682f69cd
      https://github.com/ehb54/ultrascan3/commit/e1345a3206da2fc4942f218fc813fda1682f69cd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: f51e6bac3a1d4943c3291b8db1525d9f18419844
      https://github.com/ehb54/ultrascan3/commit/f51e6bac3a1d4943c3291b8db1525d9f18419844
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 044f72440db40f7632169394d6ee0b593998562a
      https://github.com/ehb54/ultrascan3/commit/044f72440db40f7632169394d6ee0b593998562a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 37a4a06b5999bf9f3c243fbe38ede1a3fea379af
      https://github.com/ehb54/ultrascan3/commit/37a4a06b5999bf9f3c243fbe38ede1a3fea379af
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [33more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: f22ca7ce48ab875427dac618f91e473b40d937ce
      https://github.com/ehb54/ultrascan3/commit/f22ca7ce48ab875427dac618f91e473b40d937ce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [Back compatibility with a 1-channel RA-sim. data] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
      https://github.com/ehb54/ultrascan3/commit/2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP:IP+RI - prevent crush at 4. EDIT when IP loaded first due to leagcy protocol re-using and scan_nth set to 0...


  Commit: f4915d875bcf8965884d7059dab0011045ae16b8
      https://github.com/ehb54/ultrascan3/commit/f4915d875bcf8965884d7059dab0011045ae16b8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d81051ec6903d845918fcfa3b93d324988b84d52
      https://github.com/ehb54/ultrascan3/commit/d81051ec6903d845918fcfa3b93d324988b84d52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: f289321afa9b9b656d8bde7b11a50b5e27b397a2
      https://github.com/ehb54/ultrascan3/commit/f289321afa9b9b656d8bde7b11a50b5e27b397a2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 857f3efd29534ce5ce6cf14c840be389eebd9b74
      https://github.com/ehb54/ultrascan3/commit/857f3efd29534ce5ce6cf14c840be389eebd9b74
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
      https://github.com/ehb54/ultrascan3/commit/2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [[1]And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d56a96153cae267abf3f0ab713d600e6c37a16ad
      https://github.com/ehb54/ultrascan3/commit/d56a96153cae267abf3f0ab713d600e6c37a16ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [And for Audit Trail -- And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: e1a744a5b128a49750aed0f58d5b988527a78d00
      https://github.com/ehb54/ultrascan3/commit/e1a744a5b128a49750aed0f58d5b988527a78d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: beb1029bcdca1b2612f23cf65f739021388aac1f
      https://github.com/ehb54/ultrascan3/commit/beb1029bcdca1b2612f23cf65f739021388aac1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [1]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 83fbeffb53ca1d9a82583aa5a62cdc4527299f12
      https://github.com/ehb54/ultrascan3/commit/83fbeffb53ca1d9a82583aa5a62cdc4527299f12
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
      https://github.com/ehb54/ultrascan3/commit/01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [ the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 828342afc1ebd1342fb402beb9010070781b07b7
      https://github.com/ehb54/ultrascan3/commit/828342afc1ebd1342fb402beb9010070781b07b7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  [anf add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 10bd647e3ac0e99176196271ff1d6b97645cc030
      https://github.com/ehb54/ultrascan3/commit/10bd647e3ac0e99176196271ff1d6b97645cc030
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [[add option to Cancel scan, but not the first time]and add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 9d2438e1c6cec27070001ad1631548c32ccea3b4
      https://github.com/ehb54/ultrascan3/commit/9d2438e1c6cec27070001ad1631548c32ccea3b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: aea46531df9dbdab71687e604f60e8047f1e66f1
      https://github.com/ehb54/ultrascan3/commit/aea46531df9dbdab71687e604f60e8047f1e66f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  []GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: 7981a62c68b5c180b08fd48e7452601700d341e1
      https://github.com/ehb54/ultrascan3/commit/7981a62c68b5c180b08fd48e7452601700d341e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M gui/us_gui_settings.cpp
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 89695a27c955ea41f1763c6af51d62064c11c7b3
      https://github.com/ehb54/ultrascan3/commit/89695a27c955ea41f1763c6af51d62064c11c7b3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 1468dcf35170704617ae78f5e2581e0070273c8d
      https://github.com/ehb54/ultrascan3/commit/1468dcf35170704617ae78f5e2581e0070273c8d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #479 from ehb54/alexey-dev-issue954

Extend GMP:dataDisk for IP- and mixed optics RI+IP types; Improve user experiences for GMP:Audit Trail & GMP:eSigs


Compare: https://github.com/ehb54/ultrascan3/compare/a6dc6e628437...1468dcf35170

To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications

From noreply at github.com  Tue Jul 14 20:57:48 2026
From: noreply at github.com (alexsav815)
Date: Tue, 14 Jul 2026 19:57:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] 63750e: GMP:dataDisk - work towards
 extention of the uploa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue961/69bb3f-de15b6@github.com>

  Branch: refs/heads/alexey-dev-issue961
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
      https://github.com/ehb54/ultrascan3/commit/63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: e1345a3206da2fc4942f218fc813fda1682f69cd
      https://github.com/ehb54/ultrascan3/commit/e1345a3206da2fc4942f218fc813fda1682f69cd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: f51e6bac3a1d4943c3291b8db1525d9f18419844
      https://github.com/ehb54/ultrascan3/commit/f51e6bac3a1d4943c3291b8db1525d9f18419844
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 044f72440db40f7632169394d6ee0b593998562a
      https://github.com/ehb54/ultrascan3/commit/044f72440db40f7632169394d6ee0b593998562a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 37a4a06b5999bf9f3c243fbe38ede1a3fea379af
      https://github.com/ehb54/ultrascan3/commit/37a4a06b5999bf9f3c243fbe38ede1a3fea379af
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [33more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: f22ca7ce48ab875427dac618f91e473b40d937ce
      https://github.com/ehb54/ultrascan3/commit/f22ca7ce48ab875427dac618f91e473b40d937ce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [Back compatibility with a 1-channel RA-sim. data] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
      https://github.com/ehb54/ultrascan3/commit/2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP:IP+RI - prevent crush at 4. EDIT when IP loaded first due to leagcy protocol re-using and scan_nth set to 0...


  Commit: f4915d875bcf8965884d7059dab0011045ae16b8
      https://github.com/ehb54/ultrascan3/commit/f4915d875bcf8965884d7059dab0011045ae16b8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d81051ec6903d845918fcfa3b93d324988b84d52
      https://github.com/ehb54/ultrascan3/commit/d81051ec6903d845918fcfa3b93d324988b84d52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: f289321afa9b9b656d8bde7b11a50b5e27b397a2
      https://github.com/ehb54/ultrascan3/commit/f289321afa9b9b656d8bde7b11a50b5e27b397a2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 857f3efd29534ce5ce6cf14c840be389eebd9b74
      https://github.com/ehb54/ultrascan3/commit/857f3efd29534ce5ce6cf14c840be389eebd9b74
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
      https://github.com/ehb54/ultrascan3/commit/2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [[1]And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d56a96153cae267abf3f0ab713d600e6c37a16ad
      https://github.com/ehb54/ultrascan3/commit/d56a96153cae267abf3f0ab713d600e6c37a16ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [And for Audit Trail -- And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: e1a744a5b128a49750aed0f58d5b988527a78d00
      https://github.com/ehb54/ultrascan3/commit/e1a744a5b128a49750aed0f58d5b988527a78d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: beb1029bcdca1b2612f23cf65f739021388aac1f
      https://github.com/ehb54/ultrascan3/commit/beb1029bcdca1b2612f23cf65f739021388aac1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [1]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 83fbeffb53ca1d9a82583aa5a62cdc4527299f12
      https://github.com/ehb54/ultrascan3/commit/83fbeffb53ca1d9a82583aa5a62cdc4527299f12
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
      https://github.com/ehb54/ultrascan3/commit/01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [ the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 828342afc1ebd1342fb402beb9010070781b07b7
      https://github.com/ehb54/ultrascan3/commit/828342afc1ebd1342fb402beb9010070781b07b7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  [anf add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 10bd647e3ac0e99176196271ff1d6b97645cc030
      https://github.com/ehb54/ultrascan3/commit/10bd647e3ac0e99176196271ff1d6b97645cc030
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [[add option to Cancel scan, but not the first time]and add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 9d2438e1c6cec27070001ad1631548c32ccea3b4
      https://github.com/ehb54/ultrascan3/commit/9d2438e1c6cec27070001ad1631548c32ccea3b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: aea46531df9dbdab71687e604f60e8047f1e66f1
      https://github.com/ehb54/ultrascan3/commit/aea46531df9dbdab71687e604f60e8047f1e66f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  []GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: 7981a62c68b5c180b08fd48e7452601700d341e1
      https://github.com/ehb54/ultrascan3/commit/7981a62c68b5c180b08fd48e7452601700d341e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M gui/us_gui_settings.cpp
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 3a329e106454a1f26436acd02b7d43809c8fd0f6
      https://github.com/ehb54/ultrascan3/commit/3a329e106454a1f26436acd02b7d43809c8fd0f6
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  feat: add initial CMake configuration and vcpkg support for gumbo library


  Commit: a6dc6e628437424579410fe577bca9357bbb38cd
      https://github.com/ehb54/ultrascan3/commit/a6dc6e628437424579410fe577bca9357bbb38cd
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge pull request #483 from ehb54/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch

Add CMake configuration and vcpkg support for gumbo library


  Commit: 89695a27c955ea41f1763c6af51d62064c11c7b3
      https://github.com/ehb54/ultrascan3/commit/89695a27c955ea41f1763c6af51d62064c11c7b3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 1468dcf35170704617ae78f5e2581e0070273c8d
      https://github.com/ehb54/ultrascan3/commit/1468dcf35170704617ae78f5e2581e0070273c8d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #479 from ehb54/alexey-dev-issue954

Extend GMP:dataDisk for IP- and mixed optics RI+IP types; Improve user experiences for GMP:Audit Trail & GMP:eSigs


  Commit: de15b65e87559ed23515bf20079ecd0de671f983
      https://github.com/ehb54/ultrascan3/commit/de15b65e87559ed23515bf20079ecd0de671f983
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue961


Compare: https://github.com/ehb54/ultrascan3/compare/69bb3f83f418...de15b65e8755

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From noreply at github.com  Tue Jul 14 21:26:06 2026
From: noreply at github.com (alexsav815)
Date: Tue, 14 Jul 2026 20:26:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8fbfd9: 2. LIVE_UPDATE stage: GMP
 vs R&D: pass flag for th...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/1468dc-cace17@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8fbfd948e503374ba161214696f34e1ec158228f
      https://github.com/ehb54/ultrascan3/commit/8fbfd948e503374ba161214696f34e1ec158228f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  2. LIVE_UPDATE stage: GMP vs R&D: pass flag for the program mode to the live update from the top-level us_comproject, to define different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: 69bb3f83f418b000fce5d05520008f5be7e3c9d3
      https://github.com/ehb54/ultrascan3/commit/69bb3f83f418b000fce5d05520008f5be7e3c9d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  [updated]2. LIVE_UPDATE stage: GMP vs R&D: different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: de15b65e87559ed23515bf20079ecd0de671f983
      https://github.com/ehb54/ultrascan3/commit/de15b65e87559ed23515bf20079ecd0de671f983
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue961


  Commit: cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
      https://github.com/ehb54/ultrascan3/commit/cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  Merge pull request #481 from ehb54/alexey-dev-issue961

GMP vs R&D's 2. LIVE_UPDATE, stop optima / skip optima stage


Compare: https://github.com/ehb54/ultrascan3/compare/1468dcf35170...cace172cd5fe

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From noreply at github.com  Tue Jul 14 21:26:09 2026
From: noreply at github.com (alexsav815)
Date: Tue, 14 Jul 2026 20:26:09 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue961/de15b6-000000@github.com>

  Branch: refs/heads/alexey-dev-issue961
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Jul 16 08:51:30 2026
From: noreply at github.com (emre brookes)
Date: Thu, 16 Jul 2026 07:51:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] 51613b: Add headless scripting for
 extrapolate-to-zero-con...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/ba7adb-51613b@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 51613b6750f3e3f4fb4736a8498c5b1bd8731998
      https://github.com/ehb54/ultrascan3/commit/51613b6750f3e3f4fb4736a8498c5b1bd8731998
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  Add headless scripting for extrapolate-to-zero-concentration

Add a us3_somo -g gui_script command, "saxs_extrap_c0 <controlfile>", that
runs the SAXS extrapolate-to-c0 computation with no interactive dialogs, so a
run is reproducible and its result can be saved for regression testing and for
validating every option combination. The computation is identical to the
interactive path -- the same fit, options and output curve -- only the two
modal dialogs are replaced by a key/value control file.

- New us_hydrodyn_saxs_iqq_extrap_c0_script.cpp: saxs_extrap_c0_script(ctrl)
  parses the control file, clears the plot, loads each input curve (no_scaling
  so the scaling-target dialog is skipped and each curve keeps its intensity),
  sets the run options, and drives the plotted-curve extrapolation path.
- us_hydrodyn_saxs.h: script-mode gate + parsed option members + method decl.
- us_hydrodyn_saxs_loads.cpp: in script mode, skip the load-selection dialog
  (select all loaded curves) and the scaling-target dialog.
- us_hydrodyn_saxs_iqq_extrap_c0.cpp: in script mode, skip the concentration/
  options dialog and take every choice from the script members (concentrations
  from the Conc: headers, optionally overridden); route the modal warnings to
  the editor log so a headless run does not block; write the extrapolated curve
  to the control file's output path as a 3-column .dat.
- us_hydrodyn_saxs_external.cpp: echo editor_msg to stdout during a gui_script
  run so the diagnostics (curves/points used, merge point, Guinier QC, outlier
  and SD-reassessment verdicts) are visible headlessly.
- us_hydrodyn_script.cpp: wire the saxs_extrap_c0 command (opens the SAXS
  window if needed, then runs the control file).
- manual: document the scripting mode, control-file directives and an example.

Validated on the 7-curve alpha-synuclein set across model x ref_scale x merge x
weighting x recompute-inputs x SD-reassess x outlier combinations; results and
self-describing names reproduce the interactive behaviour, including the known
outlier-concentration discard at sigma 1.5 / chi^2 1.2.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 16 09:58:27 2026
From: noreply at github.com (emre brookes)
Date: Thu, 16 Jul 2026 08:58:27 -0700
Subject: [us-commits] [ehb54/us3lims_common] d72762: global_config: add
 COMPLETE finalize grace/ceiling...
Message-ID: <ehb54/us3lims_common/push/refs/heads/ehb54-issue-969/000000-d72762@github.com>

  Branch: refs/heads/ehb54-issue-969
  Home:   https://github.com/ehb54/us3lims_common
  Commit: d727624d2ede4befa5c607540ab8f307f7265f7e
      https://github.com/ehb54/us3lims_common/commit/d727624d2ede4befa5c607540ab8f307f7265f7e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  global_config: add COMPLETE finalize grace/ceiling tunables

jobmonitor finalizes a COMPLETE job without the cluster's (unreliable, UDP)
"Finished" message once a grace period has elapsed, timed on its own clock.
Expose the grace and the hard ceiling here; jobmonitor defaults to 600 /
21600 when they are not defined.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 16 09:58:26 2026
From: noreply at github.com (emre brookes)
Date: Thu, 16 Jul 2026 08:58:26 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl] c50e86: jobmonitor: finalize
 COMPLETE jobs without relying...
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/ehb54-issue-969/000000-c50e86@github.com>

  Branch: refs/heads/ehb54-issue-969
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: c50e86c1a89d96fa8bf2522f1420f903090a8974
      https://github.com/ehb54/us3lims_gridctl/commit/c50e86c1a89d96fa8bf2522f1420f903090a8974
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  jobmonitor: finalize COMPLETE jobs without relying on UDP 'Finished'

check_job()'s COMPLETE case exited the per-job monitor even when
gfac_cleanup() returned 0 ("not yet finalizable, retry later"), which
orphaned the job until a manual uslims_jobs.php --restart. Separately, the
finalize fallback compared time() to strtotime(queue_messages.time), so a
timezone/clock skew (observed ~7h at zentriforce) made the delta negative
and the fallback never fired.

- check_job() COMPLETE case now retries (returns false, keeps polling) when
  complete() returns 0; stops on 1 (finalized) or -1 (terminal).
- cleanup()/complete() propagate the gfac_cleanup()/aira_cleanup() result;
  contract: -1 terminal, 0 retry, 1 finalized.
- gfac_cleanup() times the finalize grace on the jobmonitor's own epoch clock
  via a per-job marker file ($lock_dir/complete_seen), immune to tz/clock
  skew, with a hard ceiling. Grace/ceiling read from
  $global_complete_grace_seconds / $global_complete_max_seconds (default
  600 / 21600) when defined.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 16 11:18:20 2026
From: noreply at github.com (emre brookes)
Date: Thu, 16 Jul 2026 10:18:20 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl] 060dbc: address SonarCloud:
 drop return() parens, brace si...
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/ehb54-issue-969/c50e86-060dbc@github.com>

  Branch: refs/heads/ehb54-issue-969
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: 060dbce49b93f5858119c2c584693a55cdec320a
      https://github.com/ehb54/us3lims_gridctl/commit/060dbce49b93f5858119c2c584693a55cdec320a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  address SonarCloud: drop return() parens, brace single-statement ifs

Clears 7 of the 8 new-code smells on PR #30:
- S6600: return( expr ) -> return expr (new returns only)
- S121: added braces to the new single-statement if bodies

The remaining S1142 (cleanup() has 5 returns) is accepted separately.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 16 12:56:01 2026
From: noreply at github.com (emre brookes)
Date: Thu, 16 Jul 2026 11:56:01 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5a3784: extrap_c0 CLI: warn +
 auto-repair non-positive inp...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/51613b-5a3784@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5a37845a6354c292be6fa3a219622cb3a4847013
      https://github.com/ehb54/ultrascan3/commit/5a37845a6354c292be6fa3a219622cb3a4847013
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp

  Log Message:
  -----------
  extrap_c0 CLI: warn + auto-repair non-positive input SDs (all-or-nothing errors)

A single non-positive SD point (commonly a grid edge in deposited SAXS data)
makes SOMO disable that curve's errors entirely -- error handling is
all-or-nothing by design -- silently forcing an unweighted extrapolation.
This surfaced as materially different, sometimes nonsensical, benchmark results
vs a weighted reference.

Rather than change the shared all-or-nothing convention, handle it in the
extrap-c0 scripted flow only:

- Always warn (non-blocking stdout log -- never a pop-up, so headless runs
  don't hang) which input curve carries how many non-positive SD points.
- fill_sd directive (default on): repair each non-positive SD from its nearest
  positive-SD neighbour before loading, but only when the positive SDs are the
  majority (a mostly/all-zero curve has no real errors to draw from and is left
  as-is). Since the dialog already offers "Weight regression by curve errors"
  (i.e. turn SDs off), auto-repair is a safe default; set fill_sd 0 to reproduce
  the raw unweighted result. Headers (incl. Conc:) are preserved.
- This is folded into the existing pre-load common_crop preprocessing.

do_extrap_c0: the "no usable error" note now explains the likely cause
(non-positive SD points disabling a curve's errors) and points at the
weighting-off option. It uses editor_msg (non-blocking), matching the existing
scripted-run pop-up guard.

Validated on the SASBDB Table-1 additive benchmark: lysozyme (3 edge zeros) now
warns, fills, and fits weighted; glucose isomerase went from no output to a
sensible Rg. (RNaseA/xylanase/urate-oxidase failures are separate low-q
data-quality issues, not SD/grid bugs.)

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 16 13:37:18 2026
From: noreply at github.com (emre brookes)
Date: Thu, 16 Jul 2026 12:37:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9ecb32: extrap_c0: fix Guinier-QC
 window (point-count -> q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/5a3784-9ecb32@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9ecb32097ef10d9de0f1d835f0d6319b77527b1d
      https://github.com/ehb54/ultrascan3/commit/9ecb32097ef10d9de0f1d835f0d6319b77527b1d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp

  Log Message:
  -----------
  extrap_c0: fix Guinier-QC window (point-count -> q-value) so fine grids work

The standalone Guinier QC of the extrapolated curve (us_extrap_c0_guinier, a
rough automatic ln I vs q^2 check, NOT SOMO's Guinier panel) chose its initial
low-q window by POINT COUNT (first 25 points). On a coarse grid that is ~q<0.08;
on a fine, densely sampled grid (e.g. the 2452-point SASBDB deposits, q from
0.0032) 25 points spans only q<0.008 -- a tiny, noise-dominated sliver -- so the
fit returned a nonsensical Rg (86 A on urate oxidase) or no fit at all (RNaseA,
xylanase), even though the extrapolated CURVE was correct.

Choose the initial window by q-VALUE (q <= 0.08 A^-1, grid-density independent,
matching the Python reference and SOMO's own q*Rg<=1.3 convention), fall back to
a point count only for coarse/short grids, and iterate the q*Rg<=1.3 refinement
to convergence instead of a single pass. Also label the log line as a rough
automatic check and point to the Guinier panel for a definitive fit.

Validated on the SASBDB Table-1 additive benchmark: urate oxidase 86 -> 37.0,
RNaseA/xylanase no-fit -> 15.1 / 15.0, glucose isomerase 32.7, lysozyme 14.1 --
all matching a reference Guinier run on the same output curves. Only the QC
readout changed; the extrapolated curves are unchanged.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 17 06:11:58 2026
From: noreply at github.com (emre brookes)
Date: Fri, 17 Jul 2026 05:11:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7df70d: extrap_c0: carry psv/i0se
 onto the extrapolated cu...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/9ecb32-7df70d@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7df70d240eb07142df1b0cbc8eefb73acbe763dd
      https://github.com/ehb54/ultrascan3/commit/7df70d240eb07142df1b0cbc8eefb73acbe763dd
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp

  Log Message:
  -----------
  extrap_c0: carry psv/i0se onto the extrapolated curve; stop on conflicts

The extrapolate-to-zero-concentration path was the only SAXS subsystem that did
not carry partial specific volume (psv) and standard I(0) (i0se): it wrote the
extrapolated curve's conc_csv entry (and re-wrote each input's) with the 2-arg
update_conc_csv, filling psv/i0se with the global defaults. Returning to Guinier
after the replot therefore showed reset values on both the new curve and the
inputs, and the output .dat header omitted the tokens entirely.

- capture each input's psv/i0se (parsed from PSV:/I0se: headers into conc_csv on
  load) before they are overwritten
- hard-stop with a curve-named message when explicitly-set psv/i0se disagree
  across the series; a missing header (global default) is treated as compatible
- carry the agreed values onto the inputs and the extrapolated curve, and write
  PSV:/I0se: into the scripted output header (same tokens/format as HPLC/MALS/DAD)
  so the file round-trips
- new dump_conc_csv <path> control-file directive to dump the name/conc/psv/i0se
  table for headless validation

Validated headlessly: carry (matching headers) propagates 0.712/0.000123 to the
output curve, inputs, and header; conflict (one differing psv) aborts with no
output; the 5-protein Table-1 additive benchmark (no psv/i0se headers) stays
byte-identical, confirming the change is inert on unannotated data.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 17 06:22:25 2026
From: noreply at github.com (emre brookes)
Date: Fri, 17 Jul 2026 05:22:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6775f1: extrap_c0: keep the series
 name prefix on cropped/...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/7df70d-6775f1@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6775f1828b844d7cb40aaa94e82e2d2ad4dd092d
      https://github.com/ehb54/ultrascan3/commit/6775f1828b844d7cb40aaa94e82e2d2ad4dd092d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp

  Log Message:
  -----------
  extrap_c0: keep the series name prefix on cropped/filled inputs

When the scripted crop/fill preprocessing runs, inputs were copied to temp files
prefixed with an index (0_/1_/2_). Those digit prefixes made the loaded curve
names diverge at char 0, so the extrapolated curve's common-prefix name derivation
collapsed to a bare "extrap_c0_add" -- and the index leaked into per-curve
warnings and the psv/i0se conflict message.

Name each cropped/filled copy by its original basename when the inputs' basenames
are all distinct (the normal labelled concentration series), falling back to the
index prefix only on an actual basename collision (same filename from different
dirs) that would otherwise produce identical plotted-curve names. The extrapolated
curve again derives e.g. X4_Lys_extrap_c0_add, and warnings/messages show clean
basenames.

