From noreply at github.com  Thu Oct  2 06:27:23 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 02 Oct 2025 05:27:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3eb9ae: fix: duplicate include
 removed
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/4a401e-3eb9ae@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
      https://github.com/ehb54/ultrascan3/commit/3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  fix: duplicate include removed



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From noreply at github.com  Thu Oct  2 10:23:13 2025
From: noreply at github.com (Borries Demeler)
Date: Thu, 02 Oct 2025 09:23:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] a4fcd0: GMP | 1. EXP.: AProfile &&
 4. EDIT -- init. steps ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/f286c4-003fce@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
      https://github.com/ehb54/ultrascan3/commit/a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-21 (Sun, 21 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 1246e6e3724e8a382585cc65e0208d3008bfbeeb
      https://github.com/ehb54/ultrascan3/commit/1246e6e3724e8a382585cc65e0208d3008bfbeeb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

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

  Log Message:
  -----------
  [1a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5e6c7f858d8e6163099c500c970c02e54801243b
      https://github.com/ehb54/ultrascan3/commit/5e6c7f858d8e6163099c500c970c02e54801243b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
      https://github.com/ehb54/ultrascan3/commit/5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5edb9ce91335769271fb5f593482a97dc4233059
      https://github.com/ehb54/ultrascan3/commit/5edb9ce91335769271fb5f593482a97dc4233059
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [4]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 9aff495b37873080961f8c231a3ce673377f80d3
      https://github.com/ehb54/ultrascan3/commit/9aff495b37873080961f8c231a3ce673377f80d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
      https://github.com/ehb54/ultrascan3/commit/1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 321a8cba345ec3c3f2187e0ba10f28376fd49a3e
      https://github.com/ehb54/ultrascan3/commit/321a8cba345ec3c3f2187e0ba10f28376fd49a3e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [5b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 373ac0ac501856ea0df8f4f579f953d89ec810b0
      https://github.com/ehb54/ultrascan3/commit/373ac0ac501856ea0df8f4f579f953d89ec810b0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [6b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ea3905ba9097c5eed14e034d6656fd0c84dff988
      https://github.com/ehb54/ultrascan3/commit/ea3905ba9097c5eed14e034d6656fd0c84dff988
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [6b-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
      https://github.com/ehb54/ultrascan3/commit/ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [7-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 905f41462ec9dab9667e915d639af2970e21a7a4
      https://github.com/ehb54/ultrascan3/commit/905f41462ec9dab9667e915d639af2970e21a7a4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [proper settings of min/max for scan_beg|nth|end for different optics systems] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 671b8e4d0e4951014a52280942d6a6c9712f14fa
      https://github.com/ehb54/ultrascan3/commit/671b8e4d0e4951014a52280942d6a6c9712f14fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: d584fa48438a0f9d744b750a6abe23533cc48b52
      https://github.com/ehb54/ultrascan3/commit/d584fa48438a0f9d744b750a6abe23533cc48b52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [RESTORE--UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 84f86b86f77bbcd33e113217d09cbda59701b58b
      https://github.com/ehb54/ultrascan3/commit/84f86b86f77bbcd33e113217d09cbda59701b58b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 8ecca10f20a347fd906905b16f8e85ef5afff22a
      https://github.com/ehb54/ultrascan3/commit/8ecca10f20a347fd906905b16f8e85ef5afff22a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: fe9b9031b3af683efa02792cf18ca46a51d376d8
      https://github.com/ehb54/ultrascan3/commit/fe9b9031b3af683efa02792cf18ca46a51d376d8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
      https://github.com/ehb54/ultrascan3/commit/4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: b1ff389cba607cd5f34556fb6945f050ad099ff8
      https://github.com/ehb54/ultrascan3/commit/b1ff389cba607cd5f34556fb6945f050ad099ff8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: b557af349d02a148cef58c38976319f129cf4afa
      https://github.com/ehb54/ultrascan3/commit/b557af349d02a148cef58c38976319f129cf4afa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
      https://github.com/ehb54/ultrascan3/commit/57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
      https://github.com/ehb54/ultrascan3/commit/825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 4f9217705b688c38c3e420a609c2692c23a7e160
      https://github.com/ehb54/ultrascan3/commit/4f9217705b688c38c3e420a609c2692c23a7e160
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [4]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: f8379662ac83a104ca49b29cc3b5a7f830944d05
      https://github.com/ehb54/ultrascan3/commit/f8379662ac83a104ca49b29cc3b5a7f830944d05
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [5]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 036113902d7405af0d641ad3afb98b2010cef02f
      https://github.com/ehb54/ultrascan3/commit/036113902d7405af0d641ad3afb98b2010cef02f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
      https://github.com/ehb54/ultrascan3/commit/0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [REstore form -- unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 42b30b23222d6e9b070861a382ebe34ad77611ab
      https://github.com/ehb54/ultrascan3/commit/42b30b23222d6e9b070861a382ebe34ad77611ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP | 6. REPORT -- do not display scan exclusion settings Scan section if optics type not used...


  Commit: e3282fcfa778c046776d3abf2a718a9617230b4d
      https://github.com/ehb54/ultrascan3/commit/e3282fcfa778c046776d3abf2a718a9617230b4d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  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 -- do not specify details on Scan exlusions of there were no any...


  Commit: 8a112ba9e5ae7859d58f117c486f2e52cbba2899
      https://github.com/ehb54/ultrascan3/commit/8a112ba9e5ae7859d58f117c486f2e52cbba2899
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d1287da6bdde6dcb79acc019617ea24b5d93d410
      https://github.com/ehb54/ultrascan3/commit/d1287da6bdde6dcb79acc019617ea24b5d93d410
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    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 gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    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_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge pull request #265 from ehb54/master

add master


  Commit: 8dff3550c25c2827799de8e3f245f1f34a9044ab
      https://github.com/ehb54/ultrascan3/commit/8dff3550c25c2827799de8e3f245f1f34a9044ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

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

  Log Message:
  -----------
  [2]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d927f1c7acffd7436189c83726111d960cbd1e2d
      https://github.com/ehb54/ultrascan3/commit/d927f1c7acffd7436189c83726111d960cbd1e2d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 4c3a97f136b46591a7381b85fb726ea2fb87f7f2
      https://github.com/ehb54/ultrascan3/commit/4c3a97f136b46591a7381b85fb726ea2fb87f7f2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

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

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
      https://github.com/ehb54/ultrascan3/commit/7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 07f7d5c89032aa8dac1c13fe611e51d8e076cfde
      https://github.com/ehb54/ultrascan3/commit/07f7d5c89032aa8dac1c13fe611e51d8e076cfde
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 232008ddbb42fa37d28890542961579241726f13
      https://github.com/ehb54/ultrascan3/commit/232008ddbb42fa37d28890542961579241726f13
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 003fcead31be5da3e4a5744bd8b5a9a3adb9686d
      https://github.com/ehb54/ultrascan3/commit/003fcead31be5da3e4a5744bd8b5a9a3adb9686d
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  Merge pull request #267 from ehb54/alexey-dev-issue556

Alexey dev issue556: Scan Exclusion Profile Editor for AProfile in GMP #556


Compare: https://github.com/ehb54/ultrascan3/compare/f286c4ffff80...003fcead31be

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From noreply at github.com  Thu Oct  2 13:42:50 2025
From: noreply at github.com (alexsav815)
Date: Thu, 02 Oct 2025 12:42:50 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue562/000000-003fce@github.com>

  Branch: refs/heads/alexey-dev-issue562
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From noreply at github.com  Thu Oct  2 13:54:00 2025
From: noreply at github.com (alexsav815)
Date: Thu, 02 Oct 2025 12:54:00 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9b2e06: US_intargal -- avoid
 loading editProfiles...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue562/003fce-9b2e06@github.com>

  Branch: refs/heads/alexey-dev-issue562
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9b2e06a5e4a371044a913065222c7d91603e0085
      https://github.com/ehb54/ultrascan3/commit/9b2e06a5e4a371044a913065222c7d91603e0085
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intargal -- avoid loading editProfiles...



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From noreply at github.com  Thu Oct  2 14:25:05 2025
From: noreply at github.com (alexsav815)
Date: Thu, 02 Oct 2025 13:25:05 -0700
Subject: [us-commits] [ehb54/ultrascan3] abfa96: US_intergal -- restore
 editProfiles read; add debu...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue562/9b2e06-abfa96@github.com>

  Branch: refs/heads/alexey-dev-issue562
  Home:   https://github.com/ehb54/ultrascan3
  Commit: abfa96706807a26b5b0642ed078a97acf01a3e18
      https://github.com/ehb54/ultrascan3/commit/abfa96706807a26b5b0642ed078a97acf01a3e18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intergal -- restore editProfiles read; add debugs...



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From noreply at github.com  Thu Oct  2 14:33:29 2025
From: noreply at github.com (alexsav815)
Date: Thu, 02 Oct 2025 13:33:29 -0700
Subject: [us-commits] [ehb54/ultrascan3] d712bb: [1]US_intergal -- restore
 editProfiles read; add d...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue562/abfa96-d712bb@github.com>

  Branch: refs/heads/alexey-dev-issue562
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d712bbbb0ceb306e036f428d4245c0e3b87c097b
      https://github.com/ehb54/ultrascan3/commit/d712bbbb0ceb306e036f428d4245c0e3b87c097b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [1]US_intergal -- restore editProfiles read; add debugs...



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From noreply at github.com  Thu Oct  2 14:41:54 2025
From: noreply at github.com (alexsav815)
Date: Thu, 02 Oct 2025 13:41:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 088595: [2]US_intergal -- restore
 editProfiles read; add d...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue562/d712bb-088595@github.com>

  Branch: refs/heads/alexey-dev-issue562
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 088595bbbb4e35e890cb8d2bf308945e0333f3f1
      https://github.com/ehb54/ultrascan3/commit/088595bbbb4e35e890cb8d2bf308945e0333f3f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [2]US_intergal -- restore editProfiles read; add debugs...



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From noreply at github.com  Thu Oct  2 14:46:03 2025
From: noreply at github.com (alexsav815)
Date: Thu, 02 Oct 2025 13:46:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] 153436: [3]US_intergal -- create
 curves' labels from the m...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue562/088595-153436@github.com>

  Branch: refs/heads/alexey-dev-issue562
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 15343601bc0774d196184c33adbddefab8430a11
      https://github.com/ehb54/ultrascan3/commit/15343601bc0774d196184c33adbddefab8430a11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [3]US_intergal -- create curves' labels from the model's desc...



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From noreply at github.com  Fri Oct  3 07:11:41 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:11:41 -0700
Subject: [us-commits] [ehb54/ultrascan3] e19b8e: Update
 qwtplot3d/CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/3eb9ae-e19b8e@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e19b8e845f44edf59c398eea895d16d8564b3946
      https://github.com/ehb54/ultrascan3/commit/e19b8e845f44edf59c398eea895d16d8564b3946
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  Update qwtplot3d/CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:21:29 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:21:29 -0700
Subject: [us-commits] [ehb54/ultrascan3] 24e6dc: Update
 qwtplot3d/CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/e19b8e-24e6dc@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 24e6dcb2dc6358b46e0f61426c38ca8463ed7eb6
      https://github.com/ehb54/ultrascan3/commit/24e6dcb2dc6358b46e0f61426c38ca8463ed7eb6
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  Update qwtplot3d/CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:22:19 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:22:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] 646342: Update
 qwtplot3d/CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/24e6dc-646342@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6463427a66d96b7186f8ba01da93d96ef6016f0f
      https://github.com/ehb54/ultrascan3/commit/6463427a66d96b7186f8ba01da93d96ef6016f0f
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  Update qwtplot3d/CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:23:19 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:23:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] f74e17: Update
 qwtplot3d/CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/646342-f74e17@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f74e17c3970be78c5eed03bb9c95b6550e07ca70
      https://github.com/ehb54/ultrascan3/commit/f74e17c3970be78c5eed03bb9c95b6550e07ca70
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  Update qwtplot3d/CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:24:17 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:24:17 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8e491d: Update CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/f74e17-8e491d@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8e491d3bc9c99536a2fd029a53e2e99ca6c6148a
      https://github.com/ehb54/ultrascan3/commit/8e491d3bc9c99536a2fd029a53e2e99ca6c6148a
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:25:35 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:25:35 -0700
Subject: [us-commits] [ehb54/ultrascan3] 117e2d: Update CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/8e491d-117e2d@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 117e2dcd0fb2bd04178118bdfd11a80ecde97049
      https://github.com/ehb54/ultrascan3/commit/117e2dcd0fb2bd04178118bdfd11a80ecde97049
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:40:47 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:40:47 -0700
Subject: [us-commits] [ehb54/ultrascan3] ac056c: fix: pr resolutions
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/117e2d-ac056c@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ac056cec74ce1c8883363b39d9bcb28f28efff09
      https://github.com/ehb54/ultrascan3/commit/ac056cec74ce1c8883363b39d9bcb28f28efff09
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M programs/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  fix: pr resolutions



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From noreply at github.com  Fri Oct  3 07:41:56 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:41:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5751ad: Update CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/ac056c-5751ad@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5751adc8577c166a02763e76db9e41089389c85e
      https://github.com/ehb54/ultrascan3/commit/5751adc8577c166a02763e76db9e41089389c85e
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:43:02 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:43:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7cda38: Update CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/5751ad-7cda38@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7cda3857169ade862a877fd44ab1beb72f41e02c
      https://github.com/ehb54/ultrascan3/commit/7cda3857169ade862a877fd44ab1beb72f41e02c
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 07:43:36 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 06:43:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] 53a9e1: Update CMakeLists.txt
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/7cda38-53a9e1@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 53a9e1c3b0937e678c71d8a0bf2be6c2062efe0b
      https://github.com/ehb54/ultrascan3/commit/53a9e1c3b0937e678c71d8a0bf2be6c2062efe0b
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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



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From noreply at github.com  Fri Oct  3 08:09:06 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 03 Oct 2025 07:09:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7143f0: fix: pr resolutions
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/53a9e1-707b4e@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7143f0a242abcc7c760ef7b9d3162fef09a12c00
      https://github.com/ehb54/ultrascan3/commit/7143f0a242abcc7c760ef7b9d3162fef09a12c00
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_rsa.cpp

  Log Message:
  -----------
  fix: pr resolutions


  Commit: 707b4e1b5a58b92040a59b6698a14171a4ddc279
      https://github.com/ehb54/ultrascan3/commit/707b4e1b5a58b92040a59b6698a14171a4ddc279
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/aaron-dev-test-utils' into aaron-dev-test-utils


Compare: https://github.com/ehb54/ultrascan3/compare/53a9e1c3b093...707b4e1b5a58

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From noreply at github.com  Fri Oct  3 14:37:24 2025
From: noreply at github.com (alexsav815)
Date: Fri, 03 Oct 2025 13:37:24 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/000000-003fce@github.com>

  Branch: refs/heads/alexey-dev-issue567
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From noreply at github.com  Fri Oct  3 14:56:54 2025
From: noreply at github.com (HabGab)
Date: Fri, 03 Oct 2025 13:56:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9b2e06: US_intargal -- avoid
 loading editProfiles...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/003fce-d62e7b@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9b2e06a5e4a371044a913065222c7d91603e0085
      https://github.com/ehb54/ultrascan3/commit/9b2e06a5e4a371044a913065222c7d91603e0085
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intargal -- avoid loading editProfiles...


  Commit: abfa96706807a26b5b0642ed078a97acf01a3e18
      https://github.com/ehb54/ultrascan3/commit/abfa96706807a26b5b0642ed078a97acf01a3e18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intergal -- restore editProfiles read; add debugs...


  Commit: d712bbbb0ceb306e036f428d4245c0e3b87c097b
      https://github.com/ehb54/ultrascan3/commit/d712bbbb0ceb306e036f428d4245c0e3b87c097b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [1]US_intergal -- restore editProfiles read; add debugs...


  Commit: 088595bbbb4e35e890cb8d2bf308945e0333f3f1
      https://github.com/ehb54/ultrascan3/commit/088595bbbb4e35e890cb8d2bf308945e0333f3f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [2]US_intergal -- restore editProfiles read; add debugs...


  Commit: 15343601bc0774d196184c33adbddefab8430a11
      https://github.com/ehb54/ultrascan3/commit/15343601bc0774d196184c33adbddefab8430a11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [3]US_intergal -- create curves' labels from the model's desc...


  Commit: d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
      https://github.com/ehb54/ultrascan3/commit/d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  Merge pull request #268 from ehb54/alexey-dev-issue562

Alexey dev issue562: Enable plotting CG-SG integral distr.


Compare: https://github.com/ehb54/ultrascan3/compare/003fcead31be...d62e7b57ef0e

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From noreply at github.com  Sat Oct  4 09:39:27 2025
From: noreply at github.com (ehb54)
Date: Sat, 04 Oct 2025 08:39:27 -0700
Subject: [us-commits] [ehb54/ultrascan3] e52749: qssl_probe - simple test of
 qssl to google.com
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb-issue-565/939ab2-e52749@github.com>

  Branch: refs/heads/ehb-issue-565
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e5274972b68ed56906de3ed0866fa9589a30aa64
      https://github.com/ehb54/ultrascan3/commit/e5274972b68ed56906de3ed0866fa9589a30aa64
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-04 (Sat, 04 Oct 2025)

  Changed paths:
    A admin/networktesting/qssl_probe/README
    A admin/networktesting/qssl_probe/main.cpp
    A admin/networktesting/qssl_probe/qssl_probe.pro

  Log Message:
  -----------
  qssl_probe - simple test of qssl to google.com



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From noreply at github.com  Sat Oct  4 11:55:24 2025
From: noreply at github.com (ehb54)
Date: Sat, 04 Oct 2025 10:55:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7ce5d4: qhttp_post_probe - testing
 for us_http_post with a...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb-issue-565/e52749-7ce5d4@github.com>

  Branch: refs/heads/ehb-issue-565
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7ce5d4f3d2be67ccf3913b489fc8a3fd057d4070
      https://github.com/ehb54/ultrascan3/commit/7ce5d4f3d2be67ccf3913b489fc8a3fd057d4070
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-04 (Sat, 04 Oct 2025)

  Changed paths:
    A admin/networktesting/qhttp_post_probe/README
    A admin/networktesting/qhttp_post_probe/qhttp_post_probe_libus_utils/main.cpp
    A admin/networktesting/qhttp_post_probe/qhttp_post_probe_libus_utils/qhttp_post_probe_libus_utils.pro
    A admin/networktesting/qhttp_post_probe/qhttp_post_probe_no_libus_utils/main.cpp
    A admin/networktesting/qhttp_post_probe/qhttp_post_probe_no_libus_utils/qhttp_post_probe_no_libus_utils.pro
    A admin/networktesting/qhttp_post_probe/qhttp_post_probe_no_libus_utils/us_extern.h
    A admin/networktesting/qhttp_post_probe/qhttp_post_probe_no_libus_utils/us_http_post.cpp
    A admin/networktesting/qhttp_post_probe/qhttp_post_probe_no_libus_utils/us_http_post.h

  Log Message:
  -----------
  qhttp_post_probe - testing for us_http_post with and without libus_utils



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From noreply at github.com  Sun Oct  5 09:43:29 2025
From: noreply at github.com (ehb54)
Date: Sun, 05 Oct 2025 08:43:29 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1d9106: cli tests for db
 connectivity
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb-issue-565/7ce5d4-1d9106@github.com>

  Branch: refs/heads/ehb-issue-565
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1d9106f75e2f8f56580736b42f197a094e970929
      https://github.com/ehb54/ultrascan3/commit/1d9106f75e2f8f56580736b42f197a094e970929
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-05 (Sun, 05 Oct 2025)

  Changed paths:
    A admin/networktesting/db2_tests/README
    A admin/networktesting/db2_tests/db2_test_libus_utils/db2_test_no_libus_utils.pro
    A admin/networktesting/db2_tests/db2_test_libus_utils/main.cpp
    A admin/networktesting/db2_tests/db2_test_no_libus_utils/db2_test_no_libus_utils.pro
    A admin/networktesting/db2_tests/db2_test_no_libus_utils/main.cpp
    A admin/networktesting/db2_tests/db2_test_no_libus_utils/us_db2.cpp
    A admin/networktesting/db2_tests/db2_test_no_libus_utils/us_db2.h

  Log Message:
  -----------
  cli tests for db connectivity



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From noreply at github.com  Mon Oct  6 12:57:45 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 11:57:45 -0700
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue567/000000-6ffbfa@github.com>

  Branch: refs/heads/alexey-dev-for-issue567
  Home:   https://github.com/ehb54/us3_sql

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From noreply at github.com  Mon Oct  6 13:06:53 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 12:06:53 -0700
Subject: [us-commits] [ehb54/ultrascan3] 399d84: GMP | R&D : dataDisk --
 differentiate between RI-u...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/003fce-399d84@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 399d845e5667346225803b9ac45b753c7676e39d
      https://github.com/ehb54/ultrascan3/commit/399d845e5667346225803b9ac45b753c7676e39d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_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_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...



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From noreply at github.com  Mon Oct  6 13:07:16 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 12:07:16 -0700
Subject: [us-commits] [ehb54/us3_sql] 5ea073: [SQL for -- ] GMP | R&D :
 dataDisk -- differentiat...
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue567/6ffbfa-5ea073@github.com>

  Branch: refs/heads/alexey-dev-for-issue567
  Home:   https://github.com/ehb54/us3_sql
  Commit: 5ea0736b33b19866bcc11f51efc613f2227cc97c
      https://github.com/ehb54/us3_sql/commit/5ea0736b33b19866bcc11f51efc613f2227cc97c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M us3.sql

  Log Message:
  -----------
  [SQL for -- ] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ......



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From noreply at github.com  Mon Oct  6 14:37:19 2025
From: noreply at github.com (ehb54)
Date: Mon, 06 Oct 2025 13:37:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7c3478: Redhat 9 build seems to work
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb-issue-565/1d9106-7c3478@github.com>

  Branch: refs/heads/ehb-issue-565
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7c347823c038dfbe3cce04e8f26afeef50938ac3
      https://github.com/ehb54/ultrascan3/commit/7c347823c038dfbe3cce04e8f26afeef50938ac3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M admin/release/buildpkg.pl
    M admin/release/redhat/Dockerfile

  Log Message:
  -----------
  Redhat 9 build seems to work



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From noreply at github.com  Mon Oct  6 15:27:43 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 14:27:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] f924d7: [1] GMP | R&D : dataDisk --
 differentiate between ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/399d84-f924d7@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f924d79f3ecf67db15ced074ac2b50a4cafc9c72
      https://github.com/ehb54/ultrascan3/commit/f924d79f3ecf67db15ced074ac2b50a4cafc9c72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [1] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...



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From noreply at github.com  Mon Oct  6 15:39:19 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 14:39:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] a95afc: [2] GMP | R&D : dataDisk --
 differentiate between ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/f924d7-a95afc@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
      https://github.com/ehb54/ultrascan3/commit/a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...



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From noreply at github.com  Mon Oct  6 15:46:54 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 14:46:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8f9f12: [3] GMP | R&D : dataDisk --
 differentiate between ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/a95afc-8f9f12@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8f9f1257b799c491fa5629c912071eabb435388f
      https://github.com/ehb54/ultrascan3/commit/8f9f1257b799c491fa5629c912071eabb435388f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...



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From noreply at github.com  Mon Oct  6 16:43:26 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 15:43:26 -0700
Subject: [us-commits] [ehb54/ultrascan3] c3a261: Us_Edit -- address
 non-hidden widgets in different...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/8f9f12-c3a261@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c3a261985e7e3979e7a9a11fcad5c851e739f41b
      https://github.com/ehb54/ultrascan3/commit/c3a261985e7e3979e7a9a11fcad5c851e739f41b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Us_Edit -- address non-hidden widgets in different constructors && scenarios ...



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From noreply at github.com  Mon Oct  6 17:08:47 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 16:08:47 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3ad355: [1]Us_Edit -- address
 non-hidden widgets in differ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/c3a261-3ad355@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3ad35587a1da03cc9926344ac40bb3d364a32d24
      https://github.com/ehb54/ultrascan3/commit/3ad35587a1da03cc9926344ac40bb3d364a32d24
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...



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From noreply at github.com  Mon Oct  6 17:16:54 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 16:16:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] d6a4a4: [2]Us_Edit -- address
 non-hidden widgets in differ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/3ad355-d6a4a4@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d6a4a469c86320252916565b3bd860c07cab4b1f
      https://github.com/ehb54/ultrascan3/commit/d6a4a469c86320252916565b3bd860c07cab4b1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...



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From noreply at github.com  Mon Oct  6 17:39:31 2025
From: noreply at github.com (alexsav815)
Date: Mon, 06 Oct 2025 16:39:31 -0700
Subject: [us-commits] [ehb54/ultrascan3] d3528c: [3]Us_Edit -- address
 non-hidden widgets in differ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/d6a4a4-d3528c@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d3528cb233647917b4f76c9423f9deae1983f2bd
      https://github.com/ehb54/ultrascan3/commit/d3528cb233647917b4f76c9423f9deae1983f2bd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...