Verified: Lysozyme Table-1 output name restored to X4_Lys_extrap_c0_add with
byte-identical data; the other four proteins (no preprocessing) unchanged; the
psv/i0se carry + conflict CLI tests still pass.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 17 06:31:56 2026
From: noreply at github.com (emre brookes)
Date: Fri, 17 Jul 2026 05:31:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] c02b5f: extrap_c0 doc: document
 psv/i0se carry-over, confl...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/6775f1-c02b5f@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c02b5fb523af5b3b6296fb3bbe8d0c5f939cc9b6
      https://github.com/ehb54/ultrascan3/commit/c02b5fb523af5b3b6296fb3bbe8d0c5f939cc9b6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 doc: document psv/i0se carry-over, conflict stop, dump_conc_csv

The manual page (somo_saxs_extrap_c0.html) predated the psv/i0se work. Add:
(1) a dialog-section paragraph on the per-curve PSV:/I0se: header values -- that
they must agree across a concentration series and that conflicting explicit
values abort the run, while a missing header uses the default and is compatible;
(2) an Output-section note that the extrapolated curve inherits the series'
psv/i0se (in the plot and the saved header) and that the inputs keep theirs;
(3) scripting input/output directive docs now note the PSV:/I0se: round-trip;
(4) the new dump_conc_csv directive. Date bumped to 2026-07-17.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 17 11:42:41 2026
From: noreply at github.com (emre brookes)
Date: Fri, 17 Jul 2026 10:42:41 -0700
Subject: [us-commits] [ehb54/us3lims_common] d72762: global_config: add
 COMPLETE finalize grace/ceiling...
Message-ID: <ehb54/us3lims_common/push/refs/heads/main/4e25de-fe9a51@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_common
  Commit: d727624d2ede4befa5c607540ab8f307f7265f7e
      https://github.com/ehb54/us3lims_common/commit/d727624d2ede4befa5c607540ab8f307f7265f7e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  global_config: add COMPLETE finalize grace/ceiling tunables

jobmonitor finalizes a COMPLETE job without the cluster's (unreliable, UDP)
"Finished" message once a grace period has elapsed, timed on its own clock.
Expose the grace and the hard ceiling here; jobmonitor defaults to 600 /
21600 when they are not defined.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: fe9a51dc8efded7056664654ddf5970e89187da7
      https://github.com/ehb54/us3lims_common/commit/fe9a51dc8efded7056664654ddf5970e89187da7
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  Merge pull request #25 from ehb54/ehb54-issue-969

global_config: COMPLETE finalize grace/ceiling tunables (issue #969)


Compare: https://github.com/ehb54/us3lims_common/compare/4e25de4a189a...fe9a51dc8efd

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From noreply at github.com  Fri Jul 17 11:44:04 2026
From: noreply at github.com (emre brookes)
Date: Fri, 17 Jul 2026 10:44:04 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl] c50e86: jobmonitor: finalize
 COMPLETE jobs without relying...
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/main/b0acd2-fdb69d@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: c50e86c1a89d96fa8bf2522f1420f903090a8974
      https://github.com/ehb54/us3lims_gridctl/commit/c50e86c1a89d96fa8bf2522f1420f903090a8974
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  jobmonitor: finalize COMPLETE jobs without relying on UDP 'Finished'

check_job()'s COMPLETE case exited the per-job monitor even when
gfac_cleanup() returned 0 ("not yet finalizable, retry later"), which
orphaned the job until a manual uslims_jobs.php --restart. Separately, the
finalize fallback compared time() to strtotime(queue_messages.time), so a
timezone/clock skew (observed ~7h at zentriforce) made the delta negative
and the fallback never fired.

- check_job() COMPLETE case now retries (returns false, keeps polling) when
  complete() returns 0; stops on 1 (finalized) or -1 (terminal).
- cleanup()/complete() propagate the gfac_cleanup()/aira_cleanup() result;
  contract: -1 terminal, 0 retry, 1 finalized.
- gfac_cleanup() times the finalize grace on the jobmonitor's own epoch clock
  via a per-job marker file ($lock_dir/complete_seen), immune to tz/clock
  skew, with a hard ceiling. Grace/ceiling read from
  $global_complete_grace_seconds / $global_complete_max_seconds (default
  600 / 21600) when defined.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 060dbce49b93f5858119c2c584693a55cdec320a
      https://github.com/ehb54/us3lims_gridctl/commit/060dbce49b93f5858119c2c584693a55cdec320a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  address SonarCloud: drop return() parens, brace single-statement ifs

Clears 7 of the 8 new-code smells on PR #30:
- S6600: return( expr ) -> return expr (new returns only)
- S121: added braces to the new single-statement if bodies

The remaining S1142 (cleanup() has 5 returns) is accepted separately.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: fdb69dc880499d8d05e439355288d06eafedb212
      https://github.com/ehb54/us3lims_gridctl/commit/fdb69dc880499d8d05e439355288d06eafedb212
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  Merge pull request #30 from ehb54/ehb54-issue-969

jobmonitor: finalize COMPLETE jobs robustly (issue #969)


Compare: https://github.com/ehb54/us3lims_gridctl/compare/b0acd2f3bb3a...fdb69dc88049

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From noreply at github.com  Fri Jul 17 11:44:06 2026
From: noreply at github.com (emre brookes)
Date: Fri, 17 Jul 2026 10:44:06 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl]
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/ehb54-issue-969/060dbc-000000@github.com>

  Branch: refs/heads/ehb54-issue-969
  Home:   https://github.com/ehb54/us3lims_gridctl

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From noreply at github.com  Fri Jul 17 11:50:01 2026
From: noreply at github.com (emre brookes)
Date: Fri, 17 Jul 2026 10:50:01 -0700
Subject: [us-commits] [ehb54/us3lims_common]
Message-ID: <ehb54/us3lims_common/push/refs/heads/ehb54-issue-969/d72762-000000@github.com>

  Branch: refs/heads/ehb54-issue-969
  Home:   https://github.com/ehb54/us3lims_common

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From noreply at github.com  Sat Jul 18 13:49:29 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Jul 2026 12:49:29 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl] 9299e8: fix: sha commit update
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/780-request-pbs-gfac-cleanup/5afda2-a75cdf@github.com>

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_gridctl
  Commit: 9299e856f36d6b086ae0a508a7c9b7447c5c0d5f
      https://github.com/ehb54/us3lims_gridctl/commit/9299e856f36d6b086ae0a508a7c9b7447c5c0d5f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  fix: sha commit update


  Commit: 65f411d468ae31e9a7dfa74a8969d609c4aa50b9
      https://github.com/ehb54/us3lims_gridctl/commit/65f411d468ae31e9a7dfa74a8969d609c4aa50b9
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #24 from ehb54/900-update-bump-pr-sha-us3lims_gridctl

Fix SHA commit update


  Commit: cf43a7500425d7a2057e708eb198a34abeae95f9
      https://github.com/ehb54/us3lims_gridctl/commit/cf43a7500425d7a2057e708eb198a34abeae95f9
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Bump version to 4.1.0


  Commit: c96169aa306b38ddf8516d25b1bb3341047be050
      https://github.com/ehb54/us3lims_gridctl/commit/c96169aa306b38ddf8516d25b1bb3341047be050
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Merge pull request #25 from ehb54/bump-to-v4.1.0

Bump to v4.1.0


  Commit: 2843ec5521e3abaca87929751db9d635958a789e
      https://github.com/ehb54/us3lims_gridctl/commit/2843ec5521e3abaca87929751db9d635958a789e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M cleanup.php
    M jobmonitor/cleanup.php

  Log Message:
  -----------
  Fix race condition causing intermittent "Failed data fetch"

The analysis-results.tar scp had no retry, and the only wait/backoff
loop polled for stderr's arrival, not the tar itself. If the remote
job finished writing stderr before closing the tar, the tar fetch
silently failed and was never retried, leaving gfac.analysis.tarfile
empty even though the job succeeded.

Add a retry to the tar scp matching stdout/stderr, and a dedicated
backoff loop that re-checks for and re-fetches the tar before giving
up. Applied identically to cleanup.php and jobmonitor/cleanup.php.

Fixes ehb54/ultrascan-tickets#914


  Commit: 299622e1aa03a28eb4bc2874245e56e64cce1aa5
      https://github.com/ehb54/us3lims_gridctl/commit/299622e1aa03a28eb4bc2874245e56e64cce1aa5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M cleanup.php
    M jobmonitor/cleanup.php

  Log Message:
  -----------
  Add curly braces around single-statement if blocks (SonarCloud)


  Commit: 31337ffaf7aec158264331b22425837f3697d050
      https://github.com/ehb54/us3lims_gridctl/commit/31337ffaf7aec158264331b22425837f3697d050
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-20 (Sat, 20 Jun 2026)

  Changed paths:
    M cleanup.php
    M jobmonitor/cleanup.php

  Log Message:
  -----------
  Merge pull request #26 from ehb54/ehb54-issue-914

Fix race condition causing intermittent "Failed data fetch"


  Commit: 7314df59df76c69f5b7650b1f79273e98c855fdc
      https://github.com/ehb54/us3lims_gridctl/commit/7314df59df76c69f5b7650b1f79273e98c855fdc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M submitone.php

  Log Message:
  -----------
  Detect job submission failures in submitone.php's CLI error checks

The included web pages (2DSA_1.php/2DSA_2.php, PCSA_1.php/PCSA_2.php,
etc.) never push job submission failures into $cli_errors themselves
- they only echo an ERROR: line into the dumped output. As a result,
submitone.php's check_cli_errors() saw an empty array and proceeded
as if the submission had succeeded, even when it hadn't (e.g. the
sbatch failure case fixed in ehb54/us3lims_common#21).

Add check_cli_errors_in_dump(), which scans the dump file for any
ERROR: line and folds it into $cli_errors, called right before
check_cli_errors() after both the PCSA and 2DSA job-type includes.

This doesn't change GMP/autoflow's own failure detection, which
already polls autoflowAnalysis.status directly - it only gives
submitone.php its own immediate signal that a submission it just ran
failed.

Fixes ehb54/ultrascan-tickets#917


  Commit: 5d00d5db8381168ffca0014e20c8e48ce3d7402a
      https://github.com/ehb54/us3lims_gridctl/commit/5d00d5db8381168ffca0014e20c8e48ce3d7402a
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M submitone.php

  Log Message:
  -----------
  Merge pull request #27 from ehb54/ehb54-issue-917

Detect job submission failures in submitone.php's CLI error checks


  Commit: 9cb26506131078dc3676ef1d4f163f6853e1a892
      https://github.com/ehb54/us3lims_gridctl/commit/9cb26506131078dc3676ef1d4f163f6853e1a892
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: b0acd2f3bb3a3897b2534094cccc427450087213
      https://github.com/ehb54/us3lims_gridctl/commit/b0acd2f3bb3a3897b2534094cccc427450087213
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #29 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


  Commit: c50e86c1a89d96fa8bf2522f1420f903090a8974
      https://github.com/ehb54/us3lims_gridctl/commit/c50e86c1a89d96fa8bf2522f1420f903090a8974
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  jobmonitor: finalize COMPLETE jobs without relying on UDP 'Finished'

check_job()'s COMPLETE case exited the per-job monitor even when
gfac_cleanup() returned 0 ("not yet finalizable, retry later"), which
orphaned the job until a manual uslims_jobs.php --restart. Separately, the
finalize fallback compared time() to strtotime(queue_messages.time), so a
timezone/clock skew (observed ~7h at zentriforce) made the delta negative
and the fallback never fired.

- check_job() COMPLETE case now retries (returns false, keeps polling) when
  complete() returns 0; stops on 1 (finalized) or -1 (terminal).
- cleanup()/complete() propagate the gfac_cleanup()/aira_cleanup() result;
  contract: -1 terminal, 0 retry, 1 finalized.
- gfac_cleanup() times the finalize grace on the jobmonitor's own epoch clock
  via a per-job marker file ($lock_dir/complete_seen), immune to tz/clock
  skew, with a hard ceiling. Grace/ceiling read from
  $global_complete_grace_seconds / $global_complete_max_seconds (default
  600 / 21600) when defined.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 060dbce49b93f5858119c2c584693a55cdec320a
      https://github.com/ehb54/us3lims_gridctl/commit/060dbce49b93f5858119c2c584693a55cdec320a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  address SonarCloud: drop return() parens, brace single-statement ifs

Clears 7 of the 8 new-code smells on PR #30:
- S6600: return( expr ) -> return expr (new returns only)
- S121: added braces to the new single-statement if bodies

The remaining S1142 (cleanup() has 5 returns) is accepted separately.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: fdb69dc880499d8d05e439355288d06eafedb212
      https://github.com/ehb54/us3lims_gridctl/commit/fdb69dc880499d8d05e439355288d06eafedb212
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M jobmonitor/cleanup.php
    M jobmonitor/cleanup_gfac.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  Merge pull request #30 from ehb54/ehb54-issue-969

jobmonitor: finalize COMPLETE jobs robustly (issue #969)


  Commit: eb0c70fc5589445468d5c18a8a51278d6067ad08
      https://github.com/ehb54/us3lims_gridctl/commit/eb0c70fc5589445468d5c18a8a51278d6067ad08
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    A VERSION
    M gridctl.php
    A jobmonitor/cleanup.php
    M jobmonitor/cleanup_job.php
    M jobmonitor/gridctl.php
    M jobmonitor/jobmonitor.php
    M submitone.php

  Log Message:
  -----------
  Merge origin/main: COMPLETE-finalize retry, submission-failure detection, and race-condition fixes (issues 969/917/914)


  Commit: a75cdf8991db6b8d09e9ff5e7b0e5899f4985e06
      https://github.com/ehb54/us3lims_gridctl/commit/a75cdf8991db6b8d09e9ff5e7b0e5899f4985e06
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M gridctl.php
    M jobmonitor/cleanup.php
    M jobmonitor/gridctl.php

  Log Message:
  -----------
  Finish config-driven cluster migration and remove remaining dead Airavata code in gridctl/cleanup paths


Compare: https://github.com/ehb54/us3lims_gridctl/compare/5afda25367d1...a75cdf8991db

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From noreply at github.com  Sat Jul 18 14:02:33 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Jul 2026 13:02:33 -0700
Subject: [us-commits] [ehb54/us3lims_dbinst] 056975: fix: sha commit update
Message-ID: <ehb54/us3lims_dbinst/push/refs/heads/780-request-pbs-gfac-cleanup/b25835-dcd05b@github.com>

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_dbinst
  Commit: 0569753955eea5ef47e2df04950d88921d924a9b
      https://github.com/ehb54/us3lims_dbinst/commit/0569753955eea5ef47e2df04950d88921d924a9b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-06-16 (Tue, 16 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  fix: sha commit update


  Commit: 7ab3717136cc01546d74131f49a640fcfb373e1d
      https://github.com/ehb54/us3lims_dbinst/commit/7ab3717136cc01546d74131f49a640fcfb373e1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-17 (Wed, 17 Jun 2026)

  Changed paths:
    M .github/workflows/bump-version.yml

  Log Message:
  -----------
  Merge pull request #58 from ehb54/901-update-bump-pr-us3lims_dbinst

Fix SHA commit update


  Commit: 3801e22d4f627f3fdf3808265cb64d69aee6b184
      https://github.com/ehb54/us3lims_dbinst/commit/3801e22d4f627f3fdf3808265cb64d69aee6b184
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Bump version to 4.1.0


  Commit: 222415c8a2785d7b5363fc7c665558d7efba669c
      https://github.com/ehb54/us3lims_dbinst/commit/222415c8a2785d7b5363fc7c665558d7efba669c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-19 (Fri, 19 Jun 2026)

  Changed paths:
    A VERSION

  Log Message:
  -----------
  Merge pull request #59 from ehb54/bump-to-v4.1.0

Bump to v4.1.0


  Commit: b7b60f199f538f4030991ea44b06cd0ab7e4b765
      https://github.com/ehb54/us3lims_dbinst/commit/b7b60f199f538f4030991ea44b06cd0ab7e4b765
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M 2DSA-CG_2.php
    M 2DSA_2.php
    M DMGA_2.php
    M GA_3.php
    M PCSA_2.php

  Log Message:
  -----------
  Surface job submission failures on the "job accepted" confirmation page

2DSA_2.php, 2DSA-CG_2.php, PCSA_2.php, GA_3.php, and DMGA_2.php each
print a "Thank you, your job was accepted and is currently processing"
banner unconditionally, before checking the submit class's messages.
If submission actually failed (e.g. the sbatch failure case fixed in
ehb54/us3lims_common#21), the only sign was an ERROR: line buried in
a raw print_r() dump below the success banner.

Scan the queue messages for an ERROR: line (the prefix used by
submit_local.php's failure path) and surface a clear, visible warning
when found, without changing any existing control flow.

Fixes ehb54/ultrascan-tickets#916


  Commit: 19e67efb6cd2821d04e65867e39e436ed8b44be4
      https://github.com/ehb54/us3lims_dbinst/commit/19e67efb6cd2821d04e65867e39e436ed8b44be4
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M 2DSA-CG_2.php
    M 2DSA_2.php
    M DMGA_2.php
    M GA_3.php
    M PCSA_2.php

  Log Message:
  -----------
  Merge pull request #60 from ehb54/ehb54-issue-916

Surface job submission failures on the "job accepted" confirmation page


  Commit: 79b5ae5ba6993d3c8622c09e65e149f4d33c8e82
      https://github.com/ehb54/us3lims_dbinst/commit/79b5ae5ba6993d3c8622c09e65e149f4d33c8e82
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M index.php

  Log Message:
  -----------
  updated index.php


  Commit: 45595d10d64438edb40e69ebd1ff044ccd1efd09
      https://github.com/ehb54/us3lims_dbinst/commit/45595d10d64438edb40e69ebd1ff044ccd1efd09
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-06-22 (Mon, 22 Jun 2026)

  Changed paths:
    M index.php

  Log Message:
  -----------
  Merge pull request #61 from ehb54/ehb54-issue-918

Update index.php


  Commit: 072a2fecc57c897ae7c54bd86e0f7340cf95ae40
      https://github.com/ehb54/us3lims_dbinst/commit/072a2fecc57c897ae7c54bd86e0f7340cf95ae40
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: d4ddd03e0c925cdad8eb680bab52c0dfa2cc7269
      https://github.com/ehb54/us3lims_dbinst/commit/d4ddd03e0c925cdad8eb680bab52c0dfa2cc7269
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION

  Log Message:
  -----------
  Merge pull request #62 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


  Commit: 810ee1eb8ec9963dc2495ba83eb73342e80fe604
      https://github.com/ehb54/us3lims_dbinst/commit/810ee1eb8ec9963dc2495ba83eb73342e80fe604
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-05 (Sun, 05 Jul 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    M 2DSA-CG_2.php
    M 2DSA_2.php
    M DMGA_2.php
    M GA_3.php
    M PCSA_2.php
    A VERSION
    M index.php

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 780-request-pbs-gfac-cleanup


  Commit: 2563dc027b05ebdf078e866adca713e063b1760f
      https://github.com/ehb54/us3lims_dbinst/commit/2563dc027b05ebdf078e866adca713e063b1760f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M queue_viewer.php

  Log Message:
  -----------
  Fix missing global declaration breaking single-tenant USiaB detection in queue_viewer.php


  Commit: dcd05b0c65a81ab7a14b53bbbe668ac56daac357
      https://github.com/ehb54/us3lims_dbinst/commit/dcd05b0c65a81ab7a14b53bbbe668ac56daac357
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M config.php.template
    M lib/HPC_analysis.php

  Log Message:
  -----------
  Fix SELinux-blocked login (exec to posix_getpwnam) and parameterize PCSA_Settings insert


Compare: https://github.com/ehb54/us3lims_dbinst/compare/b2583567887d...dcd05b0c65a8

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From noreply at github.com  Sat Jul 18 14:08:00 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Jul 2026 13:08:00 -0700
Subject: [us-commits] [ehb54/us3lims_newinst]
Message-ID: <ehb54/us3lims_newinst/push/refs/heads/971-request-pbs-gfac-cleanup-us3lims_newinst/000000-75f41a@github.com>

  Branch: refs/heads/971-request-pbs-gfac-cleanup-us3lims_newinst
  Home:   https://github.com/ehb54/us3lims_newinst

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From noreply at github.com  Sat Jul 18 14:10:58 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Jul 2026 13:10:58 -0700
Subject: [us-commits] [ehb54/us3lims_newinst] 4a462b: Drop dead
 Airavata/Thrift config vars from install...
Message-ID: <ehb54/us3lims_newinst/push/refs/heads/971-request-pbs-gfac-cleanup-us3lims_newinst/75f41a-4a462b@github.com>

  Branch: refs/heads/971-request-pbs-gfac-cleanup-us3lims_newinst
  Home:   https://github.com/ehb54/us3lims_newinst
  Commit: 4a462b7690f827447ea79018bb7bf8b0ad16afb3
      https://github.com/ehb54/us3lims_newinst/commit/4a462b7690f827447ea79018bb7bf8b0ad16afb3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M config.php.template
    M makeconfig.php

  Log Message:
  -----------
  Drop dead Airavata/Thrift config vars from install templates and generator



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From noreply at github.com  Sat Jul 18 14:28:57 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Jul 2026 13:28:57 -0700
Subject: [us-commits] [ehb54/us3lims_common] d72762: global_config: add
 COMPLETE finalize grace/ceiling...
Message-ID: <ehb54/us3lims_common/push/refs/heads/780-request-pbs-gfac-cleanup/9c9f98-712901@github.com>

  Branch: refs/heads/780-request-pbs-gfac-cleanup
  Home:   https://github.com/ehb54/us3lims_common
  Commit: d727624d2ede4befa5c607540ab8f307f7265f7e
      https://github.com/ehb54/us3lims_common/commit/d727624d2ede4befa5c607540ab8f307f7265f7e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-16 (Thu, 16 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  global_config: add COMPLETE finalize grace/ceiling tunables

jobmonitor finalizes a COMPLETE job without the cluster's (unreliable, UDP)
"Finished" message once a grace period has elapsed, timed on its own clock.
Expose the grace and the hard ceiling here; jobmonitor defaults to 600 /
21600 when they are not defined.

Refs ehb54/ultrascan-tickets#969

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: fe9a51dc8efded7056664654ddf5970e89187da7
      https://github.com/ehb54/us3lims_common/commit/fe9a51dc8efded7056664654ddf5970e89187da7
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-17 (Fri, 17 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  Merge pull request #25 from ehb54/ehb54-issue-969

global_config: COMPLETE finalize grace/ceiling tunables (issue #969)


  Commit: cc2ddd2736ec6c0cffe9a9097f9b0568011a815e
      https://github.com/ehb54/us3lims_common/commit/cc2ddd2736ec6c0cffe9a9097f9b0568011a815e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M class/submit_slurm.php

  Log Message:
  -----------
  fix: correct submit_slurm.php's HPCAnalysisResult write to use backend_job_id and reorder the jobmonitor launch so nice wraps sudo instead of blocking it


  Commit: 2627c414318b46de9b92273d094cd0b50496ebe9
      https://github.com/ehb54/us3lims_common/commit/2627c414318b46de9b92273d094cd0b50496ebe9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M class/submit_slurm.php

  Log Message:
  -----------
  fix: revert submit_slurm.php's HPCAnalysisResult write back to the canonical gfacID column, since backend_job_id was untracked local drift on one dev database


  Commit: d213ce9954dacaa561e7c5d4458fa0b66d56c6cb
      https://github.com/ehb54/us3lims_common/commit/d213ce9954dacaa561e7c5d4458fa0b66d56c6cb
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M global_config.php.template

  Log Message:
  -----------
  Merge origin/main: COMPLETE finalize grace/ceiling tunables (issue 969)


  Commit: 7129012efd04151aa5f2fa9c1a845e1dd374da83
      https://github.com/ehb54/us3lims_common/commit/7129012efd04151aa5f2fa9c1a845e1dd374da83
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M class/jobsubmit.php

  Log Message:
  -----------
  Fix stale submit_local.php reference in jobsubmit.php comment


Compare: https://github.com/ehb54/us3lims_common/compare/9c9f98ccd4dd...7129012efd04

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From noreply at github.com  Sat Jul 18 14:33:14 2026
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Jul 2026 13:33:14 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo] 0ee019: Fix SELinux-blocked
 login by resolving us3 home di...
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/835-request-update-webinfo/ba6174-0ee019@github.com>

  Branch: refs/heads/835-request-update-webinfo
  Home:   https://github.com/ehb54/us3lims_webinfo
  Commit: 0ee01951eb4af78ba3ff9a153aa3ce8c963c9617
      https://github.com/ehb54/us3lims_webinfo/commit/0ee01951eb4af78ba3ff9a153aa3ce8c963c9617
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M config.php.template

  Log Message:
  -----------
  Fix SELinux-blocked login by resolving us3 home dir via posix_getpwnam instead of exec



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From noreply at github.com  Sat Jul 18 22:15:15 2026
From: noreply at github.com (emre brookes)
Date: Sat, 18 Jul 2026 21:15:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] e0d57b: somo/grpy: add
 self-contained in-process GRPY modu...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-972/000000-e0d57b@github.com>

  Branch: refs/heads/ehb54-issue-972
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e0d57bc99cd1ff7d35f3b5a0a03c310b4fd4745d
      https://github.com/ehb54/ultrascan3/commit/e0d57bc99cd1ff7d35f3b5a0a03c310b4fd4745d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    A us_somo/develop/grpy/INTEGRATION.md
    A us_somo/develop/grpy/README.md
    A us_somo/develop/grpy/grpy_api.hpp
    A us_somo/develop/grpy/grpy_core.hpp
    A us_somo/develop/grpy/grpy_report.hpp
    A us_somo/develop/grpy/linalg.hpp
    A us_somo/develop/grpy/parallel_qt.hpp
    A us_somo/develop/grpy/parallel_std.hpp
    A us_somo/develop/grpy/tests/data/1znf.bead_model
    A us_somo/develop/grpy/tests/data/1znf_golden.txt
    A us_somo/develop/grpy/tests/data/dumbbell_golden.txt
    A us_somo/develop/grpy/tests/qt_proof.cpp
    A us_somo/develop/grpy/tests/run.sh
    A us_somo/develop/grpy/tests/test_api.cpp
    A us_somo/develop/grpy/tests/test_assemble.cpp
    A us_somo/develop/grpy/tests/test_linalg.cpp
    A us_somo/develop/grpy/tests/test_ooc.cpp
    A us_somo/develop/grpy/tests/test_threaded.cpp
    M us_somo/develop/libus_somo.pro

  Log Message:
  -----------
  somo/grpy: add self-contained in-process GRPY module (Eigen)

Adds us_somo/develop/grpy/: a C++ port of GRPY (generalized Rotne-Prager-Yamakawa
hydrodynamics) callable in-process, to replace the external Fortran binary run via
QProcess with stdout scraping.

The module is self-contained and isolated from the SOMO god classes:
- header-only, own namespace (grpy), dependency-injected threading (la::Parallel;
  QtParallel over QThreadPool for SOMO, std::thread for the CLI/tests);
- memory-lean tiled Cholesky (solve M X = T instead of forming the full inverse;
  upper-triangle, factored in place) with single-precision and out-of-core (mmap)
  options for large systems, and fine-grained in-inversion progress via callback;
- grpy::Solver::run(beads, params, progressCb) returns structured scalars AND the
  full report text, so the on-disk results file is preserved as before.
- tests/ validate against the captured GRPY golden (report + scalars) and prove the
  Qt in-process path; run standalone via tests/run.sh.

Wires the qmake build (QT += concurrent, INCLUDEPATH += include grpy, HEADERS).
No US_Hydrodyn changes yet; the QProcess call-site swap is a follow-up commit.

Refs ehb54/ultrascan-tickets#972

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 18 22:47:19 2026
From: noreply at github.com (emre brookes)
Date: Sat, 18 Jul 2026 21:47:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] d3e4bc: somo/grpy: run GRPY
 in-process, drop external bina...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-972/e0d57b-d3e4bc@github.com>

  Branch: refs/heads/ehb54-issue-972
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d3e4bc90e410221103f9e57d5f1aa0c0f5a0d8d7
      https://github.com/ehb54/ultrascan3/commit/d3e4bc90e410221103f9e57d5f1aa0c0f5a0d8d7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    M us_somo/develop/grpy/grpy_api.hpp
    A us_somo/develop/grpy/tests/data/dumbbell.grpy
    M us_somo/develop/grpy/tests/test_api.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp

  Log Message:
  -----------
  somo/grpy: run GRPY in-process, drop external binary + Docker path

Wire the self-contained grpy module into US_Hydrodyn::calc_grpy_hydro /
grpy_process_next: read the .grpy file SOMO already writes via
grpy::read_native_file(), run grpy::Solver over a QtParallel backend on
SOMO's thread pool, and fill grpy_stdout from Results::report so the
existing grpy_finished() parsing and .grpy_res preservation are unchanged.

Removes the QProcess launch, the US_Container_Grpy selection, and the
Docker/parallel-image plumbing -- in-process is now the sole path. Progress
is driven by the Solver callback (processEvents keeps the GUI painting).

Adds grpy::read_native_file() + a native-reader test case (dumbbell.grpy)
that reproduces the dumbbell golden.

Refs ehb54/ultrascan-tickets#972

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sat Jul 18 22:54:02 2026
From: noreply at github.com (emre brookes)
Date: Sat, 18 Jul 2026 21:54:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3647e4: somo/grpy: remove dead
 external/Docker GRPY plumbing
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-972/d3e4bc-3647e4@github.com>

  Branch: refs/heads/ehb54-issue-972
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3647e4575c4e7785585ed676e543c891f0d3c98d
      https://github.com/ehb54/ultrascan3/commit/3647e4575c4e7785585ed676e543c891f0d3c98d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-18 (Sat, 18 Jul 2026)

  Changed paths:
    R us_somo/develop/include/us_container_grpy.h
    M us_somo/develop/include/us_hydrodyn.h
    M us_somo/develop/include/us_hydrodyn_misc.h
    M us_somo/develop/libus_somo.pro
    R us_somo/develop/src/us_container_grpy.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_misc.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo/grpy: remove dead external/Docker GRPY plumbing

Now that GRPY runs in-process (the external binary + Docker path is gone),
delete the symbols that only served the old QProcess path:

- US_Container_Grpy class (src/us_container_grpy.cpp, include/us_container_grpy.h)
  and its libus_somo.pro SOURCES/HEADERS entries; the us_container_grpy member,
  its includes/init, and grpy_parallel_pulled.
- cb_parallel_grpy checkbox + set_parallel_grpy() slot and the misc.parallel_grpy
  field, incl. its settings save/load/default (old saved values are simply ignored).
- the grpy QProcess* member, grpy_prog, and the grpy_readFromStdout/Stderr/started
  slots. stop_calc()'s process-terminate block is replaced by a note: cancellation
  now flows through stopFlag, honored by the Solver progress callback and
  grpy_finished().

Objects rebuild cleanly (us_hydrodyn, us_hydrodyn_grpy, us_hydrodyn_misc,
us_hydrodyn_settings).

Refs ehb54/ultrascan-tickets#972

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 19 07:13:26 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 06:13:26 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7a83b6: somo/grpy: fix in-process
 finish hand-off + resolv...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-972/3647e4-7a83b6@github.com>

  Branch: refs/heads/ehb54-issue-972
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7a83b64352e047e10fe6bc46d68e4e6a05bd9aee
      https://github.com/ehb54/ultrascan3/commit/7a83b64352e047e10fe6bc46d68e4e6a05bd9aee
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_grpy.cpp

  Log Message:
  -----------
  somo/grpy: fix in-process finish hand-off + resolve input path

Two fixes found while validating the in-process path end-to-end via the
batch gui_script on a real bead model:

1. grpy_finished() was never invoked. It was posted with
   QMetaObject::invokeMethod(..., Qt::QueuedConnection, Q_ARG(QProcess::
   ExitStatus, ...)), but QProcess::ExitStatus is not a registered
   queued-connection metatype, so the invoke silently failed
   ("Unable to handle unregistered datatype 'QProcess::ExitStatus'").
   grpy_running then never cleared and the batch's
   while(grpy_running) processEvents() loop hung forever. Replaced both
   call sites with QTimer::singleShot(0, this, lambda) which defers to the
   event loop (still no deep recursion through the model batch) but calls
   grpy_finished() directly, needing no metatype registration.

2. read_native_file() read grpy_last_processed (a bare filename) relative
   to the process CWD. The old QProcess set its working directory to
   get_somo_dir(); resolve the path against get_somo_dir() to match, and
   guard a missing file with a clear error instead of a silent empty solve.

Validated: gui_script batch run on a 165-bead model produces a .grpy_res
whose every physical observable (rotational diffusion, sedimentation,
intrinsic viscosities, all 8 relaxation times, diagonal diffusion tensor)
matches the Fortran GRPY_osx10.11 binary on the same .grpy input exactly;
only the documented eigenvector sign-gauge and ~1e-9 coupling noise differ.

Refs ehb54/ultrascan-tickets#972

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 19 07:25:26 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 06:25:26 -0700
Subject: [us-commits] [ehb54/ultrascan3] 89f4a3: somo/grpy: expose
 single-precision + out-of-core o...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-972/7a83b6-89f4a3@github.com>

  Branch: refs/heads/ehb54-issue-972
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 89f4a3ddd7aa11db5166a243e2d5260aa746ccb4
      https://github.com/ehb54/ultrascan3/commit/89f4a3ddd7aa11db5166a243e2d5260aa746ccb4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_grpy.cpp

  Log Message:
  -----------
  somo/grpy: expose single-precision + out-of-core options

Wire grpy::Options.single and .ooc_dir at the in-process call site. These
matter only for very large bead models (memory-bound; run via batch/cluster),
so they are surfaced through the lightweight, no-UI mechanisms rather than
new god-class dialog controls:

  - gui_script `global grpy_single 1` / `global grpy_ooc_dir <dir>`
  - GRPY_SINGLE / GRPY_OOC_DIR environment-variable fallback (matches the
    standalone CLI's env knobs)

Default off = in-core double precision, byte-identical to prior behavior. A
"GRPY options: ..." editor message is emitted when either is active.

Validated: gui_script run with `global grpy_single 1` on the 165-bead model
completes and reproduces every labeled observable of the double-precision /
Fortran-golden result (single matches to 4 sig figs by design). The module's
single-precision and out-of-core paths themselves are covered by the grpy
unit tests (test_linalg float, test_ooc).

Refs ehb54/ultrascan-tickets#972

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 19 08:03:39 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 07:03:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] f17026: somo/grpy: add GRPY
 precision (double/float) contr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-972/89f4a3-f17026@github.com>

  Branch: refs/heads/ehb54-issue-972
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f17026f45075de36cb25ba4601f2fa662255683c
      https://github.com/ehb54/ultrascan3/commit/f17026f45075de36cb25ba4601f2fa662255683c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_hydro.h
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydro.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo/grpy: add GRPY precision (double/float) control to Hydro Options

Per review, surface the single-precision option as a proper control in the
SOMO Hydrodynamic Calculation Options window rather than script/env only.

Adds a "GRPY Numerical Precision:" group with "Double (default)" / "Float
(for large systems)" radios to US_Hydrodyn_Hydro, right below the existing
"Inclusion of Buried Beads (for GRPY)" group and mirroring its idiom. Backed
by hydro.grpy_single (default false = double), persisted in the SOMO settings
(save/load/default) and reported in display_default_differences() like the
sibling GRPY setting.

The in-process call site now reads hydro.grpy_single as the primary source;
the gui_script `global grpy_single` param and GRPY_SINGLE env var still
override for headless/batch automation. Out-of-core stays script/env only
(a cluster-scale knob, no GUI control).

Validated: full libus_somo rebuild clean (0 errors); default-double gui_script
run reproduces the Fortran-golden scalars (no regression).

Refs ehb54/ultrascan-tickets#972

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 19 11:47:15 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 10:47:15 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/000000-cace17@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 19 11:48:01 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 10:48:01 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8dfdc2: Remove qwt6.1.6 actions
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/cace17-8dfdc2@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8dfdc23580f00cca9ee0e30846264de12a8b48da
      https://github.com/ehb54/ultrascan3/commit/8dfdc23580f00cca9ee0e30846264de12a8b48da
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Remove qwt6.1.6 actions

Removed deprecated container version for consistency.



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From noreply at github.com  Sun Jul 19 11:50:12 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 10:50:12 -0700
Subject: [us-commits] [ehb54/ultrascan3] f0c349: Update QWT library paths to
 version 6.3.0
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/8dfdc2-f0c349@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f0c349fca126bf42f3ebfe0df308eaa92c0496aa
      https://github.com/ehb54/ultrascan3/commit/f0c349fca126bf42f3ebfe0df308eaa92c0496aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M local.pri.template

  Log Message:
  -----------
  Update QWT library paths to version 6.3.0



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From noreply at github.com  Sun Jul 19 11:53:15 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 10:53:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] 916daf: Remove obsolete Qwt6.1.6
 configuration presets
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/f0c349-916daf@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 916daffdf16dff43a9bc0d7172116cbc0351d1e3
      https://github.com/ehb54/ultrascan3/commit/916daffdf16dff43a9bc0d7172116cbc0351d1e3
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M CMakePresets.json

  Log Message:
  -----------
  Remove obsolete Qwt6.1.6 configuration presets



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From noreply at github.com  Sun Jul 19 12:00:36 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:00:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4ac366: Update README.md
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/916daf-4ac366@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4ac36652598c13e33e3fd33a81ab2e73a7c49e4d
      https://github.com/ehb54/ultrascan3/commit/4ac36652598c13e33e3fd33a81ab2e73a7c49e4d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M README.md

  Log Message:
  -----------
  Update README.md



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From noreply at github.com  Sun Jul 19 12:03:33 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:03:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6fa64b: Remove features related to
 qwt6.1.6
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/4ac366-6fa64b@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6fa64bfaeccb6f8c2e067b76d263d2b53b6e39e0
      https://github.com/ehb54/ultrascan3/commit/6fa64bfaeccb6f8c2e067b76d263d2b53b6e39e0
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M vcpkg.json

  Log Message:
  -----------
  Remove features related to qwt6.1.6



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From noreply at github.com  Sun Jul 19 12:04:06 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:04:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] 714e0a: Delete
 buildsys/vcpkg/overlay-ports/qwt-6-1-6 dire...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/6fa64b-714e0a@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 714e0af89a43a966e1b0a10b2867ce431be484b4
      https://github.com/ehb54/ultrascan3/commit/714e0af89a43a966e1b0a10b2867ce431be484b4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json

  Log Message:
  -----------
  Delete buildsys/vcpkg/overlay-ports/qwt-6-1-6 directory



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From noreply at github.com  Sun Jul 19 12:04:32 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:04:32 -0700
Subject: [us-commits] [ehb54/ultrascan3] bd2ba1: Delete
 buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/714e0a-bd2ba1@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bd2ba1eb4ca34e6d5d02a40108f830cbef743819
      https://github.com/ehb54/ultrascan3/commit/bd2ba1eb4ca34e6d5d02a40108f830cbef743819
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json

  Log Message:
  -----------
  Delete buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5 directory



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From noreply at github.com  Sun Jul 19 12:06:08 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:06:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] e9c14e: Update Qt version to
 5.15.19 and Qwt version to 6.3.0
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/bd2ba1-e9c14e@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e9c14e7d36445e310a59dd7278bd41c19438b3e6
      https://github.com/ehb54/ultrascan3/commit/e9c14e7d36445e310a59dd7278bd41c19438b3e6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M admin/modulefiles/home-gui-build

  Log Message:
  -----------
  Update Qt version to 5.15.19 and Qwt version to 6.3.0



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From noreply at github.com  Sun Jul 19 12:10:44 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:10:44 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6ad0f5: Remove deprecated container
 from CodeQL workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/e9c14e-6ad0f5@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6ad0f5088acc5230a10f42a1aa19646cfa5405e8
      https://github.com/ehb54/ultrascan3/commit/6ad0f5088acc5230a10f42a1aa19646cfa5405e8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Remove deprecated container from CodeQL workflow



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From noreply at github.com  Sun Jul 19 12:11:47 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:11:47 -0700
Subject: [us-commits] [ehb54/ultrascan3] 176c84: Update container version in
 doc-build workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/6ad0f5-176c84@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 176c84781a267671c249e6e989c9cf928d28d3f1
      https://github.com/ehb54/ultrascan3/commit/176c84781a267671c249e6e989c9cf928d28d3f1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  Update container version in doc-build workflow



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From noreply at github.com  Sun Jul 19 12:16:25 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:16:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2a9589: Add new container to CodeQL
 analysis workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/176c84-2a9589@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2a95899b28bedd085cfa2f9464a9482aeb5daf98
      https://github.com/ehb54/ultrascan3/commit/2a95899b28bedd085cfa2f9464a9482aeb5daf98
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Add new container to CodeQL analysis workflow



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From noreply at github.com  Sun Jul 19 12:24:33 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:24:33 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/unittest/000000-cace17@github.com>

  Branch: refs/heads/lukas/unittest
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 19 12:28:06 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:28:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] 99535b: Add qtmultimedia5-dev to
 unit tests workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/unittest/cace17-99535b@github.com>

  Branch: refs/heads/lukas/unittest
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 99535b73ac71970aef06bd32024f048873970c1f
      https://github.com/ehb54/ultrascan3/commit/99535b73ac71970aef06bd32024f048873970c1f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add qtmultimedia5-dev to unit tests workflow



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From noreply at github.com  Sun Jul 19 12:31:04 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 11:31:04 -0700
Subject: [us-commits] [ehb54/ultrascan3] fe5f85: Update changed files in
 unit-tests-v2 workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/unittest/99535b-fe5f85@github.com>

  Branch: refs/heads/lukas/unittest
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fe5f85278c6177d4879919a5f15f232e3ffb6cc8
      https://github.com/ehb54/ultrascan3/commit/fe5f85278c6177d4879919a5f15f232e3ffb6cc8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Update changed files in unit-tests-v2 workflow



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From noreply at github.com  Sun Jul 19 13:05:08 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 12:05:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] 00cf2e: Fix two invalid us_somo
 regex patterns breaking US...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-975/000000-00cf2e@github.com>

  Branch: refs/heads/ehb54-issue-975
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 00cf2edadbc180e095d0db4efe197d2fb86d2862
      https://github.com/ehb54/ultrascan3/commit/00cf2edadbc180e095d0db4efe197d2fb86d2862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 19 13:05:23 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 12:05:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] ec623d: Fix two invalid us_somo
 regex patterns breaking US...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-975-somo-dev/000000-ec623d@github.com>

  Branch: refs/heads/ehb54-issue-975-somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ec623de279dc648f1abba5ee7ee53b827f45d335
      https://github.com/ehb54/ultrascan3/commit/ec623de279dc648f1abba5ee7ee53b827f45d335
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Sun Jul 19 14:17:02 2026
From: noreply at github.com (aaron-auc)
Date: Sun, 19 Jul 2026 13:17:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 63750e: GMP:dataDisk - work towards
 extention of the uploa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/464018-e1a744@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
      https://github.com/ehb54/ultrascan3/commit/63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: e1345a3206da2fc4942f218fc813fda1682f69cd
      https://github.com/ehb54/ultrascan3/commit/e1345a3206da2fc4942f218fc813fda1682f69cd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: f51e6bac3a1d4943c3291b8db1525d9f18419844
      https://github.com/ehb54/ultrascan3/commit/f51e6bac3a1d4943c3291b8db1525d9f18419844
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 044f72440db40f7632169394d6ee0b593998562a
      https://github.com/ehb54/ultrascan3/commit/044f72440db40f7632169394d6ee0b593998562a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 37a4a06b5999bf9f3c243fbe38ede1a3fea379af
      https://github.com/ehb54/ultrascan3/commit/37a4a06b5999bf9f3c243fbe38ede1a3fea379af
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [33more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
      https://github.com/ehb54/ultrascan3/commit/8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Add missing execute permission to shell scripts in scripts/


  Commit: a43e638e495930eb941519ece5e33498e89fd1ec
      https://github.com/ehb54/ultrascan3/commit/a43e638e495930eb941519ece5e33498e89fd1ec
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: improve python3 version check and update-alternatives registration


  Commit: 7f15d549465db31e042d59a5686dc8e2cd2b056a
      https://github.com/ehb54/ultrascan3/commit/7f15d549465db31e042d59a5686dc8e2cd2b056a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  mod: make executable


  Commit: 36dd7367a1f0d64008dcf711a3c7265de78867f7
      https://github.com/ehb54/ultrascan3/commit/36dd7367a1f0d64008dcf711a3c7265de78867f7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  fix: conditionally include python39 packages based on python3 version


  Commit: f22ca7ce48ab875427dac618f91e473b40d937ce
      https://github.com/ehb54/ultrascan3/commit/f22ca7ce48ab875427dac618f91e473b40d937ce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [Back compatibility with a 1-channel RA-sim. data] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 73a27078af4dfa87f2178651d2907835d3cf9b92
      https://github.com/ehb54/ultrascan3/commit/73a27078af4dfa87f2178651d2907835d3cf9b92
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  fix: update default GUI style for MacOS to 'macOS' in Qt 6


  Commit: 2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
      https://github.com/ehb54/ultrascan3/commit/2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP:IP+RI - prevent crush at 4. EDIT when IP loaded first due to leagcy protocol re-using and scan_nth set to 0...


  Commit: e69cf69c249ce62533cd87f25c93dde746147ffa
      https://github.com/ehb54/ultrascan3/commit/e69cf69c249ce62533cd87f25c93dde746147ffa
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge pull request #474 from ehb54/843-request-macintosh-style-is-deprecated

Update default GUI style for macOS in Qt 6


  Commit: aa00be99171275b2c91132092e04bce0f9cace1d
      https://github.com/ehb54/ultrascan3/commit/aa00be99171275b2c91132092e04bce0f9cace1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge branch 'main' into 955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute


  Commit: 833773e788e0239ba91dae8b4fdd7110a147fb4b
      https://github.com/ehb54/ultrascan3/commit/833773e788e0239ba91dae8b4fdd7110a147fb4b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge pull request #472 from ehb54/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute

Add execute permission to shell scripts and improve version check


  Commit: f4915d875bcf8965884d7059dab0011045ae16b8
      https://github.com/ehb54/ultrascan3/commit/f4915d875bcf8965884d7059dab0011045ae16b8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d81051ec6903d845918fcfa3b93d324988b84d52
      https://github.com/ehb54/ultrascan3/commit/d81051ec6903d845918fcfa3b93d324988b84d52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: f289321afa9b9b656d8bde7b11a50b5e27b397a2
      https://github.com/ehb54/ultrascan3/commit/f289321afa9b9b656d8bde7b11a50b5e27b397a2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 857f3efd29534ce5ce6cf14c840be389eebd9b74
      https://github.com/ehb54/ultrascan3/commit/857f3efd29534ce5ce6cf14c840be389eebd9b74
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
      https://github.com/ehb54/ultrascan3/commit/2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [[1]And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d56a96153cae267abf3f0ab713d600e6c37a16ad
      https://github.com/ehb54/ultrascan3/commit/d56a96153cae267abf3f0ab713d600e6c37a16ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [And for Audit Trail -- And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: e1a744a5b128a49750aed0f58d5b988527a78d00
      https://github.com/ehb54/ultrascan3/commit/e1a744a5b128a49750aed0f58d5b988527a78d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: beb1029bcdca1b2612f23cf65f739021388aac1f
      https://github.com/ehb54/ultrascan3/commit/beb1029bcdca1b2612f23cf65f739021388aac1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [1]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 83fbeffb53ca1d9a82583aa5a62cdc4527299f12
      https://github.com/ehb54/ultrascan3/commit/83fbeffb53ca1d9a82583aa5a62cdc4527299f12
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
      https://github.com/ehb54/ultrascan3/commit/01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [ the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 828342afc1ebd1342fb402beb9010070781b07b7
      https://github.com/ehb54/ultrascan3/commit/828342afc1ebd1342fb402beb9010070781b07b7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  [anf add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 10bd647e3ac0e99176196271ff1d6b97645cc030
      https://github.com/ehb54/ultrascan3/commit/10bd647e3ac0e99176196271ff1d6b97645cc030
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [[add option to Cancel scan, but not the first time]and add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 9d2438e1c6cec27070001ad1631548c32ccea3b4
      https://github.com/ehb54/ultrascan3/commit/9d2438e1c6cec27070001ad1631548c32ccea3b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: aea46531df9dbdab71687e604f60e8047f1e66f1
      https://github.com/ehb54/ultrascan3/commit/aea46531df9dbdab71687e604f60e8047f1e66f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  []GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: 7981a62c68b5c180b08fd48e7452601700d341e1
      https://github.com/ehb54/ultrascan3/commit/7981a62c68b5c180b08fd48e7452601700d341e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M gui/us_gui_settings.cpp
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 8fbfd948e503374ba161214696f34e1ec158228f
      https://github.com/ehb54/ultrascan3/commit/8fbfd948e503374ba161214696f34e1ec158228f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  2. LIVE_UPDATE stage: GMP vs R&D: pass flag for the program mode to the live update from the top-level us_comproject, to define different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: 69bb3f83f418b000fce5d05520008f5be7e3c9d3
      https://github.com/ehb54/ultrascan3/commit/69bb3f83f418b000fce5d05520008f5be7e3c9d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  [updated]2. LIVE_UPDATE stage: GMP vs R&D: different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: 3a329e106454a1f26436acd02b7d43809c8fd0f6
      https://github.com/ehb54/ultrascan3/commit/3a329e106454a1f26436acd02b7d43809c8fd0f6
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  feat: add initial CMake configuration and vcpkg support for gumbo library


  Commit: a6dc6e628437424579410fe577bca9357bbb38cd
      https://github.com/ehb54/ultrascan3/commit/a6dc6e628437424579410fe577bca9357bbb38cd
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge pull request #483 from ehb54/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch

Add CMake configuration and vcpkg support for gumbo library


  Commit: 89695a27c955ea41f1763c6af51d62064c11c7b3
      https://github.com/ehb54/ultrascan3/commit/89695a27c955ea41f1763c6af51d62064c11c7b3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 1468dcf35170704617ae78f5e2581e0070273c8d
      https://github.com/ehb54/ultrascan3/commit/1468dcf35170704617ae78f5e2581e0070273c8d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #479 from ehb54/alexey-dev-issue954

Extend GMP:dataDisk for IP- and mixed optics RI+IP types; Improve user experiences for GMP:Audit Trail & GMP:eSigs


  Commit: de15b65e87559ed23515bf20079ecd0de671f983
      https://github.com/ehb54/ultrascan3/commit/de15b65e87559ed23515bf20079ecd0de671f983
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue961


  Commit: cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
      https://github.com/ehb54/ultrascan3/commit/cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  Merge pull request #481 from ehb54/alexey-dev-issue961

GMP vs R&D's 2. LIVE_UPDATE, stop optima / skip optima stage


  Commit: e1a744791f51869f9547406aa7b6b2fe3825c85a
      https://github.com/ehb54/ultrascan3/commit/e1a744791f51869f9547406aa7b6b2fe3825c85a
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge branch 'main' into 875-request-cmake-remove-gmp-module-from-installer-for-osx


Compare: https://github.com/ehb54/ultrascan3/compare/4640187c3364...e1a744791f51

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From noreply at github.com  Sun Jul 19 14:44:27 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 13:44:27 -0700
Subject: [us-commits] [ehb54/ultrascan3] 00cf2e: Fix two invalid us_somo
 regex patterns breaking US...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/cace17-4b3e14@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 00cf2edadbc180e095d0db4efe197d2fb86d2862
      https://github.com/ehb54/ultrascan3/commit/00cf2edadbc180e095d0db4efe197d2fb86d2862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4b3e14634cdc79f28ec75abd4093e49b82247b94
      https://github.com/ehb54/ultrascan3/commit/4b3e14634cdc79f28ec75abd4093e49b82247b94
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #490 from ehb54/ehb54-issue-975

Fix two invalid us_somo regex patterns breaking US_RegexTest (#975)


Compare: https://github.com/ehb54/ultrascan3/compare/cace172cd5fe...4b3e14634cdc

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From noreply at github.com  Sun Jul 19 14:44:32 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 13:44:32 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-975/00cf2e-000000@github.com>