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From noreply at github.com  Tue Oct  7 08:34:56 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 07 Oct 2025 07:34:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] c5ac60: fix: pr resolutions
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/707b4e-c5ac60@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c5ac6055aa2897ea08fe5150e24756655fd3f912
      https://github.com/ehb54/ultrascan3/commit/c5ac6055aa2897ea08fe5150e24756655fd3f912
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-07 (Tue, 07 Oct 2025)

  Changed paths:
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_ramp/us_ramp_gui.cpp

  Log Message:
  -----------
  fix: pr resolutions



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From noreply at github.com  Tue Oct  7 08:59:35 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 07 Oct 2025 07:59:35 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8b4d2d: Consolidated commit after
 cleanup
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/c5ac60-8b4d2d@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
      https://github.com/ehb54/ultrascan3/commit/8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-07 (Tue, 07 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_rsa.cpp

  Log Message:
  -----------
  Consolidated commit after cleanup



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From noreply at github.com  Wed Oct  8 14:34:09 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 08 Oct 2025 13:34:09 -0700
Subject: [us-commits] [ehb54/ultrascan3] 69b601: PAM for linux password for
 php
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/8b4d2d-934f49@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 69b6016db937a41c6d364bda55101d76f5564bc6
      https://github.com/ehb54/ultrascan3/commit/69b6016db937a41c6d364bda55101d76f5564bc6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    A admin/pam_auth_helper/README.md
    A admin/pam_auth_helper/pam.d/php-helper
    A admin/pam_auth_helper/pam_auth_helper.c
    A admin/pam_auth_helper/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php


  Commit: 22b88019d6a64a92f89f361f6cfd6737cab591d9
      https://github.com/ehb54/ultrascan3/commit/22b88019d6a64a92f89f361f6cfd6737cab591d9
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    M admin/pam_auth_helper/README.md

  Log Message:
  -----------
  Update README.md


  Commit: e64cf5274f1d7302ca4582ea2e138b08a870e828
      https://github.com/ehb54/ultrascan3/commit/e64cf5274f1d7302ca4582ea2e138b08a870e828
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    A admin/pam_auth_helper/Makefile

  Log Message:
  -----------
  PAM for linux password for php - makefile


  Commit: 56f6b69169ad4e990282f20f3531d347cdca36bf
      https://github.com/ehb54/ultrascan3/commit/56f6b69169ad4e990282f20f3531d347cdca36bf
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    A admin/pam/pam_no_ad/Makefile
    A admin/pam/pam_no_ad/README.md
    A admin/pam/pam_no_ad/files/php
    A admin/pam/pam_no_ad/files/sssd.conf
    R admin/pam_auth_helper/Makefile
    R admin/pam_auth_helper/README.md
    R admin/pam_auth_helper/pam.d/php-helper
    R admin/pam_auth_helper/pam_auth_helper.c
    R admin/pam_auth_helper/pam_auth_test.php

  Log Message:
  -----------
  PAM auth no AD/LDAP, Linux passwords only


  Commit: 5050f341dbde4ea01ba7f0e3aa9862fbb5fbe6b9
      https://github.com/ehb54/ultrascan3/commit/5050f341dbde4ea01ba7f0e3aa9862fbb5fbe6b9
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

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

  Log Message:
  -----------
  Merge pull request #226 from ehb54/master

merge master to issue branch


  Commit: b16f0504f2f4404db161c55323d9df63622854fc
      https://github.com/ehb54/ultrascan3/commit/b16f0504f2f4404db161c55323d9df63622854fc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: bd0a2263e0e3493aaa08624c81fcbd820f172a1d
      https://github.com/ehb54/ultrascan3/commit/bd0a2263e0e3493aaa08624c81fcbd820f172a1d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    A admin/pam/pam_no_ad/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php - pam_auth_test.php


  Commit: 1a4ce194b046f388b13ae0c04a5f361478f90700
      https://github.com/ehb54/ultrascan3/commit/1a4ce194b046f388b13ae0c04a5f361478f90700
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: df89a15dee591af68573b8840c6f78586499c3a3
      https://github.com/ehb54/ultrascan3/commit/df89a15dee591af68573b8840c6f78586499c3a3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php - pam_auth_test.php


  Commit: c65ba3d71581de0a41ee41787e66c4026190dc18
      https://github.com/ehb54/ultrascan3/commit/c65ba3d71581de0a41ee41787e66c4026190dc18
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/Makefile
    A admin/pam/pam_no_ad/files/mariadb
    M admin/pam/pam_no_ad/files/sssd.conf
    A admin/pam/pam_no_ad/files/system-auth-nosss

  Log Message:
  -----------
  pam - updated config


  Commit: 93f3f88fd38b866aad319181f61dc3e4aa8bcfe3
      https://github.com/ehb54/ultrascan3/commit/93f3f88fd38b866aad319181f61dc3e4aa8bcfe3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  pam - updated READEM


  Commit: bb52f3f31f0438cd66c01a5d7e4eb903ce4b37d0
      https://github.com/ehb54/ultrascan3/commit/bb52f3f31f0438cd66c01a5d7e4eb903ce4b37d0
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: 1eb1eb3811ccfad632482d58ed2a9ba6015609a4
      https://github.com/ehb54/ultrascan3/commit/1eb1eb3811ccfad632482d58ed2a9ba6015609a4
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/files/sssd.conf

  Log Message:
  -----------
  remove proxy_fast_switch

sssd.log reports [sssd] [sss_ini_call_validators] (0x0020): [rule/allowed_domain_options]: Attribute 'proxy_fast_switch' is not allowed in section 'domain/local'.


  Commit: 1c7bcff1b439d260af022b29abcf3f0bb17c3983
      https://github.com/ehb54/ultrascan3/commit/1c7bcff1b439d260af022b29abcf3f0bb17c3983
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md
    A admin/pam/pam_no_ad/pam_auth_pamtester.php

  Log Message:
  -----------
  issue496 - pamtester testing


  Commit: 7ce6ebcdb8cbd49311441bf7937aba4fec2bffd6
      https://github.com/ehb54/ultrascan3/commit/7ce6ebcdb8cbd49311441bf7937aba4fec2bffd6
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: 52d2e12f19167416a58de29b71876a11edd2caf6
      https://github.com/ehb54/ultrascan3/commit/52d2e12f19167416a58de29b71876a11edd2caf6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-12 (Fri, 12 Sep 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  GMP | 1. EXP.: 8.Aprofile -- [Add model ID to framework]custom grid implementation...


  Commit: 5c1814ae911784afd312e835594b931008d8bed4
      https://github.com/ehb54/ultrascan3/commit/5c1814ae911784afd312e835594b931008d8bed4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-12 (Fri, 12 Sep 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.: 8.Aprofile -- [Add model ID to framework]custom grid implementation...


  Commit: 4e5d8b4cc07c2a5c5065886cf61e61c76fafffad
      https://github.com/ehb54/ultrascan3/commit/4e5d8b4cc07c2a5c5065886cf61e61c76fafffad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-14 (Sun, 14 Sep 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  [2]GMP | 1. EXP.: 8.Aprofile -- [Add model ID to framework]custom grid implementation...ush


  Commit: 747e42f7732dc906533cbd0cd954e81e3e565d98
      https://github.com/ehb54/ultrascan3/commit/747e42f7732dc906533cbd0cd954e81e3e565d98
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

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

  Log Message:
  -----------
  GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: 0337b97ebfe25072971b60c29b4a2d390667da17
      https://github.com/ehb54/ultrascan3/commit/0337b97ebfe25072971b60c29b4a2d390667da17
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp

  Log Message:
  -----------
  [test1]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: 77987890dfd45f62499deda691795b2e88ed4c26
      https://github.com/ehb54/ultrascan3/commit/77987890dfd45f62499deda691795b2e88ed4c26
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp

  Log Message:
  -----------
  [test2]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: f0d642fb0b9364e641fb3119b5eb5f3d9a70d908
      https://github.com/ehb54/ultrascan3/commit/f0d642fb0b9364e641fb3119b5eb5f3d9a70d908
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

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

  Log Message:
  -----------
  [test4]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: cabec77d85cef315e34c7a7362b56b19524d3972
      https://github.com/ehb54/ultrascan3/commit/cabec77d85cef315e34c7a7362b56b19524d3972
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [test5]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: ffb3fb9dc2da42d44a60eaefd9a678aea956a204
      https://github.com/ehb54/ultrascan3/commit/ffb3fb9dc2da42d44a60eaefd9a678aea956a204
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M gui/us_model_loader.cpp

  Log Message:
  -----------
  [test6]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: 8373d17ba7f453a11426f8935218990b8e317f51
      https://github.com/ehb54/ultrascan3/commit/8373d17ba7f453a11426f8935218990b8e317f51
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [test77]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: d29359d571538fdcdba340546c1ace762f2585f7
      https://github.com/ehb54/ultrascan3/commit/d29359d571538fdcdba340546c1ace762f2585f7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

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

  Log Message:
  -----------
  Add function to check acceleration rate and first scan validity

Introduced `check_acceleration()` in `US_AstfemMath` to validate acceleration rates and detect potential issues with first scan timing. Enhanced error reporting for experiments with low acceleration or scans during acceleration phase. Updated header file accordingly.


  Commit: 00b9132e2f4a788b4b056a3277c0b52a4f0adec4
      https://github.com/ehb54/ultrascan3/commit/00b9132e2f4a788b4b056a3277c0b52a4f0adec4
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp

  Log Message:
  -----------
  Refactor speed step validation logic and integrate `check_acceleration()`

Replaced manual speed step validation with the `check_acceleration()` function from `US_AstfemMath`, improving modularity and error detection. Enhanced message box handling for better user feedback on scan timing and acceleration issues.


  Commit: b3b5449d21badd09a6c72964db5f09a1c6ac22ab
      https://github.com/ehb54/ultrascan3/commit/b3b5449d21badd09a6c72964db5f09a1c6ac22ab
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Replace manual acceleration checks with `check_acceleration()` helper

Streamlined acceleration validation using `US_AstfemMath::check_acceleration()` for improved modularity, reduced code redundancy, and enhanced error handling. Updated message box logic to display detailed user feedback when issues are detected.


  Commit: e7990f3902c576ee20053e446ae508e1d193ef29
      https://github.com/ehb54/ultrascan3/commit/e7990f3902c576ee20053e446ae508e1d193ef29
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Refactor message box logic and integrate updated `check_acceleration()` validation

Simplified acceleration validation by utilizing `US_AstfemMath::check_acceleration()`. Streamlined message box handling to improve readability and user feedback for experiments with acceleration issues.


  Commit: 31e99caf2928581de4943b1119be73a9436d1447
      https://github.com/ehb54/ultrascan3/commit/31e99caf2928581de4943b1119be73a9436d1447
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Remove obsolete low acceleration check and associated UI logic

Eliminated redundant low acceleration validation and message box logic from `us_experiment_gui_optima.cpp`, simplifying the code and improving maintainability.


  Commit: 91d63509d1f79d315225eff1b2d7fb5b6115ecc3
      https://github.com/ehb54/ultrascan3/commit/91d63509d1f79d315225eff1b2d7fb5b6115ecc3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_fematch/us_fematch.cpp

  Log Message:
  -----------
  Replace manual acceleration UI logic with `check_acceleration()` integration

Streamlined acceleration validation by utilizing `US_AstfemMath::check_acceleration()`. Removed redundant manual checks and simplified message box handling for improved user feedback and code maintainability.


  Commit: a460bef08c775745062f6fe891f2893e2002d117
      https://github.com/ehb54/ultrascan3/commit/a460bef08c775745062f6fe891f2893e2002d117
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp

  Log Message:
  -----------
  Replace manual acceleration UI logic with `check_acceleration()` integration

Streamlined acceleration validation by utilizing `US_AstfemMath::check_acceleration()`. Removed redundant manual checks and simplified message box handling for improved user feedback and code maintainability.


  Commit: 009aba4948371da1e6e6f05f46f5a11c092b324c
      https://github.com/ehb54/ultrascan3/commit/009aba4948371da1e6e6f05f46f5a11c092b324c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_reporter_gmp.cpp`

Replaced manual acceleration checks with `US_AstfemMath::check_acceleration()`, streamlining validation and improving error reporting with enhanced message box logic. Removed redundant code for better maintainability.


  Commit: bee67ad94ebbc7c9821dc0aad18e6bce737b4568
      https://github.com/ehb54/ultrascan3/commit/bee67ad94ebbc7c9821dc0aad18e6bce737b4568
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

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

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: 227d32eb57b85946a3d39e4643719738eeddabb5
      https://github.com/ehb54/ultrascan3/commit/227d32eb57b85946a3d39e4643719738eeddabb5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

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

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: fa44532656ec9a8863fe76d5878356f412f827fb
      https://github.com/ehb54/ultrascan3/commit/fa44532656ec9a8863fe76d5878356f412f827fb
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_vhw_enhanced.cpp`

Added validation for acceleration profiles using `US_AstfemMath::check_acceleration()`. Enhanced message box logic for user feedback and streamlined error handling for scan data issues.


  Commit: 3b4ade0ff450252975099029f53fae26589346a6
      https://github.com/ehb54/ultrascan3/commit/3b4ade0ff450252975099029f53fae26589346a6
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_analysis_base2.cpp` in order to add it to us_second_moment, us_dcdt, us_pcsa

Added acceleration validation leveraging `US_AstfemMath::check_acceleration()`. Enhanced message box logic for user feedback and streamlined error handling for scan data issues.


  Commit: 9fb462a87d5cfef990e583e0aa8dda091841052b
      https://github.com/ehb54/ultrascan3/commit/9fb462a87d5cfef990e583e0aa8dda091841052b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_fematch/us_resplot_fem.cpp

  Log Message:
  -----------
  [debug]GMP | 6. REPORT: CG -- ...


  Commit: 42982afb88ddce0d00ece507d399d59735905d72
      https://github.com/ehb54/ultrascan3/commit/42982afb88ddce0d00ece507d399d59735905d72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug1]GMP | 6. REPORT: CG -- ...


  Commit: 493798b230e227ab68985ca50882c28058efd160
      https://github.com/ehb54/ultrascan3/commit/493798b230e227ab68985ca50882c28058efd160
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug2]GMP | 6. REPORT: CG -- ...


  Commit: a468cc16f534c3769ca2b90b209848d226d596fc
      https://github.com/ehb54/ultrascan3/commit/a468cc16f534c3769ca2b90b209848d226d596fc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug3]GMP | 6. REPORT: CG -- ...


  Commit: 35851638d1fc647e0bd2dd3861e329898ac2fec1
      https://github.com/ehb54/ultrascan3/commit/35851638d1fc647e0bd2dd3861e329898ac2fec1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug4]GMP | 6. REPORT: CG -- ...


  Commit: 8de77f30a55f3d955960b24d9fc654f85a643da1
      https://github.com/ehb54/ultrascan3/commit/8de77f30a55f3d955960b24d9fc654f85a643da1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug5]GMP | 6. REPORT: CG -- ...


  Commit: 116f06f0e3cb97e592455a896ea074987b1d687d
      https://github.com/ehb54/ultrascan3/commit/116f06f0e3cb97e592455a896ea074987b1d687d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug5]GMP | 6. REPORT: CG -- ...


  Commit: ada9fc194b6107aa9234582f328928f990f49ab8
      https://github.com/ehb54/ultrascan3/commit/ada9fc194b6107aa9234582f328928f990f49ab8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug7]GMP | 6. REPORT: CG -- ...


  Commit: 32bb4b7a5dc2070311763e159ad64dab3cc648d4
      https://github.com/ehb54/ultrascan3/commit/32bb4b7a5dc2070311763e159ad64dab3cc648d4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Enhance advanced_config documentation with new flags

Added detailed descriptions for various configuration flags related to debugging and speed settings.


  Commit: b52f75b2a6792fda0bab5a3eb02250629eed0b4a
      https://github.com/ehb54/ultrascan3/commit/b52f75b2a6792fda0bab5a3eb02250629eed0b4a
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Update wording

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: 62d4ea94709d6f723457f2bc6436f79c5486ddae
      https://github.com/ehb54/ultrascan3/commit/62d4ea94709d6f723457f2bc6436f79c5486ddae
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Update hsclogo description in advanced_config


  Commit: 803cac4e0551cf55251878109066602030536089
      https://github.com/ehb54/ultrascan3/commit/803cac4e0551cf55251878109066602030536089
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M programs/us_fematch/us_fematch.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_fematch.cpp`

Replaced manual acceleration validation with `US_AstfemMath::check_acceleration()`. Improved error handling and message box logic to provide better user feedback for scan data issues.


  Commit: 6147e952e75e949c7809a98a21beb2107f87e395
      https://github.com/ehb54/ultrascan3/commit/6147e952e75e949c7809a98a21beb2107f87e395
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Clarify `check_acceleration()` documentation for return format and behavior


  Commit: d976a8685de0adc6d272b35cec81016a34e4a38e
      https://github.com/ehb54/ultrascan3/commit/d976a8685de0adc6d272b35cec81016a34e4a38e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

  Log Message:
  -----------
  Refactor `check_acceleration()` logic for improved readability and robustness

Simplified variable naming, added guards for edge cases, and clarified acceleration rate and time checks. Enhanced error messages to provide more detailed user feedback.


  Commit: 6c6ba45b05dacb1c10cf803c959c2b9b4bdbe14c
      https://github.com/ehb54/ultrascan3/commit/6c6ba45b05dacb1c10cf803c959c2b9b4bdbe14c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Fix incorrect dereference of `edata` in `check_acceleration()` call


  Commit: 103683b0b42e6d3ee23a86bb3749b3cc0aa08e11
      https://github.com/ehb54/ultrascan3/commit/103683b0b42e6d3ee23a86bb3749b3cc0aa08e11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Fix incorrect dereference of `edata` in `check_acceleration()` call within `us_reporter_gmp.cpp`


  Commit: 347ef44a538b0dfd5dd64c49aa7d9baecf6f1c03
      https://github.com/ehb54/ultrascan3/commit/347ef44a538b0dfd5dd64c49aa7d9baecf6f1c03
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Merge pull request #263 from ehb54/lukas/debug_text_docs

Document advanced settings debug text values/flags


  Commit: 9d51aa93fbdb6f1a84076e3ddd128210f701d29d
      https://github.com/ehb54/ultrascan3/commit/9d51aa93fbdb6f1a84076e3ddd128210f701d29d
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp

  Log Message:
  -----------
  Refactor speed profile and time state handling in `us_analysis_base2.cpp`

Refactored speed profile processing to improve clarity and maintainability. Added enhanced logic to handle time state files and initialization of simulation parameters. Simplified acceleration checks using `US_AstfemMath::check_acceleration()`.


  Commit: 1f7336dfecb15d81c71c88e6922196f0137c6431
      https://github.com/ehb54/ultrascan3/commit/1f7336dfecb15d81c71c88e6922196f0137c6431
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

  Log Message:
  -----------
  Adjust `kT1Factor` initialization and format specifiers in error messages

Revised `kT1Factor` to use explicit calculation for enhanced clarity. Updated float formatting in error messages from 'g' to 'f' for consistent precision in user feedback.


  Commit: b29fc424db0d4aa7e5e60d830be2fbadb73666e1
      https://github.com/ehb54/ultrascan3/commit/b29fc424db0d4aa7e5e60d830be2fbadb73666e1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp

  Log Message:
  -----------
  Remove manual `check_acceleration()` validation in `us_2dsa.cpp`

Eliminated redundant acceleration validation logic and message box handling. Streamlined by removing unused `US_AstfemMath::check_acceleration()` integration.


  Commit: 626668c35b1cdd774c6ba744a7cd473feb548602
      https://github.com/ehb54/ultrascan3/commit/626668c35b1cdd774c6ba744a7cd473feb548602
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Simplify `check_results` bounds checks in message box handling across programs


  Commit: b21a559ee9e33fed395a785dbaa8f14fe58e9831
      https://github.com/ehb54/ultrascan3/commit/b21a559ee9e33fed395a785dbaa8f14fe58e9831
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp

  Log Message:
  -----------
  Remove unused `check_acceleration` logic and disable `update(0)` call in `us_vhw_enhanced.cpp` to prevent unnecessary update cycle


  Commit: a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
      https://github.com/ehb54/ultrascan3/commit/a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-21 (Sun, 21 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: e49834c3a05a6ffbc730f24be564d3c319a06d2a
      https://github.com/ehb54/ultrascan3/commit/e49834c3a05a6ffbc730f24be564d3c319a06d2a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

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

  Log Message:
  -----------
  Add `calc_omega2t` functionality to `US_AstfemMath` for omega2t calculations

Introduced a new method `calc_omega2t` in `US_AstfemMath` to calculate omega2t values based on speed profiles, acceleration rates, and time parameters. Enhanced flexibility for processing speed step data.


  Commit: 046484c8433d54042b223de7aebd2b793424b6a9
      https://github.com/ehb54/ultrascan3/commit/046484c8433d54042b223de7aebd2b793424b6a9
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Refactor speed step simulation logic in `us_astfem_sim.cpp`

Streamlined speed profile processing by removing redundant legacy logic and incorporating `calc_omega2t` for precise omega2t and time grid calculations. Enhanced clarity and maintainability of simulation loop.


  Commit: 1246e6e3724e8a382585cc65e0208d3008bfbeeb
      https://github.com/ehb54/ultrascan3/commit/1246e6e3724e8a382585cc65e0208d3008bfbeeb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

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

  Log Message:
  -----------
  [1a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5e6c7f858d8e6163099c500c970c02e54801243b
      https://github.com/ehb54/ultrascan3/commit/5e6c7f858d8e6163099c500c970c02e54801243b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
      https://github.com/ehb54/ultrascan3/commit/5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5edb9ce91335769271fb5f593482a97dc4233059
      https://github.com/ehb54/ultrascan3/commit/5edb9ce91335769271fb5f593482a97dc4233059
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [4]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 9aff495b37873080961f8c231a3ce673377f80d3
      https://github.com/ehb54/ultrascan3/commit/9aff495b37873080961f8c231a3ce673377f80d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
      https://github.com/ehb54/ultrascan3/commit/1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 321a8cba345ec3c3f2187e0ba10f28376fd49a3e
      https://github.com/ehb54/ultrascan3/commit/321a8cba345ec3c3f2187e0ba10f28376fd49a3e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [5b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 373ac0ac501856ea0df8f4f579f953d89ec810b0
      https://github.com/ehb54/ultrascan3/commit/373ac0ac501856ea0df8f4f579f953d89ec810b0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [6b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ea3905ba9097c5eed14e034d6656fd0c84dff988
      https://github.com/ehb54/ultrascan3/commit/ea3905ba9097c5eed14e034d6656fd0c84dff988
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [6b-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
      https://github.com/ehb54/ultrascan3/commit/ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [7-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: df769b270aea86fedc2fb0da2875e71741354606
      https://github.com/ehb54/ultrascan3/commit/df769b270aea86fedc2fb0da2875e71741354606
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge pull request #262 from ehb54/lukas/bad-timestate

Bad timestate warnings


  Commit: 021924be498aba94508063128ff7d169d1d6c80c
      https://github.com/ehb54/ultrascan3/commit/021924be498aba94508063128ff7d169d1d6c80c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-23 (Tue, 23 Sep 2025)

  Changed paths:
    M gui/us_model_loader.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  Merge pull request #261 from ehb54/alexey-dev-issue553

Alexey dev issue553: GMP-Custom grid: pass also CG-modelID throught the framework


  Commit: 905f41462ec9dab9667e915d639af2970e21a7a4
      https://github.com/ehb54/ultrascan3/commit/905f41462ec9dab9667e915d639af2970e21a7a4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [proper settings of min/max for scan_beg|nth|end for different optics systems] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 671b8e4d0e4951014a52280942d6a6c9712f14fa
      https://github.com/ehb54/ultrascan3/commit/671b8e4d0e4951014a52280942d6a6c9712f14fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: d584fa48438a0f9d744b750a6abe23533cc48b52
      https://github.com/ehb54/ultrascan3/commit/d584fa48438a0f9d744b750a6abe23533cc48b52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [RESTORE--UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 84f86b86f77bbcd33e113217d09cbda59701b58b
      https://github.com/ehb54/ultrascan3/commit/84f86b86f77bbcd33e113217d09cbda59701b58b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 8ecca10f20a347fd906905b16f8e85ef5afff22a
      https://github.com/ehb54/ultrascan3/commit/8ecca10f20a347fd906905b16f8e85ef5afff22a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: fe9b9031b3af683efa02792cf18ca46a51d376d8
      https://github.com/ehb54/ultrascan3/commit/fe9b9031b3af683efa02792cf18ca46a51d376d8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
      https://github.com/ehb54/ultrascan3/commit/4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: b1ff389cba607cd5f34556fb6945f050ad099ff8
      https://github.com/ehb54/ultrascan3/commit/b1ff389cba607cd5f34556fb6945f050ad099ff8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: b557af349d02a148cef58c38976319f129cf4afa
      https://github.com/ehb54/ultrascan3/commit/b557af349d02a148cef58c38976319f129cf4afa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
      https://github.com/ehb54/ultrascan3/commit/57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
      https://github.com/ehb54/ultrascan3/commit/825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 4f9217705b688c38c3e420a609c2692c23a7e160
      https://github.com/ehb54/ultrascan3/commit/4f9217705b688c38c3e420a609c2692c23a7e160
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [4]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: f8379662ac83a104ca49b29cc3b5a7f830944d05
      https://github.com/ehb54/ultrascan3/commit/f8379662ac83a104ca49b29cc3b5a7f830944d05
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [5]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 036113902d7405af0d641ad3afb98b2010cef02f
      https://github.com/ehb54/ultrascan3/commit/036113902d7405af0d641ad3afb98b2010cef02f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 2e456f0922765ab66ffb5844fc6ef570a37ce431
      https://github.com/ehb54/ultrascan3/commit/2e456f0922765ab66ffb5844fc6ef570a37ce431
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    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

  Log Message:
  -----------
  Merge pull request #225 from ehb54/ehb54-issue-496

PAM for linux password for php


  Commit: 0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
      https://github.com/ehb54/ultrascan3/commit/0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [REstore form -- unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 154500215bfe391bf9dd7fda43456fe170c3c834
      https://github.com/ehb54/ultrascan3/commit/154500215bfe391bf9dd7fda43456fe170c3c834
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

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

  Log Message:
  -----------
  us_grid_editor: update the program GUI to get the cusotm grid from the users


  Commit: 42b30b23222d6e9b070861a382ebe34ad77611ab
      https://github.com/ehb54/ultrascan3/commit/42b30b23222d6e9b070861a382ebe34ad77611ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP | 6. REPORT -- do not display scan exclusion settings Scan section if optics type not used...