  Branch: refs/heads/ehb54-issue-975
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 19 14:44:56 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 13:44:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] ec623d: Fix two invalid us_somo
 regex patterns breaking US...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/d9d2b4-8fc78b@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ec623de279dc648f1abba5ee7ee53b827f45d335
      https://github.com/ehb54/ultrascan3/commit/ec623de279dc648f1abba5ee7ee53b827f45d335
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 8fc78be3a6ca3abe1dac66484e802358129f3536
      https://github.com/ehb54/ultrascan3/commit/8fc78be3a6ca3abe1dac66484e802358129f3536
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #491 from ehb54/ehb54-issue-975-somo-dev

Fix two invalid us_somo regex patterns breaking US_RegexTest (#975) [somo-dev]


Compare: https://github.com/ehb54/ultrascan3/compare/d9d2b46041a5...8fc78be3a6ca

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From noreply at github.com  Sun Jul 19 14:44:58 2026
From: noreply at github.com (emre brookes)
Date: Sun, 19 Jul 2026 13:44:58 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-975-somo-dev/ec623d-000000@github.com>

  Branch: refs/heads/ehb54-issue-975-somo-dev
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 19 14:46:23 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 13:46:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] 00cf2e: Fix two invalid us_somo
 regex patterns breaking US...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/unittest/fe5f85-3eaf20@github.com>

  Branch: refs/heads/lukas/unittest
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 00cf2edadbc180e095d0db4efe197d2fb86d2862
      https://github.com/ehb54/ultrascan3/commit/00cf2edadbc180e095d0db4efe197d2fb86d2862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4b3e14634cdc79f28ec75abd4093e49b82247b94
      https://github.com/ehb54/ultrascan3/commit/4b3e14634cdc79f28ec75abd4093e49b82247b94
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #490 from ehb54/ehb54-issue-975

Fix two invalid us_somo regex patterns breaking US_RegexTest (#975)


  Commit: 3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
      https://github.com/ehb54/ultrascan3/commit/3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/unittest


Compare: https://github.com/ehb54/ultrascan3/compare/fe5f85278c61...3eaf20cfd32e

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From noreply at github.com  Sun Jul 19 14:47:17 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 13:47:17 -0700
Subject: [us-commits] [ehb54/ultrascan3] 00cf2e: Fix two invalid us_somo
 regex patterns breaking US...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/2a9589-71b90e@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 00cf2edadbc180e095d0db4efe197d2fb86d2862
      https://github.com/ehb54/ultrascan3/commit/00cf2edadbc180e095d0db4efe197d2fb86d2862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4b3e14634cdc79f28ec75abd4093e49b82247b94
      https://github.com/ehb54/ultrascan3/commit/4b3e14634cdc79f28ec75abd4093e49b82247b94
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #490 from ehb54/ehb54-issue-975

Fix two invalid us_somo regex patterns breaking US_RegexTest (#975)


  Commit: 71b90e81d955f9c4c383d86ebbfd2942e9198495
      https://github.com/ehb54/ultrascan3/commit/71b90e81d955f9c4c383d86ebbfd2942e9198495
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/qwt616


Compare: https://github.com/ehb54/ultrascan3/compare/2a95899b28be...71b90e81d955

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From noreply at github.com  Sun Jul 19 14:53:46 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 13:53:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 99535b: Add qtmultimedia5-dev to
 unit tests workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/4b3e14-9722a6@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 99535b73ac71970aef06bd32024f048873970c1f
      https://github.com/ehb54/ultrascan3/commit/99535b73ac71970aef06bd32024f048873970c1f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add qtmultimedia5-dev to unit tests workflow


  Commit: fe5f85278c6177d4879919a5f15f232e3ffb6cc8
      https://github.com/ehb54/ultrascan3/commit/fe5f85278c6177d4879919a5f15f232e3ffb6cc8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Update changed files in unit-tests-v2 workflow


  Commit: 3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
      https://github.com/ehb54/ultrascan3/commit/3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/unittest


  Commit: 9722a6463cb01bd8170e5e3ee87082561cc756c9
      https://github.com/ehb54/ultrascan3/commit/9722a6463cb01bd8170e5e3ee87082561cc756c9
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Merge pull request #489 from ehb54/lukas/unittest

Add qtmultimedia5-dev to unit tests workflow


Compare: https://github.com/ehb54/ultrascan3/compare/4b3e14634cdc...9722a6463cb0

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From noreply at github.com  Sun Jul 19 14:54:12 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 13:54:12 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/unittest/3eaf20-000000@github.com>

  Branch: refs/heads/lukas/unittest
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Jul 19 14:54:25 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 13:54:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 99535b: Add qtmultimedia5-dev to
 unit tests workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/71b90e-ff82e8@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 99535b73ac71970aef06bd32024f048873970c1f
      https://github.com/ehb54/ultrascan3/commit/99535b73ac71970aef06bd32024f048873970c1f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add qtmultimedia5-dev to unit tests workflow


  Commit: fe5f85278c6177d4879919a5f15f232e3ffb6cc8
      https://github.com/ehb54/ultrascan3/commit/fe5f85278c6177d4879919a5f15f232e3ffb6cc8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Update changed files in unit-tests-v2 workflow


  Commit: 3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
      https://github.com/ehb54/ultrascan3/commit/3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/unittest


  Commit: 9722a6463cb01bd8170e5e3ee87082561cc756c9
      https://github.com/ehb54/ultrascan3/commit/9722a6463cb01bd8170e5e3ee87082561cc756c9
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Merge pull request #489 from ehb54/lukas/unittest

Add qtmultimedia5-dev to unit tests workflow


  Commit: ff82e871483b4d4618e39a453f7ff78c85fe6a79
      https://github.com/ehb54/ultrascan3/commit/ff82e871483b4d4618e39a453f7ff78c85fe6a79
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Merge branch 'main' into lukas/qwt616


Compare: https://github.com/ehb54/ultrascan3/compare/71b90e81d955...ff82e871483b

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From noreply at github.com  Sun Jul 19 17:03:09 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 16:03:09 -0700
Subject: [us-commits] [ehb54/ultrascan3] bcc6dc: Removal of qwt6.1.6 in
 github actions, documentati...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/9722a6-bcc6dc@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
      https://github.com/ehb54/ultrascan3/commit/bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M CMakePresets.json
    M README.md
    M admin/modulefiles/home-gui-build
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M local.pri.template
    M vcpkg.json

  Log Message:
  -----------
  Removal of qwt6.1.6 in github actions, documentation, cmkae and vcpkg configuration (#488)

* Remove qwt6.1.6 actions

Removed deprecated container version for consistency.

* Update QWT library paths to version 6.3.0

* Remove obsolete Qwt6.1.6 configuration presets

* Update README.md

* Remove features related to qwt6.1.6

* Delete buildsys/vcpkg/overlay-ports/qwt-6-1-6 directory

* Delete buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5 directory

* Update Qt version to 5.15.19 and Qwt version to 6.3.0

* Remove deprecated container from CodeQL workflow

* Update container version in doc-build workflow

* Add new container to CodeQL analysis workflow



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From noreply at github.com  Sun Jul 19 17:03:19 2026
From: noreply at github.com (Lukas Dobler)
Date: Sun, 19 Jul 2026 16:03:19 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qwt616/ff82e8-000000@github.com>

  Branch: refs/heads/lukas/qwt616
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Jul 20 07:14:36 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 06:14:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] a997ae: extrap_c0: fix unweighted
 GCV wiping out low q; re...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/c02b5f-a997ae@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a997aef8d438a5599240a6ef7cbefe853d9604ab
      https://github.com/ehb54/ultrascan3/commit/a997aef8d438a5599240a6ef7cbefe853d9604ab
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: fix unweighted GCV wiping out low q; report real skip causes

Reported: "non weighted seems to not work -- q-points could not be extrapolated
(fewer than 2 valid data points) and were skipped, regardless of merge etc."

Root cause. With unit weights the joint GCV objective on the reciprocal (c/I) axis is
dominated by the high-q points, whose values are orders of magnitude larger than the
low-q ones. GCV therefore selected lambda ~7.7e6 (effective slope dof 9.8, vs 259/19.7
for the same data weighted), over-smoothing alpha(q) into a near-constant until
Iex = (Q - B*alpha)/C went negative starting at the LOWEST q. Every such q was dropped,
so the Guinier region was destroyed and Rg blew up to 111 A. merge_ref cannot help
because it splices the reference at HIGH q while the damage is at low q.

This was previously recorded as "genuine algorithm behavior, validates why sd_weights
defaults ON". That was wrong: the same data unweighted with GCV OFF gives Rg 37.5 A with
1 skip, i.e. unweighted fitting is fine -- the regularization was the problem.

Fixes:
- (C, root cause) In the unweighted case, weight each q by 1/scale^2 where scale is that
  q's mean |y|. The factor is CONSTANT WITHIN a q, so it leaves every per-q fit (slope
  R/M and intercept Iex) algebraically unchanged -- it only rebalances the q against one
  another in the joint penalized solve, restoring the conditioning the 1/sigma^2 path
  gets for free. Equivalent to assuming constant relative error, the standard default
  when error bars are absent or distrusted. The weighted path is untouched.
- (A) Report the ACTUAL skip cause(s) with per-cause counts. All four causes previously
  reported as "fewer than 2 valid data points", which is wrong for three of them and hid
  the real one (non-positive 1/I(0) intercept) -- that message is what sent the original
  diagnosis down the wrong path.
- (B, safety net) If the GCV-smoothed intercept is still non-positive at some q, fall back
  to the unregularized per-q intercept there instead of dropping the point, and tell the
  user how many q that happened at (those points are not regularized).

Validated on the 7-curve alpha-syn set: recip_uw 506 skips / Rg 111 -> 0 skips / Rg 38.4
(in family with recip 38.1, additive 38.4, nogcv 38.3, unweighted-nogcv 37.5); same for
the merge variant. 8 of 9 regression baselines and all 5 SASBDB Table-1 outputs are
byte-identical, confirming the default weighted+GCV path is unchanged. Safety net (B) did
not need to fire in any test -- it is defensive only. Manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 08:19:29 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 07:19:29 -0700
Subject: [us-commits] [ehb54/ultrascan3] 53f39f: Fix deoxynucleotide C2'
 hybridization: C4H1 -> C4H2
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-976/000000-af7923@github.com>

  Branch: refs/heads/ehb54-issue-976
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 53f39f42b231277e413ace83e548826caa3ab7a4
      https://github.com/ehb54/ultrascan3/commit/53f39f42b231277e413ace83e548826caa3ab7a4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.residue.new

  Log Message:
  -----------
  Fix deoxynucleotide C2' hybridization: C4H1 -> C4H2

Deoxyribose C2' is bonded to C1', C3' and two hydrogens, so it is a CH2
(C4H2, 14.03). It was typed C4H1 (13.02), the ribose value, where C2'
carries O2' and only one hydrogen.

The deoxy blocks were created by copying the corresponding ribo block and
deleting the O2' atom line, but C2' was never retyped. Every deoxy residue
therefore came out 1.01 Da light, and since residue mass is the sum of its
atom hybrid masses, the error propagated into MW, vbar-weighted quantities
and bead masses for every DNA run.

Corrected in all 22 affected blocks (DA/DC/DG/DT, both the primed and the
starred atom-naming variants, with and without phosphate). Each deoxy
residue is now exactly 16.00 Da below its ribo counterpart, i.e. the loss
of one oxygen and nothing else; previously the gap was 17.01 Da:

  A ->DA   266.27 -> 250.27  (-16.00, was -17.01)
  C ->DC   242.24 -> 226.24  (-16.00, was -17.01)
  G ->DG   282.27 -> 266.27  (-16.00, was -17.01)
  U ->DT   243.22 -> 241.25  (-1.97 = -O +CH2, was -2.98)

Ribose C2' (A/C/G/U, and sugars such as LMT) is untouched.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4ae31a8922b1bca3ae30d07dd6f66d2b5ac7c3bb
      https://github.com/ehb54/ultrascan3/commit/4ae31a8922b1bca3ae30d07dd6f66d2b5ac7c3bb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new
    M us_somo/etc/somo.residue.new
    M us_somo/etc/somo.saxs_atoms.new

  Log Message:
  -----------
  Add molybdenum cluster support to the SOMO parameter files

Adopts the additive part of Mattia's updated parameter files: support for
polyoxomolybdate clusters, which previously could not be typed at all.

  somo.hybrid      O2H02- (oxide O2-), MO+5, MO+6
  somo.atom        MO1-MO6 as MO+6, MO7/MO8 as MO+5; O2H02- oxide, O2H2
                   water and further O1H0 entries for the O1-O27 cluster
                   oxygens (38 rows)
  somo.saxs_atoms  Cromer-Mann form factors for MO+5 and MO+6, both the
                   9- and 11-parameter variants, matching the MO+3 rows
  somo.residue     two new residues, Molybdenum Cluster Subunit 1 (MO2)
                   and Subunit 2 (MO6)

Purely additive - no existing row is modified, so no current result can
change. Verified: every hybrid referenced by somo.residue resolves in
somo.hybrid; every (atom name, hybrid) pair used by the two new residues
exists in somo.atom; and the new electron counts are correct for Z minus
formal charge (O2- 10, MO+5 37, MO+6 36).

Mattia's copy of somo.residue predates 78465e20, so it is missing glucose;
GLC is deliberately retained here and only his new blocks were taken.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: b112dfd5c5fe820c5ddbac261d394c8ea900d844
      https://github.com/ehb54/ultrascan3/commit/b112dfd5c5fe820c5ddbac261d394c8ea900d844
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new

  Log Message:
  -----------
  Fix SAXS excluded volume for four hydroxyl entries in somo.atom

O10, O1A, O1B and O1N carried 9.13 A^3 as their O2H1 excluded volume, the
value belonging to a bare oxygen (O1H0/O2H0), rather than the 14.28 A^3 used
by every other hydroxyl. The four rows sit directly below O1H0/O2H0 rows for
the same atom names, so this reads as a copy-paste slip.

All 43 O2H1 rows in the file now use 14.28; before this change 39 did and
these 4 did not. Affects the excluded-volume term in SAXS curve computation
for structures containing those atom names.

>From Mattia's updated parameter files.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 1f0b373b0887e359bf2dd08e7ef193f0800b2f56
      https://github.com/ehb54/ultrascan3/commit/1f0b373b0887e359bf2dd08e7ef193f0800b2f56
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.residue.new

  Log Message:
  -----------
  Fix NDP ionized-state vbar: 0.599 -> 0.589

NADPH (NDP) declared vbar 0.589 for the neutral form but 0.599 for both
ionized states. 0.599 is NAD's vbar, and the NDP header otherwise matches
NAD's line, so the two ionized values were carried over when the entry was
copied from NAD.

Every other multi-state residue in the file repeats the same vbar across all
of its protonation states; NDP was the only one of the 20 that did not. It
now uses 0.589 throughout, so vbar no longer jumps by 1.7% as a function of
pH for NADPH-containing models.

>From Mattia's updated parameter files.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: af79233b29bed30e8f53969b0280ff14eef0aa04
      https://github.com/ehb54/ultrascan3/commit/af79233b29bed30e8f53969b0280ff14eef0aa04
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new

  Log Message:
  -----------
  Set MO+3 radius to 0.69 (NEEDS CONFIRMATION FROM MATTIA)

Mattia's files change the Mo(III) radius from 0.83 to 0.69 A in both
somo.atom and somo.hybrid. Kept as the last commit on this branch because,
unlike everything before it, it changes results for existing structures:
it is not additive and not a demonstrable typo.

Evidence for: his three Mo radii, 0.69 (+3), 0.61 (+5) and 0.73 (+6), are
Shannon effective ionic radii for Mo(III) and Mo(V) six-coordinate and
Mo(VI) seven-coordinate. 0.83 corresponds to no standard Mo radius, and it
entered in 623ce9cc (2020) together with the rest of the multi-pKa support
files, with no stated source.

Evidence against: the metal radii in these tables are not uniformly Shannon
values (ZN+2 is 1.04 where Shannon gives 0.74, CA+2 is 1.26 where Shannon
gives 1.00), so the series may be on a different scale, and mixing a
seven-coordinate value for Mo(VI) with six-coordinate values for Mo(III)
and Mo(V) leaves the radius rising from +3 to +6 rather than falling.

Drop this commit if Mattia cannot confirm the provenance; the preceding
commits do not depend on it.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


Compare: https://github.com/ehb54/ultrascan3/compare/53f39f42b231%5E...af79233b29be

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From noreply at github.com  Mon Jul 20 08:44:40 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 07:44:40 -0700
Subject: [us-commits] [ehb54/ultrascan3] f00f0b: Set MO+3 radius to 0.69,
 completing the Mo series
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-976/af7923-f00f0b@github.com>

  Branch: refs/heads/ehb54-issue-976
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f00f0bfd2facda5de8de10142e040f2c8b2db1e9
      https://github.com/ehb54/ultrascan3/commit/f00f0bfd2facda5de8de10142e040f2c8b2db1e9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new

  Log Message:
  -----------
  Set MO+3 radius to 0.69, completing the Mo series

Mattia changed the Mo(III) radius from 0.83 to 0.69 A in both somo.atom and
somo.hybrid when adding the MO+5 and MO+6 entries, and has confirmed 0.69 is
the value to use.

This makes the three Mo radii one consistently sourced set: 0.69 (+3), 0.61
(+5) and 0.73 (+6) are Shannon effective ionic radii, six-coordinate for
Mo(III) and Mo(V) and seven-coordinate for Mo(VI). The previous 0.83
corresponds to no standard Mo radius; it entered in 623ce9cc (2020) with the
multi-pKa support files, with no stated source.

Note for anyone reading the table later: the radius rises from +3 to +6
rather than falling, because the Mo(VI) value is seven-coordinate while the
other two are six-coordinate. That is intentional, not a transcription error.

Unlike the rest of this branch this change is not additive. It alters bead
radii, and hence hydrodynamic results, for existing structures containing
Mo(III).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 09:04:06 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 08:04:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] 246fd4: extrap_c0: allow the
 outlier QC to discard more th...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/a997ae-246fd4@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 246fd4b747a296ab696167e6e4f479499ad5f412
      https://github.com/ehb54/ultrascan3/commit/246fd4b747a296ab696167e6e4f479499ad5f412
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp

  Log Message:
  -----------
  extrap_c0: allow the outlier QC to discard more than one curve

Motivated by Mattia's alpha-syn evaluation: he identifies TWO contaminated curves
(conc 2.41176 as an outlier in MW-vs-concentration, and 0.694246 with an
overestimated MW), while the QC discards at most one and nominates a third
(1.81792). With more than one bad curve present, a single pass judges every curve
against a trend that still contains the other offender, so the nomination itself
can be unreliable.

Detection is now repeated on the CLEANED set while curves keep qualifying, bounded
by a new outlier_max limit. Default 1 reproduces the previous behavior exactly
(and is what the GUI uses, since the dialog is unchanged); the headless driver
exposes it as the `outlier_max <int>` control-file directive so the effect can be
evaluated. Each discard is logged with its ordinal, and hitting the cap while a
further curve still qualifies is reported rather than silently ignored. The
regression-plot red "x" marks the first (strongest) discard; the log records all.

Verified: all 9 regression baselines byte-identical with the default, so nothing
changes unless the limit is raised. On the 7-curve alpha-syn set with the limit
raised, pass 2 nominates 0.694246 -- one of the two curves Mattia flagged -- but
it is correctly kept, failing the systematic gate at 64% one-sided (needs >=70%).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 09:20:20 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 08:20:20 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3b3ffa: extrap_c0: studentize the
 outlier nomination resid...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/246fd4-3b3ffa@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3b3ffaec747d5e17d2777dc5cb4bdaaaecfd980c
      https://github.com/ehb54/ultrascan3/commit/3b3ffaec747d5e17d2777dc5cb4bdaaaecfd980c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp

  Log Message:
  -----------
  extrap_c0: studentize the outlier nomination residual (leverage correction)

The QC nominated the curve with the largest mean |standardized residual|, with no
leverage adjustment. In a regression of y against concentration the HIGHEST-
concentration curve is the extreme x and therefore the highest-leverage point: it
drags the fitted line onto itself and shrinks its own residual, so a genuinely bad
top-concentration curve is masked by construction.

Measured on the 7-curve alpha-syn set: the top curve (conc 2.41176) carries mean
leverage 0.802 against ~0.29 average, giving raw mean|t| 0.822 -- rank 5 of 7, i.e.
apparently clean -- while the leverage-corrected value is 1.803, rank 2.

Nomination now uses the internally-studentized residual r/(sigma*sqrt(1-h)), with
h = w*(1/S + (x-xbar_w)^2/M) the point's leverage in the weighted line fit (sum h = 2).
Since Var(r_i) = sigma_i^2 (1-h_i), this is the standard statistic rather than a
heuristic. Controlled by the new `outlier_leverage 0|1` control-file directive
(default 1) so the previous behavior can still be reproduced.

Verified: all 9 regression baselines byte-identical -- on that set the same curve is
nominated either way, only the reported statistic changes (1.62 -> 1.97). The C++
values reproduce an independent Python computation of the same quantity exactly.

Note for the record: leverage correction alone does NOT let the detector find the
curve Mattia flags (conc 2.41176). Once the first outlier is removed that curve's
leverage rises to 0.987 -- the fit passes almost exactly through it, its raw residual
collapses to 0.123, and even an 8.8x studentized inflation leaves it below the next
candidate. At h ~ 1 the regression has essentially no information about that point,
so NO residual-based criterion can judge it. Identifying it requires external
information, which is exactly what Mattia's MW-vs-concentration check supplies.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 09:22:41 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 08:22:41 -0700
Subject: [us-commits] [ehb54/ultrascan3] be9437: Complete the SAXS excluded
 volume fix: 31 further ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-976/f00f0b-be9437@github.com>

  Branch: refs/heads/ehb54-issue-976
  Home:   https://github.com/ehb54/ultrascan3
  Commit: be9437cf7e072474c7e06337c0716df2ad1d3c34
      https://github.com/ehb54/ultrascan3/commit/be9437cf7e072474c7e06337c0716df2ad1d3c34
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new

  Log Message:
  -----------
  Complete the SAXS excluded volume fix: 31 further rows in somo.atom

Extends the O2H1 correction to every other row carrying the same mistake.

Throughout somo.atom a hybrid's excluded volume is the bare heavy-atom value
plus 5.15 A^3 per attached hydrogen, 5.15 being hydrogen's own excluded volume
in somo.saxs_atoms. These 31 rows carried the bare value despite the hybrid
having hydrogens, i.e. the hydrogen contribution was omitted:

  C4H3  16.44 -> 31.89  x20   C13 C15 C1Q C1R C1T C1U C2 C20 C22 C25 C28
                              C2A C3 C35 C36 C38 C3P C4 C42 C5
  C4H2  16.44 -> 26.74  x8    C14 C15 C16 C17 C18 C19 C1P C21
  C3H2  16.44 -> 26.74  x2    CBB CBC
  C4H1  16.44 -> 21.59  x1    C40

With the four O2H1 rows already corrected earlier on this branch, all 35 rows
of this error class are now consistent. The number of hybrids carrying more
than one excluded volume drops from 6 to 2.

Four rows deviate from the rule in some other way and are deliberately left
untouched, since they need a judgement call rather than arithmetic:

  SG   S2H1   25.1   rule gives 25.01  - looks like a dropped digit, but the
                                         effect is negligible either way
  NE2  N3H1+  12.79  rule gives  7.64  - carries the two-hydrogen value while
                                         its mass 15.02 says one hydrogen
  B    B4H0    2.14  rule gives 29.65  - 2.14 is boron's volume in
                                         somo.saxs_atoms; B1/B2 use 29.65
  OW   O2H2   24     rule gives 19.43  - water oxygen; 24 may well be
                                         deliberate for explicit water

Affects the excluded-volume term in SAXS curve computation for structures
containing these atom names.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 09:27:48 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 08:27:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] 53f39f: Fix deoxynucleotide C2'
 hybridization: C4H1 -> C4H2
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/8fc78b-bf1c73@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 53f39f42b231277e413ace83e548826caa3ab7a4
      https://github.com/ehb54/ultrascan3/commit/53f39f42b231277e413ace83e548826caa3ab7a4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.residue.new

  Log Message:
  -----------
  Fix deoxynucleotide C2' hybridization: C4H1 -> C4H2

Deoxyribose C2' is bonded to C1', C3' and two hydrogens, so it is a CH2
(C4H2, 14.03). It was typed C4H1 (13.02), the ribose value, where C2'
carries O2' and only one hydrogen.

The deoxy blocks were created by copying the corresponding ribo block and
deleting the O2' atom line, but C2' was never retyped. Every deoxy residue
therefore came out 1.01 Da light, and since residue mass is the sum of its
atom hybrid masses, the error propagated into MW, vbar-weighted quantities
and bead masses for every DNA run.