  Commit: 9f8fa54c2859fc4a8c4f996ef37443963f0e4ab2
      https://github.com/ehb54/ultrascan3/commit/9f8fa54c2859fc4a8c4f996ef37443963f0e4ab2
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

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

  Log Message:
  -----------
  us_grid_editor: add function to parse a grid file


  Commit: f6b215b4f73633db8bee542cefd88da89761620b
      https://github.com/ehb54/ultrascan3/commit/f6b215b4f73633db8bee542cefd88da89761620b
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_grid_editor/us_grid_editor.cpp

  Log Message:
  -----------
  us_grid_editor: save the user grid model locally and on DB


  Commit: 4ec94c4a344d53369ca022d39c166df3b0859490
      https://github.com/ehb54/ultrascan3/commit/4ec94c4a344d53369ca022d39c166df3b0859490
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-27 (Sat, 27 Sep 2025)

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

  Log Message:
  -----------
  fixed the issue with resetting to the default after pasrsing the CSV file. Refine the functions to reload the model from DB and local drive


  Commit: f286c4ffff8050ccb898b5446f3915031c6b7585
      https://github.com/ehb54/ultrascan3/commit/f286c4ffff8050ccb898b5446f3915031c6b7585
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-27 (Sat, 27 Sep 2025)

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

  Log Message:
  -----------
  Merge pull request #264 from samo38/issue_563

Issue 563: Custom Grid Program


  Commit: e3282fcfa778c046776d3abf2a718a9617230b4d
      https://github.com/ehb54/ultrascan3/commit/e3282fcfa778c046776d3abf2a718a9617230b4d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  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 -- do not specify details on Scan exlusions of there were no any...


  Commit: 8a112ba9e5ae7859d58f117c486f2e52cbba2899
      https://github.com/ehb54/ultrascan3/commit/8a112ba9e5ae7859d58f117c486f2e52cbba2899
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d1287da6bdde6dcb79acc019617ea24b5d93d410
      https://github.com/ehb54/ultrascan3/commit/d1287da6bdde6dcb79acc019617ea24b5d93d410
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    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 gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    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_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge pull request #265 from ehb54/master

add master


  Commit: 8dff3550c25c2827799de8e3f245f1f34a9044ab
      https://github.com/ehb54/ultrascan3/commit/8dff3550c25c2827799de8e3f245f1f34a9044ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

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

  Log Message:
  -----------
  [2]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d927f1c7acffd7436189c83726111d960cbd1e2d
      https://github.com/ehb54/ultrascan3/commit/d927f1c7acffd7436189c83726111d960cbd1e2d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 4c3a97f136b46591a7381b85fb726ea2fb87f7f2
      https://github.com/ehb54/ultrascan3/commit/4c3a97f136b46591a7381b85fb726ea2fb87f7f2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

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

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
      https://github.com/ehb54/ultrascan3/commit/7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 07f7d5c89032aa8dac1c13fe611e51d8e076cfde
      https://github.com/ehb54/ultrascan3/commit/07f7d5c89032aa8dac1c13fe611e51d8e076cfde
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 232008ddbb42fa37d28890542961579241726f13
      https://github.com/ehb54/ultrascan3/commit/232008ddbb42fa37d28890542961579241726f13
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 003fcead31be5da3e4a5744bd8b5a9a3adb9686d
      https://github.com/ehb54/ultrascan3/commit/003fcead31be5da3e4a5744bd8b5a9a3adb9686d
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  Merge pull request #267 from ehb54/alexey-dev-issue556

Alexey dev issue556: Scan Exclusion Profile Editor for AProfile in GMP #556


  Commit: 9b2e06a5e4a371044a913065222c7d91603e0085
      https://github.com/ehb54/ultrascan3/commit/9b2e06a5e4a371044a913065222c7d91603e0085
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intargal -- avoid loading editProfiles...


  Commit: abfa96706807a26b5b0642ed078a97acf01a3e18
      https://github.com/ehb54/ultrascan3/commit/abfa96706807a26b5b0642ed078a97acf01a3e18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intergal -- restore editProfiles read; add debugs...


  Commit: d712bbbb0ceb306e036f428d4245c0e3b87c097b
      https://github.com/ehb54/ultrascan3/commit/d712bbbb0ceb306e036f428d4245c0e3b87c097b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [1]US_intergal -- restore editProfiles read; add debugs...


  Commit: 088595bbbb4e35e890cb8d2bf308945e0333f3f1
      https://github.com/ehb54/ultrascan3/commit/088595bbbb4e35e890cb8d2bf308945e0333f3f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [2]US_intergal -- restore editProfiles read; add debugs...


  Commit: 15343601bc0774d196184c33adbddefab8430a11
      https://github.com/ehb54/ultrascan3/commit/15343601bc0774d196184c33adbddefab8430a11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [3]US_intergal -- create curves' labels from the model's desc...


  Commit: d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
      https://github.com/ehb54/ultrascan3/commit/d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  Merge pull request #268 from ehb54/alexey-dev-issue562

Alexey dev issue562: Enable plotting CG-SG integral distr.


  Commit: 934f494e4683d95677c5a7051705426df529cf13
      https://github.com/ehb54/ultrascan3/commit/934f494e4683d95677c5a7051705426df529cf13
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-08 (Wed, 08 Oct 2025)

  Changed paths:
    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 doc/manual/advanced_config.body
    M gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.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_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    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_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


Compare: https://github.com/ehb54/ultrascan3/compare/8b4d2dc93db3...934f494e4683

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From noreply at github.com  Wed Oct  8 16:57:30 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 08 Oct 2025 15:57:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] af1a5c: Additional Unit Testing
 us_ana_profile, us_crc, us...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/d62e7b-4e54cb@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af1a5c8bc4252ae4bf9c3467711811c2f536d72f
      https://github.com/ehb54/ultrascan3/commit/af1a5c8bc4252ae4bf9c3467711811c2f536d72f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    A test/utils/test_us_ana_profile.cpp
    A test/utils/test_us_ana_profile.h
    A test/utils/test_us_crc.cpp
    A test/utils/test_us_crc.h
    A test/utils/test_us_crypto.cpp
    A test/utils/test_us_crypto.h
    A test/utils/test_us_dataIO.cpp
    A test/utils/test_us_dataIO.h
    A test/utils/test_us_math2.cpp
    A test/utils/test_us_math2.h
    A test/utils/test_us_matrix.cpp
    A test/utils/test_us_matrix.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Additional Unit Testing us_ana_profile, us_crc, us_crypto, us_dataio, us_math2, and us_matrix.


  Commit: 1408abf68cb2d299a8ad20905a1898d9f12c0958
      https://github.com/ehb54/ultrascan3/commit/1408abf68cb2d299a8ad20905a1898d9f12c0958
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    A test/utils/test_us_simparms.cpp
    A test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Tests pass locally except for TestUSMath2::test_linefit() and TestUSAnaProfile::testEqualityOperator() which have issues submitted to resolve.


  Commit: f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
      https://github.com/ehb54/ultrascan3/commit/f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_memory.cpp
    A test/utils/test_us_memory.h
    A test/utils/test_us_settings.cpp
    A test/utils/test_us_settings.h
    A test/utils/test_us_time_state.cpp
    A test/utils/test_us_time_state.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_memory, us_settings, and us_time_state


  Commit: 4abb61bbcc128d9293b4ff30674448f285671ab1
      https://github.com/ehb54/ultrascan3/commit/4abb61bbcc128d9293b4ff30674448f285671ab1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_analyte.cpp
    A test/utils/test_us_analyte.h
    A test/utils/test_us_db2.cpp
    A test/utils/test_us_db2.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_analyte and us_db2


  Commit: e9390c59f666fcc05efbd47251b28fe67c3e0b91
      https://github.com/ehb54/ultrascan3/commit/e9390c59f666fcc05efbd47251b28fe67c3e0b91
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_math.cpp
    A test/utils/test_us_astfem_math.h
    A test/utils/test_us_project.cpp
    A test/utils/test_us_project.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_math and us_project


  Commit: a9e23b7e83f8210188d4489c503430d9c26f97ee
      https://github.com/ehb54/ultrascan3/commit/a9e23b7e83f8210188d4489c503430d9c26f97ee
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    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_mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    A test/utils/test_us_project_gtest.cpp
    A test/utils/test_us_project_gtest.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Add gtest


  Commit: eaf6180d144d0c86dc4caec50879155740cc76e3
      https://github.com/ehb54/ultrascan3/commit/eaf6180d144d0c86dc4caec50879155740cc76e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_rsa.cpp
    A test/utils/test_us_astfem_rsa.h
    A test/utils/test_us_model.cpp
    A test/utils/test_us_model.h
    A test/utils/test_us_stiffbase.cpp
    A test/utils/test_us_stiffbase.h
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_rsa, us_model, and us_stiffbase


  Commit: 824605af8d275da7234b0a9d7f3672a8c001ea43
      https://github.com/ehb54/ultrascan3/commit/824605af8d275da7234b0a9d7f3672a8c001ea43
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_project_gtest.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Rebase merge


  Commit: 60e801e42c2edfe91afb422f4031c95eaae2d4da
      https://github.com/ehb54/ultrascan3/commit/60e801e42c2edfe91afb422f4031c95eaae2d4da
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A admin/codeql/custom-queries/cpp/codeql-pack.yml
    M admin/codeql/custom-queries/cpp/find-unused-functions.ql

  Log Message:
  -----------
  Update codeql custom query


  Commit: 7b370a88e30b380b1e40382cecb82aa1310eba3f
      https://github.com/ehb54/ultrascan3/commit/7b370a88e30b380b1e40382cecb82aa1310eba3f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A test/utils/test_us_buffer.cpp
    M test/utils/test_us_datafiles.cpp

  Log Message:
  -----------
  Add test_us_buffer.cpp


  Commit: 363e32b18e6f47106c9dd75c7f1793511472a3b0
      https://github.com/ehb54/ultrascan3/commit/363e32b18e6f47106c9dd75c7f1793511472a3b0
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  Add apt-get install libmysqlclient-dev


  Commit: 77a89e083d64e4c862e61b9716a1e7d1f1892df4
      https://github.com/ehb54/ultrascan3/commit/77a89e083d64e4c862e61b9716a1e7d1f1892df4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update to find mysql during build


  Commit: 69b88e6a47d8369f97892eddcbfa839473ce9120
      https://github.com/ehb54/ultrascan3/commit/69b88e6a47d8369f97892eddcbfa839473ce9120
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h

  Log Message:
  -----------
  removed query test


  Commit: 3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
      https://github.com/ehb54/ultrascan3/commit/3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  run specific test


  Commit: d84cc16735556c0d8fb706bc768a6a4dc10db9a8
      https://github.com/ehb54/ultrascan3/commit/d84cc16735556c0d8fb706bc768a6a4dc10db9a8
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-03 (Tue, 03 Sep 2024)

  Changed paths:
    M test/utils/test_us_math2.cpp

  Log Message:
  -----------
  test_us_math2 was updated after sigma calculation was verified.


  Commit: 6276beb67d5181eba36861791acef5e415723e89
      https://github.com/ehb54/ultrascan3/commit/6276beb67d5181eba36861791acef5e415723e89
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-06-29 (Sun, 29 Jun 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A CITATION.cff
    M CMakeLists.txt
    M LICENSE.txt
    M admin/codeql/docker/docker/Dockerfile
    M admin/codeql/docker/dockerdev/Dockerfile
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    A admin/release/ubuntu/mathops.h
    M admin/release/ubuntu_qt6/Dockerfile
    A admin/us_branch/README.md
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php
    M alpha/us.cpp
    A doc/calc_model_coefficient_documentation.pdf
    A doc/calc_timestate_documentation.pdf
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    R doc/manual/2dsa_advan.body
    R doc/manual/2dsa_analvv.body
    R doc/manual/2dsa_analys.body
    M doc/manual/Makefile
    M doc/manual/README
    M doc/manual/advanced_config.body
    M doc/manual/astfem_sim.body
    M doc/manual/cfa_viewer.body
    M doc/manual/colorgradient.body
    M doc/manual/config.body
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    R doc/manual/experiment_rotor.body
    R doc/manual/experiment_solutions.body
    R doc/manual/experiment_speeds.body
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    R doc/manual/load_noise_details.body
    M doc/manual/mainstyle.css
    M doc/manual/make-html.sh
    M doc/manual/make-wraps.sh
    M doc/manual/manage_data.body
    M doc/manual/manage_data_cmenu.body
    M doc/manual/manage_data_thelp.body
    M doc/manual/manual.qhp
    M doc/manual/mwlr_view_load.body
    M doc/manual/mwlr_viewer.body
    M doc/manual/pcsa.body
    M doc/manual/pcsa_analys.body
    M doc/manual/pcsa_mlines.body
    M doc/manual/pcsa_rpscan.body
    M doc/manual/pseudo3d_combine.body
    M doc/manual/register.body
    M doc/manual/reporter.body
    A doc/manual/sassoc.body
    M doc/manual/second_moment.body
    M doc/manual/simparams.body
    A doc/manual/somo.body
    M doc/manual/time_derivative.body
    M doc/manual/ultrascan3.txt
    M doc/manual/us_edit.body
    M doc/manual/us_edit_mwl.body
    M doc/manual/us_fds_filemanager.body
    M doc/manual/uscolor2.body
    M doc/manual/vhw_combine.body
    M doc/manual/vhw_distrib_plot.body
    M doc/manual/vhw_enhanced.body
    M gui/images.qrc
    A gui/images/table.png
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_gui_util.cpp
    M gui/us_gui_util.h
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_license.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_rotor_gui.cpp
    M gui/us_rotor_gui.h
    M gui/us_run_details2.cpp
    M gui/us_run_details2.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M library.pri
    M makeall.sh
    M programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.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_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.h
    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_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_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project.pro
    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/us_com_project_academic.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_database.h
    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_experiment.cpp
    M programs/us_convert/us_get_run.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_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    R programs/us_esigner_gmp_aux/us_esigner_gmp.pro
    R programs/us_esigner_gmp_aux/us_esigner_gmp_main.cpp
    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/us_fematch.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.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_tree.cpp
    M programs/us_manage_data/us_data_tree.h
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.h
    R programs/us_mwl_db_query/us_mwl_db_query.pro
    R programs/us_mwl_db_query/us_mwl_pltctrl.cpp
    R programs/us_mwl_db_query/us_mwl_pltctrl.h
    R programs/us_mwl_db_query/us_mwl_run.cpp
    R programs/us_mwl_db_query/us_mwl_run.h
    R programs/us_mwl_db_query/us_mwlr_viewer.cpp
    R programs/us_mwl_db_query/us_mwlr_viewer.h
    M programs/us_mwl_species_fit/us_load_run_noise.cpp
    M programs/us_mwl_species_fit/us_load_run_noise.h
    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_fit/us_mwl_species_fit.pro
    A programs/us_mwl_species_fit/us_mwl_species_fit_main.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    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_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_query_rmsd/us_query_rmsd.pro
    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_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M test/utils/CMakeLists.txt
    A test/utils/test_us_simparams.cpp
    A test/utils/test_us_simparams.h
    M test/utils/test_us_utils_main.cpp
    M us_somo/attic/INSTALL
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_util.cpp
    M us_somo/extra/haddock/bin_i73/mpi/runjob
    M us_somo/somo/doc/manual/somo/IntegralBaselineTheory.html
    M us_somo/somo/doc/manual/somo/baseline_best.html
    M us_somo/somo/doc/manual/somo/copyright.html
    M us_somo/somo/doc/manual/somo/cormap.html
    M us_somo/somo/doc/manual/somo/dad_parameters.html
    M us_somo/somo/doc/manual/somo/fractal_dimension_options.html
    M us_somo/somo/doc/manual/somo/mals_options.html
    M us_somo/somo/doc/manual/somo/mals_parameters.html
    M us_somo/somo/doc/manual/somo/mals_saxs_options.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_Gaussian_theory.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_ciq.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_conc_csv_frames.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_dctr.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_nth.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_options.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_p3d.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_parameters.html
    M us_somo/somo/doc/manual/somo/saxs_ift.html
    M us_somo/somo/doc/manual/somo/somo.html
    M us_somo/somo/doc/manual/somo/somo_BEST_Analysis.html
    M us_somo/somo/doc/manual/somo/somo_BEST_setup.html
    M us_somo/somo/doc/manual/somo/somo_Dammin_Dammif_bead_model_properties.html
    M us_somo/somo/doc/manual/somo/somo_SAXS_search.html
    M us_somo/somo/doc/manual/somo/somo_add_saxs.html
    M us_somo/somo/doc/manual/somo/somo_addatom.html
    M us_somo/somo/doc/manual/somo/somo_addhybridization.html
    M us_somo/somo/doc/manual/somo/somo_advanced_config.html
    M us_somo/somo/doc/manual/somo/somo_anaflex_options.html
    M us_somo/somo/doc/manual/somo/somo_asa.html
    M us_somo/somo/doc/manual/somo/somo_batch.html
    M us_somo/somo/doc/manual/somo/somo_bd_options.html
    M us_somo/somo/doc/manual/somo/somo_bead_model_format.html
    M us_somo/somo/doc/manual/somo/somo_bead_output.html
    M us_somo/somo/doc/manual/somo/somo_cluster.html
    M us_somo/somo/doc/manual/somo/somo_cluster_advanced_options.html
    M us_somo/somo/doc/manual/somo/somo_cluster_config.html
    M us_somo/somo/doc/manual/somo/somo_cluster_dmd.html
    M us_somo/somo/doc/manual/somo/somo_cluster_results.html
    M us_somo/somo/doc/manual/somo/somo_cluster_status.html
    M us_somo/somo/doc/manual/somo/somo_cluster_submit.html
    M us_somo/somo/doc/manual/somo/somo_comparative.html
    M us_somo/somo/doc/manual/somo/somo_dammin_opts.html
    M us_somo/somo/doc/manual/somo/somo_dmd_options.html
    M us_somo/somo/doc/manual/somo/somo_file.html
    M us_somo/somo/doc/manual/somo/somo_grid.html
    M us_somo/somo/doc/manual/somo/somo_grid_overlap.html
    M us_somo/somo/doc/manual/somo/somo_hydro.html
    M us_somo/somo/doc/manual/somo/somo_hydro_expert_mode.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html_old
    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_misc.html
    M us_somo/somo/doc/manual/somo/somo_overlap.html
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    M us_somo/somo/doc/manual/somo/somo_pdb_visualization.html
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    M us_somo/somo/doc/manual/somo/somo_results.html
    M us_somo/somo/doc/manual/somo/somo_save.html
    M us_somo/somo/doc/manual/somo/somo_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_buffer.html
    M us_somo/somo/doc/manual/somo/somo_saxs_conc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_baseline_corr.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_fit.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_linear_baselines.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_movie.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_skewedGauss.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_svd.html
    M us_somo/somo/doc/manual/somo/somo_saxs_iqq_residuals.html
    M us_somo/somo/doc/manual/somo/somo_saxs_load_csv.html
    M us_somo/somo/doc/manual/somo/somo_saxs_mw.html
    M us_somo/somo/doc/manual/somo/somo_saxs_options.html
    M us_somo/somo/doc/manual/somo/somo_saxs_residuals.html
    M us_somo/somo/doc/manual/somo/somo_show_hydro.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html
    M us_somo/somo/doc/manual/somo/somo_vdw_overlap.html
    M us_somo/somo/doc/manual/somo/underconstruction.html
    M us_somo/somo/doc/manual/somo/uv_vis_options.html
    M utils/CMakeLists.txt
    R utils/calc_coefficient_documentation.pdf
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    A utils/us_archive.cpp
    A utils/us_archive.h
    M utils/us_astfem_math.cpp
    A utils/us_csv_data.cpp
    A utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_geturl.h
    M utils/us_hydrosim.cpp
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_math2.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_report_gmp.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	CMakeLists.txt
#	test/utils/CMakeLists.txt
#	test/utils/test_us_utils_main.cpp
#	utils/CMakeLists.txt


  Commit: a423656c7a4997ae177e5406c7b8f846d5cda459
      https://github.com/ehb54/ultrascan3/commit/a423656c7a4997ae177e5406c7b8f846d5cda459
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-01 (Tue, 01 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/test/docker/Dockerfile
    A test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    M test/utils/test_mock_us_db2.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_project.h
    R test/utils/test_us_project_gtest.cpp
    R test/utils/test_us_project_gtest.h
    R test/utils/test_us_simparams.cpp
    R test/utils/test_us_simparams.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_project.cpp
    M utils/us_project.h

  Log Message:
  -----------
  dependency injection, docker, and remove duplicates


  Commit: b10a7ddbde27cb31ff6ce03fac85921856c2c90f
      https://github.com/ehb54/ultrascan3/commit/b10a7ddbde27cb31ff6ce03fac85921856c2c90f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_math.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    M test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_memory.h
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_dataIO.h

  Log Message:
  -----------
  convert qtests to google tests


  Commit: 54099cb2ff6ed13d069418492a1d7c6430277fb4
      https://github.com/ehb54/ultrascan3/commit/54099cb2ff6ed13d069418492a1d7c6430277fb4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

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

  Log Message:
  -----------
  remove specific test logic


  Commit: 5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
      https://github.com/ehb54/ultrascan3/commit/5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  test failing test


  Commit: 29b485c94b6bfd0e1f7be5ca07da8449cefe8081
      https://github.com/ehb54/ultrascan3/commit/29b485c94b6bfd0e1f7be5ca07da8449cefe8081
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  disabled failing test


  Commit: 9f15926c85f745d67b489772eb640400a916ad92
      https://github.com/ehb54/ultrascan3/commit/9f15926c85f745d67b489772eb640400a916ad92
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-05 (Sat, 05 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/README.md

  Log Message:
  -----------
  fixed comment, added readme


  Commit: 3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
      https://github.com/ehb54/ultrascan3/commit/3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis


  Commit: a9025670cc855940cf159141a10a5e0648312794
      https://github.com/ehb54/ultrascan3/commit/a9025670cc855940cf159141a10a5e0648312794
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis removed sudo


  Commit: bbdf69b0fef6c0be255ef3bdecfba8597797c668
      https://github.com/ehb54/ultrascan3/commit/bbdf69b0fef6c0be255ef3bdecfba8597797c668
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  moved static analysis to separate file


  Commit: d208f8e88de47207cc309f9b9e25483681973e03
      https://github.com/ehb54/ultrascan3/commit/d208f8e88de47207cc309f9b9e25483681973e03
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  fix iwyu


  Commit: 3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
      https://github.com/ehb54/ultrascan3/commit/3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    R doc/manual/README
    A doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
      https://github.com/ehb54/ultrascan3/commit/cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M test/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: a65be797990b6aa12a17b160b052482c930fb9ce
      https://github.com/ehb54/ultrascan3/commit/a65be797990b6aa12a17b160b052482c930fb9ce
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: 0ce7f8bbe5702044fddc573c6c7ea2002b72510d
      https://github.com/ehb54/ultrascan3/commit/0ce7f8bbe5702044fddc573c6c7ea2002b72510d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-13 (Sun, 13 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M test-docker.sh
    M test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    R test/utils/test_mock_us_db2.h
    M test/utils/test_us_ana_profile.cpp
    R test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    R test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_math.h
    M test/utils/test_us_astfem_rsa.cpp
    R test/utils/test_us_astfem_rsa.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    R test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    R test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    R test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    R test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    R test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    R test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    R test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    R test/utils/test_us_memory.h
    M test/utils/test_us_model.cpp
    R test/utils/test_us_model.h
    M test/utils/test_us_project.cpp
    R test/utils/test_us_project.h
    M test/utils/test_us_settings.cpp
    R test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    R test/utils/test_us_simparms.h
    M test/utils/test_us_stiffbase.cpp
    R test/utils/test_us_stiffbase.h
    M test/utils/test_us_time_state.cpp
    R test/utils/test_us_time_state.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    M utils/us_analyte.cpp
    M utils/us_analyte.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_dataIO.cpp
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_rotor.cpp
    M utils/us_rotor.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_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  ius_db2 build


  Commit: 76e2cf6ae4e764993cbd9d37d1bd086413514e3d
      https://github.com/ehb54/ultrascan3/commit/76e2cf6ae4e764993cbd9d37d1bd086413514e3d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .gitignore
    M test-docker.sh
    A test/README
    R test/README.md
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_model.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_stiffbase.cpp
    M test/utils/test_us_time_state.cpp
    M test/utils/test_us_util.cpp

  Log Message:
  -----------
  working set of util unit tests


  Commit: 3a4240895ec21be113a64f6d852aa70cdc0f9455
      https://github.com/ehb54/ultrascan3/commit/3a4240895ec21be113a64f6d852aa70cdc0f9455
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_tmst_plot.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	utils/us_simparms.cpp


  Commit: eb5398d2831269197d566f36400b5f80c87ac2b1
      https://github.com/ehb54/ultrascan3/commit/eb5398d2831269197d566f36400b5f80c87ac2b1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.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/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_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_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_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/us_model.cpp
    M utils/us_model.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 6c17ff96ca055f6cc43eeb2532d0eceab53580b3
      https://github.com/ehb54/ultrascan3/commit/6c17ff96ca055f6cc43eeb2532d0eceab53580b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_solution.cpp

  Log Message:
  -----------
  set to lowercase ius_db2.h


  Commit: 483c6d095b00b75710d4feeb2d9b996f0a4bd213
      https://github.com/ehb54/ultrascan3/commit/483c6d095b00b75710d4feeb2d9b996f0a4bd213
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M test-docker.sh

  Log Message:
  -----------
  add cmake hint file


  Commit: 76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
      https://github.com/ehb54/ultrascan3/commit/76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_simparms.cpp

  Log Message:
  -----------
  iusdb changes


  Commit: 295b4c9f222964264a4f4f2c9890d5b9f9d61f24
      https://github.com/ehb54/ultrascan3/commit/295b4c9f222964264a4f4f2c9890d5b9f9d61f24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M utils/ius_db2.h

  Log Message:
  -----------
  iusdb add qstring constuctor, turn off static analysis, move safe directory config


  Commit: 4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
      https://github.com/ehb54/ultrascan3/commit/4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