Corrected in all 22 affected blocks (DA/DC/DG/DT, both the primed and the
starred atom-naming variants, with and without phosphate). Each deoxy
residue is now exactly 16.00 Da below its ribo counterpart, i.e. the loss
of one oxygen and nothing else; previously the gap was 17.01 Da:

  A ->DA   266.27 -> 250.27  (-16.00, was -17.01)
  C ->DC   242.24 -> 226.24  (-16.00, was -17.01)
  G ->DG   282.27 -> 266.27  (-16.00, was -17.01)
  U ->DT   243.22 -> 241.25  (-1.97 = -O +CH2, was -2.98)

Ribose C2' (A/C/G/U, and sugars such as LMT) is untouched.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4ae31a8922b1bca3ae30d07dd6f66d2b5ac7c3bb
      https://github.com/ehb54/ultrascan3/commit/4ae31a8922b1bca3ae30d07dd6f66d2b5ac7c3bb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new
    M us_somo/etc/somo.residue.new
    M us_somo/etc/somo.saxs_atoms.new

  Log Message:
  -----------
  Add molybdenum cluster support to the SOMO parameter files

Adopts the additive part of Mattia's updated parameter files: support for
polyoxomolybdate clusters, which previously could not be typed at all.

  somo.hybrid      O2H02- (oxide O2-), MO+5, MO+6
  somo.atom        MO1-MO6 as MO+6, MO7/MO8 as MO+5; O2H02- oxide, O2H2
                   water and further O1H0 entries for the O1-O27 cluster
                   oxygens (38 rows)
  somo.saxs_atoms  Cromer-Mann form factors for MO+5 and MO+6, both the
                   9- and 11-parameter variants, matching the MO+3 rows
  somo.residue     two new residues, Molybdenum Cluster Subunit 1 (MO2)
                   and Subunit 2 (MO6)

Purely additive - no existing row is modified, so no current result can
change. Verified: every hybrid referenced by somo.residue resolves in
somo.hybrid; every (atom name, hybrid) pair used by the two new residues
exists in somo.atom; and the new electron counts are correct for Z minus
formal charge (O2- 10, MO+5 37, MO+6 36).

Mattia's copy of somo.residue predates 78465e20, so it is missing glucose;
GLC is deliberately retained here and only his new blocks were taken.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: b112dfd5c5fe820c5ddbac261d394c8ea900d844
      https://github.com/ehb54/ultrascan3/commit/b112dfd5c5fe820c5ddbac261d394c8ea900d844
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new

  Log Message:
  -----------
  Fix SAXS excluded volume for four hydroxyl entries in somo.atom

O10, O1A, O1B and O1N carried 9.13 A^3 as their O2H1 excluded volume, the
value belonging to a bare oxygen (O1H0/O2H0), rather than the 14.28 A^3 used
by every other hydroxyl. The four rows sit directly below O1H0/O2H0 rows for
the same atom names, so this reads as a copy-paste slip.

All 43 O2H1 rows in the file now use 14.28; before this change 39 did and
these 4 did not. Affects the excluded-volume term in SAXS curve computation
for structures containing those atom names.

>From Mattia's updated parameter files.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 1f0b373b0887e359bf2dd08e7ef193f0800b2f56
      https://github.com/ehb54/ultrascan3/commit/1f0b373b0887e359bf2dd08e7ef193f0800b2f56
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.residue.new

  Log Message:
  -----------
  Fix NDP ionized-state vbar: 0.599 -> 0.589

NADPH (NDP) declared vbar 0.589 for the neutral form but 0.599 for both
ionized states. 0.599 is NAD's vbar, and the NDP header otherwise matches
NAD's line, so the two ionized values were carried over when the entry was
copied from NAD.

Every other multi-state residue in the file repeats the same vbar across all
of its protonation states; NDP was the only one of the 20 that did not. It
now uses 0.589 throughout, so vbar no longer jumps by 1.7% as a function of
pH for NADPH-containing models.

>From Mattia's updated parameter files.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: f00f0bfd2facda5de8de10142e040f2c8b2db1e9
      https://github.com/ehb54/ultrascan3/commit/f00f0bfd2facda5de8de10142e040f2c8b2db1e9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new

  Log Message:
  -----------
  Set MO+3 radius to 0.69, completing the Mo series

Mattia changed the Mo(III) radius from 0.83 to 0.69 A in both somo.atom and
somo.hybrid when adding the MO+5 and MO+6 entries, and has confirmed 0.69 is
the value to use.

This makes the three Mo radii one consistently sourced set: 0.69 (+3), 0.61
(+5) and 0.73 (+6) are Shannon effective ionic radii, six-coordinate for
Mo(III) and Mo(V) and seven-coordinate for Mo(VI). The previous 0.83
corresponds to no standard Mo radius; it entered in 623ce9cc (2020) with the
multi-pKa support files, with no stated source.

Note for anyone reading the table later: the radius rises from +3 to +6
rather than falling, because the Mo(VI) value is seven-coordinate while the
other two are six-coordinate. That is intentional, not a transcription error.

Unlike the rest of this branch this change is not additive. It alters bead
radii, and hence hydrodynamic results, for existing structures containing
Mo(III).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: be9437cf7e072474c7e06337c0716df2ad1d3c34
      https://github.com/ehb54/ultrascan3/commit/be9437cf7e072474c7e06337c0716df2ad1d3c34
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new

  Log Message:
  -----------
  Complete the SAXS excluded volume fix: 31 further rows in somo.atom

Extends the O2H1 correction to every other row carrying the same mistake.

Throughout somo.atom a hybrid's excluded volume is the bare heavy-atom value
plus 5.15 A^3 per attached hydrogen, 5.15 being hydrogen's own excluded volume
in somo.saxs_atoms. These 31 rows carried the bare value despite the hybrid
having hydrogens, i.e. the hydrogen contribution was omitted:

  C4H3  16.44 -> 31.89  x20   C13 C15 C1Q C1R C1T C1U C2 C20 C22 C25 C28
                              C2A C3 C35 C36 C38 C3P C4 C42 C5
  C4H2  16.44 -> 26.74  x8    C14 C15 C16 C17 C18 C19 C1P C21
  C3H2  16.44 -> 26.74  x2    CBB CBC
  C4H1  16.44 -> 21.59  x1    C40

With the four O2H1 rows already corrected earlier on this branch, all 35 rows
of this error class are now consistent. The number of hybrids carrying more
than one excluded volume drops from 6 to 2.

Four rows deviate from the rule in some other way and are deliberately left
untouched, since they need a judgement call rather than arithmetic:

  SG   S2H1   25.1   rule gives 25.01  - looks like a dropped digit, but the
                                         effect is negligible either way
  NE2  N3H1+  12.79  rule gives  7.64  - carries the two-hydrogen value while
                                         its mass 15.02 says one hydrogen
  B    B4H0    2.14  rule gives 29.65  - 2.14 is boron's volume in
                                         somo.saxs_atoms; B1/B2 use 29.65
  OW   O2H2   24     rule gives 19.43  - water oxygen; 24 may well be
                                         deliberate for explicit water

Affects the excluded-volume term in SAXS curve computation for structures
containing these atom names.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: bf1c7305fc74d7d30908e9423dea0a3fbc47e195
      https://github.com/ehb54/ultrascan3/commit/bf1c7305fc74d7d30908e9423dea0a3fbc47e195
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/etc/somo.atom.new
    M us_somo/etc/somo.hybrid.new
    M us_somo/etc/somo.residue.new
    M us_somo/etc/somo.saxs_atoms.new

  Log Message:
  -----------
  Merge pull request #492 from ehb54/ehb54-issue-976

SOMO parameter files: adopt Mattia's updates and fix deoxynucleotide C2' hybridization


Compare: https://github.com/ehb54/ultrascan3/compare/8fc78be3a6ca...bf1c7305fc74

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From noreply at github.com  Mon Jul 20 09:27:51 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 08:27:51 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-976/be9437-000000@github.com>

  Branch: refs/heads/ehb54-issue-976
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Jul 20 09:28:45 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 08:28:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] f6be52: extrap_c0 doc:
 multi-discard, studentized residual...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/3b3ffa-f6be52@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f6be52fa2c657a7ea9ddbc48c3e51d5f2fbf7268
      https://github.com/ehb54/ultrascan3/commit/f6be52fa2c657a7ea9ddbc48c3e51d5f2fbf7268
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 doc: multi-discard, studentized residual, and its limitation

The manual was not updated alongside 246fd4b74 (multi-discard) and 3b3ffaec7
(leverage-corrected nomination), leaving two stale claims and two undocumented
directives.

- Outlier QC section: "at most one curve is ever discarded" now correctly scoped to
  the interactive dialog, with the scripted outlier_max limit and the reason raising
  it matters (a single pass judges each curve against a trend still containing the
  other offender). Ranking statistic corrected to the studentized residual. Output
  token generalized _qc1 -> _qcN, noting the red "x" marks the first discard while
  the log records all.
- New paragraph on WHY the residual is leverage-corrected: the highest-concentration
  curve is the extreme x, carries the most leverage, pulls the fit onto itself and
  masks its own residual (measured: leverage 0.80 vs 0.29 average moved a curve from
  5th to 2nd of 7). Var(r) = sigma^2 (1-h), so it is the standard statistic.
- New paragraph on the limitation: when one concentration sits far above the rest its
  leverage approaches 1, the fit passes through it and its residual is near zero
  however it is scaled -- no residual-based test can judge such a curve, and doing so
  needs information from outside the regression (e.g. MW from I(0) vs the known value).
- Scripting section: documented outlier_max and outlier_leverage. Date bumped.

Rendered and checked; the pre-existing bare-<p> imbalance is unchanged (delta 5 both
before and after), so no tag nesting was introduced.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 13:58:03 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 12:58:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] 579add: Perceive hybridization/vdW
 radius/electron count f...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-978/000000-eb57f1@github.com>

  Branch: refs/heads/ehb54-issue-978
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 579add03864b4311b5016d778c65e660dd753e77
      https://github.com/ehb54/ultrascan3/commit/579add03864b4311b5016d778c65e660dd753e77
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    A us_somo/develop/include/us_hydrodyn_perceive.h
    A us_somo/develop/include/us_hydrodyn_perceive_elements.h
    A us_somo/develop/include/us_hydrodyn_perceive_hybrid.h
    A us_somo/develop/include/us_hydrodyn_perceive_saxs.h
    A us_somo/develop/include/us_hydrodyn_perceive_somo.h
    M us_somo/develop/libus_somo.pro
    A us_somo/develop/perceiver/.gitignore
    A us_somo/develop/perceiver/DECISIONS.md
    A us_somo/develop/perceiver/README.md
    A us_somo/develop/perceiver/data/ref/f0_WaasKirf.dat
    A us_somo/develop/perceiver/data/ref/it1992.cpp
    A us_somo/develop/perceiver/data/ref/somo.saxs_atoms.generated
    A us_somo/develop/perceiver/pdb_lite.h
    A us_somo/develop/perceiver/residue_oracle.h
    A us_somo/develop/perceiver/tests/coverage.cpp
    A us_somo/develop/perceiver/tests/emit_residue.cpp
    A us_somo/develop/perceiver/tests/regression.cpp
    A us_somo/develop/perceiver/tests/tests_unit.cpp
    A us_somo/develop/perceiver/tinytest.h
    A us_somo/develop/perceiver/tools/gen_saxs_entries.py
    A us_somo/develop/src/us_hydrodyn_perceive.cpp
    A us_somo/develop/src/us_hydrodyn_perceive_somo.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp

  Log Message:
  -----------
  Perceive hybridization/vdW radius/electron count for non-coded residues

Phases A and B of ehb54/ultrascan-tickets#978.

SOMO needs an atom's hybridization, vdW radius and electron count to build a
bead model, and today they come only from the hand-curated somo.residue. For a
residue that table does not code, SOMO synthesises a "<RESNAME>_NC<n>"
placeholder and models it as a generic ABB average bead. This adds a chemical
perceiver that derives the real per-atom chemistry from element + coordinates,
so such a residue can be given a proper entry instead of an averaged one.

somo.residue remains the master: perception runs only for residues SOMO itself
recorded in unknown_residues.

Phase A - core compiled into libus_somo:
  include/us_hydrodyn_perceive{,_elements,_hybrid,_saxs}.h
  src/us_hydrodyn_perceive.cpp
Pipeline: spatial-grid bond perception (honouring CONECT where present, and
H-/ion-agnostic so implicit-H inference is identical with or without explicit
hydrogens) -> ring detection + planarity aromaticity -> Kekule bond orders ->
per-element classification -> emit a somo.residue block plus any somo.hybrid
rows for novel types.

The core is deliberately Qt-free, so the standalone harness in
us_somo/develop/perceiver builds the very same sources without Qt: 23 unit
tests plus a regression that takes residues somo.residue DOES code, pretends
they are unknown, and checks they are reproduced - 41,219 atoms over 8 demo
structures, 99.83% geometric perception, 0.17% genuine error. The residual is
protonation/tautomer state, which heavy-atom geometry cannot resolve in
principle. The harness reads us_somo/etc directly so it cannot drift from the
real tables.

us_hydrodyn_perceive_somo.{h,cpp} is the only Qt-aware layer: it converts
PDB_model/PDB_chain/PDB_atom, reads CONECT and HETNAM from the source file,
and returns tentative entries. It converts the whole model rather than one
residue because bond perception needs surrounding context (peptide links,
disulfides, metal coordination) to get coordination numbers, and hence
implicit-H counts, right. Instances are de-duplicated back to the base residue
name so one confirmation covers all instances of the same chemistry.

Phase B - headless "perceive <pdbfile>" gui_script command, so the whole path
is exercisable against real structures with no GUI:
  us3_somo _pad -I -g <script>
Entries carry a REVIEW block naming every atom whose perception was uncertain
(ambiguous protonation, assumed oxidation state, estimated vbar), which is what
the confirmation UI in ehb54/ultrascan-tickets#979 will present to the user.

No existing behaviour changes: nothing calls the perceiver outside the new
command.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: 3e3fd3f51164a3220ab3b6d3d51b724d747040db
      https://github.com/ehb54/ultrascan3/commit/3e3fd3f51164a3220ab3b6d3d51b724d747040db
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_perceive_somo.h
    M us_somo/develop/perceiver/README.md
    A us_somo/develop/perceiver/examples/perceive.somo
    M us_somo/develop/src/us_hydrodyn_perceive_somo.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp

  Log Message:
  -----------
  Add "perceive compare" hand-testing sub-command

Part of ehb54/ultrascan-tickets#978.

"perceive compare <pdb>" runs perception over the residues somo.residue DOES
code and diffs the result against the curated types, reporting exact-match and
physics-match rates, a curated->perceived difference histogram, and the first
differing atoms. It is the interactive equivalent of the standalone regression
harness, but run inside SOMO against the user's own installed ~/ultrascan/etc
tables - so it also reveals when an installed table is out of date.

Cross-validation on 1HEL: the in-SOMO path and the standalone harness agree
exactly (1000 atoms scored, 984 exact 98.40%, 995 physics 99.50%), despite
using different PDB parsers and different copies of the tables. The five
physics differences are all known, explainable categories: the chain
N-terminus (a real -NH3+, where the perceiver is chemically right and the
residue template cannot know), the His tautomer and its charge, and the
Asp carboxylate protonation convention.

Also adds examples/perceive.somo documenting the invocation, including the
gotchas that cost time otherwise: the throwaway "_pad" argument is required on
macOS and must be omitted on Linux, "-I" avoids blocking config dialogs, and
the first run after rebuilding libus_somo only re-installs configs and exits,
so it must be run twice.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: eb57f12bd7b373cf3efba41e691eb607024cafc3
      https://github.com/ehb54/ultrascan3/commit/eb57f12bd7b373cf3efba41e691eb607024cafc3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/develop/perceiver/README.md

  Log Message:
  -----------
  Correct perceiver README: tables are read from us_somo/etc, not copied

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


Compare: https://github.com/ehb54/ultrascan3/compare/579add03864b%5E...eb57f12bd7b3

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From noreply at github.com  Mon Jul 20 14:16:43 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 13:16:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6ba2c5: extrap_c0: allow explicit
 reference-curve selectio...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/f6be52-6ba2c5@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6ba2c51a18bf32051322bdf25b0c0d66d05b3678
      https://github.com/ehb54/ultrascan3/commit/6ba2c51a18bf32051322bdf25b0c0d66d05b3678
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: allow explicit reference-curve selection, with guards

The reference used for the absolute scale and the high-q splice was always the
highest-concentration curve. That is the right DEFAULT -- intensity scales with
concentration, so the top curve normally has the best high-q signal-to-noise, which
is exactly what the splice consumes -- but it is wrong when that curve is itself
unsound (aggregation, mis-set concentration, radiation damage, bad subtraction).

The program cannot detect that case: the top-concentration curve is the extreme x in
the per-q fit, so its leverage approaches 1, the line passes essentially through it,
and its residual carries almost no information about it. Judging it needs knowledge
from outside the regression (e.g. MW from I(0) against the known value), which the
user may have. So expose the choice rather than guess: new `reference <name|conc>`
control-file directive, matching either a curve name (or a distinctive part of one)
or a concentration. A non-matching value is reported and the default used, never
silently ignored.

Two guards, because overriding interacts badly with the splice:
- selecting a non-highest concentration while merge_ref is on is warned about. The
  merge point is where the extrapolation stops differing from the reference, and a
  lower-concentration reference is both nearer dilute already and noisier, so the
  test passes almost immediately.
- a merge point in the first 10% of the grid is flagged: the output is then the raw
  reference curve rather than the extrapolation, discarding both the de-noising and
  the c=0 correction. This guard also protects the default path.

Verified: override selects correctly by concentration and by name substring;
non-matching falls back with a warning; both guards fire on a lower-concentration
reference (merge collapses to index 0 of 1045, as predicted); all 9 regression
baselines byte-identical, so the default path is unchanged. Manual updated with the
directive, why highest-concentration is the right default, why the program cannot
audit that curve itself, and the splice caveat.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 14:53:12 2026
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Jul 2026 13:53:12 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/packaging_sphinx/cc049b-000000@github.com>

  Branch: refs/heads/lukas/packaging_sphinx
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Jul 20 16:14:07 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Jul 2026 15:14:07 -0700
Subject: [us-commits] [ehb54/ultrascan3] cb55c6: Remove the XQuartz/X11
 rasmol dependency from macO...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/e1a744-cb55c6@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cb55c62623e1816ffe6d7924419a7723874c752f
      https://github.com/ehb54/ultrascan3/commit/cb55c62623e1816ffe6d7924419a7723874c752f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/linux/LinuxHpcDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/macos/MacHpcDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    M doc/manual/source/start_page-new.rst
    M pkg/macos/README.md
    M pkg/macos/preinstall
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  Remove the XQuartz/X11 rasmol dependency from macOS/Windows/Linux packaging in favor of the new static ehb54/rasmol build, add a VERSION file consistency check to packaging, and fix HPC Linux builds that unconditionally required GLU/X11.



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From noreply at github.com  Mon Jul 20 16:15:58 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Jul 2026 15:15:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 56ac62: add: nightly build
Message-ID: <ehb54/ultrascan3/push/refs/heads/bump-to-v4.2.0-dev/435b89-0b31fc@github.com>

  Branch: refs/heads/bump-to-v4.2.0-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 56ac62aee0f30eb92b6ba1c4fb11e0b3a4be919c
      https://github.com/ehb54/ultrascan3/commit/56ac62aee0f30eb92b6ba1c4fb11e0b3a4be919c
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    A .github/workflows/nightly-builds.yml
    A .github/workflows/nightly-macos-arm.yml
    A .github/workflows/nightly-macos-intel.yml
    A .github/workflows/nightly-oraclelinux8.yml
    A .github/workflows/nightly-ubuntu.yml
    A .github/workflows/nightly-windows.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    M programs/us/CMakeLists.txt
    M scripts/bootstrap-linux.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M vcpkg.json

  Log Message:
  -----------
  add: nightly build


  Commit: 2d14470510d03383cc580dc728ceaf34b28a9111
      https://github.com/ehb54/ultrascan3/commit/2d14470510d03383cc580dc728ceaf34b28a9111
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: ce0e7bc73c888397b643b77a02254123918c717f
      https://github.com/ehb54/ultrascan3/commit/ce0e7bc73c888397b643b77a02254123918c717f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .gitignore
    M doc/manual/Makefile
    M doc/manual/source/2dsa/2dsa_analys.rst
    M doc/manual/source/2dsa/2dsa_main.rst
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    A doc/manual/source/_static/UltraScanIII.pdf
    A doc/manual/source/_static/images/cmenu_help.png
    A doc/manual/source/_static/images/load_us3.png
    A doc/manual/source/_static/images/reporter_comrep.png
    A doc/manual/source/_static/images/us_spectrum-0-upded.png
    M doc/manual/source/_static/images/us_spectrum-1.png
    M doc/manual/source/_static/js/sphinx_highlight.js
    M doc/manual/source/analysprof_general.rst
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_new.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/astfem_sim.rst
    M doc/manual/source/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/buffer/buffer_settings.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/convert.rst
    M doc/manual/source/dmga_init.rst
    M doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/experiment/general.rst
    M doc/manual/source/experiment/import.rst
    M doc/manual/source/experiment/liveupdate.rst
    M doc/manual/source/experiment/range.rst
    M doc/manual/source/experiment/rotor.rst
    M doc/manual/source/experiment/solutions.rst
    M doc/manual/source/experiment/speeds.rst
    M doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_dmga_adv.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/fe_match/index.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp/gmp_automation.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    M doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_protocol_development.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    M doc/manual/source/multi-wavelength/index.rst
    M doc/manual/source/multi-wavelength/mwl_species_fit.rst
    M doc/manual/source/multi-wavelength/mwl_species_sim.rst
    M doc/manual/source/multi-wavelength/mwl_spectra.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/pseudo3d.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rmsd_query.rst
    R doc/manual/source/rotor.rst
    M doc/manual/source/rotor_calibration.rst
    A doc/manual/source/rotors.rst
    M doc/manual/source/run_details.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/simparams.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/start_page-int.rst
    M doc/manual/source/start_page-mw.rst
    M doc/manual/source/start_page-new.rst
    M doc/manual/source/start_page-rpt.rst
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_administrator.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst
    M doc/manual/source/us_investigator.rst
    M doc/manual/source/us_project.rst
    M doc/manual/source/us_spectrum.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/xpn_viewer.rst
    M gui/us_abstractrotor_gui.h
    M gui/us_rotor_gui.h
    M utils/us_run_protocol.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: b61ed7ce96981f2cb26951cc5d14ba599e34ae18
      https://github.com/ehb54/ultrascan3/commit/b61ed7ce96981f2cb26951cc5d14ba599e34ae18
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:

  Log Message:
  -----------
  Merge branch '800-enhancement-nightly-build-using-vcpkg' of github.com:ehb54/ultrascan3 into 800-enhancement-nightly-build-using-vcpkg


  Commit: 438ca1c0535b533e30d747dbfaaea341f80130df
      https://github.com/ehb54/ultrascan3/commit/438ca1c0535b533e30d747dbfaaea341f80130df
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-04-22 (Wed, 22 Apr 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  mod: rollback to match main


  Commit: 97bcfb0c7e017363e4cad1a6b8cf95a30bed82be
      https://github.com/ehb54/ultrascan3/commit/97bcfb0c7e017363e4cad1a6b8cf95a30bed82be
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-01 (Fri, 01 May 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  fix: resolve warning


  Commit: 2964bb347925c13d2a1dcfe7b03f3ce469c6190a
      https://github.com/ehb54/ultrascan3/commit/2964bb347925c13d2a1dcfe7b03f3ce469c6190a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-02 (Sat, 02 May 2026)

  Changed paths:
    M .github/workflows/nightly-builds.yml
    M .github/workflows/nightly-oraclelinux8.yml
    M .github/workflows/nightly-ubuntu.yml
    M .github/workflows/release.yml
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M scripts/build.sh

  Log Message:
  -----------
  mod: standard naming and xz used


  Commit: a7f952b2fbd09af29abbe74039f4d006e6662f42
      https://github.com/ehb54/ultrascan3/commit/a7f952b2fbd09af29abbe74039f4d006e6662f42
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-18 (Mon, 18 May 2026)

  Changed paths:
    M .github/workflows/nightly-builds.yml
    M .github/workflows/nightly-macos-arm.yml
    M .github/workflows/nightly-macos-intel.yml
    M .github/workflows/nightly-oraclelinux8.yml
    M .github/workflows/nightly-ubuntu.yml
    M .github/workflows/nightly-windows.yml
    M .github/workflows/release.yml
    M scripts/bootstrap-linux.sh
    M us-build

  Log Message:
  -----------
  fix(ci): nightly gate logic, bootstrap improvements, SHA bump to d40ab4b6


  Commit: 3aca19dec6d034a4606e10eee12ebc053f6bcbd7
      https://github.com/ehb54/ultrascan3/commit/3aca19dec6d034a4606e10eee12ebc053f6bcbd7
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-05-18 (Mon, 18 May 2026)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 46622569dc9e5cae5f731a56d2200b57fc981db8
      https://github.com/ehb54/ultrascan3/commit/46622569dc9e5cae5f731a56d2200b57fc981db8
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-19 (Tue, 19 May 2026)

  Changed paths:
    M programs/us_analyte/CMakeLists.txt
    M programs/us_export_legacy/CMakeLists.txt

  Log Message:
  -----------
  fix: changed program names to match what us_win_data.cpp uses.