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

  Log Message:
  -----------
  error in gui build related to iusdb2


  Commit: 217485a90c5e92e0e810e5e3dfe2dac0177b8b35
      https://github.com/ehb54/ultrascan3/commit/217485a90c5e92e0e810e5e3dfe2dac0177b8b35
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    R admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakelists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_convert/us_select_triples.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
    A programs/us_experiment/CMakeLists.txt
    A programs/us_fematch/CMakeLists.txt
    A programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_pcsa/us_pcsa.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    A programs/us_query_rmsd/CMakeLists.txt
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_db2.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  error in build related to iusdb2, cmake build for programs, and working unit tests


  Commit: 8401655782f10eb593ea8537ea59378e3da8f03b
      https://github.com/ehb54/ultrascan3/commit/8401655782f10eb593ea8537ea59378e3da8f03b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  move unit tests trigger to separate file


  Commit: 73021e71e98437f3583fc6edcaf0fe2faf72d5fd
      https://github.com/ehb54/ultrascan3/commit/73021e71e98437f3583fc6edcaf0fe2faf72d5fd
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M programs/us_com_project/CMakelists.txt
    A qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  add us_com_project cmakelists


  Commit: c9030ec25f5d2ce4547c140beaf0d06baa785f4a
      https://github.com/ehb54/ultrascan3/commit/c9030ec25f5d2ce4547c140beaf0d06baa785f4a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    A programs/us_com_project/CMakeLists.txt
    R programs/us_com_project/CMakelists.txt

  Log Message:
  -----------
  fix us_com_project cmakelists had lowercase l in name


  Commit: 7edcb7cb1815454a3c1517671b8f46ba157b7fd5
      https://github.com/ehb54/ultrascan3/commit/7edcb7cb1815454a3c1517671b8f46ba157b7fd5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml should not run and not send email


  Commit: a414cfc8f6a9b899f987a41925b89b2a948b954a
      https://github.com/ehb54/ultrascan3/commit/a414cfc8f6a9b899f987a41925b89b2a948b954a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml running but non-failing


  Commit: 09d7e2075e6ba517445079e50e2410866d36ef05
      https://github.com/ehb54/ultrascan3/commit/09d7e2075e6ba517445079e50e2410866d36ef05
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml install libqwt-qt5-dev


  Commit: 6014d3b78be1f58f196982b8e963eb9a1fd10650
      https://github.com/ehb54/ultrascan3/commit/6014d3b78be1f58f196982b8e963eb9a1fd10650
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 86802e7c8b63d5dafae200d92ab4edd449a76122
      https://github.com/ehb54/ultrascan3/commit/86802e7c8b63d5dafae200d92ab4edd449a76122
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 1c1fe3aebbc7885934e26733499fdc6e3443cd25
      https://github.com/ehb54/ultrascan3/commit/1c1fe3aebbc7885934e26733499fdc6e3443cd25
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml remove format check


  Commit: 545dd0c591ceb5f40b85403fe9d72a8dc2079608
      https://github.com/ehb54/ultrascan3/commit/545dd0c591ceb5f40b85403fe9d72a8dc2079608
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml only check changed files


  Commit: ff38446e4155e613f61b9ccfdadc5141796dba1d
      https://github.com/ehb54/ultrascan3/commit/ff38446e4155e613f61b9ccfdadc5141796dba1d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: 44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
      https://github.com/ehb54/ultrascan3/commit/44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
      https://github.com/ehb54/ultrascan3/commit/ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  mod workflow triggers to push or pr on master only


  Commit: 42e26337f0dd52027b91e41ba3af0f9e1b626a24
      https://github.com/ehb54/ultrascan3/commit/42e26337f0dd52027b91e41ba3af0f9e1b626a24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .gitignore
    R admin/codeql/custom-queries/cpp/codeql-pack.yml
    R admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_model_editor.cpp
    R gui/us_model_editor.h
    M gui/us_model_gui.cpp
    M gui/us_model_loader.h
    M gui/us_noise_loader.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_edit/us_edit.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  code cleanup before PR review


  Commit: 895bcceea66cf95608da4f456620659d8e9517d5
      https://github.com/ehb54/ultrascan3/commit/895bcceea66cf95608da4f456620659d8e9517d5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #260 from ehb54/master

commit update


  Commit: 19e27c3ec7093c10f143441101c85d0af09b12ac
      https://github.com/ehb54/ultrascan3/commit/19e27c3ec7093c10f143441101c85d0af09b12ac
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: better reporting of critical issues


  Commit: 3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
      https://github.com/ehb54/ultrascan3/commit/3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/aaron-dev-test-utils' into aaron-dev-test-utils


  Commit: eaf7d5bc8dae71e71e890cbec10deb318fe0862c
      https://github.com/ehb54/ultrascan3/commit/eaf7d5bc8dae71e71e890cbec10deb318fe0862c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: artifact upload fix


  Commit: f04888d7116e9c5498dd5a316307e9f4dc238d40
      https://github.com/ehb54/ultrascan3/commit/f04888d7116e9c5498dd5a316307e9f4dc238d40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

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

  Log Message:
  -----------
  fix: critical static analysis only


  Commit: d9ed24af5742fb54910d7c1d9873b57c528b4661
      https://github.com/ehb54/ultrascan3/commit/d9ed24af5742fb54910d7c1d9873b57c528b4661
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/FindQwt.cmake
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/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
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_settings.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: address review comments


  Commit: dd3e9be9669f28156c33235c7e73db3040c614a5
      https://github.com/ehb54/ultrascan3/commit/dd3e9be9669f28156c33235c7e73db3040c614a5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: 93c11d987df52db6a1d9484f4f49a7acb54bd4dc
      https://github.com/ehb54/ultrascan3/commit/93c11d987df52db6a1d9484f4f49a7acb54bd4dc
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: ea99232fad84d9c9e2e785ee18794694bb22b883
      https://github.com/ehb54/ultrascan3/commit/ea99232fad84d9c9e2e785ee18794694bb22b883
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Update utils/CMakeLists.txt

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


  Commit: a1344544e53b2158a855ac3ddb3296bbb15d21e0
      https://github.com/ehb54/ultrascan3/commit/a1344544e53b2158a855ac3ddb3296bbb15d21e0
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Update gui/CMakeLists.txt

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


  Commit: 6115f78b236f317ecc7ce852c9541d8ac10084e4
      https://github.com/ehb54/ultrascan3/commit/6115f78b236f317ecc7ce852c9541d8ac10084e4
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  Update test/utils/CMakeLists.txt

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


  Commit: e87ab944bf93815dda5842e3dadee3249c11a52c
      https://github.com/ehb54/ultrascan3/commit/e87ab944bf93815dda5842e3dadee3249c11a52c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_vector.cpp

  Log Message:
  -----------
  fix: cmake collision during build


  Commit: 4a401e5be566119b5510674930f3b4365211a052
      https://github.com/ehb54/ultrascan3/commit/4a401e5be566119b5510674930f3b4365211a052
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  fix: add QWT to us_program_common


  Commit: 3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
      https://github.com/ehb54/ultrascan3/commit/3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  fix: duplicate include removed


  Commit: 8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
      https://github.com/ehb54/ultrascan3/commit/8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-07 (Tue, 07 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_rsa.cpp

  Log Message:
  -----------
  Consolidated commit after cleanup


  Commit: 934f494e4683d95677c5a7051705426df529cf13
      https://github.com/ehb54/ultrascan3/commit/934f494e4683d95677c5a7051705426df529cf13
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-08 (Wed, 08 Oct 2025)

  Changed paths:
    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 doc/manual/advanced_config.body
    M gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.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_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    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_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 4e54cb0bd0e5eda0aebea648780b89b67b47d482
      https://github.com/ehb54/ultrascan3/commit/4e54cb0bd0e5eda0aebea648780b89b67b47d482
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #234 from ehb54/aaron-dev-test-utils

Add: google mock framework, static code analysis


Compare: https://github.com/ehb54/ultrascan3/compare/d62e7b57ef0e...4e54cb0bd0e5

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From noreply at github.com  Wed Oct  8 16:57:39 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 08 Oct 2025 15:57:39 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/934f49-000000@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Oct  8 17:00:30 2025
From: noreply at github.com (alexsav815)
Date: Wed, 08 Oct 2025 16:00:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] af1a5c: Additional Unit Testing
 us_ana_profile, us_crc, us...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/d3528c-6dc675@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af1a5c8bc4252ae4bf9c3467711811c2f536d72f
      https://github.com/ehb54/ultrascan3/commit/af1a5c8bc4252ae4bf9c3467711811c2f536d72f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    A test/utils/test_us_ana_profile.cpp
    A test/utils/test_us_ana_profile.h
    A test/utils/test_us_crc.cpp
    A test/utils/test_us_crc.h
    A test/utils/test_us_crypto.cpp
    A test/utils/test_us_crypto.h
    A test/utils/test_us_dataIO.cpp
    A test/utils/test_us_dataIO.h
    A test/utils/test_us_math2.cpp
    A test/utils/test_us_math2.h
    A test/utils/test_us_matrix.cpp
    A test/utils/test_us_matrix.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Additional Unit Testing us_ana_profile, us_crc, us_crypto, us_dataio, us_math2, and us_matrix.


  Commit: 1408abf68cb2d299a8ad20905a1898d9f12c0958
      https://github.com/ehb54/ultrascan3/commit/1408abf68cb2d299a8ad20905a1898d9f12c0958
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    A test/utils/test_us_simparms.cpp
    A test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Tests pass locally except for TestUSMath2::test_linefit() and TestUSAnaProfile::testEqualityOperator() which have issues submitted to resolve.


  Commit: f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
      https://github.com/ehb54/ultrascan3/commit/f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_memory.cpp
    A test/utils/test_us_memory.h
    A test/utils/test_us_settings.cpp
    A test/utils/test_us_settings.h
    A test/utils/test_us_time_state.cpp
    A test/utils/test_us_time_state.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_memory, us_settings, and us_time_state


  Commit: 4abb61bbcc128d9293b4ff30674448f285671ab1
      https://github.com/ehb54/ultrascan3/commit/4abb61bbcc128d9293b4ff30674448f285671ab1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_analyte.cpp
    A test/utils/test_us_analyte.h
    A test/utils/test_us_db2.cpp
    A test/utils/test_us_db2.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_analyte and us_db2


  Commit: e9390c59f666fcc05efbd47251b28fe67c3e0b91
      https://github.com/ehb54/ultrascan3/commit/e9390c59f666fcc05efbd47251b28fe67c3e0b91
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_math.cpp
    A test/utils/test_us_astfem_math.h
    A test/utils/test_us_project.cpp
    A test/utils/test_us_project.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_math and us_project


  Commit: a9e23b7e83f8210188d4489c503430d9c26f97ee
      https://github.com/ehb54/ultrascan3/commit/a9e23b7e83f8210188d4489c503430d9c26f97ee
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    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_mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    A test/utils/test_us_project_gtest.cpp
    A test/utils/test_us_project_gtest.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Add gtest


  Commit: eaf6180d144d0c86dc4caec50879155740cc76e3
      https://github.com/ehb54/ultrascan3/commit/eaf6180d144d0c86dc4caec50879155740cc76e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_rsa.cpp
    A test/utils/test_us_astfem_rsa.h
    A test/utils/test_us_model.cpp
    A test/utils/test_us_model.h
    A test/utils/test_us_stiffbase.cpp
    A test/utils/test_us_stiffbase.h
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_rsa, us_model, and us_stiffbase


  Commit: 824605af8d275da7234b0a9d7f3672a8c001ea43
      https://github.com/ehb54/ultrascan3/commit/824605af8d275da7234b0a9d7f3672a8c001ea43
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_project_gtest.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Rebase merge


  Commit: 60e801e42c2edfe91afb422f4031c95eaae2d4da
      https://github.com/ehb54/ultrascan3/commit/60e801e42c2edfe91afb422f4031c95eaae2d4da
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A admin/codeql/custom-queries/cpp/codeql-pack.yml
    M admin/codeql/custom-queries/cpp/find-unused-functions.ql

  Log Message:
  -----------
  Update codeql custom query


  Commit: 7b370a88e30b380b1e40382cecb82aa1310eba3f
      https://github.com/ehb54/ultrascan3/commit/7b370a88e30b380b1e40382cecb82aa1310eba3f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A test/utils/test_us_buffer.cpp
    M test/utils/test_us_datafiles.cpp

  Log Message:
  -----------
  Add test_us_buffer.cpp


  Commit: 363e32b18e6f47106c9dd75c7f1793511472a3b0
      https://github.com/ehb54/ultrascan3/commit/363e32b18e6f47106c9dd75c7f1793511472a3b0
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  Add apt-get install libmysqlclient-dev


  Commit: 77a89e083d64e4c862e61b9716a1e7d1f1892df4
      https://github.com/ehb54/ultrascan3/commit/77a89e083d64e4c862e61b9716a1e7d1f1892df4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update to find mysql during build


  Commit: 69b88e6a47d8369f97892eddcbfa839473ce9120
      https://github.com/ehb54/ultrascan3/commit/69b88e6a47d8369f97892eddcbfa839473ce9120
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h

  Log Message:
  -----------
  removed query test


  Commit: 3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
      https://github.com/ehb54/ultrascan3/commit/3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  run specific test


  Commit: d84cc16735556c0d8fb706bc768a6a4dc10db9a8
      https://github.com/ehb54/ultrascan3/commit/d84cc16735556c0d8fb706bc768a6a4dc10db9a8
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-03 (Tue, 03 Sep 2024)

  Changed paths:
    M test/utils/test_us_math2.cpp

  Log Message:
  -----------
  test_us_math2 was updated after sigma calculation was verified.


  Commit: 6276beb67d5181eba36861791acef5e415723e89
      https://github.com/ehb54/ultrascan3/commit/6276beb67d5181eba36861791acef5e415723e89
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-06-29 (Sun, 29 Jun 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A CITATION.cff
    M CMakeLists.txt
    M LICENSE.txt
    M admin/codeql/docker/docker/Dockerfile
    M admin/codeql/docker/dockerdev/Dockerfile
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    A admin/release/ubuntu/mathops.h
    M admin/release/ubuntu_qt6/Dockerfile
    A admin/us_branch/README.md
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php
    M alpha/us.cpp
    A doc/calc_model_coefficient_documentation.pdf
    A doc/calc_timestate_documentation.pdf
    R doc/manual/2dsa.body
    A doc/manual/2dsa/2dsa.body
    A doc/manual/2dsa/2dsa_advan.body
    A doc/manual/2dsa/2dsa_analvv.body
    A doc/manual/2dsa/2dsa_analys.body
    R doc/manual/2dsa_advan.body
    R doc/manual/2dsa_analvv.body
    R doc/manual/2dsa_analys.body
    M doc/manual/Makefile
    M doc/manual/README
    M doc/manual/advanced_config.body
    M doc/manual/astfem_sim.body
    M doc/manual/cfa_viewer.body
    M doc/manual/colorgradient.body
    M doc/manual/config.body
    M doc/manual/config2.body
    M doc/manual/convert.body
    M doc/manual/data_loader.body
    M doc/manual/ddist_combine.body
    M doc/manual/dens_match.body
    A doc/manual/experiment/experiment_cells.body
    A doc/manual/experiment/experiment_general.body
    A doc/manual/experiment/experiment_photomult.body
    A doc/manual/experiment/experiment_rotor.body
    A doc/manual/experiment/experiment_solutions.body
    A doc/manual/experiment/experiment_speeds.body
    A doc/manual/experiment/experiment_upload.body
    R doc/manual/experiment_cells.body
    R doc/manual/experiment_general.body
    R doc/manual/experiment_photomult.body
    R doc/manual/experiment_rotor.body
    R doc/manual/experiment_solutions.body
    R doc/manual/experiment_speeds.body
    R doc/manual/experiment_upload.body
    M doc/manual/export_legacy.body
    R doc/manual/fe_match.body
    A doc/manual/fe_match/fe_match.body
    A doc/manual/fe_match/fe_match_adv.body
    A doc/manual/fe_match/fe_match_controls.body
    A doc/manual/fe_match/fe_match_lddat.body
    A doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fe_match_adv.body
    R doc/manual/fe_match_controls.body
    R doc/manual/fe_match_lddat.body
    R doc/manual/fe_match_simulate.body
    M doc/manual/fit_meniscus.body
    M doc/manual/ga_initialize.body
    A doc/manual/gmp/gmp.body
    A doc/manual/gmp/gmp_audit_trail.body
    A doc/manual/gmp/gmp_data_acquisition.body
    A doc/manual/gmp/gmp_data_acquisition_experiment.body
    A doc/manual/gmp/gmp_data_acquisition_gmp.body
    A doc/manual/gmp/gmp_protocol_development.body
    A doc/manual/gmp/gmp_report_generator.body
    A doc/manual/gmp/gmp_signature.body
    M doc/manual/grid_editor.body
    A doc/manual/images/gmp/audit_trail/gmp_audit_trail_01.png
    A doc/manual/images/gmp/audit_trail/gmp_audit_trail_02.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_01.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_02.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_03.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_04.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_05.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_06.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_07.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_08.png
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    M us_somo/somo/doc/manual/somo/somo_results.html
    M us_somo/somo/doc/manual/somo/somo_save.html
    M us_somo/somo/doc/manual/somo/somo_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_buffer.html
    M us_somo/somo/doc/manual/somo/somo_saxs_conc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_baseline_corr.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_fit.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_linear_baselines.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_movie.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_skewedGauss.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_svd.html
    M us_somo/somo/doc/manual/somo/somo_saxs_iqq_residuals.html
    M us_somo/somo/doc/manual/somo/somo_saxs_load_csv.html
    M us_somo/somo/doc/manual/somo/somo_saxs_mw.html
    M us_somo/somo/doc/manual/somo/somo_saxs_options.html
    M us_somo/somo/doc/manual/somo/somo_saxs_residuals.html
    M us_somo/somo/doc/manual/somo/somo_show_hydro.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html
    M us_somo/somo/doc/manual/somo/somo_vdw_overlap.html
    M us_somo/somo/doc/manual/somo/underconstruction.html
    M us_somo/somo/doc/manual/somo/uv_vis_options.html
    M utils/CMakeLists.txt
    R utils/calc_coefficient_documentation.pdf
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    A utils/us_archive.cpp
    A utils/us_archive.h
    M utils/us_astfem_math.cpp
    A utils/us_csv_data.cpp
    A utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_geturl.h
    M utils/us_hydrosim.cpp
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_math2.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_report_gmp.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	CMakeLists.txt
#	test/utils/CMakeLists.txt
#	test/utils/test_us_utils_main.cpp
#	utils/CMakeLists.txt


  Commit: a423656c7a4997ae177e5406c7b8f846d5cda459
      https://github.com/ehb54/ultrascan3/commit/a423656c7a4997ae177e5406c7b8f846d5cda459
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-01 (Tue, 01 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/test/docker/Dockerfile
    A test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    M test/utils/test_mock_us_db2.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_project.h
    R test/utils/test_us_project_gtest.cpp
    R test/utils/test_us_project_gtest.h
    R test/utils/test_us_simparams.cpp
    R test/utils/test_us_simparams.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_project.cpp
    M utils/us_project.h

  Log Message:
  -----------
  dependency injection, docker, and remove duplicates


  Commit: b10a7ddbde27cb31ff6ce03fac85921856c2c90f
      https://github.com/ehb54/ultrascan3/commit/b10a7ddbde27cb31ff6ce03fac85921856c2c90f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_math.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    M test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_memory.h
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_dataIO.h

  Log Message:
  -----------
  convert qtests to google tests


  Commit: 54099cb2ff6ed13d069418492a1d7c6430277fb4
      https://github.com/ehb54/ultrascan3/commit/54099cb2ff6ed13d069418492a1d7c6430277fb4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

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

  Log Message:
  -----------
  remove specific test logic


  Commit: 5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
      https://github.com/ehb54/ultrascan3/commit/5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  test failing test


  Commit: 29b485c94b6bfd0e1f7be5ca07da8449cefe8081
      https://github.com/ehb54/ultrascan3/commit/29b485c94b6bfd0e1f7be5ca07da8449cefe8081
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  disabled failing test


  Commit: 9f15926c85f745d67b489772eb640400a916ad92
      https://github.com/ehb54/ultrascan3/commit/9f15926c85f745d67b489772eb640400a916ad92
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-05 (Sat, 05 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/README.md

  Log Message:
  -----------
  fixed comment, added readme


  Commit: 3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
      https://github.com/ehb54/ultrascan3/commit/3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis


  Commit: a9025670cc855940cf159141a10a5e0648312794
      https://github.com/ehb54/ultrascan3/commit/a9025670cc855940cf159141a10a5e0648312794
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis removed sudo


  Commit: bbdf69b0fef6c0be255ef3bdecfba8597797c668
      https://github.com/ehb54/ultrascan3/commit/bbdf69b0fef6c0be255ef3bdecfba8597797c668
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  moved static analysis to separate file


  Commit: d208f8e88de47207cc309f9b9e25483681973e03
      https://github.com/ehb54/ultrascan3/commit/d208f8e88de47207cc309f9b9e25483681973e03
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  fix iwyu


  Commit: 3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
      https://github.com/ehb54/ultrascan3/commit/3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    R doc/manual/README
    A doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
      https://github.com/ehb54/ultrascan3/commit/cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M test/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: a65be797990b6aa12a17b160b052482c930fb9ce
      https://github.com/ehb54/ultrascan3/commit/a65be797990b6aa12a17b160b052482c930fb9ce
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: 0ce7f8bbe5702044fddc573c6c7ea2002b72510d
      https://github.com/ehb54/ultrascan3/commit/0ce7f8bbe5702044fddc573c6c7ea2002b72510d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-13 (Sun, 13 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M test-docker.sh
    M test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    R test/utils/test_mock_us_db2.h
    M test/utils/test_us_ana_profile.cpp
    R test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    R test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_math.h
    M test/utils/test_us_astfem_rsa.cpp
    R test/utils/test_us_astfem_rsa.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    R test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    R test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    R test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    R test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    R test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    R test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    R test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    R test/utils/test_us_memory.h
    M test/utils/test_us_model.cpp
    R test/utils/test_us_model.h
    M test/utils/test_us_project.cpp
    R test/utils/test_us_project.h
    M test/utils/test_us_settings.cpp
    R test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    R test/utils/test_us_simparms.h
    M test/utils/test_us_stiffbase.cpp
    R test/utils/test_us_stiffbase.h
    M test/utils/test_us_time_state.cpp
    R test/utils/test_us_time_state.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    M utils/us_analyte.cpp
    M utils/us_analyte.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_dataIO.cpp
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_rotor.cpp
    M utils/us_rotor.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_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  ius_db2 build


  Commit: 76e2cf6ae4e764993cbd9d37d1bd086413514e3d
      https://github.com/ehb54/ultrascan3/commit/76e2cf6ae4e764993cbd9d37d1bd086413514e3d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .gitignore
    M test-docker.sh
    A test/README
    R test/README.md
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_model.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_stiffbase.cpp
    M test/utils/test_us_time_state.cpp
    M test/utils/test_us_util.cpp

  Log Message:
  -----------
  working set of util unit tests


  Commit: 3a4240895ec21be113a64f6d852aa70cdc0f9455
      https://github.com/ehb54/ultrascan3/commit/3a4240895ec21be113a64f6d852aa70cdc0f9455
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_tmst_plot.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	utils/us_simparms.cpp


  Commit: eb5398d2831269197d566f36400b5f80c87ac2b1
      https://github.com/ehb54/ultrascan3/commit/eb5398d2831269197d566f36400b5f80c87ac2b1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.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/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_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_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_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/us_model.cpp
    M utils/us_model.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 6c17ff96ca055f6cc43eeb2532d0eceab53580b3
      https://github.com/ehb54/ultrascan3/commit/6c17ff96ca055f6cc43eeb2532d0eceab53580b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_solution.cpp

  Log Message:
  -----------
  set to lowercase ius_db2.h


  Commit: 483c6d095b00b75710d4feeb2d9b996f0a4bd213
      https://github.com/ehb54/ultrascan3/commit/483c6d095b00b75710d4feeb2d9b996f0a4bd213
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M test-docker.sh

  Log Message:
  -----------
  add cmake hint file


  Commit: 76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
      https://github.com/ehb54/ultrascan3/commit/76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_simparms.cpp

  Log Message:
  -----------
  iusdb changes


  Commit: 295b4c9f222964264a4f4f2c9890d5b9f9d61f24
      https://github.com/ehb54/ultrascan3/commit/295b4c9f222964264a4f4f2c9890d5b9f9d61f24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M utils/ius_db2.h

  Log Message:
  -----------
  iusdb add qstring constuctor, turn off static analysis, move safe directory config


  Commit: 4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
      https://github.com/ehb54/ultrascan3/commit/4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

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

  Log Message:
  -----------
  error in gui build related to iusdb2


  Commit: 217485a90c5e92e0e810e5e3dfe2dac0177b8b35
      https://github.com/ehb54/ultrascan3/commit/217485a90c5e92e0e810e5e3dfe2dac0177b8b35
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    R admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakelists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_convert/us_select_triples.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
    A programs/us_experiment/CMakeLists.txt
    A programs/us_fematch/CMakeLists.txt
    A programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_pcsa/us_pcsa.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    A programs/us_query_rmsd/CMakeLists.txt
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_db2.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  error in build related to iusdb2, cmake build for programs, and working unit tests


  Commit: 8401655782f10eb593ea8537ea59378e3da8f03b
      https://github.com/ehb54/ultrascan3/commit/8401655782f10eb593ea8537ea59378e3da8f03b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  move unit tests trigger to separate file


  Commit: 73021e71e98437f3583fc6edcaf0fe2faf72d5fd
      https://github.com/ehb54/ultrascan3/commit/73021e71e98437f3583fc6edcaf0fe2faf72d5fd
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M programs/us_com_project/CMakelists.txt
    A qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  add us_com_project cmakelists


  Commit: c9030ec25f5d2ce4547c140beaf0d06baa785f4a
      https://github.com/ehb54/ultrascan3/commit/c9030ec25f5d2ce4547c140beaf0d06baa785f4a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    A programs/us_com_project/CMakeLists.txt
    R programs/us_com_project/CMakelists.txt

  Log Message:
  -----------
  fix us_com_project cmakelists had lowercase l in name


  Commit: 7edcb7cb1815454a3c1517671b8f46ba157b7fd5
      https://github.com/ehb54/ultrascan3/commit/7edcb7cb1815454a3c1517671b8f46ba157b7fd5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml should not run and not send email


  Commit: a414cfc8f6a9b899f987a41925b89b2a948b954a
      https://github.com/ehb54/ultrascan3/commit/a414cfc8f6a9b899f987a41925b89b2a948b954a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml running but non-failing


  Commit: 09d7e2075e6ba517445079e50e2410866d36ef05
      https://github.com/ehb54/ultrascan3/commit/09d7e2075e6ba517445079e50e2410866d36ef05
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml install libqwt-qt5-dev


  Commit: 6014d3b78be1f58f196982b8e963eb9a1fd10650
      https://github.com/ehb54/ultrascan3/commit/6014d3b78be1f58f196982b8e963eb9a1fd10650
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 86802e7c8b63d5dafae200d92ab4edd449a76122
      https://github.com/ehb54/ultrascan3/commit/86802e7c8b63d5dafae200d92ab4edd449a76122
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 1c1fe3aebbc7885934e26733499fdc6e3443cd25
      https://github.com/ehb54/ultrascan3/commit/1c1fe3aebbc7885934e26733499fdc6e3443cd25
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml remove format check


  Commit: 545dd0c591ceb5f40b85403fe9d72a8dc2079608
      https://github.com/ehb54/ultrascan3/commit/545dd0c591ceb5f40b85403fe9d72a8dc2079608
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml only check changed files


  Commit: ff38446e4155e613f61b9ccfdadc5141796dba1d
      https://github.com/ehb54/ultrascan3/commit/ff38446e4155e613f61b9ccfdadc5141796dba1d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: 44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
      https://github.com/ehb54/ultrascan3/commit/44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
      https://github.com/ehb54/ultrascan3/commit/ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  mod workflow triggers to push or pr on master only


  Commit: 42e26337f0dd52027b91e41ba3af0f9e1b626a24
      https://github.com/ehb54/ultrascan3/commit/42e26337f0dd52027b91e41ba3af0f9e1b626a24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .gitignore
    R admin/codeql/custom-queries/cpp/codeql-pack.yml
    R admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_model_editor.cpp
    R gui/us_model_editor.h
    M gui/us_model_gui.cpp
    M gui/us_model_loader.h
    M gui/us_noise_loader.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_edit/us_edit.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  code cleanup before PR review


  Commit: 895bcceea66cf95608da4f456620659d8e9517d5
      https://github.com/ehb54/ultrascan3/commit/895bcceea66cf95608da4f456620659d8e9517d5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #260 from ehb54/master

commit update


  Commit: 19e27c3ec7093c10f143441101c85d0af09b12ac
      https://github.com/ehb54/ultrascan3/commit/19e27c3ec7093c10f143441101c85d0af09b12ac
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: better reporting of critical issues


  Commit: 3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
      https://github.com/ehb54/ultrascan3/commit/3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/aaron-dev-test-utils' into aaron-dev-test-utils


  Commit: eaf7d5bc8dae71e71e890cbec10deb318fe0862c
      https://github.com/ehb54/ultrascan3/commit/eaf7d5bc8dae71e71e890cbec10deb318fe0862c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: artifact upload fix


  Commit: f04888d7116e9c5498dd5a316307e9f4dc238d40
      https://github.com/ehb54/ultrascan3/commit/f04888d7116e9c5498dd5a316307e9f4dc238d40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

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

  Log Message:
  -----------
  fix: critical static analysis only


  Commit: d9ed24af5742fb54910d7c1d9873b57c528b4661
      https://github.com/ehb54/ultrascan3/commit/d9ed24af5742fb54910d7c1d9873b57c528b4661
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/FindQwt.cmake
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/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
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_settings.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: address review comments


  Commit: dd3e9be9669f28156c33235c7e73db3040c614a5
      https://github.com/ehb54/ultrascan3/commit/dd3e9be9669f28156c33235c7e73db3040c614a5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: 93c11d987df52db6a1d9484f4f49a7acb54bd4dc
      https://github.com/ehb54/ultrascan3/commit/93c11d987df52db6a1d9484f4f49a7acb54bd4dc
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: ea99232fad84d9c9e2e785ee18794694bb22b883
      https://github.com/ehb54/ultrascan3/commit/ea99232fad84d9c9e2e785ee18794694bb22b883
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Update utils/CMakeLists.txt

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


  Commit: a1344544e53b2158a855ac3ddb3296bbb15d21e0
      https://github.com/ehb54/ultrascan3/commit/a1344544e53b2158a855ac3ddb3296bbb15d21e0
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Update gui/CMakeLists.txt

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


  Commit: 6115f78b236f317ecc7ce852c9541d8ac10084e4
      https://github.com/ehb54/ultrascan3/commit/6115f78b236f317ecc7ce852c9541d8ac10084e4
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  Update test/utils/CMakeLists.txt

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


  Commit: e87ab944bf93815dda5842e3dadee3249c11a52c
      https://github.com/ehb54/ultrascan3/commit/e87ab944bf93815dda5842e3dadee3249c11a52c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_vector.cpp

  Log Message:
  -----------
  fix: cmake collision during build


  Commit: 4a401e5be566119b5510674930f3b4365211a052
      https://github.com/ehb54/ultrascan3/commit/4a401e5be566119b5510674930f3b4365211a052
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  fix: add QWT to us_program_common


  Commit: 3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
      https://github.com/ehb54/ultrascan3/commit/3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  fix: duplicate include removed


  Commit: 9b2e06a5e4a371044a913065222c7d91603e0085
      https://github.com/ehb54/ultrascan3/commit/9b2e06a5e4a371044a913065222c7d91603e0085
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intargal -- avoid loading editProfiles...


  Commit: abfa96706807a26b5b0642ed078a97acf01a3e18
      https://github.com/ehb54/ultrascan3/commit/abfa96706807a26b5b0642ed078a97acf01a3e18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intergal -- restore editProfiles read; add debugs...


  Commit: d712bbbb0ceb306e036f428d4245c0e3b87c097b
      https://github.com/ehb54/ultrascan3/commit/d712bbbb0ceb306e036f428d4245c0e3b87c097b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [1]US_intergal -- restore editProfiles read; add debugs...


  Commit: 088595bbbb4e35e890cb8d2bf308945e0333f3f1
      https://github.com/ehb54/ultrascan3/commit/088595bbbb4e35e890cb8d2bf308945e0333f3f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [2]US_intergal -- restore editProfiles read; add debugs...


  Commit: 15343601bc0774d196184c33adbddefab8430a11
      https://github.com/ehb54/ultrascan3/commit/15343601bc0774d196184c33adbddefab8430a11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [3]US_intergal -- create curves' labels from the model's desc...


  Commit: d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
      https://github.com/ehb54/ultrascan3/commit/d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  Merge pull request #268 from ehb54/alexey-dev-issue562

Alexey dev issue562: Enable plotting CG-SG integral distr.


  Commit: 8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
      https://github.com/ehb54/ultrascan3/commit/8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-07 (Tue, 07 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_rsa.cpp

  Log Message:
  -----------
  Consolidated commit after cleanup


  Commit: 934f494e4683d95677c5a7051705426df529cf13
      https://github.com/ehb54/ultrascan3/commit/934f494e4683d95677c5a7051705426df529cf13
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-08 (Wed, 08 Oct 2025)

  Changed paths:
    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 doc/manual/advanced_config.body
    M gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.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_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    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_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 4e54cb0bd0e5eda0aebea648780b89b67b47d482
      https://github.com/ehb54/ultrascan3/commit/4e54cb0bd0e5eda0aebea648780b89b67b47d482
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #234 from ehb54/aaron-dev-test-utils

Add: google mock framework, static code analysis


  Commit: 6dc67538e4d0efedcf66715d9f44781f3f8e27e4
      https://github.com/ehb54/ultrascan3/commit/6dc67538e4d0efedcf66715d9f44781f3f8e27e4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #269 from ehb54/master

Bring this branch to the latest master state


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From noreply at github.com  Wed Oct  8 17:21:54 2025
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Date: Wed, 08 Oct 2025 16:21:54 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/000000-4e54cb@github.com>

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Date: Thu, 09 Oct 2025 08:32:10 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/demeler-simparams/1e85b9-000000@github.com>

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Date: Thu, 09 Oct 2025 08:34:37 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/Issue422/42a14e-000000@github.com>

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Date: Thu, 09 Oct 2025 11:46:48 -0700
Subject: [us-commits] [ehb54/ultrascan3]
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Date: Thu, 09 Oct 2025 11:47:47 -0700
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From noreply at github.com  Thu Oct  9 12:47:50 2025
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Date: Thu, 09 Oct 2025 11:47:50 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue367-backup/bcc377-000000@github.com>

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From noreply at github.com  Thu Oct  9 12:47:56 2025
From: noreply at github.com (alexsav815)
Date: Thu, 09 Oct 2025 11:47:56 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev/11d6ae-000000@github.com>

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From noreply at github.com  Thu Oct  9 14:06:17 2025
From: noreply at github.com (alexsav815)
Date: Thu, 09 Oct 2025 13:06:17 -0700
Subject: [us-commits] [ehb54/ultrascan3] 72add4: GMP-ABDE: 5. ANALYSIS --
 honor AProfile's setting ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue574/4e54cb-72add4@github.com>

  Branch: refs/heads/alexey-dev-issue574
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 72add4bba839a101a1cd875f5ff266fa9a91ccc9
      https://github.com/ehb54/ultrascan3/commit/72add4bba839a101a1cd875f5ff266fa9a91ccc9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  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:
  -----------
  GMP-ABDE: 5. ANALYSIS -- honor AProfile's setting (channels selection) in MWL-species fit and normalization...



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From noreply at github.com  Thu Oct  9 14:38:51 2025
From: noreply at github.com (alexsav815)
Date: Thu, 09 Oct 2025 13:38:51 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue576/000000-4e54cb@github.com>

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From noreply at github.com  Thu Oct  9 14:53:03 2025
From: noreply at github.com (alexsav815)
Date: Thu, 09 Oct 2025 13:53:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] af2045: GMP: 1. EXP. -- for
 dataDisk option, do not block ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue576/4e54cb-af2045@github.com>

  Branch: refs/heads/alexey-dev-issue576
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...



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From noreply at github.com  Thu Oct  9 14:59:35 2025
From: noreply at github.com (alexsav815)
Date: Thu, 09 Oct 2025 13:59:35 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue575/000000-4e54cb@github.com>

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From noreply at github.com  Thu Oct  9 15:43:35 2025
From: noreply at github.com (alexsav815)
Date: Thu, 09 Oct 2025 14:43:35 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8d1c1b: GMP: 5. ANALYSIS: FITMEN --
 disable update btn rig...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue575/4e54cb-8d1c1b@github.com>

  Branch: refs/heads/alexey-dev-issue575
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8d1c1b4dcbf1b2c698688d5aad236d07578858d5
      https://github.com/ehb54/ultrascan3/commit/8d1c1b4dcbf1b2c698688d5aad236d07578858d5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  GMP: 5. ANALYSIS: FITMEN -- disable update btn right after it's clicked...



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From noreply at github.com  Fri Oct 10 14:31:46 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 10 Oct 2025 13:31:46 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue576/af2045-000000@github.com>

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From noreply at github.com  Fri Oct 10 14:31:44 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 10 Oct 2025 13:31:44 -0700
Subject: [us-commits] [ehb54/ultrascan3] af2045: GMP: 1. EXP. -- for
 dataDisk option, do not block ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/4e54cb-34e199@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...


  Commit: 34e1993274025890c5cceda224c19973aa5b2ae2
      https://github.com/ehb54/ultrascan3/commit/34e1993274025890c5cceda224c19973aa5b2ae2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #271 from ehb54/alexey-dev-issue576

GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise..


Compare: https://github.com/ehb54/ultrascan3/compare/4e54cb0bd0e5...34e199327402

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From noreply at github.com  Fri Oct 10 18:33:50 2025
From: noreply at github.com (alexsav815)
Date: Fri, 10 Oct 2025 17:33:50 -0700
Subject: [us-commits] [ehb54/ultrascan3] af2045: GMP: 1. EXP. -- for
 dataDisk option, do not block ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/6dc675-bdba96@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...


  Commit: 34e1993274025890c5cceda224c19973aa5b2ae2
      https://github.com/ehb54/ultrascan3/commit/34e1993274025890c5cceda224c19973aa5b2ae2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #271 from ehb54/alexey-dev-issue576

GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise..


  Commit: bdba96a7dc97bb081790098cfb3d72bc10a32c18
      https://github.com/ehb54/ultrascan3/commit/bdba96a7dc97bb081790098cfb3d72bc10a32c18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #274 from ehb54/master

Bring to the current master state


Compare: https://github.com/ehb54/ultrascan3/compare/6dc67538e4d0...bdba96a7dc97

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From noreply at github.com  Fri Oct 10 18:34:13 2025
From: noreply at github.com (alexsav815)
Date: Fri, 10 Oct 2025 17:34:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] af2045: GMP: 1. EXP. -- for
 dataDisk option, do not block ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue575/8d1c1b-7c722f@github.com>

  Branch: refs/heads/alexey-dev-issue575
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...


  Commit: 34e1993274025890c5cceda224c19973aa5b2ae2
      https://github.com/ehb54/ultrascan3/commit/34e1993274025890c5cceda224c19973aa5b2ae2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #271 from ehb54/alexey-dev-issue576

GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise..


  Commit: 7c722f2fc3f2a82a9d5063fe4aecc128f465873d
      https://github.com/ehb54/ultrascan3/commit/7c722f2fc3f2a82a9d5063fe4aecc128f465873d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #275 from ehb54/master

Bring to current master state


Compare: https://github.com/ehb54/ultrascan3/compare/8d1c1b4dcbf1...7c722f2fc3f2

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From noreply at github.com  Fri Oct 10 18:34:24 2025
From: noreply at github.com (alexsav815)
Date: Fri, 10 Oct 2025 17:34:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] af2045: GMP: 1. EXP. -- for
 dataDisk option, do not block ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue574/72add4-60b0a4@github.com>

  Branch: refs/heads/alexey-dev-issue574
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...


  Commit: 34e1993274025890c5cceda224c19973aa5b2ae2
      https://github.com/ehb54/ultrascan3/commit/34e1993274025890c5cceda224c19973aa5b2ae2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #271 from ehb54/alexey-dev-issue576

GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise..


  Commit: 60b0a4d52d2f57ac00206f32b33f7a01c943bf8e
      https://github.com/ehb54/ultrascan3/commit/60b0a4d52d2f57ac00206f32b33f7a01c943bf8e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #276 from ehb54/master

Bring to current master


Compare: https://github.com/ehb54/ultrascan3/compare/72add4bba839...60b0a4d52d2f

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From noreply at github.com  Sat Oct 11 02:07:57 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 11 Oct 2025 01:07:57 -0700
Subject: [us-commits] [ehb54/ultrascan3] af1a5c: Additional Unit Testing
 us_ana_profile, us_crc, us...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_xpn_viewer_timestate/bb0aa9-b18731@github.com>

  Branch: refs/heads/lukas/us_xpn_viewer_timestate
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af1a5c8bc4252ae4bf9c3467711811c2f536d72f
      https://github.com/ehb54/ultrascan3/commit/af1a5c8bc4252ae4bf9c3467711811c2f536d72f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    A test/utils/test_us_ana_profile.cpp
    A test/utils/test_us_ana_profile.h
    A test/utils/test_us_crc.cpp
    A test/utils/test_us_crc.h
    A test/utils/test_us_crypto.cpp
    A test/utils/test_us_crypto.h
    A test/utils/test_us_dataIO.cpp
    A test/utils/test_us_dataIO.h
    A test/utils/test_us_math2.cpp
    A test/utils/test_us_math2.h
    A test/utils/test_us_matrix.cpp
    A test/utils/test_us_matrix.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Additional Unit Testing us_ana_profile, us_crc, us_crypto, us_dataio, us_math2, and us_matrix.


  Commit: 1408abf68cb2d299a8ad20905a1898d9f12c0958
      https://github.com/ehb54/ultrascan3/commit/1408abf68cb2d299a8ad20905a1898d9f12c0958
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    A test/utils/test_us_simparms.cpp
    A test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Tests pass locally except for TestUSMath2::test_linefit() and TestUSAnaProfile::testEqualityOperator() which have issues submitted to resolve.


  Commit: f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
      https://github.com/ehb54/ultrascan3/commit/f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_memory.cpp
    A test/utils/test_us_memory.h
    A test/utils/test_us_settings.cpp
    A test/utils/test_us_settings.h
    A test/utils/test_us_time_state.cpp
    A test/utils/test_us_time_state.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_memory, us_settings, and us_time_state


  Commit: 4abb61bbcc128d9293b4ff30674448f285671ab1
      https://github.com/ehb54/ultrascan3/commit/4abb61bbcc128d9293b4ff30674448f285671ab1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_analyte.cpp
    A test/utils/test_us_analyte.h
    A test/utils/test_us_db2.cpp
    A test/utils/test_us_db2.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_analyte and us_db2


  Commit: e9390c59f666fcc05efbd47251b28fe67c3e0b91
      https://github.com/ehb54/ultrascan3/commit/e9390c59f666fcc05efbd47251b28fe67c3e0b91
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_math.cpp
    A test/utils/test_us_astfem_math.h
    A test/utils/test_us_project.cpp
    A test/utils/test_us_project.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_math and us_project


  Commit: a9e23b7e83f8210188d4489c503430d9c26f97ee
      https://github.com/ehb54/ultrascan3/commit/a9e23b7e83f8210188d4489c503430d9c26f97ee
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    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_mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    A test/utils/test_us_project_gtest.cpp
    A test/utils/test_us_project_gtest.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Add gtest


  Commit: eaf6180d144d0c86dc4caec50879155740cc76e3
      https://github.com/ehb54/ultrascan3/commit/eaf6180d144d0c86dc4caec50879155740cc76e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_rsa.cpp
    A test/utils/test_us_astfem_rsa.h
    A test/utils/test_us_model.cpp
    A test/utils/test_us_model.h
    A test/utils/test_us_stiffbase.cpp
    A test/utils/test_us_stiffbase.h
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_rsa, us_model, and us_stiffbase


  Commit: 824605af8d275da7234b0a9d7f3672a8c001ea43
      https://github.com/ehb54/ultrascan3/commit/824605af8d275da7234b0a9d7f3672a8c001ea43
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_project_gtest.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Rebase merge


  Commit: 60e801e42c2edfe91afb422f4031c95eaae2d4da
      https://github.com/ehb54/ultrascan3/commit/60e801e42c2edfe91afb422f4031c95eaae2d4da
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A admin/codeql/custom-queries/cpp/codeql-pack.yml
    M admin/codeql/custom-queries/cpp/find-unused-functions.ql

  Log Message:
  -----------
  Update codeql custom query


  Commit: 7b370a88e30b380b1e40382cecb82aa1310eba3f
      https://github.com/ehb54/ultrascan3/commit/7b370a88e30b380b1e40382cecb82aa1310eba3f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A test/utils/test_us_buffer.cpp
    M test/utils/test_us_datafiles.cpp

  Log Message:
  -----------
  Add test_us_buffer.cpp


  Commit: 363e32b18e6f47106c9dd75c7f1793511472a3b0
      https://github.com/ehb54/ultrascan3/commit/363e32b18e6f47106c9dd75c7f1793511472a3b0
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  Add apt-get install libmysqlclient-dev


  Commit: 77a89e083d64e4c862e61b9716a1e7d1f1892df4
      https://github.com/ehb54/ultrascan3/commit/77a89e083d64e4c862e61b9716a1e7d1f1892df4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update to find mysql during build


  Commit: 69b88e6a47d8369f97892eddcbfa839473ce9120
      https://github.com/ehb54/ultrascan3/commit/69b88e6a47d8369f97892eddcbfa839473ce9120
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h

  Log Message:
  -----------
  removed query test


  Commit: 3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
      https://github.com/ehb54/ultrascan3/commit/3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  run specific test


  Commit: d84cc16735556c0d8fb706bc768a6a4dc10db9a8
      https://github.com/ehb54/ultrascan3/commit/d84cc16735556c0d8fb706bc768a6a4dc10db9a8
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-03 (Tue, 03 Sep 2024)

  Changed paths:
    M test/utils/test_us_math2.cpp

  Log Message:
  -----------
  test_us_math2 was updated after sigma calculation was verified.


  Commit: 69b6016db937a41c6d364bda55101d76f5564bc6
      https://github.com/ehb54/ultrascan3/commit/69b6016db937a41c6d364bda55101d76f5564bc6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    A admin/pam_auth_helper/README.md
    A admin/pam_auth_helper/pam.d/php-helper
    A admin/pam_auth_helper/pam_auth_helper.c
    A admin/pam_auth_helper/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php


  Commit: 22b88019d6a64a92f89f361f6cfd6737cab591d9
      https://github.com/ehb54/ultrascan3/commit/22b88019d6a64a92f89f361f6cfd6737cab591d9
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    M admin/pam_auth_helper/README.md

  Log Message:
  -----------
  Update README.md


  Commit: e64cf5274f1d7302ca4582ea2e138b08a870e828
      https://github.com/ehb54/ultrascan3/commit/e64cf5274f1d7302ca4582ea2e138b08a870e828
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    A admin/pam_auth_helper/Makefile

  Log Message:
  -----------
  PAM for linux password for php - makefile


  Commit: 56f6b69169ad4e990282f20f3531d347cdca36bf
      https://github.com/ehb54/ultrascan3/commit/56f6b69169ad4e990282f20f3531d347cdca36bf
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    A admin/pam/pam_no_ad/Makefile
    A admin/pam/pam_no_ad/README.md
    A admin/pam/pam_no_ad/files/php
    A admin/pam/pam_no_ad/files/sssd.conf
    R admin/pam_auth_helper/Makefile
    R admin/pam_auth_helper/README.md
    R admin/pam_auth_helper/pam.d/php-helper
    R admin/pam_auth_helper/pam_auth_helper.c
    R admin/pam_auth_helper/pam_auth_test.php

  Log Message:
  -----------
  PAM auth no AD/LDAP, Linux passwords only


  Commit: 5050f341dbde4ea01ba7f0e3aa9862fbb5fbe6b9
      https://github.com/ehb54/ultrascan3/commit/5050f341dbde4ea01ba7f0e3aa9862fbb5fbe6b9
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

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

  Log Message:
  -----------
  Merge pull request #226 from ehb54/master

merge master to issue branch


  Commit: b16f0504f2f4404db161c55323d9df63622854fc
      https://github.com/ehb54/ultrascan3/commit/b16f0504f2f4404db161c55323d9df63622854fc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: bd0a2263e0e3493aaa08624c81fcbd820f172a1d
      https://github.com/ehb54/ultrascan3/commit/bd0a2263e0e3493aaa08624c81fcbd820f172a1d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    A admin/pam/pam_no_ad/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php - pam_auth_test.php


  Commit: 1a4ce194b046f388b13ae0c04a5f361478f90700
      https://github.com/ehb54/ultrascan3/commit/1a4ce194b046f388b13ae0c04a5f361478f90700
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: df89a15dee591af68573b8840c6f78586499c3a3
      https://github.com/ehb54/ultrascan3/commit/df89a15dee591af68573b8840c6f78586499c3a3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php - pam_auth_test.php


  Commit: c65ba3d71581de0a41ee41787e66c4026190dc18
      https://github.com/ehb54/ultrascan3/commit/c65ba3d71581de0a41ee41787e66c4026190dc18
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/Makefile
    A admin/pam/pam_no_ad/files/mariadb
    M admin/pam/pam_no_ad/files/sssd.conf
    A admin/pam/pam_no_ad/files/system-auth-nosss

  Log Message:
  -----------
  pam - updated config


  Commit: 93f3f88fd38b866aad319181f61dc3e4aa8bcfe3
      https://github.com/ehb54/ultrascan3/commit/93f3f88fd38b866aad319181f61dc3e4aa8bcfe3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  pam - updated READEM


  Commit: bb52f3f31f0438cd66c01a5d7e4eb903ce4b37d0
      https://github.com/ehb54/ultrascan3/commit/bb52f3f31f0438cd66c01a5d7e4eb903ce4b37d0
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: 1eb1eb3811ccfad632482d58ed2a9ba6015609a4
      https://github.com/ehb54/ultrascan3/commit/1eb1eb3811ccfad632482d58ed2a9ba6015609a4
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/files/sssd.conf

  Log Message:
  -----------
  remove proxy_fast_switch

sssd.log reports [sssd] [sss_ini_call_validators] (0x0020): [rule/allowed_domain_options]: Attribute 'proxy_fast_switch' is not allowed in section 'domain/local'.