  Commit: 0b97fc731d6dc06bcc6f64ed95c91667a0f8a591
      https://github.com/ehb54/ultrascan3/commit/0b97fc731d6dc06bcc6f64ed95c91667a0f8a591
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-19 (Tue, 19 May 2026)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/800-enhancement-nightly-build-using-vcpkg' into 800-enhancement-nightly-build-using-vcpkg


  Commit: aa28f848f31dce5d87784af68a9ce96752fb6584
      https://github.com/ehb54/ultrascan3/commit/aa28f848f31dce5d87784af68a9ce96752fb6584
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  fix(cmake): find qhelpgenerator before add_subdirectory(doc/manual) so Qt help files are built on first configure


  Commit: ee3c66db7273692c74d982760682c646a13ed113
      https://github.com/ehb54/ultrascan3/commit/ee3c66db7273692c74d982760682c646a13ed113
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-05-29 (Fri, 29 May 2026)

  Changed paths:
    M gui/us_extinction_gui.cpp
    M gui/us_properties.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 07f813016ff39565ddcf9e01ce3ca3a29ecc863a
      https://github.com/ehb54/ultrascan3/commit/07f813016ff39565ddcf9e01ce3ca3a29ecc863a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    A .github/workflows/nightly-build.yml
    R .github/workflows/nightly-builds.yml
    R .github/workflows/nightly-macos-arm.yml
    R .github/workflows/nightly-macos-intel.yml
    R .github/workflows/nightly-oraclelinux8.yml
    R .github/workflows/nightly-ubuntu.yml
    R .github/workflows/nightly-windows.yml
    M .github/workflows/on-demand-build.yml
    M .github/workflows/release.yml

  Log Message:
  -----------
  refactor: rename nightly build workflow files and update references for consistency


  Commit: 8ee0408d863d9af9868a15ba00610567482b5d1d
      https://github.com/ehb54/ultrascan3/commit/8ee0408d863d9af9868a15ba00610567482b5d1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-05-31 (Sun, 31 May 2026)

  Changed paths:
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 74a065b515b243ce83392ca76022b87d3d4dcb6c
      https://github.com/ehb54/ultrascan3/commit/74a065b515b243ce83392ca76022b87d3d4dcb6c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-02 (Tue, 02 Jun 2026)

  Changed paths:
    R .github/workflows/unit-tests.yml
    M .gitignore
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/macos/MacDeploy.cmake
    M admin/cmake/packaging/windows/WinDeploy.cmake
    M admin/cmake/toolchain.cmake
    M programs/us/us.cpp
    M scripts/build.ps1
    M scripts/build.sh

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 32aff34ae2377dd1854ab45ea784dcac5a4731d0
      https://github.com/ehb54/ultrascan3/commit/32aff34ae2377dd1854ab45ea784dcac5a4731d0
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-06-04 (Thu, 04 Jun 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_database.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: 0e41a20a321c39a27e8379902ef769bd1c537011
      https://github.com/ehb54/ultrascan3/commit/0e41a20a321c39a27e8379902ef769bd1c537011
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-06 (Mon, 06 Jul 2026)

  Changed paths:
    M .github/workflows/bump-version.yml
    M .github/workflows/codeql-analysis.yml
    M .gitignore
    A VERSION
    M admin/codeql/docker/local.pri.somo
    M admin/release/linux.pl
    R doc/manual/source/__pycache__/auto_index.cpython-39.pyc
    M doc/manual/source/conf.py
    M gui/libus_gui.pro
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_help.cpp
    M gui/us_select_item.cpp
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M local.pri.template
    M makeall.sh
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    M utils/us_lm.cpp
    M utils/us_matrix.cpp
    M utils/us_settings.cpp
    M utils/us_solve_sim.cpp

  Log Message:
  -----------
  Merge branch 'main' into 800-enhancement-nightly-build-using-vcpkg


  Commit: dc00acf48dd3b8ab26645b2b104a19d152e81d4a
      https://github.com/ehb54/ultrascan3/commit/dc00acf48dd3b8ab26645b2b104a19d152e81d4a
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-06 (Mon, 06 Jul 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    A .github/workflows/nightly-build.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    M programs/us/CMakeLists.txt
    M programs/us_analyte/CMakeLists.txt
    M programs/us_export_legacy/CMakeLists.txt
    M scripts/bootstrap-linux.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M us-build
    M vcpkg.json

  Log Message:
  -----------
  Merge pull request #417 from ehb54/800-enhancement-nightly-build-using-vcpkg

Add nightly build configuration


  Commit: 63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
      https://github.com/ehb54/ultrascan3/commit/63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: e1345a3206da2fc4942f218fc813fda1682f69cd
      https://github.com/ehb54/ultrascan3/commit/e1345a3206da2fc4942f218fc813fda1682f69cd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: f51e6bac3a1d4943c3291b8db1525d9f18419844
      https://github.com/ehb54/ultrascan3/commit/f51e6bac3a1d4943c3291b8db1525d9f18419844
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 044f72440db40f7632169394d6ee0b593998562a
      https://github.com/ehb54/ultrascan3/commit/044f72440db40f7632169394d6ee0b593998562a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 37a4a06b5999bf9f3c243fbe38ede1a3fea379af
      https://github.com/ehb54/ultrascan3/commit/37a4a06b5999bf9f3c243fbe38ede1a3fea379af
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [33more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
      https://github.com/ehb54/ultrascan3/commit/8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Add missing execute permission to shell scripts in scripts/


  Commit: a43e638e495930eb941519ece5e33498e89fd1ec
      https://github.com/ehb54/ultrascan3/commit/a43e638e495930eb941519ece5e33498e89fd1ec
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: improve python3 version check and update-alternatives registration


  Commit: 7f15d549465db31e042d59a5686dc8e2cd2b056a
      https://github.com/ehb54/ultrascan3/commit/7f15d549465db31e042d59a5686dc8e2cd2b056a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  mod: make executable


  Commit: 36dd7367a1f0d64008dcf711a3c7265de78867f7
      https://github.com/ehb54/ultrascan3/commit/36dd7367a1f0d64008dcf711a3c7265de78867f7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  fix: conditionally include python39 packages based on python3 version


  Commit: f22ca7ce48ab875427dac618f91e473b40d937ce
      https://github.com/ehb54/ultrascan3/commit/f22ca7ce48ab875427dac618f91e473b40d937ce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [Back compatibility with a 1-channel RA-sim. data] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 73a27078af4dfa87f2178651d2907835d3cf9b92
      https://github.com/ehb54/ultrascan3/commit/73a27078af4dfa87f2178651d2907835d3cf9b92
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  fix: update default GUI style for MacOS to 'macOS' in Qt 6


  Commit: 2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
      https://github.com/ehb54/ultrascan3/commit/2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP:IP+RI - prevent crush at 4. EDIT when IP loaded first due to leagcy protocol re-using and scan_nth set to 0...


  Commit: e69cf69c249ce62533cd87f25c93dde746147ffa
      https://github.com/ehb54/ultrascan3/commit/e69cf69c249ce62533cd87f25c93dde746147ffa
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge pull request #474 from ehb54/843-request-macintosh-style-is-deprecated

Update default GUI style for macOS in Qt 6


  Commit: aa00be99171275b2c91132092e04bce0f9cace1d
      https://github.com/ehb54/ultrascan3/commit/aa00be99171275b2c91132092e04bce0f9cace1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge branch 'main' into 955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute


  Commit: 833773e788e0239ba91dae8b4fdd7110a147fb4b
      https://github.com/ehb54/ultrascan3/commit/833773e788e0239ba91dae8b4fdd7110a147fb4b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge pull request #472 from ehb54/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute

Add execute permission to shell scripts and improve version check


  Commit: f4915d875bcf8965884d7059dab0011045ae16b8
      https://github.com/ehb54/ultrascan3/commit/f4915d875bcf8965884d7059dab0011045ae16b8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d81051ec6903d845918fcfa3b93d324988b84d52
      https://github.com/ehb54/ultrascan3/commit/d81051ec6903d845918fcfa3b93d324988b84d52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: f289321afa9b9b656d8bde7b11a50b5e27b397a2
      https://github.com/ehb54/ultrascan3/commit/f289321afa9b9b656d8bde7b11a50b5e27b397a2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 857f3efd29534ce5ce6cf14c840be389eebd9b74
      https://github.com/ehb54/ultrascan3/commit/857f3efd29534ce5ce6cf14c840be389eebd9b74
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
      https://github.com/ehb54/ultrascan3/commit/2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [[1]And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d56a96153cae267abf3f0ab713d600e6c37a16ad
      https://github.com/ehb54/ultrascan3/commit/d56a96153cae267abf3f0ab713d600e6c37a16ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [And for Audit Trail -- And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: e1a744a5b128a49750aed0f58d5b988527a78d00
      https://github.com/ehb54/ultrascan3/commit/e1a744a5b128a49750aed0f58d5b988527a78d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: beb1029bcdca1b2612f23cf65f739021388aac1f
      https://github.com/ehb54/ultrascan3/commit/beb1029bcdca1b2612f23cf65f739021388aac1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [1]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 83fbeffb53ca1d9a82583aa5a62cdc4527299f12
      https://github.com/ehb54/ultrascan3/commit/83fbeffb53ca1d9a82583aa5a62cdc4527299f12
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
      https://github.com/ehb54/ultrascan3/commit/01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [ the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 828342afc1ebd1342fb402beb9010070781b07b7
      https://github.com/ehb54/ultrascan3/commit/828342afc1ebd1342fb402beb9010070781b07b7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  [anf add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 10bd647e3ac0e99176196271ff1d6b97645cc030
      https://github.com/ehb54/ultrascan3/commit/10bd647e3ac0e99176196271ff1d6b97645cc030
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [[add option to Cancel scan, but not the first time]and add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 9d2438e1c6cec27070001ad1631548c32ccea3b4
      https://github.com/ehb54/ultrascan3/commit/9d2438e1c6cec27070001ad1631548c32ccea3b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: aea46531df9dbdab71687e604f60e8047f1e66f1
      https://github.com/ehb54/ultrascan3/commit/aea46531df9dbdab71687e604f60e8047f1e66f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  []GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: 7981a62c68b5c180b08fd48e7452601700d341e1
      https://github.com/ehb54/ultrascan3/commit/7981a62c68b5c180b08fd48e7452601700d341e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M gui/us_gui_settings.cpp
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 8fbfd948e503374ba161214696f34e1ec158228f
      https://github.com/ehb54/ultrascan3/commit/8fbfd948e503374ba161214696f34e1ec158228f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  2. LIVE_UPDATE stage: GMP vs R&D: pass flag for the program mode to the live update from the top-level us_comproject, to define different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: 69bb3f83f418b000fce5d05520008f5be7e3c9d3
      https://github.com/ehb54/ultrascan3/commit/69bb3f83f418b000fce5d05520008f5be7e3c9d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  [updated]2. LIVE_UPDATE stage: GMP vs R&D: different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: 3a329e106454a1f26436acd02b7d43809c8fd0f6
      https://github.com/ehb54/ultrascan3/commit/3a329e106454a1f26436acd02b7d43809c8fd0f6
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  feat: add initial CMake configuration and vcpkg support for gumbo library


  Commit: a6dc6e628437424579410fe577bca9357bbb38cd
      https://github.com/ehb54/ultrascan3/commit/a6dc6e628437424579410fe577bca9357bbb38cd
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge pull request #483 from ehb54/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch

Add CMake configuration and vcpkg support for gumbo library


  Commit: 89695a27c955ea41f1763c6af51d62064c11c7b3
      https://github.com/ehb54/ultrascan3/commit/89695a27c955ea41f1763c6af51d62064c11c7b3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 1468dcf35170704617ae78f5e2581e0070273c8d
      https://github.com/ehb54/ultrascan3/commit/1468dcf35170704617ae78f5e2581e0070273c8d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #479 from ehb54/alexey-dev-issue954

Extend GMP:dataDisk for IP- and mixed optics RI+IP types; Improve user experiences for GMP:Audit Trail & GMP:eSigs


  Commit: de15b65e87559ed23515bf20079ecd0de671f983
      https://github.com/ehb54/ultrascan3/commit/de15b65e87559ed23515bf20079ecd0de671f983
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue961


  Commit: cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
      https://github.com/ehb54/ultrascan3/commit/cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  Merge pull request #481 from ehb54/alexey-dev-issue961

GMP vs R&D's 2. LIVE_UPDATE, stop optima / skip optima stage


  Commit: 99535b73ac71970aef06bd32024f048873970c1f
      https://github.com/ehb54/ultrascan3/commit/99535b73ac71970aef06bd32024f048873970c1f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add qtmultimedia5-dev to unit tests workflow


  Commit: fe5f85278c6177d4879919a5f15f232e3ffb6cc8
      https://github.com/ehb54/ultrascan3/commit/fe5f85278c6177d4879919a5f15f232e3ffb6cc8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Update changed files in unit-tests-v2 workflow


  Commit: 00cf2edadbc180e095d0db4efe197d2fb86d2862
      https://github.com/ehb54/ultrascan3/commit/00cf2edadbc180e095d0db4efe197d2fb86d2862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4b3e14634cdc79f28ec75abd4093e49b82247b94
      https://github.com/ehb54/ultrascan3/commit/4b3e14634cdc79f28ec75abd4093e49b82247b94
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #490 from ehb54/ehb54-issue-975

Fix two invalid us_somo regex patterns breaking US_RegexTest (#975)


  Commit: 3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
      https://github.com/ehb54/ultrascan3/commit/3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/unittest


  Commit: 9722a6463cb01bd8170e5e3ee87082561cc756c9
      https://github.com/ehb54/ultrascan3/commit/9722a6463cb01bd8170e5e3ee87082561cc756c9
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Merge pull request #489 from ehb54/lukas/unittest

Add qtmultimedia5-dev to unit tests workflow


  Commit: bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
      https://github.com/ehb54/ultrascan3/commit/bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M CMakePresets.json
    M README.md
    M admin/modulefiles/home-gui-build
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M local.pri.template
    M vcpkg.json

  Log Message:
  -----------
  Removal of qwt6.1.6 in github actions, documentation, cmkae and vcpkg configuration (#488)

* Remove qwt6.1.6 actions

Removed deprecated container version for consistency.

* Update QWT library paths to version 6.3.0

* Remove obsolete Qwt6.1.6 configuration presets

* Update README.md

* Remove features related to qwt6.1.6

* Delete buildsys/vcpkg/overlay-ports/qwt-6-1-6 directory

* Delete buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5 directory

* Update Qt version to 5.15.19 and Qwt version to 6.3.0

* Remove deprecated container from CodeQL workflow

* Update container version in doc-build workflow

* Add new container to CodeQL analysis workflow


  Commit: 0b31fc702d62f9465a90923164934c2f0021d61b
      https://github.com/ehb54/ultrascan3/commit/0b31fc702d62f9465a90923164934c2f0021d61b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/nightly-build.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakeLists.txt
    M CMakePresets.json
    M README.md
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    M admin/modulefiles/home-gui-build
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M local.pri.template
    M programs/us/CMakeLists.txt
    M programs/us_analyte/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_export_legacy/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M us-build
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.2.0-dev


Compare: https://github.com/ehb54/ultrascan3/compare/435b89afe6c3...0b31fc702d62

To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications

From noreply at github.com  Mon Jul 20 16:19:46 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Jul 2026 15:19:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 63750e: GMP:dataDisk - work towards
 extention of the uploa...
Message-ID: <ehb54/ultrascan3/push/refs/heads/758-bug-extra-logos/a2f9d2-100d7a@github.com>

  Branch: refs/heads/758-bug-extra-logos
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
      https://github.com/ehb54/ultrascan3/commit/63750ef614b0f6abe2a34e9d0bf8bed3dde39d9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: e1345a3206da2fc4942f218fc813fda1682f69cd
      https://github.com/ehb54/ultrascan3/commit/e1345a3206da2fc4942f218fc813fda1682f69cd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-08 (Wed, 08 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: f51e6bac3a1d4943c3291b8db1525d9f18419844
      https://github.com/ehb54/ultrascan3/commit/f51e6bac3a1d4943c3291b8db1525d9f18419844
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 044f72440db40f7632169394d6ee0b593998562a
      https://github.com/ehb54/ultrascan3/commit/044f72440db40f7632169394d6ee0b593998562a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...


  Commit: 37a4a06b5999bf9f3c243fbe38ede1a3fea379af
      https://github.com/ehb54/ultrascan3/commit/37a4a06b5999bf9f3c243fbe38ede1a3fea379af
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [33more Work on] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
      https://github.com/ehb54/ultrascan3/commit/8567f6bb8d1e49dcb74695ac1860c8f4573faa9b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Add missing execute permission to shell scripts in scripts/


  Commit: a43e638e495930eb941519ece5e33498e89fd1ec
      https://github.com/ehb54/ultrascan3/commit/a43e638e495930eb941519ece5e33498e89fd1ec
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: improve python3 version check and update-alternatives registration


  Commit: 7f15d549465db31e042d59a5686dc8e2cd2b056a
      https://github.com/ehb54/ultrascan3/commit/7f15d549465db31e042d59a5686dc8e2cd2b056a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  mod: make executable


  Commit: 36dd7367a1f0d64008dcf711a3c7265de78867f7
      https://github.com/ehb54/ultrascan3/commit/36dd7367a1f0d64008dcf711a3c7265de78867f7
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  fix: conditionally include python39 packages based on python3 version


  Commit: f22ca7ce48ab875427dac618f91e473b40d937ce
      https://github.com/ehb54/ultrascan3/commit/f22ca7ce48ab875427dac618f91e473b40d937ce
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-09 (Thu, 09 Jul 2026)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [Back compatibility with a 1-channel RA-sim. data] GMP:dataDisk - work towards extention of the uploaded data for cases like IP-, mixed IP+RI...ush


  Commit: 73a27078af4dfa87f2178651d2907835d3cf9b92
      https://github.com/ehb54/ultrascan3/commit/73a27078af4dfa87f2178651d2907835d3cf9b92
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  fix: update default GUI style for MacOS to 'macOS' in Qt 6


  Commit: 2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
      https://github.com/ehb54/ultrascan3/commit/2cd235232ef4f83871ccf60cf8b9efd0bb38fbfe
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP:IP+RI - prevent crush at 4. EDIT when IP loaded first due to leagcy protocol re-using and scan_nth set to 0...


  Commit: e69cf69c249ce62533cd87f25c93dde746147ffa
      https://github.com/ehb54/ultrascan3/commit/e69cf69c249ce62533cd87f25c93dde746147ffa
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge pull request #474 from ehb54/843-request-macintosh-style-is-deprecated

Update default GUI style for macOS in Qt 6


  Commit: aa00be99171275b2c91132092e04bce0f9cace1d
      https://github.com/ehb54/ultrascan3/commit/aa00be99171275b2c91132092e04bce0f9cace1d
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_gui_settings.cpp

  Log Message:
  -----------
  Merge branch 'main' into 955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute


  Commit: 833773e788e0239ba91dae8b4fdd7110a147fb4b
      https://github.com/ehb54/ultrascan3/commit/833773e788e0239ba91dae8b4fdd7110a147fb4b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge pull request #472 from ehb54/955-bug-file-permissions-of-scripts-in-scripts-are-missing-execute

Add execute permission to shell scripts and improve version check


  Commit: f4915d875bcf8965884d7059dab0011045ae16b8
      https://github.com/ehb54/ultrascan3/commit/f4915d875bcf8965884d7059dab0011045ae16b8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d81051ec6903d845918fcfa3b93d324988b84d52
      https://github.com/ehb54/ultrascan3/commit/d81051ec6903d845918fcfa3b93d324988b84d52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [1]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: f289321afa9b9b656d8bde7b11a50b5e27b397a2
      https://github.com/ehb54/ultrascan3/commit/f289321afa9b9b656d8bde7b11a50b5e27b397a2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [2]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 857f3efd29534ce5ce6cf14c840be389eebd9b74
      https://github.com/ehb54/ultrascan3/commit/857f3efd29534ce5ce6cf14c840be389eebd9b74
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: 2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
      https://github.com/ehb54/ultrascan3/commit/2a4da2f7bd60a033f274e9e9c2ee8f0bbdcda96d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp

  Log Message:
  -----------
  [[1]And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: d56a96153cae267abf3f0ab713d600e6c37a16ad
      https://github.com/ehb54/ultrascan3/commit/d56a96153cae267abf3f0ab713d600e6c37a16ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [And for Audit Trail -- And pass to 6.REPORT && print it]GMP:3. IMPORT - test: capture message for disparate scans...


  Commit: e1a744a5b128a49750aed0f58d5b988527a78d00
      https://github.com/ehb54/ultrascan3/commit/e1a744a5b128a49750aed0f58d5b988527a78d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: beb1029bcdca1b2612f23cf65f739021388aac1f
      https://github.com/ehb54/ultrascan3/commit/beb1029bcdca1b2612f23cf65f739021388aac1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [1]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 83fbeffb53ca1d9a82583aa5a62cdc4527299f12
      https://github.com/ehb54/ultrascan3/commit/83fbeffb53ca1d9a82583aa5a62cdc4527299f12
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
      https://github.com/ehb54/ultrascan3/commit/01574252f1b9c11b6e9b38c1f94934f1fdaf28ae
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [ the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 828342afc1ebd1342fb402beb9010070781b07b7
      https://github.com/ehb54/ultrascan3/commit/828342afc1ebd1342fb402beb9010070781b07b7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h

  Log Message:
  -----------
  [anf add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 10bd647e3ac0e99176196271ff1d6b97645cc030
      https://github.com/ehb54/ultrascan3/commit/10bd647e3ac0e99176196271ff1d6b97645cc030
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [[add option to Cancel scan, but not the first time]and add Refresh list from inside GMP run list:  the GMP run list is now cached for the life of this window, so no long re-scanning][2]GMP:Audit Trail - add progress dialog for fetching GMP runs associated with the user-role before generating runs list - can take long times, and use ris uninformed...


  Commit: 9d2438e1c6cec27070001ad1631548c32ccea3b4
      https://github.com/ehb54/ultrascan3/commit/9d2438e1c6cec27070001ad1631548c32ccea3b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: aea46531df9dbdab71687e604f60e8047f1e66f1
      https://github.com/ehb54/ultrascan3/commit/aea46531df9dbdab71687e604f60e8047f1e66f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h

  Log Message:
  -----------
  []GMP:eSignatures -- same user experience improvements as for Audit_trail: for long checks against db records for matches of the logged-in user to reviwers, add dialog; add refreshign list option from withing the list; add cancel refresh option not changing the cached list...


  Commit: 7981a62c68b5c180b08fd48e7452601700d341e1
      https://github.com/ehb54/ultrascan3/commit/7981a62c68b5c180b08fd48e7452601700d341e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-11 (Sat, 11 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M gui/us_gui_settings.cpp
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 8fbfd948e503374ba161214696f34e1ec158228f
      https://github.com/ehb54/ultrascan3/commit/8fbfd948e503374ba161214696f34e1ec158228f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  2. LIVE_UPDATE stage: GMP vs R&D: pass flag for the program mode to the live update from the top-level us_comproject, to define different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: 69bb3f83f418b000fce5d05520008f5be7e3c9d3
      https://github.com/ehb54/ultrascan3/commit/69bb3f83f418b000fce5d05520008f5be7e3c9d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  [updated]2. LIVE_UPDATE stage: GMP vs R&D: different behavior upon Optima STOP & SKIP STAGE actions; do not require signing off and the reason for an action in R&D mdoe ...


  Commit: 3a329e106454a1f26436acd02b7d43809c8fd0f6
      https://github.com/ehb54/ultrascan3/commit/3a329e106454a1f26436acd02b7d43809c8fd0f6
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-12 (Sun, 12 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  feat: add initial CMake configuration and vcpkg support for gumbo library


  Commit: a6dc6e628437424579410fe577bca9357bbb38cd
      https://github.com/ehb54/ultrascan3/commit/a6dc6e628437424579410fe577bca9357bbb38cd
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge pull request #483 from ehb54/964-bug-nightly-build-fails-on-macos-intel-windows-x64-vcpkg-gumbo-port-hash-mismatch

Add CMake configuration and vcpkg support for gumbo library


  Commit: 89695a27c955ea41f1763c6af51d62064c11c7b3
      https://github.com/ehb54/ultrascan3/commit/89695a27c955ea41f1763c6af51d62064c11c7b3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-13 (Mon, 13 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue954


  Commit: 1468dcf35170704617ae78f5e2581e0070273c8d
      https://github.com/ehb54/ultrascan3/commit/1468dcf35170704617ae78f5e2581e0070273c8d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #479 from ehb54/alexey-dev-issue954

Extend GMP:dataDisk for IP- and mixed optics RI+IP types; Improve user experiences for GMP:Audit Trail & GMP:eSigs


  Commit: de15b65e87559ed23515bf20079ecd0de671f983
      https://github.com/ehb54/ultrascan3/commit/de15b65e87559ed23515bf20079ecd0de671f983
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_select_item.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue961


  Commit: cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
      https://github.com/ehb54/ultrascan3/commit/cace172cd5fe2cd5eb58a1c3eed60c0d5962a5b6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2026-07-14 (Tue, 14 Jul 2026)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h

  Log Message:
  -----------
  Merge pull request #481 from ehb54/alexey-dev-issue961

GMP vs R&D's 2. LIVE_UPDATE, stop optima / skip optima stage


  Commit: 99535b73ac71970aef06bd32024f048873970c1f
      https://github.com/ehb54/ultrascan3/commit/99535b73ac71970aef06bd32024f048873970c1f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add qtmultimedia5-dev to unit tests workflow


  Commit: fe5f85278c6177d4879919a5f15f232e3ffb6cc8
      https://github.com/ehb54/ultrascan3/commit/fe5f85278c6177d4879919a5f15f232e3ffb6cc8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Update changed files in unit-tests-v2 workflow


  Commit: 00cf2edadbc180e095d0db4efe197d2fb86d2862
      https://github.com/ehb54/ultrascan3/commit/00cf2edadbc180e095d0db4efe197d2fb86d2862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4b3e14634cdc79f28ec75abd4093e49b82247b94
      https://github.com/ehb54/ultrascan3/commit/4b3e14634cdc79f28ec75abd4093e49b82247b94
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #490 from ehb54/ehb54-issue-975

Fix two invalid us_somo regex patterns breaking US_RegexTest (#975)


  Commit: 3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
      https://github.com/ehb54/ultrascan3/commit/3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/unittest


  Commit: 9722a6463cb01bd8170e5e3ee87082561cc756c9
      https://github.com/ehb54/ultrascan3/commit/9722a6463cb01bd8170e5e3ee87082561cc756c9
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Merge pull request #489 from ehb54/lukas/unittest

Add qtmultimedia5-dev to unit tests workflow


  Commit: bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
      https://github.com/ehb54/ultrascan3/commit/bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M CMakePresets.json
    M README.md
    M admin/modulefiles/home-gui-build
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M local.pri.template
    M vcpkg.json

  Log Message:
  -----------
  Removal of qwt6.1.6 in github actions, documentation, cmkae and vcpkg configuration (#488)

* Remove qwt6.1.6 actions

Removed deprecated container version for consistency.