  Commit: 1c7bcff1b439d260af022b29abcf3f0bb17c3983
      https://github.com/ehb54/ultrascan3/commit/1c7bcff1b439d260af022b29abcf3f0bb17c3983
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md
    A admin/pam/pam_no_ad/pam_auth_pamtester.php

  Log Message:
  -----------
  issue496 - pamtester testing


  Commit: 7ce6ebcdb8cbd49311441bf7937aba4fec2bffd6
      https://github.com/ehb54/ultrascan3/commit/7ce6ebcdb8cbd49311441bf7937aba4fec2bffd6
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: 6276beb67d5181eba36861791acef5e415723e89
      https://github.com/ehb54/ultrascan3/commit/6276beb67d5181eba36861791acef5e415723e89
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-06-29 (Sun, 29 Jun 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A CITATION.cff
    M CMakeLists.txt
    M LICENSE.txt
    M admin/codeql/docker/docker/Dockerfile
    M admin/codeql/docker/dockerdev/Dockerfile
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    A admin/release/ubuntu/mathops.h
    M admin/release/ubuntu_qt6/Dockerfile
    A admin/us_branch/README.md
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php
    M alpha/us.cpp
    A doc/calc_model_coefficient_documentation.pdf
    A doc/calc_timestate_documentation.pdf
    R doc/manual/2dsa.body
    A doc/manual/2dsa/2dsa.body
    A doc/manual/2dsa/2dsa_advan.body
    A doc/manual/2dsa/2dsa_analvv.body
    A doc/manual/2dsa/2dsa_analys.body
    R doc/manual/2dsa_advan.body
    R doc/manual/2dsa_analvv.body
    R doc/manual/2dsa_analys.body
    M doc/manual/Makefile
    M doc/manual/README
    M doc/manual/advanced_config.body
    M doc/manual/astfem_sim.body
    M doc/manual/cfa_viewer.body
    M doc/manual/colorgradient.body
    M doc/manual/config.body
    M doc/manual/config2.body
    M doc/manual/convert.body
    M doc/manual/data_loader.body
    M doc/manual/ddist_combine.body
    M doc/manual/dens_match.body
    A doc/manual/experiment/experiment_cells.body
    A doc/manual/experiment/experiment_general.body
    A doc/manual/experiment/experiment_photomult.body
    A doc/manual/experiment/experiment_rotor.body
    A doc/manual/experiment/experiment_solutions.body
    A doc/manual/experiment/experiment_speeds.body
    A doc/manual/experiment/experiment_upload.body
    R doc/manual/experiment_cells.body
    R doc/manual/experiment_general.body
    R doc/manual/experiment_photomult.body
    R doc/manual/experiment_rotor.body
    R doc/manual/experiment_solutions.body
    R doc/manual/experiment_speeds.body
    R doc/manual/experiment_upload.body
    M doc/manual/export_legacy.body
    R doc/manual/fe_match.body
    A doc/manual/fe_match/fe_match.body
    A doc/manual/fe_match/fe_match_adv.body
    A doc/manual/fe_match/fe_match_controls.body
    A doc/manual/fe_match/fe_match_lddat.body
    A doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fe_match_adv.body
    R doc/manual/fe_match_controls.body
    R doc/manual/fe_match_lddat.body
    R doc/manual/fe_match_simulate.body
    M doc/manual/fit_meniscus.body
    M doc/manual/ga_initialize.body
    A doc/manual/gmp/gmp.body
    A doc/manual/gmp/gmp_audit_trail.body
    A doc/manual/gmp/gmp_data_acquisition.body
    A doc/manual/gmp/gmp_data_acquisition_experiment.body
    A doc/manual/gmp/gmp_data_acquisition_gmp.body
    A doc/manual/gmp/gmp_protocol_development.body
    A doc/manual/gmp/gmp_report_generator.body
    A doc/manual/gmp/gmp_signature.body
    M doc/manual/grid_editor.body
    A doc/manual/images/gmp/audit_trail/gmp_audit_trail_01.png
    A doc/manual/images/gmp/audit_trail/gmp_audit_trail_02.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_01.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_02.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_03.png
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    M us_somo/somo/doc/manual/somo/somo_pdb_editor_merge.html
    M us_somo/somo/doc/manual/somo/somo_pdb_parsing.html
    M us_somo/somo/doc/manual/somo/somo_pdb_parsing_expert_mode.html
    M us_somo/somo/doc/manual/somo/somo_pdb_visualization.html
    M us_somo/somo/doc/manual/somo/somo_residue.html
    M us_somo/somo/doc/manual/somo/somo_results.html
    M us_somo/somo/doc/manual/somo/somo_save.html
    M us_somo/somo/doc/manual/somo/somo_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_buffer.html
    M us_somo/somo/doc/manual/somo/somo_saxs_conc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_baseline_corr.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_fit.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_linear_baselines.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_movie.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_skewedGauss.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_svd.html
    M us_somo/somo/doc/manual/somo/somo_saxs_iqq_residuals.html
    M us_somo/somo/doc/manual/somo/somo_saxs_load_csv.html
    M us_somo/somo/doc/manual/somo/somo_saxs_mw.html
    M us_somo/somo/doc/manual/somo/somo_saxs_options.html
    M us_somo/somo/doc/manual/somo/somo_saxs_residuals.html
    M us_somo/somo/doc/manual/somo/somo_show_hydro.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html
    M us_somo/somo/doc/manual/somo/somo_vdw_overlap.html
    M us_somo/somo/doc/manual/somo/underconstruction.html
    M us_somo/somo/doc/manual/somo/uv_vis_options.html
    M utils/CMakeLists.txt
    R utils/calc_coefficient_documentation.pdf
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    A utils/us_archive.cpp
    A utils/us_archive.h
    M utils/us_astfem_math.cpp
    A utils/us_csv_data.cpp
    A utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_geturl.h
    M utils/us_hydrosim.cpp
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_math2.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_report_gmp.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	CMakeLists.txt
#	test/utils/CMakeLists.txt
#	test/utils/test_us_utils_main.cpp
#	utils/CMakeLists.txt


  Commit: a423656c7a4997ae177e5406c7b8f846d5cda459
      https://github.com/ehb54/ultrascan3/commit/a423656c7a4997ae177e5406c7b8f846d5cda459
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-01 (Tue, 01 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/test/docker/Dockerfile
    A test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    M test/utils/test_mock_us_db2.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_project.h
    R test/utils/test_us_project_gtest.cpp
    R test/utils/test_us_project_gtest.h
    R test/utils/test_us_simparams.cpp
    R test/utils/test_us_simparams.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_project.cpp
    M utils/us_project.h

  Log Message:
  -----------
  dependency injection, docker, and remove duplicates


  Commit: b10a7ddbde27cb31ff6ce03fac85921856c2c90f
      https://github.com/ehb54/ultrascan3/commit/b10a7ddbde27cb31ff6ce03fac85921856c2c90f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_math.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    M test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_memory.h
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_dataIO.h

  Log Message:
  -----------
  convert qtests to google tests


  Commit: 54099cb2ff6ed13d069418492a1d7c6430277fb4
      https://github.com/ehb54/ultrascan3/commit/54099cb2ff6ed13d069418492a1d7c6430277fb4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

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

  Log Message:
  -----------
  remove specific test logic


  Commit: 5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
      https://github.com/ehb54/ultrascan3/commit/5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  test failing test


  Commit: 29b485c94b6bfd0e1f7be5ca07da8449cefe8081
      https://github.com/ehb54/ultrascan3/commit/29b485c94b6bfd0e1f7be5ca07da8449cefe8081
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  disabled failing test


  Commit: 9f15926c85f745d67b489772eb640400a916ad92
      https://github.com/ehb54/ultrascan3/commit/9f15926c85f745d67b489772eb640400a916ad92
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-05 (Sat, 05 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/README.md

  Log Message:
  -----------
  fixed comment, added readme


  Commit: 3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
      https://github.com/ehb54/ultrascan3/commit/3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis


  Commit: a9025670cc855940cf159141a10a5e0648312794
      https://github.com/ehb54/ultrascan3/commit/a9025670cc855940cf159141a10a5e0648312794
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis removed sudo


  Commit: bbdf69b0fef6c0be255ef3bdecfba8597797c668
      https://github.com/ehb54/ultrascan3/commit/bbdf69b0fef6c0be255ef3bdecfba8597797c668
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  moved static analysis to separate file


  Commit: d208f8e88de47207cc309f9b9e25483681973e03
      https://github.com/ehb54/ultrascan3/commit/d208f8e88de47207cc309f9b9e25483681973e03
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  fix iwyu


  Commit: 3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
      https://github.com/ehb54/ultrascan3/commit/3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    R doc/manual/README
    A doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
      https://github.com/ehb54/ultrascan3/commit/cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M test/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: a65be797990b6aa12a17b160b052482c930fb9ce
      https://github.com/ehb54/ultrascan3/commit/a65be797990b6aa12a17b160b052482c930fb9ce
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: 0ce7f8bbe5702044fddc573c6c7ea2002b72510d
      https://github.com/ehb54/ultrascan3/commit/0ce7f8bbe5702044fddc573c6c7ea2002b72510d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-13 (Sun, 13 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M test-docker.sh
    M test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    R test/utils/test_mock_us_db2.h
    M test/utils/test_us_ana_profile.cpp
    R test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    R test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_math.h
    M test/utils/test_us_astfem_rsa.cpp
    R test/utils/test_us_astfem_rsa.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    R test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    R test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    R test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    R test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    R test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    R test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    R test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    R test/utils/test_us_memory.h
    M test/utils/test_us_model.cpp
    R test/utils/test_us_model.h
    M test/utils/test_us_project.cpp
    R test/utils/test_us_project.h
    M test/utils/test_us_settings.cpp
    R test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    R test/utils/test_us_simparms.h
    M test/utils/test_us_stiffbase.cpp
    R test/utils/test_us_stiffbase.h
    M test/utils/test_us_time_state.cpp
    R test/utils/test_us_time_state.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    M utils/us_analyte.cpp
    M utils/us_analyte.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_dataIO.cpp
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_rotor.cpp
    M utils/us_rotor.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_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  ius_db2 build


  Commit: 76e2cf6ae4e764993cbd9d37d1bd086413514e3d
      https://github.com/ehb54/ultrascan3/commit/76e2cf6ae4e764993cbd9d37d1bd086413514e3d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .gitignore
    M test-docker.sh
    A test/README
    R test/README.md
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_model.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_stiffbase.cpp
    M test/utils/test_us_time_state.cpp
    M test/utils/test_us_util.cpp

  Log Message:
  -----------
  working set of util unit tests


  Commit: 3a4240895ec21be113a64f6d852aa70cdc0f9455
      https://github.com/ehb54/ultrascan3/commit/3a4240895ec21be113a64f6d852aa70cdc0f9455
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_tmst_plot.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	utils/us_simparms.cpp


  Commit: eb5398d2831269197d566f36400b5f80c87ac2b1
      https://github.com/ehb54/ultrascan3/commit/eb5398d2831269197d566f36400b5f80c87ac2b1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.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/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_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_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_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/us_model.cpp
    M utils/us_model.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 6c17ff96ca055f6cc43eeb2532d0eceab53580b3
      https://github.com/ehb54/ultrascan3/commit/6c17ff96ca055f6cc43eeb2532d0eceab53580b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_solution.cpp

  Log Message:
  -----------
  set to lowercase ius_db2.h


  Commit: 483c6d095b00b75710d4feeb2d9b996f0a4bd213
      https://github.com/ehb54/ultrascan3/commit/483c6d095b00b75710d4feeb2d9b996f0a4bd213
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M test-docker.sh

  Log Message:
  -----------
  add cmake hint file


  Commit: 76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
      https://github.com/ehb54/ultrascan3/commit/76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_simparms.cpp

  Log Message:
  -----------
  iusdb changes


  Commit: 295b4c9f222964264a4f4f2c9890d5b9f9d61f24
      https://github.com/ehb54/ultrascan3/commit/295b4c9f222964264a4f4f2c9890d5b9f9d61f24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M utils/ius_db2.h

  Log Message:
  -----------
  iusdb add qstring constuctor, turn off static analysis, move safe directory config


  Commit: 4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
      https://github.com/ehb54/ultrascan3/commit/4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

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

  Log Message:
  -----------
  error in gui build related to iusdb2


  Commit: 217485a90c5e92e0e810e5e3dfe2dac0177b8b35
      https://github.com/ehb54/ultrascan3/commit/217485a90c5e92e0e810e5e3dfe2dac0177b8b35
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    R admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakelists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_convert/us_select_triples.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
    A programs/us_experiment/CMakeLists.txt
    A programs/us_fematch/CMakeLists.txt
    A programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_pcsa/us_pcsa.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    A programs/us_query_rmsd/CMakeLists.txt
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_db2.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  error in build related to iusdb2, cmake build for programs, and working unit tests


  Commit: 8401655782f10eb593ea8537ea59378e3da8f03b
      https://github.com/ehb54/ultrascan3/commit/8401655782f10eb593ea8537ea59378e3da8f03b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  move unit tests trigger to separate file


  Commit: 73021e71e98437f3583fc6edcaf0fe2faf72d5fd
      https://github.com/ehb54/ultrascan3/commit/73021e71e98437f3583fc6edcaf0fe2faf72d5fd
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M programs/us_com_project/CMakelists.txt
    A qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  add us_com_project cmakelists


  Commit: c9030ec25f5d2ce4547c140beaf0d06baa785f4a
      https://github.com/ehb54/ultrascan3/commit/c9030ec25f5d2ce4547c140beaf0d06baa785f4a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    A programs/us_com_project/CMakeLists.txt
    R programs/us_com_project/CMakelists.txt

  Log Message:
  -----------
  fix us_com_project cmakelists had lowercase l in name


  Commit: 7edcb7cb1815454a3c1517671b8f46ba157b7fd5
      https://github.com/ehb54/ultrascan3/commit/7edcb7cb1815454a3c1517671b8f46ba157b7fd5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml should not run and not send email


  Commit: a414cfc8f6a9b899f987a41925b89b2a948b954a
      https://github.com/ehb54/ultrascan3/commit/a414cfc8f6a9b899f987a41925b89b2a948b954a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml running but non-failing


  Commit: 09d7e2075e6ba517445079e50e2410866d36ef05
      https://github.com/ehb54/ultrascan3/commit/09d7e2075e6ba517445079e50e2410866d36ef05
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml install libqwt-qt5-dev


  Commit: 6014d3b78be1f58f196982b8e963eb9a1fd10650
      https://github.com/ehb54/ultrascan3/commit/6014d3b78be1f58f196982b8e963eb9a1fd10650
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 86802e7c8b63d5dafae200d92ab4edd449a76122
      https://github.com/ehb54/ultrascan3/commit/86802e7c8b63d5dafae200d92ab4edd449a76122
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 1c1fe3aebbc7885934e26733499fdc6e3443cd25
      https://github.com/ehb54/ultrascan3/commit/1c1fe3aebbc7885934e26733499fdc6e3443cd25
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml remove format check


  Commit: 545dd0c591ceb5f40b85403fe9d72a8dc2079608
      https://github.com/ehb54/ultrascan3/commit/545dd0c591ceb5f40b85403fe9d72a8dc2079608
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml only check changed files


  Commit: ff38446e4155e613f61b9ccfdadc5141796dba1d
      https://github.com/ehb54/ultrascan3/commit/ff38446e4155e613f61b9ccfdadc5141796dba1d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: 44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
      https://github.com/ehb54/ultrascan3/commit/44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
      https://github.com/ehb54/ultrascan3/commit/ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  mod workflow triggers to push or pr on master only


  Commit: 42e26337f0dd52027b91e41ba3af0f9e1b626a24
      https://github.com/ehb54/ultrascan3/commit/42e26337f0dd52027b91e41ba3af0f9e1b626a24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .gitignore
    R admin/codeql/custom-queries/cpp/codeql-pack.yml
    R admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_model_editor.cpp
    R gui/us_model_editor.h
    M gui/us_model_gui.cpp
    M gui/us_model_loader.h
    M gui/us_noise_loader.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_edit/us_edit.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  code cleanup before PR review


  Commit: 895bcceea66cf95608da4f456620659d8e9517d5
      https://github.com/ehb54/ultrascan3/commit/895bcceea66cf95608da4f456620659d8e9517d5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #260 from ehb54/master

commit update


  Commit: 19e27c3ec7093c10f143441101c85d0af09b12ac
      https://github.com/ehb54/ultrascan3/commit/19e27c3ec7093c10f143441101c85d0af09b12ac
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: better reporting of critical issues


  Commit: 3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
      https://github.com/ehb54/ultrascan3/commit/3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/aaron-dev-test-utils' into aaron-dev-test-utils


  Commit: eaf7d5bc8dae71e71e890cbec10deb318fe0862c
      https://github.com/ehb54/ultrascan3/commit/eaf7d5bc8dae71e71e890cbec10deb318fe0862c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: artifact upload fix


  Commit: f04888d7116e9c5498dd5a316307e9f4dc238d40
      https://github.com/ehb54/ultrascan3/commit/f04888d7116e9c5498dd5a316307e9f4dc238d40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

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

  Log Message:
  -----------
  fix: critical static analysis only


  Commit: d9ed24af5742fb54910d7c1d9873b57c528b4661
      https://github.com/ehb54/ultrascan3/commit/d9ed24af5742fb54910d7c1d9873b57c528b4661
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/FindQwt.cmake
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/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
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_settings.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: address review comments


  Commit: a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
      https://github.com/ehb54/ultrascan3/commit/a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-21 (Sun, 21 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 1246e6e3724e8a382585cc65e0208d3008bfbeeb
      https://github.com/ehb54/ultrascan3/commit/1246e6e3724e8a382585cc65e0208d3008bfbeeb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

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

  Log Message:
  -----------
  [1a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5e6c7f858d8e6163099c500c970c02e54801243b
      https://github.com/ehb54/ultrascan3/commit/5e6c7f858d8e6163099c500c970c02e54801243b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
      https://github.com/ehb54/ultrascan3/commit/5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5edb9ce91335769271fb5f593482a97dc4233059
      https://github.com/ehb54/ultrascan3/commit/5edb9ce91335769271fb5f593482a97dc4233059
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [4]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 9aff495b37873080961f8c231a3ce673377f80d3
      https://github.com/ehb54/ultrascan3/commit/9aff495b37873080961f8c231a3ce673377f80d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
      https://github.com/ehb54/ultrascan3/commit/1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 321a8cba345ec3c3f2187e0ba10f28376fd49a3e
      https://github.com/ehb54/ultrascan3/commit/321a8cba345ec3c3f2187e0ba10f28376fd49a3e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [5b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 373ac0ac501856ea0df8f4f579f953d89ec810b0
      https://github.com/ehb54/ultrascan3/commit/373ac0ac501856ea0df8f4f579f953d89ec810b0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [6b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ea3905ba9097c5eed14e034d6656fd0c84dff988
      https://github.com/ehb54/ultrascan3/commit/ea3905ba9097c5eed14e034d6656fd0c84dff988
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [6b-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
      https://github.com/ehb54/ultrascan3/commit/ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [7-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 905f41462ec9dab9667e915d639af2970e21a7a4
      https://github.com/ehb54/ultrascan3/commit/905f41462ec9dab9667e915d639af2970e21a7a4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [proper settings of min/max for scan_beg|nth|end for different optics systems] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 671b8e4d0e4951014a52280942d6a6c9712f14fa
      https://github.com/ehb54/ultrascan3/commit/671b8e4d0e4951014a52280942d6a6c9712f14fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: d584fa48438a0f9d744b750a6abe23533cc48b52
      https://github.com/ehb54/ultrascan3/commit/d584fa48438a0f9d744b750a6abe23533cc48b52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [RESTORE--UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 84f86b86f77bbcd33e113217d09cbda59701b58b
      https://github.com/ehb54/ultrascan3/commit/84f86b86f77bbcd33e113217d09cbda59701b58b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 8ecca10f20a347fd906905b16f8e85ef5afff22a
      https://github.com/ehb54/ultrascan3/commit/8ecca10f20a347fd906905b16f8e85ef5afff22a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: fe9b9031b3af683efa02792cf18ca46a51d376d8
      https://github.com/ehb54/ultrascan3/commit/fe9b9031b3af683efa02792cf18ca46a51d376d8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
      https://github.com/ehb54/ultrascan3/commit/4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: dd3e9be9669f28156c33235c7e73db3040c614a5
      https://github.com/ehb54/ultrascan3/commit/dd3e9be9669f28156c33235c7e73db3040c614a5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: 93c11d987df52db6a1d9484f4f49a7acb54bd4dc
      https://github.com/ehb54/ultrascan3/commit/93c11d987df52db6a1d9484f4f49a7acb54bd4dc
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: ea99232fad84d9c9e2e785ee18794694bb22b883
      https://github.com/ehb54/ultrascan3/commit/ea99232fad84d9c9e2e785ee18794694bb22b883
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Update utils/CMakeLists.txt

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


  Commit: a1344544e53b2158a855ac3ddb3296bbb15d21e0
      https://github.com/ehb54/ultrascan3/commit/a1344544e53b2158a855ac3ddb3296bbb15d21e0
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Update gui/CMakeLists.txt

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


  Commit: 6115f78b236f317ecc7ce852c9541d8ac10084e4
      https://github.com/ehb54/ultrascan3/commit/6115f78b236f317ecc7ce852c9541d8ac10084e4
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  Update test/utils/CMakeLists.txt

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


  Commit: b1ff389cba607cd5f34556fb6945f050ad099ff8
      https://github.com/ehb54/ultrascan3/commit/b1ff389cba607cd5f34556fb6945f050ad099ff8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: b557af349d02a148cef58c38976319f129cf4afa
      https://github.com/ehb54/ultrascan3/commit/b557af349d02a148cef58c38976319f129cf4afa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
      https://github.com/ehb54/ultrascan3/commit/57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
      https://github.com/ehb54/ultrascan3/commit/825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 4f9217705b688c38c3e420a609c2692c23a7e160
      https://github.com/ehb54/ultrascan3/commit/4f9217705b688c38c3e420a609c2692c23a7e160
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [4]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: f8379662ac83a104ca49b29cc3b5a7f830944d05
      https://github.com/ehb54/ultrascan3/commit/f8379662ac83a104ca49b29cc3b5a7f830944d05
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [5]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: e87ab944bf93815dda5842e3dadee3249c11a52c
      https://github.com/ehb54/ultrascan3/commit/e87ab944bf93815dda5842e3dadee3249c11a52c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_vector.cpp

  Log Message:
  -----------
  fix: cmake collision during build


  Commit: 4a401e5be566119b5510674930f3b4365211a052
      https://github.com/ehb54/ultrascan3/commit/4a401e5be566119b5510674930f3b4365211a052
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  fix: add QWT to us_program_common


  Commit: 036113902d7405af0d641ad3afb98b2010cef02f
      https://github.com/ehb54/ultrascan3/commit/036113902d7405af0d641ad3afb98b2010cef02f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 2e456f0922765ab66ffb5844fc6ef570a37ce431
      https://github.com/ehb54/ultrascan3/commit/2e456f0922765ab66ffb5844fc6ef570a37ce431
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    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

  Log Message:
  -----------
  Merge pull request #225 from ehb54/ehb54-issue-496

PAM for linux password for php


  Commit: 0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
      https://github.com/ehb54/ultrascan3/commit/0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [REstore form -- unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 154500215bfe391bf9dd7fda43456fe170c3c834
      https://github.com/ehb54/ultrascan3/commit/154500215bfe391bf9dd7fda43456fe170c3c834
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

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

  Log Message:
  -----------
  us_grid_editor: update the program GUI to get the cusotm grid from the users


  Commit: 42b30b23222d6e9b070861a382ebe34ad77611ab
      https://github.com/ehb54/ultrascan3/commit/42b30b23222d6e9b070861a382ebe34ad77611ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP | 6. REPORT -- do not display scan exclusion settings Scan section if optics type not used...


  Commit: 9f8fa54c2859fc4a8c4f996ef37443963f0e4ab2
      https://github.com/ehb54/ultrascan3/commit/9f8fa54c2859fc4a8c4f996ef37443963f0e4ab2
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

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

  Log Message:
  -----------
  us_grid_editor: add function to parse a grid file


  Commit: f6b215b4f73633db8bee542cefd88da89761620b
      https://github.com/ehb54/ultrascan3/commit/f6b215b4f73633db8bee542cefd88da89761620b
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_grid_editor/us_grid_editor.cpp

  Log Message:
  -----------
  us_grid_editor: save the user grid model locally and on DB


  Commit: 4ec94c4a344d53369ca022d39c166df3b0859490
      https://github.com/ehb54/ultrascan3/commit/4ec94c4a344d53369ca022d39c166df3b0859490
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-27 (Sat, 27 Sep 2025)

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

  Log Message:
  -----------
  fixed the issue with resetting to the default after pasrsing the CSV file. Refine the functions to reload the model from DB and local drive


  Commit: f286c4ffff8050ccb898b5446f3915031c6b7585
      https://github.com/ehb54/ultrascan3/commit/f286c4ffff8050ccb898b5446f3915031c6b7585
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-27 (Sat, 27 Sep 2025)

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

  Log Message:
  -----------
  Merge pull request #264 from samo38/issue_563

Issue 563: Custom Grid Program


  Commit: e3282fcfa778c046776d3abf2a718a9617230b4d
      https://github.com/ehb54/ultrascan3/commit/e3282fcfa778c046776d3abf2a718a9617230b4d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  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 -- do not specify details on Scan exlusions of there were no any...


  Commit: 8a112ba9e5ae7859d58f117c486f2e52cbba2899
      https://github.com/ehb54/ultrascan3/commit/8a112ba9e5ae7859d58f117c486f2e52cbba2899
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d1287da6bdde6dcb79acc019617ea24b5d93d410
      https://github.com/ehb54/ultrascan3/commit/d1287da6bdde6dcb79acc019617ea24b5d93d410
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    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 gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    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_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge pull request #265 from ehb54/master

add master


  Commit: 8dff3550c25c2827799de8e3f245f1f34a9044ab
      https://github.com/ehb54/ultrascan3/commit/8dff3550c25c2827799de8e3f245f1f34a9044ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

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

  Log Message:
  -----------
  [2]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d927f1c7acffd7436189c83726111d960cbd1e2d
      https://github.com/ehb54/ultrascan3/commit/d927f1c7acffd7436189c83726111d960cbd1e2d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 4c3a97f136b46591a7381b85fb726ea2fb87f7f2
      https://github.com/ehb54/ultrascan3/commit/4c3a97f136b46591a7381b85fb726ea2fb87f7f2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

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

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
      https://github.com/ehb54/ultrascan3/commit/7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 07f7d5c89032aa8dac1c13fe611e51d8e076cfde
      https://github.com/ehb54/ultrascan3/commit/07f7d5c89032aa8dac1c13fe611e51d8e076cfde
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 232008ddbb42fa37d28890542961579241726f13
      https://github.com/ehb54/ultrascan3/commit/232008ddbb42fa37d28890542961579241726f13
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
      https://github.com/ehb54/ultrascan3/commit/3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  fix: duplicate include removed


  Commit: 003fcead31be5da3e4a5744bd8b5a9a3adb9686d
      https://github.com/ehb54/ultrascan3/commit/003fcead31be5da3e4a5744bd8b5a9a3adb9686d
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  Merge pull request #267 from ehb54/alexey-dev-issue556

Alexey dev issue556: Scan Exclusion Profile Editor for AProfile in GMP #556


  Commit: 9b2e06a5e4a371044a913065222c7d91603e0085
      https://github.com/ehb54/ultrascan3/commit/9b2e06a5e4a371044a913065222c7d91603e0085
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intargal -- avoid loading editProfiles...