* Update QWT library paths to version 6.3.0

* Remove obsolete Qwt6.1.6 configuration presets

* Update README.md

* Remove features related to qwt6.1.6

* Delete buildsys/vcpkg/overlay-ports/qwt-6-1-6 directory

* Delete buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5 directory

* Update Qt version to 5.15.19 and Qwt version to 6.3.0

* Remove deprecated container from CodeQL workflow

* Update container version in doc-build workflow

* Add new container to CodeQL analysis workflow


  Commit: 100d7aacaf6c3a88239f872ff853eea0c86bb950
      https://github.com/ehb54/ultrascan3/commit/100d7aacaf6c3a88239f872ff853eea0c86bb950
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakePresets.json
    M README.md
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/modulefiles/home-gui-build
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M local.pri.template
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into 758-bug-extra-logos


Compare: https://github.com/ehb54/ultrascan3/compare/a2f9d27b561c...100d7aacaf6c

To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications

From noreply at github.com  Mon Jul 20 16:22:52 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Jul 2026 15:22:52 -0700
Subject: [us-commits] [ehb54/ultrascan3] 99535b: Add qtmultimedia5-dev to
 unit tests workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/cb55c6-6c88b1@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 99535b73ac71970aef06bd32024f048873970c1f
      https://github.com/ehb54/ultrascan3/commit/99535b73ac71970aef06bd32024f048873970c1f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add qtmultimedia5-dev to unit tests workflow


  Commit: fe5f85278c6177d4879919a5f15f232e3ffb6cc8
      https://github.com/ehb54/ultrascan3/commit/fe5f85278c6177d4879919a5f15f232e3ffb6cc8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Update changed files in unit-tests-v2 workflow


  Commit: 00cf2edadbc180e095d0db4efe197d2fb86d2862
      https://github.com/ehb54/ultrascan3/commit/00cf2edadbc180e095d0db4efe197d2fb86d2862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Fix two invalid us_somo regex patterns breaking US_RegexTest

- us_saxs_util.cpp: remove dead, commented-out rxdigits pattern that was
  missing three closing parens (superseded by the working "^\s*\d").
  The regex-validation test scrapes commented lines too, so it flagged it.
- us_saxs_cmds_t/main.cpp:1262: "^.*((\|/)" had an extra '(' and used
  "\\|" (regex \| = literal pipe) instead of a backslash; replace with
  the path-separator class "^.*[\\\\/]" to strip the directory prefix.
- us_saxs_cmds_t/main.cpp:1266: same \|-vs-backslash bug ("^(\|/)"); fix
  to "^[\\\\/]" so it detects a leading path separator. Not caught by the
  test (it compiles), but the same latent defect.

Fixes ehb54/ultrascan-tickets#975

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>


  Commit: 4b3e14634cdc79f28ec75abd4093e49b82247b94
      https://github.com/ehb54/ultrascan3/commit/4b3e14634cdc79f28ec75abd4093e49b82247b94
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #490 from ehb54/ehb54-issue-975

Fix two invalid us_somo regex patterns breaking US_RegexTest (#975)


  Commit: 3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
      https://github.com/ehb54/ultrascan3/commit/3eaf20cfd32e222cdc0e1acaaf17cdfe9c165677
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge branch 'main' into lukas/unittest


  Commit: 9722a6463cb01bd8170e5e3ee87082561cc756c9
      https://github.com/ehb54/ultrascan3/commit/9722a6463cb01bd8170e5e3ee87082561cc756c9
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-19 (Sun, 19 Jul 2026)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Merge pull request #489 from ehb54/lukas/unittest

Add qtmultimedia5-dev to unit tests workflow


  Commit: bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
      https://github.com/ehb54/ultrascan3/commit/bcc6dc98d8b8ad1b927e7451b6c771d662b3d425
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M CMakePresets.json
    M README.md
    M admin/modulefiles/home-gui-build
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M local.pri.template
    M vcpkg.json

  Log Message:
  -----------
  Removal of qwt6.1.6 in github actions, documentation, cmkae and vcpkg configuration (#488)

* Remove qwt6.1.6 actions

Removed deprecated container version for consistency.

* Update QWT library paths to version 6.3.0

* Remove obsolete Qwt6.1.6 configuration presets

* Update README.md

* Remove features related to qwt6.1.6

* Delete buildsys/vcpkg/overlay-ports/qwt-6-1-6 directory

* Delete buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5 directory

* Update Qt version to 5.15.19 and Qwt version to 6.3.0

* Remove deprecated container from CodeQL workflow

* Update container version in doc-build workflow

* Add new container to CodeQL analysis workflow


  Commit: 6c88b17bcea6d4bea20e90f9ade1c93f4cd632e9
      https://github.com/ehb54/ultrascan3/commit/6c88b17bcea6d4bea20e90f9ade1c93f4cd632e9
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakePresets.json
    M README.md
    M admin/modulefiles/home-gui-build
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M local.pri.template
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into 875-request-cmake-remove-gmp-module-from-installer-for-osx


Compare: https://github.com/ehb54/ultrascan3/compare/cb55c62623e1...6c88b17bcea6

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From noreply at github.com  Mon Jul 20 16:29:02 2026
From: noreply at github.com (emre brookes)
Date: Mon, 20 Jul 2026 15:29:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] f860ad: extrap_c0: add the
 reference-curve selector to the...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/6ba2c5-f860ad@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f860addaae4ef58d3d20e7f59a3f681ff9f5ae0d
      https://github.com/ehb54/ultrascan3/commit/f860addaae4ef58d3d20e7f59a3f681ff9f5ae0d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: add the reference-curve selector to the concentration dialog

The reference override was scripted-only, so the users who most need it -- the ones
working interactively, who have the outside knowledge the program lacks -- could not
reach it. Adds a "Reference curve" combo to the concentration dialog: entry 0 is
"Automatic (highest concentration)" (the unchanged default), the rest name each
selected curve. The control is enabled only when the absolute-scale or high-q-splice
option is ticked, since nothing else consumes a reference.

The tooltip states why automatic is the right default (intensity scales with
concentration, so the top curve normally has the best high-q signal-to-noise, which
is what the splice copies), why the program cannot audit that curve itself (it is the
extreme x, carries nearly all the leverage, so its residual is near zero whatever its
quality), and warns that choosing a lower concentration with the splice on tends to
drag the merge point down.

Verified: builds clean; the dialog is compiled into libus_somo and the new strings are
present in the built library; all 9 regression baselines byte-identical and the CLI
reference override still behaves (selection by name and by concentration, plus the
non-matching fallback warning). Manual updated to describe the dialog control
alongside the scripted directive.

NOT verified interactively -- the widget has not been exercised in a running GUI, only
compiled and linked. The dialog defaults to "Automatic", so an untouched dialog cannot
change behaviour, but the combo's population and enable/disable behaviour should be
eyeballed once in a real session.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Mon Jul 20 18:23:17 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Jul 2026 17:23:17 -0700
Subject: [us-commits] [ehb54/ultrascan3] 435b89: Bump version to 4.2.0-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/bcc6dc-58024e@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 435b89afe6c30e42df5aba726ea83b875be9a649
      https://github.com/ehb54/ultrascan3/commit/435b89afe6c30e42df5aba726ea83b875be9a649
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: 0b31fc702d62f9465a90923164934c2f0021d61b
      https://github.com/ehb54/ultrascan3/commit/0b31fc702d62f9465a90923164934c2f0021d61b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/nightly-build.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakeLists.txt
    M CMakePresets.json
    M README.md
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    M admin/modulefiles/home-gui-build
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M local.pri.template
    M programs/us/CMakeLists.txt
    M programs/us_analyte/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_export_legacy/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M us-build
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.2.0-dev


  Commit: 58024eb57fdab1949486e2ab93da69601227067e
      https://github.com/ehb54/ultrascan3/commit/58024eb57fdab1949486e2ab93da69601227067e
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge pull request #471 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


Compare: https://github.com/ehb54/ultrascan3/compare/bcc6dc98d8b8...58024eb57fda

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From noreply at github.com  Mon Jul 20 18:23:48 2026
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Jul 2026 17:23:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] 435b89: Bump version to 4.2.0-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/758-bug-extra-logos/100d7a-fd6baa@github.com>

  Branch: refs/heads/758-bug-extra-logos
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 435b89afe6c30e42df5aba726ea83b875be9a649
      https://github.com/ehb54/ultrascan3/commit/435b89afe6c30e42df5aba726ea83b875be9a649
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: 0b31fc702d62f9465a90923164934c2f0021d61b
      https://github.com/ehb54/ultrascan3/commit/0b31fc702d62f9465a90923164934c2f0021d61b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/nightly-build.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakeLists.txt
    M CMakePresets.json
    M README.md
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    M admin/modulefiles/home-gui-build
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M local.pri.template
    M programs/us/CMakeLists.txt
    M programs/us_analyte/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_export_legacy/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M us-build
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.2.0-dev


  Commit: 58024eb57fdab1949486e2ab93da69601227067e
      https://github.com/ehb54/ultrascan3/commit/58024eb57fdab1949486e2ab93da69601227067e
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge pull request #471 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


  Commit: fd6baacc3759c1e45df31c234cb2c18e8fe2b8f5
      https://github.com/ehb54/ultrascan3/commit/fd6baacc3759c1e45df31c234cb2c18e8fe2b8f5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into 758-bug-extra-logos


Compare: https://github.com/ehb54/ultrascan3/compare/100d7aacaf6c...fd6baacc3759

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From noreply at github.com  Tue Jul 21 07:17:13 2026
From: noreply at github.com (emre brookes)
Date: Tue, 21 Jul 2026 06:17:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] fdf85a: extrap_c0: report per-curve
 I(0)/c diagnostic (sur...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/f860ad-fdf85a@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fdf85a3561ea2a81545442e018d2402c0b912a51
      https://github.com/ehb54/ultrascan3/commit/fdf85a3561ea2a81545442e018d2402c0b912a51
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: report per-curve I(0)/c diagnostic (surface evidence, not a verdict)

Closes out the reference-quality question. Two candidate automatic checks were built
and tested first, and both failed:

- a residual-derived sigma(q) as the regularization noise model: on simulated series
  swept from 4 to 32 concentrations it never beat the existing weighting, and did not
  improve with more curves, so the failure was not degrees of freedom.
- a high-q shape veto for reference quality: on simulated series with defects injected
  into the top curve it separated only a constant buffer-subtraction offset (8.7x), and
  missed mis-set concentration, aggregation and damage entirely (0% of seeds). Worse, the
  statistic tracks signal-to-noise, which rises with concentration, so in the CLEAN case
  the top curve scores best of the set (0.093 vs 0.145) -- a veto built on it is biased
  against ever firing.

Both fail for the same structural reason: the highest-concentration curve is at once the
highest-leverage point in the regression and the highest-SNR curve, so it looks good by
every measure available from inside the series. The information is not there.

So report the evidence instead of guessing. Each run now logs, per curve, the Guinier Rg
and I(0), the ratio I(0)/c, and its deviation from (a) the series median and (b) the trend
predicted by the OTHER curves. I(0)/c is constant in the dilute limit and falls smoothly
as the interparticle term grows, so a curve off the others indicates a mis-set
concentration or aggregation. The trend column is leave-one-out, so the curve cannot pull
the line onto itself -- the only form of this comparison that says anything about the
extreme concentration. Deviations beyond 15% are highlighted. Nothing is discarded or
re-selected on this basis; it feeds the reference selector, which the user drives.

On the 7-curve alpha-syn set this independently reproduces Mattia's assessment of the
0.694246 curve (+12.2% vs trend, i.e. the overestimated MW he reports). It does NOT
reproduce his call on 2.41176, which sits at -5.9% and is unremarkable by either measure.

Verified: all 9 regression baselines byte-identical (the diagnostic is log-only) and the
table is emitted on all 9 runs. Manual updated.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 21 07:32:25 2026
From: noreply at github.com (emre brookes)
Date: Tue, 21 Jul 2026 06:32:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2616d4: Add psv group-contribution
 probe (analysis for tic...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-978/eb57f1-2616d4@github.com>

  Branch: refs/heads/ehb54-issue-978
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2616d4c1ebdfc9a2920da2b7f3e2f0be113dee78
      https://github.com/ehb54/ultrascan3/commit/2616d4c1ebdfc9a2920da2b7f3e2f0be113dee78
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    A us_somo/develop/perceiver/tools/psv_model.py

  Log Message:
  -----------
  Add psv group-contribution probe (analysis for ticket #980)

Tests Mattia's suggestion that a rough psv can be suggested for a non-coded
residue from similarity to the hybridizations already in somo.residue, by
fitting a Cohn-Edsall / Durchschlag-Zipper style group-contribution model over
the ~100 genuine polyatomic residues somo.residue codes and scoring it
leave-one-out.

Result (MAE in vbar, cm^3/g; typical vbar ~0.73):
  global mean                     0.110
  sum-of-vdW-spheres (emitted now) 0.193   <- worst option available
  residue-type group average      0.070
  hybrid group-contribution       0.054   (organic only: 0.036, metals: 0.222)

So the estimate the perceiver currently emits is worse than guessing the mean,
the group-contribution model is good for organic residues, and it should not
be trusted for metal-containing ones. Findings recorded on
ehb54/ultrascan-tickets#980.

NOT pushed: this belongs with the #980 work rather than the #978 PR.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 21 07:33:08 2026
From: noreply at github.com (emre brookes)
Date: Tue, 21 Jul 2026 06:33:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] d57f01: Remove the psv/molvol
 estimate from generated entries
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-978/2616d4-d57f01@github.com>

  Branch: refs/heads/ehb54-issue-978
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d57f0171950500cb1161cc86fdfac4738c9574b4
      https://github.com/ehb54/ultrascan3/commit/d57f0171950500cb1161cc86fdfac4738c9574b4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M us_somo/develop/perceiver/DECISIONS.md
    M us_somo/develop/src/us_hydrodyn_perceive.cpp

  Log Message:
  -----------
  Remove the psv/molvol estimate from generated entries

The tentative entry emitted a vbar (and molvol) from a sum of vdW spheres.
Fitting a group-contribution model over the ~100 polyatomic residues
somo.residue codes, scored leave-one-out (perceiver/tools/psv_model.py),
shows that estimate is the WORST option available: mean absolute error 0.193
in vbar, against 0.110 for simply assuming the global mean. Summing spheres
ignores bond overlap and runs systematically high.

vbar enters hydrodynamics through the buoyancy term (1 - vbar*rho), so
emitting a number worse than a guess is actively misleading. Both fields are
now left at 0 = unset, and the entry says why and points at
ehb54/ultrascan-tickets#980, where the tiered replacement is tracked
(group-contribution for organic residues, MAE 0.036; residue-type group
average for out-of-domain cases such as metal-containing residues, where the
fit degrades to 0.222 - worse than that average; always user-overridable).

0 rather than omission because the header must keep its 7 fields to parse,
0 reads unambiguously as unset (the convention somo.saxs_atoms already uses
for F and SE), and it fails loudly: a 0 vbar is obviously wrong if used,
whereas a plausible-looking 0.80 is not.

The entry now reports the residue mass instead, since what decides whether an
imprecise psv matters is its mass fraction of the model - molecular vbar is
mass-weighted, so a 616 Da heme in a 50 kDa protein shifts it ~0.5% even with
a 0.34 vbar error.

Also tightens the REVIEW block to genuinely uncertain atoms: a confident
classification carrying an informational note was being listed as uncertain,
disagreeing with the flagged count callers report.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 21 07:38:13 2026
From: noreply at github.com (emre brookes)
Date: Tue, 21 Jul 2026 06:38:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] cda2c9: extrap_c0 doc: document the
 common_crop and fill_s...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/fdf85a-cda2c9@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cda2c97bd74c2a801631809e0513eaffb5bb0f2c
      https://github.com/ehb54/ultrascan3/commit/cda2c97bd74c2a801631809e0513eaffb5bb0f2c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 doc: document the common_crop and fill_sd directives

Found by auditing every key the control-file parser accepts against the manual rather
than assuming: 18 of 20 directives were documented, and these two never had been. They
were described in the driver's header comment when the SD-repair work landed but never
reached the user-facing manual.

fill_sd is the one that matters. It defaults to ON and changes whether the fit is
weighted at all: SOMO's error handling is all-or-nothing, so a single non-positive SD --
typically one zero at a grid edge in deposited data -- disables that curve's errors
entirely and silently forces an unweighted fit. A user reading the manual had no way to
know either that this repair happens by default or how to turn it off.

common_crop (also default ON) documents why grid-aligned inputs are cropped to their
shared q-overlap first: otherwise the loader resamples mismatched grids and
spline-extrapolates the higher-starting curves below their own data.

Audit now reports 20/20; the pre-existing bare-<p> imbalance is unchanged (delta 5).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 21 08:11:05 2026
From: noreply at github.com (aaron-auc)
Date: Tue, 21 Jul 2026 07:11:05 -0700
Subject: [us-commits] [ehb54/ultrascan3] b1e9a6: Remove hsclogo, becklogo,
 and us3logo debug text o...
Message-ID: <ehb54/ultrascan3/push/refs/heads/758-bug-extra-logos/fd6baa-b1e9a6@github.com>

  Branch: refs/heads/758-bug-extra-logos
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b1e9a6ede5d92dffc87dde24f9bda9ccf586feed
      https://github.com/ehb54/ultrascan3/commit/b1e9a6ede5d92dffc87dde24f9bda9ccf586feed
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M doc/manual/source/config.rst

  Log Message:
  -----------
  Remove hsclogo, becklogo, and us3logo debug text options from the config docs since the underlying logo code was removed.



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From noreply at github.com  Tue Jul 21 09:41:29 2026
From: noreply at github.com (aaron-auc)
Date: Tue, 21 Jul 2026 08:41:29 -0700
Subject: [us-commits] [ehb54/ultrascan3] a2f9d2: fix: remove unused logo
 handling from US_Reporter
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/58024e-5859c0@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a2f9d27b561cba63475ff3dda2637d308c1654e9
      https://github.com/ehb54/ultrascan3/commit/a2f9d27b561cba63475ff3dda2637d308c1654e9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    R etc/beckman_logo.png
    M etc/etc_belongs_list.txt
    R etc/logo_hsc.png
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h

  Log Message:
  -----------
  fix: remove unused logo handling from US_Reporter


  Commit: 100d7aacaf6c3a88239f872ff853eea0c86bb950
      https://github.com/ehb54/ultrascan3/commit/100d7aacaf6c3a88239f872ff853eea0c86bb950
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakePresets.json
    M README.md
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/modulefiles/home-gui-build
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M local.pri.template
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into 758-bug-extra-logos


  Commit: fd6baacc3759c1e45df31c234cb2c18e8fe2b8f5
      https://github.com/ehb54/ultrascan3/commit/fd6baacc3759c1e45df31c234cb2c18e8fe2b8f5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into 758-bug-extra-logos


  Commit: b1e9a6ede5d92dffc87dde24f9bda9ccf586feed
      https://github.com/ehb54/ultrascan3/commit/b1e9a6ede5d92dffc87dde24f9bda9ccf586feed
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M doc/manual/source/config.rst

  Log Message:
  -----------
  Remove hsclogo, becklogo, and us3logo debug text options from the config docs since the underlying logo code was removed.


  Commit: 5859c047d607e6b17f8f08ba43049c3a3c982a83
      https://github.com/ehb54/ultrascan3/commit/5859c047d607e6b17f8f08ba43049c3a3c982a83
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M doc/manual/source/config.rst
    R etc/beckman_logo.png
    M etc/etc_belongs_list.txt
    R etc/logo_hsc.png
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h

  Log Message:
  -----------
  Merge pull request #475 from ehb54/758-bug-extra-logos

Remove unused logo handling from US_Reporter


Compare: https://github.com/ehb54/ultrascan3/compare/58024eb57fda...5859c047d607

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From noreply at github.com  Tue Jul 21 09:41:33 2026
From: noreply at github.com (aaron-auc)
Date: Tue, 21 Jul 2026 08:41:33 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/758-bug-extra-logos/b1e9a6-000000@github.com>

  Branch: refs/heads/758-bug-extra-logos
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Jul 21 14:32:01 2026
From: noreply at github.com (emre brookes)
Date: Tue, 21 Jul 2026 13:32:01 -0700
Subject: [us-commits] [ehb54/ultrascan3] ab5571: extrap_c0: encode every
 result-changing option in ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/cda2c9-ab5571@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ab5571e2f6ed60a083b1f7f2d2076acf0260bddb
      https://github.com/ehb54/ultrascan3/commit/ab5571e2f6ed60a083b1f7f2d2076acf0260bddb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0: encode every result-changing option in the output curve name

Reported from testing: a GCV run and a no-GCV run produced the SAME curve name, so the
two were distinguishable only by an arbitrary -1 suffix. Confirmed in our own regression
set, where recip.dat and recip_nogcv.dat both carried "Sub_extrap_c0_recip".

Auditing the namer against the option list found four options that change the result but
were absent from the name:

  _nogcv          automatic slope regularization switched off
  _fb<N>          manual fit-broadening window (only active when GCV is off)
  _refc<c>        an explicitly chosen reference curve, tagged with its concentration
  _rawres         the outlier leverage correction disabled -- appended to _qcN because it
                  can change WHICH curve was dropped, so two runs could otherwise both
                  read _qc1 while resting on different curves

Tokens are emitted only for non-default choices, so an ordinary run keeps a short name.
The comment on the namer now states the invariant explicitly -- every option that can
change the result must appear here -- since the failure mode is silent and only shows up
later as two curves that cannot be told apart.

Verified: all 9 regression combos now yield unique names (previously two collided), and
the new tokens appear correctly (_refc1_8179, _nogcv_fb9, _qc1_rawres vs _qc1). Exactly
one baseline changed, name-only with 0 data-line differences, and was refreshed. Manual
updated; all 15 tokens the namer can emit are now documented.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Tue Jul 21 14:32:30 2026
From: noreply at github.com (aaron-auc)
Date: Tue, 21 Jul 2026 13:32:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] 435b89: Bump version to 4.2.0-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/6c88b1-e1a775@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 435b89afe6c30e42df5aba726ea83b875be9a649
      https://github.com/ehb54/ultrascan3/commit/435b89afe6c30e42df5aba726ea83b875be9a649
  Author: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
  Date:   2026-07-02 (Thu, 02 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Bump version to 4.2.0-dev


  Commit: a2f9d27b561cba63475ff3dda2637d308c1654e9
      https://github.com/ehb54/ultrascan3/commit/a2f9d27b561cba63475ff3dda2637d308c1654e9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-10 (Fri, 10 Jul 2026)

  Changed paths:
    R etc/beckman_logo.png
    M etc/etc_belongs_list.txt
    R etc/logo_hsc.png
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h

  Log Message:
  -----------
  fix: remove unused logo handling from US_Reporter


  Commit: 0b31fc702d62f9465a90923164934c2f0021d61b
      https://github.com/ehb54/ultrascan3/commit/0b31fc702d62f9465a90923164934c2f0021d61b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    A .github/workflows/build-macos-arm.yml
    A .github/workflows/build-macos-intel.yml
    A .github/workflows/build-oraclelinux.yml
    A .github/workflows/build-ubuntu.yml
    A .github/workflows/build-windows.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    A .github/workflows/nightly-build.yml
    A .github/workflows/on-demand-build.yml
    A .github/workflows/release.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakeLists.txt
    M CMakePresets.json
    M README.md
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/cmake/packaging/linux/LinuxHpcPkg.cmake
    M admin/cmake/packaging/linux/LinuxPkg.cmake
    M admin/cmake/triplets/arm64-linux.cmake
    A admin/cmake/triplets/x64-linux-dynamic.cmake
    A admin/cmake/triplets/x64-linux.cmake
    M admin/modulefiles/home-gui-build
    A buildsys/vcpkg/overlay-ports/at-spi2-core/portfile.cmake
    A buildsys/vcpkg/overlay-ports/at-spi2-core/vcpkg.json
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/GLIB2-static.patch
    A buildsys/vcpkg/overlay-ports/qtbase/allow_outside_prefix.patch
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_QGADGET_fix.diff
    A buildsys/vcpkg/overlay-ports/qtbase/clang-cl_source_location.patch
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_copyright.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_install_submodule.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/cmake/qt_port_details.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/config_install.patch
    A buildsys/vcpkg/overlay-ports/qtbase/dont_force_cmakecache_latest.patch
    A buildsys/vcpkg/overlay-ports/qtbase/env.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-host-aliasing.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-libresolv-test.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-link-lib-discovery.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix-missing-include.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_cmake_build.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_deploy_windows.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl.patch
    A buildsys/vcpkg/overlay-ports/qtbase/fix_egl_2.patch
    A buildsys/vcpkg/overlay-ports/qtbase/framework.patch
    A buildsys/vcpkg/overlay-ports/qtbase/harfbuzz.patch
    A buildsys/vcpkg/overlay-ports/qtbase/installed_dir.patch
    A buildsys/vcpkg/overlay-ports/qtbase/macdeployqt-symlinks.patch
    A buildsys/vcpkg/overlay-ports/qtbase/moltenvk.patch
    A buildsys/vcpkg/overlay-ports/qtbase/port.data.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qtbase/qmake.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/qt.conf.in
    A buildsys/vcpkg/overlay-ports/qtbase/qtpaths.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/use-shared-mime-info.patch
    A buildsys/vcpkg/overlay-ports/qtbase/use_inotify_on_freebsd.patch
    A buildsys/vcpkg/overlay-ports/qtbase/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qtbase/windeployqt.debug.bat
    A buildsys/vcpkg/overlay-ports/qtbase/xcodebuild-not-installed.patch
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M local.pri.template
    M programs/us/CMakeLists.txt
    M programs/us_analyte/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_export_legacy/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/build.sh
    A scripts/warm-cache.sh
    M us-build
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into bump-to-v4.2.0-dev


  Commit: 100d7aacaf6c3a88239f872ff853eea0c86bb950
      https://github.com/ehb54/ultrascan3/commit/100d7aacaf6c3a88239f872ff853eea0c86bb950
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/unit-tests-v2.yml
    M CMakePresets.json
    M README.md
    M admin/cmake/packaging/linux/LinuxDeploy.cmake
    M admin/modulefiles/home-gui-build
    A buildsys/vcpkg/overlay-ports/gumbo/CMakeLists.txt
    A buildsys/vcpkg/overlay-ports/gumbo/portfile.cmake
    A buildsys/vcpkg/overlay-ports/gumbo/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwt-6-1-6/vcpkg.json
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/portfile.cmake
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/qwtplot3d-config.cmake.in
    R buildsys/vcpkg/overlay-ports/qwtplot3d-qwt-6-1-6-qt5/vcpkg.json
    M gui/us_convert_gui.cpp
    M gui/us_convert_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_select_item.cpp
    M local.pri.template
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_edit/us_edit.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M scripts/bootstrap-linux.sh
    M scripts/bootstrap-macos.sh
    M scripts/warm-cache.sh
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into 758-bug-extra-logos


  Commit: 58024eb57fdab1949486e2ab93da69601227067e
      https://github.com/ehb54/ultrascan3/commit/58024eb57fdab1949486e2ab93da69601227067e
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge pull request #471 from ehb54/bump-to-v4.2.0-dev

Bump to v4.2.0-dev


  Commit: fd6baacc3759c1e45df31c234cb2c18e8fe2b8f5
      https://github.com/ehb54/ultrascan3/commit/fd6baacc3759c1e45df31c234cb2c18e8fe2b8f5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-20 (Mon, 20 Jul 2026)

  Changed paths:
    M VERSION
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into 758-bug-extra-logos


  Commit: b1e9a6ede5d92dffc87dde24f9bda9ccf586feed
      https://github.com/ehb54/ultrascan3/commit/b1e9a6ede5d92dffc87dde24f9bda9ccf586feed
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M doc/manual/source/config.rst

  Log Message:
  -----------
  Remove hsclogo, becklogo, and us3logo debug text options from the config docs since the underlying logo code was removed.


  Commit: 5859c047d607e6b17f8f08ba43049c3a3c982a83
      https://github.com/ehb54/ultrascan3/commit/5859c047d607e6b17f8f08ba43049c3a3c982a83
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M doc/manual/source/config.rst
    R etc/beckman_logo.png
    M etc/etc_belongs_list.txt
    R etc/logo_hsc.png
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h

  Log Message:
  -----------
  Merge pull request #475 from ehb54/758-bug-extra-logos

Remove unused logo handling from US_Reporter


  Commit: e1a77567936a0d9b3938f18f623dc326aebc183a
      https://github.com/ehb54/ultrascan3/commit/e1a77567936a0d9b3938f18f623dc326aebc183a
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M VERSION
    M doc/manual/source/config.rst
    R etc/beckman_logo.png
    M etc/etc_belongs_list.txt
    R etc/logo_hsc.png
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h
    M utils/us_defines.h

  Log Message:
  -----------
  Merge branch 'main' into 875-request-cmake-remove-gmp-module-from-installer-for-osx


Compare: https://github.com/ehb54/ultrascan3/compare/6c88b17bcea6...e1a77567936a

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From noreply at github.com  Tue Jul 21 17:44:44 2026
From: noreply at github.com (aaron-auc)
Date: Tue, 21 Jul 2026 16:44:44 -0700
Subject: [us-commits] [ehb54/ultrascan3] 99a60a: fix: bootstrap-linux.sh
 required nonexistent libti...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/e1a775-99a60a@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 99a60af96fe7b9d1c799ef9ec0416bed1b0dbd6e
      https://github.com/ehb54/ultrascan3/commit/99a60af96fe7b9d1c799ef9ec0416bed1b0dbd6e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M scripts/bootstrap-linux.sh

  Log Message:
  -----------
  fix: bootstrap-linux.sh required nonexistent libtime-piece-perl apt package

Replace with the perl metapackage, which provides Time::Piece via
perl-modules-X.YY. libtime-piece-perl never existed as a package on any
Ubuntu or Debian suite, so apt-get install for it always failed and the
same package was reported missing on every run. Also fail apt-get
install loudly on any error instead of silently retrying next run.



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From noreply at github.com  Tue Jul 21 19:05:43 2026
From: noreply at github.com (aaron-auc)
Date: Tue, 21 Jul 2026 18:05:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] 461a13: feat: add
 dependency-completeness pass using linux...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/99a60a-461a13@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 461a138367b5fc570f0f40b8234dc40ad631a1e2
      https://github.com/ehb54/ultrascan3/commit/461a138367b5fc570f0f40b8234dc40ad631a1e2
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake

  Log Message:
  -----------
  feat: add dependency-completeness pass using linuxdeploy for runtime library bundling



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From noreply at github.com  Tue Jul 21 19:13:24 2026
From: noreply at github.com (aaron-auc)
Date: Tue, 21 Jul 2026 18:13:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] d3bb6d: fix: explicitly bundle
 libxcb-cursor for linuxdepl...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/461a13-d3bb6d@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d3bb6d805cdbf851359dc8d9fbc3b4a64205290b
      https://github.com/ehb54/ultrascan3/commit/d3bb6d805cdbf851359dc8d9fbc3b4a64205290b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-21 (Tue, 21 Jul 2026)

  Changed paths:
    M admin/cmake/packaging/linux/LinuxDeploy.cmake

  Log Message:
  -----------
  fix: explicitly bundle libxcb-cursor for linuxdeploy to ensure runtime availability



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From noreply at github.com  Wed Jul 22 04:34:23 2026
From: noreply at github.com (github-actions[bot])
Date: Wed, 22 Jul 2026 03:34:23 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/tags/nightly/dc00ac-000000@github.com>

  Branch: refs/tags/nightly
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Jul 22 04:34:34 2026
From: noreply at github.com (github-actions[bot])
Date: Wed, 22 Jul 2026 03:34:34 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/tags/nightly/000000-5859c0@github.com>

  Branch: refs/tags/nightly
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Jul 22 10:53:56 2026
From: noreply at github.com (emre brookes)
Date: Wed, 22 Jul 2026 09:53:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6dd62b: extrap_c0: allow a manual q
 for the high-q splice ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/ab5571-6dd62b@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6dd62b87829b1b3e7212ac0d40698595a2b50e6f
      https://github.com/ehb54/ultrascan3/commit/6dd62b87829b1b3e7212ac0d40698595a2b50e6f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-22 (Wed, 22 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp

  Log Message:
  -----------
  extrap_c0: allow a manual q for the high-q splice switchover

Requested by Mattia: to test these data he needs to impose the merge/switchover q
rather than accept the automatic placement. The automatic point is the first q where
the extrapolation agrees with the reference within its errors; that can land where the
regularization has distorted the curve, and there is currently no way to move it.

Adds a manual switchover:
- concentration dialog: a "switchover q (blank = auto)" field next to the splice
  checkbox, enabled only when the splice is on;
- scripted driver: a `merge_q <value>` directive (requires merge_ref 1).

Blank / 0 / non-positive means automatic (unchanged behaviour). A positive value pins
the merge to the nearest output grid point and is reported in the log as a manual
switchover. The value flows into the existing _merge_q<q> name token, so pinned runs
already get distinct, self-describing names.

Verified: pinned 0.10 -> q 0.0999 idx 207, pinned 0.25 -> q 0.250 idx 536, auto ->
q 0.465 idx 995 (unchanged); merge_q given without merge_ref is correctly ignored. All
9 regression baselines byte-identical, so nothing changes unless a q is pinned. GUI
field compiles and links but has not been exercised in a live session.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Wed Jul 22 10:55:02 2026
From: noreply at github.com (emre brookes)
Date: Wed, 22 Jul 2026 09:55:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 355cff: extrap_c0 doc: document the
 manual switchover q (m...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/6dd62b-355cff@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 355cffc5da765598fd689b1360b1be6aafd311ad
      https://github.com/ehb54/ultrascan3/commit/355cffc5da765598fd689b1360b1be6aafd311ad
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-22 (Wed, 22 Jul 2026)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap_c0 doc: document the manual switchover q (merge_q)

Follows 6dd62b878. Adds the "switchover q" field to the reference-splice description
(pin the merge to a chosen q, blank = automatic) and the scripted merge_q directive to
the directive list. Directive audit back to 20/20; bare-<p> imbalance unchanged.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 23 08:45:22 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 23 Jul 2026 07:45:22 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9c6e1c: fix: exclude HPC files from
 nightly build artifact...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/d3bb6d-9c6e1c@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9c6e1cb0178e71db280fad6253be5d241738e497
      https://github.com/ehb54/ultrascan3/commit/9c6e1cb0178e71db280fad6253be5d241738e497
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M .github/workflows/nightly-build.yml

  Log Message:
  -----------
  fix: exclude HPC files from nightly build artifact copying for APP



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From noreply at github.com  Thu Jul 23 10:00:36 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 09:00:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] ed1512: extrap_c0: warn when
 fit_broaden is ignored; keep ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/355cff-ed1512@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ed15126d5c2b3a05f5f03cee6a3e404857003123
      https://github.com/ehb54/ultrascan3/commit/ed15126d5c2b3a05f5f03cee6a3e404857003123
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp

  Log Message:
  -----------
  extrap_c0: warn when fit_broaden is ignored; keep it out of the name

The manual fit-broadening window applies only to the additive model with automatic GCV
off and no reference-scale/splice. In every other case it was silently accepted and
silently dropped -- most importantly it is INERT in reciprocal mode (the default), so a
user could set it, see no effect, and have no idea why. The output name also gained a
_fbN token even when the window did nothing, falsely advertising a broadened run.

Now: when fit_broaden > 1 is requested but will not be used, log exactly why (reciprocal
model / GCV on / reference-scale or splice on). And the name is built from
fit_broaden_effective -- the value that actually took effect -- so _fbN appears only when
the window was really applied.

Found while sweeping regularization strength as a mechanism test: fit_broaden turned out
to change nothing in reciprocal, which is what exposed the silent no-op.

Verified on all four cases: reciprocal / additive+GCV / additive+ref-scale each warn and
drop the _fb token; plain additive+nogcv applies it and keeps _fb9. All 9 regression
baselines byte-identical (none use fit_broaden).

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 23 10:27:23 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 09:27:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8b57a9: release Dockerfiles: pull
 modernized statically-li...
Message-ID: <ehb54/ultrascan3/push/refs/heads/update-rasmol-sdl3-main/000000-8b57a9@github.com>

  Branch: refs/heads/update-rasmol-sdl3-main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8b57a903e8d4fde8bba207bb1282bddc53c43261
      https://github.com/ehb54/ultrascan3/commit/8b57a903e8d4fde8bba207bb1282bddc53c43261
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  release Dockerfiles: pull modernized statically-linked RasMol

redhat/centos7/ubuntu Dockerfiles now clone ehb54/rasmol (somo-modernize) and copy rasmol + rasmol.hlp from binaries/linux-x86_64 into /ultrascan3/bin, dropping the lib/* copy (statically linked, no shipped .so). Unifying the source also retires the centos7 Dockerfile's stale 'ubuntu rasmol' clone.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 23 10:27:22 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 09:27:22 -0700
Subject: [us-commits] [ehb54/ultrascan3] 653065: release Dockerfiles: pull
 modernized statically-li...
Message-ID: <ehb54/ultrascan3/push/refs/heads/update-rasmol-sdl3/000000-653065@github.com>

  Branch: refs/heads/update-rasmol-sdl3
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 653065788e7c12eca1238597b3fc9b3391a557bb
      https://github.com/ehb54/ultrascan3/commit/653065788e7c12eca1238597b3fc9b3391a557bb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  release Dockerfiles: pull modernized statically-linked RasMol

redhat/centos7/ubuntu Dockerfiles now clone ehb54/rasmol (somo-modernize) and copy rasmol + rasmol.hlp from binaries/linux-x86_64 into /ultrascan3/bin, dropping the lib/* copy (statically linked, no shipped .so). Unifying the source also retires the centos7 Dockerfile's stale 'ubuntu rasmol' clone.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 23 16:22:36 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 15:22:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] 653065: release Dockerfiles: pull
 modernized statically-li...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/f82e19-700e64@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 653065788e7c12eca1238597b3fc9b3391a557bb
      https://github.com/ehb54/ultrascan3/commit/653065788e7c12eca1238597b3fc9b3391a557bb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  release Dockerfiles: pull modernized statically-linked RasMol

redhat/centos7/ubuntu Dockerfiles now clone ehb54/rasmol (somo-modernize) and copy rasmol + rasmol.hlp from binaries/linux-x86_64 into /ultrascan3/bin, dropping the lib/* copy (statically linked, no shipped .so). Unifying the source also retires the centos7 Dockerfile's stale 'ubuntu rasmol' clone.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: 700e645d9d40cc244606d6c8a3e1ec1cdd33f8a8
      https://github.com/ehb54/ultrascan3/commit/700e645d9d40cc244606d6c8a3e1ec1cdd33f8a8
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  Merge pull request #494 from ehb54/update-rasmol-sdl3

release Dockerfiles: pull modernized statically-linked RasMol


Compare: https://github.com/ehb54/ultrascan3/compare/f82e19a70716...700e645d9d40

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From noreply at github.com  Thu Jul 23 16:22:50 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 15:22:50 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/update-rasmol-sdl3/653065-000000@github.com>

  Branch: refs/heads/update-rasmol-sdl3
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Jul 23 16:23:13 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 15:23:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8b57a9: release Dockerfiles: pull
 modernized statically-li...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/5859c0-16e2cb@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8b57a903e8d4fde8bba207bb1282bddc53c43261
      https://github.com/ehb54/ultrascan3/commit/8b57a903e8d4fde8bba207bb1282bddc53c43261
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  release Dockerfiles: pull modernized statically-linked RasMol

redhat/centos7/ubuntu Dockerfiles now clone ehb54/rasmol (somo-modernize) and copy rasmol + rasmol.hlp from binaries/linux-x86_64 into /ultrascan3/bin, dropping the lib/* copy (statically linked, no shipped .so). Unifying the source also retires the centos7 Dockerfile's stale 'ubuntu rasmol' clone.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: 16e2cb7573926eca2fc337f0ea4fb00955418108
      https://github.com/ehb54/ultrascan3/commit/16e2cb7573926eca2fc337f0ea4fb00955418108
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  Merge pull request #495 from ehb54/update-rasmol-sdl3-main

release Dockerfiles: pull modernized statically-linked RasMol (main)


Compare: https://github.com/ehb54/ultrascan3/compare/5859c047d607...16e2cb757392

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From noreply at github.com  Thu Jul 23 16:23:17 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 15:23:17 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/update-rasmol-sdl3-main/8b57a9-000000@github.com>

  Branch: refs/heads/update-rasmol-sdl3-main
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Jul 23 16:26:35 2026
From: noreply at github.com (emre brookes)
Date: Thu, 23 Jul 2026 15:26:35 -0700
Subject: [us-commits] [ehb54/ultrascan3] ad06eb: extrap-c0: default
 reciprocal->additive (wave unfi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/ed1512-ad06eb@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ad06ebcf32fff89fd4162a573227d937f14925ff
      https://github.com/ehb54/ultrascan3/commit/ad06ebcf32fff89fd4162a573227d937f14925ff
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap-c0: default reciprocal->additive (wave unfixable), reciprocal wave warning, virial2/GUI cleanup

The reciprocal+GCV concentration model develops a coherent low-q "wave" in the extrapolated
profile on few-concentration series, and it has no robust lambda cure: GCV selects lambda to fit
the c/I axis, but I(0)=1/u, and the nonlinear inversion decouples "good lambda for the fit" from
"good lambda for I(0)". Proven with a faithful GCV replica plus a lambda-sweep run through SOMO
(new gcv_lambda diagnostic directive, reading GNOM waviness off datgnom): alpha-syn is clean only
at edof ~= n / ~5 / 1 and wavy across edof 10-169, while SASBDB needs edof ~60-130 (Xylanase
R^2=0.065 otherwise) -- the good bands do not intersect, so no lambda-selection rule works.
Full analysis: extrap_c0_paper/results/reciprocal_lambda_fix_final.txt.

- Default concentration model reciprocal -> additive (dialog, CLI, header, fallback, tooltip,
  manual). Additive is clean on every dataset tested; reciprocal stays available (dropdown +
  gparam saxs_extrap_c0_model). Reciprocal's MW advantage is unvalidated (no absolute-scale data)
  while its wave cost is now demonstrated on real data.
- Reciprocal-only low-q wave warning: a Wald-Wolfowitz runs test on the EXCESS low-q coherence of
  the reciprocal profile over an additive GCV baseline (a single-curve test cannot separate the
  artifact from genuine globular form-factor structure; the Guinier R^2 does not catch the wave).
- virial2 uses a per-q quadratic and ignores GCV, so the wave cannot occur there (verified: GNOM
  z ~ -1.8 where reciprocal is -11, 0 warnings); skip the wasted GCV solve and its spurious
  "Zimm GCV applied" log line for virial2.
- GUI: gray out the GCV checkbox for virial2, the fit-broadening field for non-additive models,
  and the recompute-input mode when its checkbox is off (settable-but-ignored groupings).
- New gcv_lambda control-file directive (default 0 = automatic GCV; diagnostic/power-user knob).

Behavior-preserving on pinned-model runs: all 9 regression baselines byte-identical.

Co-Authored-By: Claude Fable 5 <noreply at anthropic.com>



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From noreply at github.com  Thu Jul 23 21:02:32 2026
From: noreply at github.com (aaron-auc)
Date: Thu, 23 Jul 2026 20:02:32 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8b57a9: release Dockerfiles: pull
 modernized statically-li...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/9c6e1c-de8c83@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8b57a903e8d4fde8bba207bb1282bddc53c43261
      https://github.com/ehb54/ultrascan3/commit/8b57a903e8d4fde8bba207bb1282bddc53c43261
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  release Dockerfiles: pull modernized statically-linked RasMol

redhat/centos7/ubuntu Dockerfiles now clone ehb54/rasmol (somo-modernize) and copy rasmol + rasmol.hlp from binaries/linux-x86_64 into /ultrascan3/bin, dropping the lib/* copy (statically linked, no shipped .so). Unifying the source also retires the centos7 Dockerfile's stale 'ubuntu rasmol' clone.

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>


  Commit: 16e2cb7573926eca2fc337f0ea4fb00955418108
      https://github.com/ehb54/ultrascan3/commit/16e2cb7573926eca2fc337f0ea4fb00955418108
  Author: emre brookes <ehb54 at users.noreply.github.com>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile

  Log Message:
  -----------
  Merge pull request #495 from ehb54/update-rasmol-sdl3-main

release Dockerfiles: pull modernized statically-linked RasMol (main)


  Commit: de8c830701bad1b9778721d8adc35799fccd2567
      https://github.com/ehb54/ultrascan3/commit/de8c830701bad1b9778721d8adc35799fccd2567
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-23 (Thu, 23 Jul 2026)

  Changed paths:

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 875-request-cmake-remove-gmp-module-from-installer-for-osx

# Conflicts:
#	admin/release/centos7/Dockerfile
#	admin/release/redhat/Dockerfile
#	admin/release/ubuntu/Dockerfile


Compare: https://github.com/ehb54/ultrascan3/compare/9c6e1cb0178e...de8c830701ba

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From noreply at github.com  Sat Jul 25 11:54:39 2026
From: noreply at github.com (github-actions[bot])
Date: Sat, 25 Jul 2026 10:54:39 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/tags/nightly/5859c0-000000@github.com>

  Branch: refs/tags/nightly
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sat Jul 25 11:55:00 2026
From: noreply at github.com (github-actions[bot])
Date: Sat, 25 Jul 2026 10:55:00 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/tags/nightly/000000-16e2cb@github.com>

  Branch: refs/tags/nightly
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Jul 30 13:53:04 2026
From: noreply at github.com (emre brookes)
Date: Thu, 30 Jul 2026 12:53:04 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5ea9ec: extrap-c0:
 model-independent low-q SE-correction Q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-920/ad06eb-5ea9ec@github.com>

  Branch: refs/heads/ehb54-issue-920
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5ea9ec80d9f3c1ef2847d4d0b1800c08e6cd77ed
      https://github.com/ehb54/ultrascan3/commit/5ea9ec80d9f3c1ef2847d4d0b1800c08e6cd77ed
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2026-07-30 (Thu, 30 Jul 2026)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_extrap_c0_conc.h
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_extrap_c0_script.cpp
    M us_somo/somo/doc/manual/somo/somo_saxs_extrap_c0.html

  Log Message:
  -----------
  extrap-c0: model-independent low-q SE-correction QC + wave flag (replaces reciprocal-only warning)

A low-q point the extrapolation places far off the smooth low-q trend is almost always a
correlated buffer-subtraction / detector artifact: because the input curves agree on it, its
extrapolated intercept SE comes out falsely tiny, giving it ~10-100x false weight in any
1/sigma^2 downstream fit (Guinier, GNOM, an NNLS reconstruction). Diagnosed on Mattia Rocco's
alpha-syn curves (2026-07-30): two such points at q~0.0068/0.0073 drove a low-q wave and a bad
SAF NNLS P-value, and the fix is to widen their error bars, not to smooth.

New file-scope helper us_extrap_c0_lowq_serepair (replaces the reciprocal-only
us_extrap_c0_wave_runsz): fits a ROBUST (iteratively reweighted, Tukey biweight) quadratic-in-q^2
trend to ln I over q <= 2/Rg, then WITHOUT changing any intensity:
  (a) SE-CORRECTION: widens each low-q error bar in place to max(sd, |I - trend|) -- model
      independent, upward only, no threshold. Removes the artifacts' false leverage.
  (b) WAVE FLAG: returns the trend-residual runs-z. When automatic GCV smoothing is on it can
      spread such artifacts into a coherent low-q wave in the VALUES (which widening the errors
      cannot undo); a strongly negative z warns and recommends turning GCV off (the unsmoothed
      extrapolation keeps the artifact local, where the SE-correction handles it).

Why this replaces the earlier reciprocal-only differential wave warning: the low-q artifact and
the GCV wave are model-independent (additive waves too), so a reciprocal-vs-additive test was the
wrong tool.

- On by default (se_repair): CLI directive `se_repair 0|1`, and a GUI checkbox
  "Low-q SD correction ...". Manual updated (new section; old reciprocal wave caveat removed).
- Changes only the output sd column. Regression: se_repair 0 reproduces all 9 baselines
  byte-identical (isolation); with it on, only recip_nogcv (2) and virial2 (56) change, sd-only
  (q and I identical). Validated on compiled SOMO: the SE-correction fires on the two alpha-syn
  bad points (sd 1.5e-4 -> 2.4e-3, x16.5) and the wave flag fires on reciprocal+GCV (runs-z -4.6).

Co-Authored-By: Claude Opus 4.8 <noreply at anthropic.com>



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From noreply at github.com  Fri Jul 31 09:23:08 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 31 Jul 2026 08:23:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4c17f2: fix: update build scripts
 to retain vcpkg_installe...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/de8c83-4c17f2@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4c17f285b4959c8641cdbcffd1caad68ea584784
      https://github.com/ehb54/ultrascan3/commit/4c17f285b4959c8641cdbcffd1caad68ea584784
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-31 (Fri, 31 Jul 2026)

  Changed paths:
    M admin/cmake/toolchain.cmake
    M scripts/build.ps1
    M scripts/build.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: update build scripts to retain vcpkg_installed dependencies during rebuild



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From noreply at github.com  Fri Jul 31 14:02:49 2026
From: noreply at github.com (aaron-auc)
Date: Fri, 31 Jul 2026 13:02:49 -0700
Subject: [us-commits] [ehb54/ultrascan3] b9f933: fix: update build scripts
 to clarify handling of l...
Message-ID: <ehb54/ultrascan3/push/refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx/4c17f2-b9f933@github.com>

  Branch: refs/heads/875-request-cmake-remove-gmp-module-from-installer-for-osx
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b9f9333f14e358df639c11a68b3d21b71857f515
      https://github.com/ehb54/ultrascan3/commit/b9f9333f14e358df639c11a68b3d21b71857f515
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2026-07-31 (Fri, 31 Jul 2026)

  Changed paths:
    M admin/cmake/toolchain.cmake
    M scripts/build.ps1
    M scripts/build.sh
    M scripts/warm-cache.sh

  Log Message:
  -----------
  fix: update build scripts to clarify handling of legacy vcpkg bookkeeping and improve path management



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