  Commit: abfa96706807a26b5b0642ed078a97acf01a3e18
      https://github.com/ehb54/ultrascan3/commit/abfa96706807a26b5b0642ed078a97acf01a3e18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intergal -- restore editProfiles read; add debugs...


  Commit: d712bbbb0ceb306e036f428d4245c0e3b87c097b
      https://github.com/ehb54/ultrascan3/commit/d712bbbb0ceb306e036f428d4245c0e3b87c097b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [1]US_intergal -- restore editProfiles read; add debugs...


  Commit: 088595bbbb4e35e890cb8d2bf308945e0333f3f1
      https://github.com/ehb54/ultrascan3/commit/088595bbbb4e35e890cb8d2bf308945e0333f3f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [2]US_intergal -- restore editProfiles read; add debugs...


  Commit: 15343601bc0774d196184c33adbddefab8430a11
      https://github.com/ehb54/ultrascan3/commit/15343601bc0774d196184c33adbddefab8430a11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [3]US_intergal -- create curves' labels from the model's desc...


  Commit: d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
      https://github.com/ehb54/ultrascan3/commit/d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  Merge pull request #268 from ehb54/alexey-dev-issue562

Alexey dev issue562: Enable plotting CG-SG integral distr.


  Commit: 8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
      https://github.com/ehb54/ultrascan3/commit/8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-07 (Tue, 07 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_rsa.cpp

  Log Message:
  -----------
  Consolidated commit after cleanup


  Commit: 934f494e4683d95677c5a7051705426df529cf13
      https://github.com/ehb54/ultrascan3/commit/934f494e4683d95677c5a7051705426df529cf13
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-08 (Wed, 08 Oct 2025)

  Changed paths:
    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 doc/manual/advanced_config.body
    M gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.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_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    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_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 4e54cb0bd0e5eda0aebea648780b89b67b47d482
      https://github.com/ehb54/ultrascan3/commit/4e54cb0bd0e5eda0aebea648780b89b67b47d482
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #234 from ehb54/aaron-dev-test-utils

Add: google mock framework, static code analysis


  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...


  Commit: 34e1993274025890c5cceda224c19973aa5b2ae2
      https://github.com/ehb54/ultrascan3/commit/34e1993274025890c5cceda224c19973aa5b2ae2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #271 from ehb54/alexey-dev-issue576

GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise..


  Commit: b1873114bd77180edf8229767b79afb615d0c045
      https://github.com/ehb54/ultrascan3/commit/b1873114bd77180edf8229767b79afb615d0c045
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    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
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.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_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    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_rsa.cpp
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #277 from ehb54/master

update lukas/us_xpn_viewer_timestate


Compare: https://github.com/ehb54/ultrascan3/compare/bb0aa9e39a0d...b1873114bd77

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From noreply at github.com  Sat Oct 11 02:14:57 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 11 Oct 2025 01:14:57 -0700
Subject: [us-commits] [ehb54/ultrascan3] 37fd8b: Refactor scan handling in
 `us_xpn_data.cpp` to use...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_xpn_viewer_timestate/b18731-37fd8b@github.com>

  Branch: refs/heads/lukas/us_xpn_viewer_timestate
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 37fd8b74401f5fce733a3c71524b9b1548508256
      https://github.com/ehb54/ultrascan3/commit/37fd8b74401f5fce733a3c71524b9b1548508256
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Refactor scan handling in `us_xpn_data.cpp` to use a sorted `scans` vector

Replaced direct iterations over `scanData` with a centralized `scans` vector, sorted by time for consistent and efficient speed step calculations. Updated associated logic to improve maintainability and clarity.



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From noreply at github.com  Sat Oct 11 03:12:38 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 11 Oct 2025 02:12:38 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_buffer_saveToDB/000000-34e199@github.com>

  Branch: refs/heads/lukas/us_buffer_saveToDB
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sat Oct 11 03:33:28 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 11 Oct 2025 02:33:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] 236ab6: Prevent early exit when
 saving a new buffer to dat...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_buffer_saveToDB/34e199-236ab6@github.com>

  Branch: refs/heads/lukas/us_buffer_saveToDB
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 236ab6f7717916a81de574fbe27299f18683a06c
      https://github.com/ehb54/ultrascan3/commit/236ab6f7717916a81de574fbe27299f18683a06c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Prevent early exit when saving a new buffer to database



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From noreply at github.com  Sat Oct 11 04:07:02 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 11 Oct 2025 03:07:02 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/static_analysis_warnings/000000-34e199@github.com>

  Branch: refs/heads/lukas/static_analysis_warnings
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sat Oct 11 04:09:37 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 11 Oct 2025 03:09:37 -0700
Subject: [us-commits] [ehb54/ultrascan3] 738825: Add null checks before
 adding child items to make ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/static_analysis_warnings/34e199-738825@github.com>

  Branch: refs/heads/lukas/static_analysis_warnings
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7388255d2bb422f8dca061365e459ac69e9267a4
      https://github.com/ehb54/ultrascan3/commit/7388255d2bb422f8dca061365e459ac69e9267a4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Add null checks before adding child items to make static analysis happy



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From noreply at github.com  Sat Oct 11 04:14:08 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 11 Oct 2025 03:14:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] f3022f: Fix formatting in
 us_data_loader.cpp
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/static_analysis_warnings/738825-f3022f@github.com>

  Branch: refs/heads/lukas/static_analysis_warnings
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f3022f734322210c7a6d74c4d72f7d5871d7f9c2
      https://github.com/ehb54/ultrascan3/commit/f3022f734322210c7a6d74c4d72f7d5871d7f9c2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Fix formatting in us_data_loader.cpp



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From noreply at github.com  Mon Oct 13 02:15:25 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 13 Oct 2025 01:15:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3edada: Include *.ui and *.qrc in
 gui build to ensure all ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-gui-resources/000000-3edada@github.com>

  Branch: refs/heads/lukas/cmake-gui-resources
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3edada407972c86d03c8f30822ebf6a3c1166357
      https://github.com/ehb54/ultrascan3/commit/3edada407972c86d03c8f30822ebf6a3c1166357
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Include *.ui and *.qrc in gui build to ensure all resources and forms are available



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From noreply at github.com  Mon Oct 13 10:02:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 13 Oct 2025 09:02:59 -0700
Subject: [us-commits] [ehb54/ultrascan3] 427e60: Clean up debug statements
 and enhance comments
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_buffer_saveToDB/236ab6-427e60@github.com>

  Branch: refs/heads/lukas/us_buffer_saveToDB
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 427e601f770f5eb39efb249bca9eb81b557561ae
      https://github.com/ehb54/ultrascan3/commit/427e601f770f5eb39efb249bca9eb81b557561ae
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Clean up debug statements and enhance comments

Removed commented debug statements and added clarifying comments for variable assignments.



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From noreply at github.com  Mon Oct 13 10:17:02 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 13 Oct 2025 09:17:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3edada: Include *.ui and *.qrc in
 gui build to ensure all ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/34e199-0bd193@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3edada407972c86d03c8f30822ebf6a3c1166357
      https://github.com/ehb54/ultrascan3/commit/3edada407972c86d03c8f30822ebf6a3c1166357
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Include *.ui and *.qrc in gui build to ensure all resources and forms are available


  Commit: 0bd193389e5967e65d03d34b4ce6dcf0f3817f84
      https://github.com/ehb54/ultrascan3/commit/0bd193389e5967e65d03d34b4ce6dcf0f3817f84
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Merge pull request #280 from ehb54/lukas/cmake-gui-resources

Include *.ui and *.qrc in us_gui library


Compare: https://github.com/ehb54/ultrascan3/compare/34e199327402...0bd193389e59

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From noreply at github.com  Mon Oct 13 10:17:24 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 13 Oct 2025 09:17:24 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-gui-resources/3edada-000000@github.com>

  Branch: refs/heads/lukas/cmake-gui-resources
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 13 13:05:23 2025
From: noreply at github.com (ehb54)
Date: Mon, 13 Oct 2025 12:05:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] b15c24: saxs hplc advanced
 selection - move p value select...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/4efac0-b15c24@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b15c2407b19ca357854b6767c1faf81212307bd6
      https://github.com/ehb54/ultrascan3/commit/b15c2407b19ca357854b6767c1faf81212307bd6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp

  Log Message:
  -----------
  saxs hplc advanced selection - move p value selection to non-expert mode



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From noreply at github.com  Mon Oct 13 13:43:09 2025
From: noreply at github.com (ehb54)
Date: Mon, 13 Oct 2025 12:43:09 -0700
Subject: [us-commits] [ehb54/ultrascan3] aa99fd: somo hplc saxs advanced
 selection - verify all cur...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/b15c24-aa99fd@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: aa99fd347d02fce3bc738d89afa1fcdb5445bb8a
      https://github.com/ehb54/ultrascan3/commit/aa99fd347d02fce3bc738d89afa1fcdb5445bb8a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp

  Log Message:
  -----------
  somo hplc saxs advanced selection - verify all curves have computed pvalues before allowing pvalue selection



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From noreply at github.com  Mon Oct 13 13:44:22 2025
From: noreply at github.com (alexsav815)
Date: Mon, 13 Oct 2025 12:44:22 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue577/000000-0bd193@github.com>

  Branch: refs/heads/alexey-dev-issue577
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 13 14:22:51 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 13 Oct 2025 13:22:51 -0700
Subject: [us-commits] [ehb54/ultrascan3] 399d84: GMP | R&D : dataDisk --
 differentiate between RI-u...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/0bd193-72ff57@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 399d845e5667346225803b9ac45b753c7676e39d
      https://github.com/ehb54/ultrascan3/commit/399d845e5667346225803b9ac45b753c7676e39d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_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_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: f924d79f3ecf67db15ced074ac2b50a4cafc9c72
      https://github.com/ehb54/ultrascan3/commit/f924d79f3ecf67db15ced074ac2b50a4cafc9c72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [1] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
      https://github.com/ehb54/ultrascan3/commit/a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: 8f9f1257b799c491fa5629c912071eabb435388f
      https://github.com/ehb54/ultrascan3/commit/8f9f1257b799c491fa5629c912071eabb435388f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: c3a261985e7e3979e7a9a11fcad5c851e739f41b
      https://github.com/ehb54/ultrascan3/commit/c3a261985e7e3979e7a9a11fcad5c851e739f41b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: 3ad35587a1da03cc9926344ac40bb3d364a32d24
      https://github.com/ehb54/ultrascan3/commit/3ad35587a1da03cc9926344ac40bb3d364a32d24
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: d6a4a469c86320252916565b3bd860c07cab4b1f
      https://github.com/ehb54/ultrascan3/commit/d6a4a469c86320252916565b3bd860c07cab4b1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: d3528cb233647917b4f76c9423f9deae1983f2bd
      https://github.com/ehb54/ultrascan3/commit/d3528cb233647917b4f76c9423f9deae1983f2bd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: 6dc67538e4d0efedcf66715d9f44781f3f8e27e4
      https://github.com/ehb54/ultrascan3/commit/6dc67538e4d0efedcf66715d9f44781f3f8e27e4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #269 from ehb54/master

Bring this branch to the latest master state


  Commit: bdba96a7dc97bb081790098cfb3d72bc10a32c18
      https://github.com/ehb54/ultrascan3/commit/bdba96a7dc97bb081790098cfb3d72bc10a32c18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #274 from ehb54/master

Bring to the current master state


  Commit: 72ff576e489d378f03adc4296b68bd001b1c649e
      https://github.com/ehb54/ultrascan3/commit/72ff576e489d378f03adc4296b68bd001b1c649e
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.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_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #273 from ehb54/alexey-dev-issue567

Alexey dev issue567: Deal with dataDisk Pseudoabsorbance type && correct GUI representaitons of US_Edit scenarios


Compare: https://github.com/ehb54/ultrascan3/compare/0bd193389e59...72ff576e489d

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From noreply at github.com  Mon Oct 13 14:24:54 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 13 Oct 2025 13:24:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8d1c1b: GMP: 5. ANALYSIS: FITMEN --
 disable update btn rig...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/72ff57-eb8022@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8d1c1b4dcbf1b2c698688d5aad236d07578858d5
      https://github.com/ehb54/ultrascan3/commit/8d1c1b4dcbf1b2c698688d5aad236d07578858d5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  GMP: 5. ANALYSIS: FITMEN -- disable update btn right after it's clicked...


  Commit: 7c722f2fc3f2a82a9d5063fe4aecc128f465873d
      https://github.com/ehb54/ultrascan3/commit/7c722f2fc3f2a82a9d5063fe4aecc128f465873d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #275 from ehb54/master

Bring to current master state


  Commit: eb8022621705540d2e5a0010b5141f3bd1620591
      https://github.com/ehb54/ultrascan3/commit/eb8022621705540d2e5a0010b5141f3bd1620591
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  Merge pull request #272 from ehb54/alexey-dev-issue575

GMP: 5. ANALYSIS: FITMEN -- disable update btn right after it's clicked..


Compare: https://github.com/ehb54/ultrascan3/compare/72ff576e489d...eb8022621705

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From noreply at github.com  Mon Oct 13 14:25:09 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 13 Oct 2025 13:25:09 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue575/7c722f-000000@github.com>

  Branch: refs/heads/alexey-dev-issue575
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 13 14:27:06 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 13 Oct 2025 13:27:06 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue567/bdba96-000000@github.com>

  Branch: refs/heads/alexey-dev-issue567
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 13 15:12:10 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 13 Oct 2025 14:12:10 -0700
Subject: [us-commits] [ehb54/ultrascan3] ea0b94: 8. AProfile: Report -- a
 sublte bug fixed for corr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/eb8022-18b990@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ea0b94a1f952fafffb14e048ef59ac09de4dae31
      https://github.com/ehb54/ultrascan3/commit/ea0b94a1f952fafffb14e048ef59ac09de4dae31
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

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

  Log Message:
  -----------
  8. AProfile: Report -- a sublte bug fixed for correctly inheriting exp. duration timefrom the main protocol into AProfile's->reports when setting protocol from scratch for the first time; also make exp. dur. fileds read-only ...


  Commit: 5ea9fa1c7dd4d0508386d70cc3f96d2f33275adf
      https://github.com/ehb54/ultrascan3/commit/5ea9fa1c7dd4d0508386d70cc3f96d2f33275adf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-10 (Thu, 10 Jul 2025)

  Changed paths:
    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:
  -----------
  GMP | R&D -- replace all QwtCounters with QSpinBoxes, to better control and validate inputs ...


  Commit: f8117c1eed92f953f483005cb49d40818b971cc9
      https://github.com/ehb54/ultrascan3/commit/f8117c1eed92f953f483005cb49d40818b971cc9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-28 (Mon, 28 Jul 2025)

  Changed paths:
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp

  Log Message:
  -----------
  GMP | R&D -- change ranges for dd-hh-mm-ss QSpinBoxes in 1. EXP.: 3. Speeds...


  Commit: 18b990073be39e32a749536729cba62d576e6c98
      https://github.com/ehb54/ultrascan3/commit/18b990073be39e32a749536729cba62d576e6c98
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_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 #237 from ehb54/alexey-dev-issue521

Alexey dev issue521: Correct and read-only exp. time in channels reports, qspinboxes instead of qwtcounters to control input


Compare: https://github.com/ehb54/ultrascan3/compare/eb8022621705...18b990073be3

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From noreply at github.com  Mon Oct 13 15:12:13 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 13 Oct 2025 14:12:13 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue521/f8117c-000000@github.com>

  Branch: refs/heads/alexey-dev-issue521
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 13 23:32:10 2025
From: noreply at github.com (alexsav815)
Date: Mon, 13 Oct 2025 22:32:10 -0700
Subject: [us-commits] [ehb54/ultrascan3] d131cb: GMP: 4. EDIT -- add rotor
 stretch to bottom in edi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue577/0bd193-d131cb@github.com>

  Branch: refs/heads/alexey-dev-issue577
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d131cbbccf4b88f4a39d285fb99a84ccfaacb536
      https://github.com/ehb54/ultrascan3/commit/d131cbbccf4b88f4a39d285fb99a84ccfaacb536
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...



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From noreply at github.com  Tue Oct 14 09:13:15 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 14 Oct 2025 08:13:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] 236ab6: Prevent early exit when
 saving a new buffer to dat...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/18b990-567202@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 236ab6f7717916a81de574fbe27299f18683a06c
      https://github.com/ehb54/ultrascan3/commit/236ab6f7717916a81de574fbe27299f18683a06c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Prevent early exit when saving a new buffer to database


  Commit: 427e601f770f5eb39efb249bca9eb81b557561ae
      https://github.com/ehb54/ultrascan3/commit/427e601f770f5eb39efb249bca9eb81b557561ae
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Clean up debug statements and enhance comments

Removed commented debug statements and added clarifying comments for variable assignments.


  Commit: 567202c3572f02c0b782f92791cac022e863829c
      https://github.com/ehb54/ultrascan3/commit/567202c3572f02c0b782f92791cac022e863829c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Merge pull request #278 from ehb54/lukas/us_buffer_saveToDB

Prevent early exit when saving a new buffer to database


Compare: https://github.com/ehb54/ultrascan3/compare/18b990073be3...567202c3572f

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From noreply at github.com  Tue Oct 14 09:13:25 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 14 Oct 2025 08:13:25 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_buffer_saveToDB/427e60-000000@github.com>

  Branch: refs/heads/lukas/us_buffer_saveToDB
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Oct 14 17:22:08 2025
From: noreply at github.com (alexsav815)
Date: Tue, 14 Oct 2025 16:22:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2bb6c5: [debug version,
 stops at XML write]GMP: 4. EDIT --...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue577/d131cb-2bb6c5@github.com>

  Branch: refs/heads/alexey-dev-issue577
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2bb6c53d1c011cceb17b9ebabc3e0700fea48879
      https://github.com/ehb54/ultrascan3/commit/2bb6c53d1c011cceb17b9ebabc3e0700fea48879
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...



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From noreply at github.com  Tue Oct 14 17:29:46 2025
From: noreply at github.com (alexsav815)
Date: Tue, 14 Oct 2025 16:29:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2dfbe7: [[1]debug version,
 stops at XML write]GMP: 4. EDIT...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue577/2bb6c5-2dfbe7@github.com>

  Branch: refs/heads/alexey-dev-issue577
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
      https://github.com/ehb54/ultrascan3/commit/2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [[1]debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...



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From noreply at github.com  Tue Oct 14 19:58:34 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 14 Oct 2025 18:58:34 -0700
Subject: [us-commits] [ehb54/ultrascan3] d131cb: GMP: 4. EDIT -- add rotor
 stretch to bottom in edi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/567202-883d73@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d131cbbccf4b88f4a39d285fb99a84ccfaacb536
      https://github.com/ehb54/ultrascan3/commit/d131cbbccf4b88f4a39d285fb99a84ccfaacb536
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 2bb6c53d1c011cceb17b9ebabc3e0700fea48879
      https://github.com/ehb54/ultrascan3/commit/2bb6c53d1c011cceb17b9ebabc3e0700fea48879
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
      https://github.com/ehb54/ultrascan3/commit/2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [[1]debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 883d73df2ac05d1717a2f924737d36a6ddda5a49
      https://github.com/ehb54/ultrascan3/commit/883d73df2ac05d1717a2f924737d36a6ddda5a49
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge pull request #282 from ehb54/alexey-dev-issue577

GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


Compare: https://github.com/ehb54/ultrascan3/compare/567202c3572f...883d73df2ac0

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From noreply at github.com  Tue Oct 14 19:58:42 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 14 Oct 2025 18:58:42 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue577/2dfbe7-000000@github.com>

  Branch: refs/heads/alexey-dev-issue577
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Oct 14 20:45:28 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 14 Oct 2025 19:45:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2d1d55: us_astfem_sim: save TI,
 RI noises in the result di...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/883d73-1de51a@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2d1d5599a18b1105dd622fb570a284c2af9b3027
      https://github.com/ehb54/ultrascan3/commit/2d1d5599a18b1105dd622fb570a284c2af9b3027
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  us_astfem_sim: save TI, RI noises in the result directory


  Commit: 52692bf1ec74f08f07f036d50913983f0cb4902c
      https://github.com/ehb54/ultrascan3/commit/52692bf1ec74f08f07f036d50913983f0cb4902c
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  us_astfem_sim.cpp: fix writing the RI csv profile for multi-speed experiments


  Commit: 5d05e1a2439de5fa9adb431619c350ae188fcf31
      https://github.com/ehb54/ultrascan3/commit/5d05e1a2439de5fa9adb431619c350ae188fcf31
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

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

  Log Message:
  -----------
  us_astfem_sim: save TI,RI noise profiles into the outout directory


  Commit: 1de51a8c4fb82a5cbb3cf09653f9e235a54c327c
      https://github.com/ehb54/ultrascan3/commit/1de51a8c4fb82a5cbb3cf09653f9e235a54c327c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

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

  Log Message:
  -----------
  Merge pull request #281 from samo38/issue_587

us_astfem_sim: save TI, RI noises in the result directory


Compare: https://github.com/ehb54/ultrascan3/compare/883d73df2ac0...1de51a8c4fb8

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From noreply at github.com  Wed Oct 15 01:23:15 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 15 Oct 2025 00:23:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] 63f4dd: Add `auto_positioning` flag
 for enhanced global po...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/window_positioning/000000-a7dbc8@github.com>

  Branch: refs/heads/lukas/window_positioning
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63f4dd275fb6537a334793979a632cbb9ff8fca6
      https://github.com/ehb54/ultrascan3/commit/63f4dd275fb6537a334793979a632cbb9ff8fca6
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_second_moment/us_second_moment.cpp

  Log Message:
  -----------
  Add `auto_positioning` flag for enhanced global positioning control across widgets and programs

Introduced a new `auto_positioning` setting for managing global positioning more dynamically. Adjusted logic to conditionally apply global positioning based on this flag, improving flexibility and consistency across multiple components.


  Commit: a7dbc87be55a513b6131ca8187578669f29e213d
      https://github.com/ehb54/ultrascan3/commit/a7dbc87be55a513b6131ca8187578669f29e213d
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Refactor `us.cpp` for improved readability and consistency

Replaced `application` with `QApplication` for static calls, updated container checks to use `.empty()`, added explicit timeouts for `waitForStarted`, and revised variable declarations to use `const` where appropriate. Simplified code and ensured consistent outcomes.


Compare: https://github.com/ehb54/ultrascan3/compare/63f4dd275fb6%5E...a7dbc87be55a

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From noreply at github.com  Wed Oct 15 05:29:21 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 15 Oct 2025 04:29:21 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1d74e9: Add `debug_positions`
 functionality and refine pro...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/window_positioning/a7dbc8-f84caa@github.com>

  Branch: refs/heads/lukas/window_positioning
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1d74e9e01956f78a618fe0431a68817877a3b3ff
      https://github.com/ehb54/ultrascan3/commit/1d74e9e01956f78a618fe0431a68817877a3b3ff
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

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

  Log Message:
  -----------
  Add `debug_positions` functionality and refine process channel handling

Introduced a new `debug_positions` method for automated debugging of position logic, integrating it into the menu system. Updated `QProcess` to utilize `ForwardedChannels` mode and removed redundant channel closure calls for improved process management.


  Commit: f84caaa7b14b6f40a98ab8b17e576b701f261d5f
      https://github.com/ehb54/ultrascan3/commit/f84caaa7b14b6f40a98ab8b17e576b701f261d5f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M programs/us_fematch/us_fematch_main.cpp

  Log Message:
  -----------
  Add debug logging for widget position and global positioning events

Implemented `showEvent` and `moveEvent` overrides in `US_Widgets` for detailed debugging of widget positioning data. Enhanced `US_FeMatch` main to log initial position and frame geometry details. These changes improve traceability for debugging global positioning logic.


Compare: https://github.com/ehb54/ultrascan3/compare/a7dbc87be55a...f84caaa7b14b

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From noreply at github.com  Wed Oct 15 05:33:28 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 15 Oct 2025 04:33:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] f70cdd: Comment out redundant
 widget movement and debug lo...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/window_positioning/f84caa-f70cdd@github.com>

  Branch: refs/heads/lukas/window_positioning
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f70cdd2c5f08ff6ae3e6708bdeeccf1e157b7061
      https://github.com/ehb54/ultrascan3/commit/f70cdd2c5f08ff6ae3e6708bdeeccf1e157b7061
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M programs/us_fematch/us_fematch_main.cpp

  Log Message:
  -----------
  Comment out redundant widget movement and debug logging in `US_FeMatch::main` for cleaner output.



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From noreply at github.com  Wed Oct 15 13:49:23 2025
From: noreply at github.com (ehb54)
Date: Wed, 15 Oct 2025 12:49:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] af1a5c: Additional Unit Testing
 us_ana_profile, us_crc, us...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-533/3fd011-ecfbe0@github.com>

  Branch: refs/heads/ehb54-issue-533
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af1a5c8bc4252ae4bf9c3467711811c2f536d72f
      https://github.com/ehb54/ultrascan3/commit/af1a5c8bc4252ae4bf9c3467711811c2f536d72f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    A test/utils/test_us_ana_profile.cpp
    A test/utils/test_us_ana_profile.h
    A test/utils/test_us_crc.cpp
    A test/utils/test_us_crc.h
    A test/utils/test_us_crypto.cpp
    A test/utils/test_us_crypto.h
    A test/utils/test_us_dataIO.cpp
    A test/utils/test_us_dataIO.h
    A test/utils/test_us_math2.cpp
    A test/utils/test_us_math2.h
    A test/utils/test_us_matrix.cpp
    A test/utils/test_us_matrix.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Additional Unit Testing us_ana_profile, us_crc, us_crypto, us_dataio, us_math2, and us_matrix.


  Commit: 1408abf68cb2d299a8ad20905a1898d9f12c0958
      https://github.com/ehb54/ultrascan3/commit/1408abf68cb2d299a8ad20905a1898d9f12c0958
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    A test/utils/test_us_simparms.cpp
    A test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Tests pass locally except for TestUSMath2::test_linefit() and TestUSAnaProfile::testEqualityOperator() which have issues submitted to resolve.


  Commit: f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
      https://github.com/ehb54/ultrascan3/commit/f87d9a2ed4bbc9a4d91dd3543dbaf4b62edca765
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_memory.cpp
    A test/utils/test_us_memory.h
    A test/utils/test_us_settings.cpp
    A test/utils/test_us_settings.h
    A test/utils/test_us_time_state.cpp
    A test/utils/test_us_time_state.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_memory, us_settings, and us_time_state


  Commit: 4abb61bbcc128d9293b4ff30674448f285671ab1
      https://github.com/ehb54/ultrascan3/commit/4abb61bbcc128d9293b4ff30674448f285671ab1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_analyte.cpp
    A test/utils/test_us_analyte.h
    A test/utils/test_us_db2.cpp
    A test/utils/test_us_db2.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_analyte and us_db2


  Commit: e9390c59f666fcc05efbd47251b28fe67c3e0b91
      https://github.com/ehb54/ultrascan3/commit/e9390c59f666fcc05efbd47251b28fe67c3e0b91
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_math.cpp
    A test/utils/test_us_astfem_math.h
    A test/utils/test_us_project.cpp
    A test/utils/test_us_project.h
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_math and us_project


  Commit: a9e23b7e83f8210188d4489c503430d9c26f97ee
      https://github.com/ehb54/ultrascan3/commit/a9e23b7e83f8210188d4489c503430d9c26f97ee
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt
    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_mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    A test/utils/test_us_project_gtest.cpp
    A test/utils/test_us_project_gtest.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Add gtest


  Commit: eaf6180d144d0c86dc4caec50879155740cc76e3
      https://github.com/ehb54/ultrascan3/commit/eaf6180d144d0c86dc4caec50879155740cc76e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/CMakeLists.txt
    A test/utils/test_us_astfem_rsa.cpp
    A test/utils/test_us_astfem_rsa.h
    A test/utils/test_us_model.cpp
    A test/utils/test_us_model.h
    A test/utils/test_us_stiffbase.cpp
    A test/utils/test_us_stiffbase.h
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Add tests for us_astfem_rsa, us_model, and us_stiffbase


  Commit: 824605af8d275da7234b0a9d7f3672a8c001ea43
      https://github.com/ehb54/ultrascan3/commit/824605af8d275da7234b0a9d7f3672a8c001ea43
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_project_gtest.cpp
    M utils/us_db2.h

  Log Message:
  -----------
  Rebase merge


  Commit: 60e801e42c2edfe91afb422f4031c95eaae2d4da
      https://github.com/ehb54/ultrascan3/commit/60e801e42c2edfe91afb422f4031c95eaae2d4da
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A admin/codeql/custom-queries/cpp/codeql-pack.yml
    M admin/codeql/custom-queries/cpp/find-unused-functions.ql

  Log Message:
  -----------
  Update codeql custom query


  Commit: 7b370a88e30b380b1e40382cecb82aa1310eba3f
      https://github.com/ehb54/ultrascan3/commit/7b370a88e30b380b1e40382cecb82aa1310eba3f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    A test/utils/test_us_buffer.cpp
    M test/utils/test_us_datafiles.cpp

  Log Message:
  -----------
  Add test_us_buffer.cpp


  Commit: 363e32b18e6f47106c9dd75c7f1793511472a3b0
      https://github.com/ehb54/ultrascan3/commit/363e32b18e6f47106c9dd75c7f1793511472a3b0
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  Add apt-get install libmysqlclient-dev


  Commit: 77a89e083d64e4c862e61b9716a1e7d1f1892df4
      https://github.com/ehb54/ultrascan3/commit/77a89e083d64e4c862e61b9716a1e7d1f1892df4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update to find mysql during build


  Commit: 69b88e6a47d8369f97892eddcbfa839473ce9120
      https://github.com/ehb54/ultrascan3/commit/69b88e6a47d8369f97892eddcbfa839473ce9120
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

  Changed paths:
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h

  Log Message:
  -----------
  removed query test


  Commit: 3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
      https://github.com/ehb54/ultrascan3/commit/3f7d4721cc43cb9f79fb187ebb5aa7f15babd257
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-01 (Sun, 01 Sep 2024)

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

  Log Message:
  -----------
  run specific test


  Commit: d84cc16735556c0d8fb706bc768a6a4dc10db9a8
      https://github.com/ehb54/ultrascan3/commit/d84cc16735556c0d8fb706bc768a6a4dc10db9a8
  Author: aaron <aaron at aucsolutions.com>
  Date:   2024-09-03 (Tue, 03 Sep 2024)

  Changed paths:
    M test/utils/test_us_math2.cpp

  Log Message:
  -----------
  test_us_math2 was updated after sigma calculation was verified.


  Commit: 69b6016db937a41c6d364bda55101d76f5564bc6
      https://github.com/ehb54/ultrascan3/commit/69b6016db937a41c6d364bda55101d76f5564bc6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    A admin/pam_auth_helper/README.md
    A admin/pam_auth_helper/pam.d/php-helper
    A admin/pam_auth_helper/pam_auth_helper.c
    A admin/pam_auth_helper/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php


  Commit: 22b88019d6a64a92f89f361f6cfd6737cab591d9
      https://github.com/ehb54/ultrascan3/commit/22b88019d6a64a92f89f361f6cfd6737cab591d9
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    M admin/pam_auth_helper/README.md

  Log Message:
  -----------
  Update README.md


  Commit: e64cf5274f1d7302ca4582ea2e138b08a870e828
      https://github.com/ehb54/ultrascan3/commit/e64cf5274f1d7302ca4582ea2e138b08a870e828
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

  Changed paths:
    A admin/pam_auth_helper/Makefile

  Log Message:
  -----------
  PAM for linux password for php - makefile


  Commit: 56f6b69169ad4e990282f20f3531d347cdca36bf
      https://github.com/ehb54/ultrascan3/commit/56f6b69169ad4e990282f20f3531d347cdca36bf
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    A admin/pam/pam_no_ad/Makefile
    A admin/pam/pam_no_ad/README.md
    A admin/pam/pam_no_ad/files/php
    A admin/pam/pam_no_ad/files/sssd.conf
    R admin/pam_auth_helper/Makefile
    R admin/pam_auth_helper/README.md
    R admin/pam_auth_helper/pam.d/php-helper
    R admin/pam_auth_helper/pam_auth_helper.c
    R admin/pam_auth_helper/pam_auth_test.php

  Log Message:
  -----------
  PAM auth no AD/LDAP, Linux passwords only


  Commit: 5050f341dbde4ea01ba7f0e3aa9862fbb5fbe6b9
      https://github.com/ehb54/ultrascan3/commit/5050f341dbde4ea01ba7f0e3aa9862fbb5fbe6b9
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

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

  Log Message:
  -----------
  Merge pull request #226 from ehb54/master

merge master to issue branch


  Commit: b16f0504f2f4404db161c55323d9df63622854fc
      https://github.com/ehb54/ultrascan3/commit/b16f0504f2f4404db161c55323d9df63622854fc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: bd0a2263e0e3493aaa08624c81fcbd820f172a1d
      https://github.com/ehb54/ultrascan3/commit/bd0a2263e0e3493aaa08624c81fcbd820f172a1d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    A admin/pam/pam_no_ad/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php - pam_auth_test.php


  Commit: 1a4ce194b046f388b13ae0c04a5f361478f90700
      https://github.com/ehb54/ultrascan3/commit/1a4ce194b046f388b13ae0c04a5f361478f90700
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: df89a15dee591af68573b8840c6f78586499c3a3
      https://github.com/ehb54/ultrascan3/commit/df89a15dee591af68573b8840c6f78586499c3a3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/pam_auth_test.php

  Log Message:
  -----------
  PAM for linux password for php - pam_auth_test.php


  Commit: c65ba3d71581de0a41ee41787e66c4026190dc18
      https://github.com/ehb54/ultrascan3/commit/c65ba3d71581de0a41ee41787e66c4026190dc18
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/Makefile
    A admin/pam/pam_no_ad/files/mariadb
    M admin/pam/pam_no_ad/files/sssd.conf
    A admin/pam/pam_no_ad/files/system-auth-nosss

  Log Message:
  -----------
  pam - updated config


  Commit: 93f3f88fd38b866aad319181f61dc3e4aa8bcfe3
      https://github.com/ehb54/ultrascan3/commit/93f3f88fd38b866aad319181f61dc3e4aa8bcfe3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  pam - updated READEM


  Commit: bb52f3f31f0438cd66c01a5d7e4eb903ce4b37d0
      https://github.com/ehb54/ultrascan3/commit/bb52f3f31f0438cd66c01a5d7e4eb903ce4b37d0
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-12 (Thu, 12 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: 1eb1eb3811ccfad632482d58ed2a9ba6015609a4
      https://github.com/ehb54/ultrascan3/commit/1eb1eb3811ccfad632482d58ed2a9ba6015609a4
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/files/sssd.conf

  Log Message:
  -----------
  remove proxy_fast_switch

sssd.log reports [sssd] [sss_ini_call_validators] (0x0020): [rule/allowed_domain_options]: Attribute 'proxy_fast_switch' is not allowed in section 'domain/local'.


  Commit: 1c7bcff1b439d260af022b29abcf3f0bb17c3983
      https://github.com/ehb54/ultrascan3/commit/1c7bcff1b439d260af022b29abcf3f0bb17c3983
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md
    A admin/pam/pam_no_ad/pam_auth_pamtester.php

  Log Message:
  -----------
  issue496 - pamtester testing


  Commit: 7ce6ebcdb8cbd49311441bf7937aba4fec2bffd6
      https://github.com/ehb54/ultrascan3/commit/7ce6ebcdb8cbd49311441bf7937aba4fec2bffd6
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-06-13 (Fri, 13 Jun 2025)

  Changed paths:
    M admin/pam/pam_no_ad/README.md

  Log Message:
  -----------
  Update README.md


  Commit: 6276beb67d5181eba36861791acef5e415723e89
      https://github.com/ehb54/ultrascan3/commit/6276beb67d5181eba36861791acef5e415723e89
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-06-29 (Sun, 29 Jun 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A CITATION.cff
    M CMakeLists.txt
    M LICENSE.txt
    M admin/codeql/docker/docker/Dockerfile
    M admin/codeql/docker/dockerdev/Dockerfile
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    A admin/release/ubuntu/mathops.h
    M admin/release/ubuntu_qt6/Dockerfile
    A admin/us_branch/README.md
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php
    M alpha/us.cpp
    A doc/calc_model_coefficient_documentation.pdf
    A doc/calc_timestate_documentation.pdf
    R doc/manual/2dsa.body
    A doc/manual/2dsa/2dsa.body
    A doc/manual/2dsa/2dsa_advan.body
    A doc/manual/2dsa/2dsa_analvv.body
    A doc/manual/2dsa/2dsa_analys.body
    R doc/manual/2dsa_advan.body
    R doc/manual/2dsa_analvv.body
    R doc/manual/2dsa_analys.body
    M doc/manual/Makefile
    M doc/manual/README
    M doc/manual/advanced_config.body
    M doc/manual/astfem_sim.body
    M doc/manual/cfa_viewer.body
    M doc/manual/colorgradient.body
    M doc/manual/config.body
    M doc/manual/config2.body
    M doc/manual/convert.body
    M doc/manual/data_loader.body
    M doc/manual/ddist_combine.body
    M doc/manual/dens_match.body
    A doc/manual/experiment/experiment_cells.body
    A doc/manual/experiment/experiment_general.body
    A doc/manual/experiment/experiment_photomult.body
    A doc/manual/experiment/experiment_rotor.body
    A doc/manual/experiment/experiment_solutions.body
    A doc/manual/experiment/experiment_speeds.body
    A doc/manual/experiment/experiment_upload.body
    R doc/manual/experiment_cells.body
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    R doc/manual/experiment_photomult.body
    R doc/manual/experiment_rotor.body
    R doc/manual/experiment_solutions.body
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    R doc/manual/experiment_upload.body
    M doc/manual/export_legacy.body
    R doc/manual/fe_match.body
    A doc/manual/fe_match/fe_match.body
    A doc/manual/fe_match/fe_match_adv.body
    A doc/manual/fe_match/fe_match_controls.body
    A doc/manual/fe_match/fe_match_lddat.body
    A doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/fe_match_adv.body
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    A doc/manual/gmp/gmp.body
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    M doc/manual/index.body
    A doc/manual/load/load_auc.body
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    A doc/manual/load/load_noise.body
    A doc/manual/load/load_noise_details.body
    R doc/manual/load_auc.body
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    R doc/manual/load_noise.body
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    M doc/manual/mainstyle.css
    M doc/manual/make-html.sh
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    M doc/manual/manage_data.body
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    M doc/manual/manage_data_thelp.body
    M doc/manual/manual.qhp
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    M doc/manual/register.body
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    A doc/manual/sassoc.body
    M doc/manual/second_moment.body
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    A doc/manual/somo.body
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    M doc/manual/vhw_combine.body
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    M doc/manual/vhw_enhanced.body
    M gui/images.qrc
    A gui/images/table.png
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_gui_util.cpp
    M gui/us_gui_util.h
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_license.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_rotor_gui.cpp
    M gui/us_rotor_gui.h
    M gui/us_run_details2.cpp
    M gui/us_run_details2.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M library.pri
    M makeall.sh
    M programs/us/us_de_DE.ts
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.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_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.h
    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_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_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project.pro
    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/us_com_project_academic.pro
    M programs/us_config/us_database.cpp
    M programs/us_config/us_database.h
    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_experiment.cpp
    M programs/us_convert/us_get_run.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_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    R programs/us_esigner_gmp_aux/us_esigner_gmp.pro
    R programs/us_esigner_gmp_aux/us_esigner_gmp_main.cpp
    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/us_fematch.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.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_tree.cpp
    M programs/us_manage_data/us_data_tree.h
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.h
    R programs/us_mwl_db_query/us_mwl_db_query.pro
    R programs/us_mwl_db_query/us_mwl_pltctrl.cpp
    R programs/us_mwl_db_query/us_mwl_pltctrl.h
    R programs/us_mwl_db_query/us_mwl_run.cpp
    R programs/us_mwl_db_query/us_mwl_run.h
    R programs/us_mwl_db_query/us_mwlr_viewer.cpp
    R programs/us_mwl_db_query/us_mwlr_viewer.h
    M programs/us_mwl_species_fit/us_load_run_noise.cpp
    M programs/us_mwl_species_fit/us_load_run_noise.h
    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_fit/us_mwl_species_fit.pro
    A programs/us_mwl_species_fit/us_mwl_species_fit_main.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    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_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_query_rmsd/us_query_rmsd.pro
    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_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M test/utils/CMakeLists.txt
    A test/utils/test_us_simparams.cpp
    A test/utils/test_us_simparams.h
    M test/utils/test_us_utils_main.cpp
    M us_somo/attic/INSTALL
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_util.cpp
    M us_somo/extra/haddock/bin_i73/mpi/runjob
    M us_somo/somo/doc/manual/somo/IntegralBaselineTheory.html
    M us_somo/somo/doc/manual/somo/baseline_best.html
    M us_somo/somo/doc/manual/somo/copyright.html
    M us_somo/somo/doc/manual/somo/cormap.html
    M us_somo/somo/doc/manual/somo/dad_parameters.html
    M us_somo/somo/doc/manual/somo/fractal_dimension_options.html
    M us_somo/somo/doc/manual/somo/mals_options.html
    M us_somo/somo/doc/manual/somo/mals_parameters.html
    M us_somo/somo/doc/manual/somo/mals_saxs_options.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_Gaussian_theory.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_ciq.html
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    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
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    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_fit.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_linear_baselines.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_movie.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_skewedGauss.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_svd.html
    M us_somo/somo/doc/manual/somo/somo_saxs_iqq_residuals.html
    M us_somo/somo/doc/manual/somo/somo_saxs_load_csv.html
    M us_somo/somo/doc/manual/somo/somo_saxs_mw.html
    M us_somo/somo/doc/manual/somo/somo_saxs_options.html
    M us_somo/somo/doc/manual/somo/somo_saxs_residuals.html
    M us_somo/somo/doc/manual/somo/somo_show_hydro.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html
    M us_somo/somo/doc/manual/somo/somo_vdw_overlap.html
    M us_somo/somo/doc/manual/somo/underconstruction.html
    M us_somo/somo/doc/manual/somo/uv_vis_options.html
    M utils/CMakeLists.txt
    R utils/calc_coefficient_documentation.pdf
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    A utils/us_archive.cpp
    A utils/us_archive.h
    M utils/us_astfem_math.cpp
    A utils/us_csv_data.cpp
    A utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_geturl.h
    M utils/us_hydrosim.cpp
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_math2.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_report_gmp.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	CMakeLists.txt
#	test/utils/CMakeLists.txt
#	test/utils/test_us_utils_main.cpp
#	utils/CMakeLists.txt


  Commit: a423656c7a4997ae177e5406c7b8f846d5cda459
      https://github.com/ehb54/ultrascan3/commit/a423656c7a4997ae177e5406c7b8f846d5cda459
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-01 (Tue, 01 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/test/docker/Dockerfile
    A test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    M test/utils/test_mock_us_db2.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_project.h
    R test/utils/test_us_project_gtest.cpp
    R test/utils/test_us_project_gtest.h
    R test/utils/test_us_simparams.cpp
    R test/utils/test_us_simparams.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_utils_main.cpp
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_project.cpp
    M utils/us_project.h

  Log Message:
  -----------
  dependency injection, docker, and remove duplicates


  Commit: b10a7ddbde27cb31ff6ce03fac85921856c2c90f
      https://github.com/ehb54/ultrascan3/commit/b10a7ddbde27cb31ff6ce03fac85921856c2c90f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_math.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    M test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    M test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    M test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_memory.h
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    M test/utils/test_us_simparms.h
    M test/utils/test_us_utils_main.cpp
    M utils/us_dataIO.h

  Log Message:
  -----------
  convert qtests to google tests


  Commit: 54099cb2ff6ed13d069418492a1d7c6430277fb4
      https://github.com/ehb54/ultrascan3/commit/54099cb2ff6ed13d069418492a1d7c6430277fb4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

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

  Log Message:
  -----------
  remove specific test logic


  Commit: 5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
      https://github.com/ehb54/ultrascan3/commit/5e9fb44fd3876b7e28a86b61c5cc8ceed76a903a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  test failing test


  Commit: 29b485c94b6bfd0e1f7be5ca07da8449cefe8081
      https://github.com/ehb54/ultrascan3/commit/29b485c94b6bfd0e1f7be5ca07da8449cefe8081
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-03 (Thu, 03 Jul 2025)

  Changed paths:
    M test/utils/test_us_crypto.cpp

  Log Message:
  -----------
  disabled failing test


  Commit: 9f15926c85f745d67b489772eb640400a916ad92
      https://github.com/ehb54/ultrascan3/commit/9f15926c85f745d67b489772eb640400a916ad92
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-05 (Sat, 05 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M test-docker.sh
    A test/README.md

  Log Message:
  -----------
  fixed comment, added readme


  Commit: 3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
      https://github.com/ehb54/ultrascan3/commit/3212f77418d1cedfe0dbc2db7f9d1a47a672d8f4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis


  Commit: a9025670cc855940cf159141a10a5e0648312794
      https://github.com/ehb54/ultrascan3/commit/a9025670cc855940cf159141a10a5e0648312794
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  code analysis removed sudo


  Commit: bbdf69b0fef6c0be255ef3bdecfba8597797c668
      https://github.com/ehb54/ultrascan3/commit/bbdf69b0fef6c0be255ef3bdecfba8597797c668
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  moved static analysis to separate file


  Commit: d208f8e88de47207cc309f9b9e25483681973e03
      https://github.com/ehb54/ultrascan3/commit/d208f8e88de47207cc309f9b9e25483681973e03
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-06 (Sun, 06 Jul 2025)

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

  Log Message:
  -----------
  fix iwyu


  Commit: 3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
      https://github.com/ehb54/ultrascan3/commit/3df3a60b840e7b78e9c6cbf9fe581f08a77f3d6e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    R doc/manual/README
    A doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
      https://github.com/ehb54/ultrascan3/commit/cbf13444f00522dfc1c7ba1dc91c9ba64c39e782
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M test/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: a65be797990b6aa12a17b160b052482c930fb9ce
      https://github.com/ehb54/ultrascan3/commit/a65be797990b6aa12a17b160b052482c930fb9ce
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

  Changed paths:
    M doc/manual/README.md

  Log Message:
  -----------
  update manual creation instructions


  Commit: ea0b94a1f952fafffb14e048ef59ac09de4dae31
      https://github.com/ehb54/ultrascan3/commit/ea0b94a1f952fafffb14e048ef59ac09de4dae31
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

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

  Log Message:
  -----------
  8. AProfile: Report -- a sublte bug fixed for correctly inheriting exp. duration timefrom the main protocol into AProfile's->reports when setting protocol from scratch for the first time; also make exp. dur. fileds read-only ...


  Commit: 5ea9fa1c7dd4d0508386d70cc3f96d2f33275adf
      https://github.com/ehb54/ultrascan3/commit/5ea9fa1c7dd4d0508386d70cc3f96d2f33275adf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-10 (Thu, 10 Jul 2025)

  Changed paths:
    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:
  -----------
  GMP | R&D -- replace all QwtCounters with QSpinBoxes, to better control and validate inputs ...


  Commit: 0ce7f8bbe5702044fddc573c6c7ea2002b72510d
      https://github.com/ehb54/ultrascan3/commit/0ce7f8bbe5702044fddc573c6c7ea2002b72510d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-07-13 (Sun, 13 Jul 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M test-docker.sh
    M test/common/qt_test_base.h
    M test/utils/CMakeLists.txt
    M test/utils/mock/mock_us_db2.h
    M test/utils/test_mock_us_db2.cpp
    R test/utils/test_mock_us_db2.h
    M test/utils/test_us_ana_profile.cpp
    R test/utils/test_us_ana_profile.h
    M test/utils/test_us_analyte.cpp
    R test/utils/test_us_analyte.h
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_math.h
    M test/utils/test_us_astfem_rsa.cpp
    R test/utils/test_us_astfem_rsa.h
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crc.cpp
    R test/utils/test_us_crc.h
    M test/utils/test_us_crypto.cpp
    R test/utils/test_us_crypto.h
    M test/utils/test_us_dataIO.cpp
    R test/utils/test_us_dataIO.h
    M test/utils/test_us_datafiles.cpp
    R test/utils/test_us_datafiles.h
    M test/utils/test_us_db2.cpp
    R test/utils/test_us_db2.h
    M test/utils/test_us_math2.cpp
    R test/utils/test_us_math2.h
    M test/utils/test_us_matrix.cpp
    R test/utils/test_us_matrix.h
    M test/utils/test_us_memory.cpp
    R test/utils/test_us_memory.h
    M test/utils/test_us_model.cpp
    R test/utils/test_us_model.h
    M test/utils/test_us_project.cpp
    R test/utils/test_us_project.h
    M test/utils/test_us_settings.cpp
    R test/utils/test_us_settings.h
    M test/utils/test_us_simparms.cpp
    R test/utils/test_us_simparms.h
    M test/utils/test_us_stiffbase.cpp
    R test/utils/test_us_stiffbase.h
    M test/utils/test_us_time_state.cpp
    R test/utils/test_us_time_state.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    M utils/us_analyte.cpp
    M utils/us_analyte.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_dataIO.cpp
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_rotor.cpp
    M utils/us_rotor.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_time_state.cpp
    M utils/us_time_state.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  ius_db2 build


  Commit: f8117c1eed92f953f483005cb49d40818b971cc9
      https://github.com/ehb54/ultrascan3/commit/f8117c1eed92f953f483005cb49d40818b971cc9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-28 (Mon, 28 Jul 2025)

  Changed paths:
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp

  Log Message:
  -----------
  GMP | R&D -- change ranges for dd-hh-mm-ss QSpinBoxes in 1. EXP.: 3. Speeds...


  Commit: b04c6a0e3ca869fe82ecb0c371d7429d546a479c
      https://github.com/ehb54/ultrascan3/commit/b04c6a0e3ca869fe82ecb0c371d7429d546a479c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-29 (Tue, 29 Jul 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  GMP | R&D -- MWL exp.: remove lambda-start/end buttons as spurious user interactions.....


  Commit: 95345c95c9d0a94b098e06a51f808abb44eca73c
      https://github.com/ehb54/ultrascan3/commit/95345c95c9d0a94b098e06a51f808abb44eca73c
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

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

  Log Message:
  -----------
  add widgets and methods to switch between the constant and varying z-values


  Commit: f1bc04efe3561e38ed1e9efb0ea052d095e0bdc9
      https://github.com/ehb54/ultrascan3/commit/f1bc04efe3561e38ed1e9efb0ea052d095e0bdc9
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-05 (Tue, 05 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: a new widget US_Grid_ZFunction added to set a function for varying z-values


  Commit: 9fefa61cdfe86961bddcc680ce15393cc20a58a4
      https://github.com/ehb54/ultrascan3/commit/9fefa61cdfe86961bddcc680ce15393cc20a58a4
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor.cpp: large update in GUI in the z-value function setter


  Commit: 16bf97037e8256a037e5ebe4007eafefbb000e2c
      https://github.com/ehb54/ultrascan3/commit/16bf97037e8256a037e5ebe4007eafefbb000e2c
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: fixed the issue with labeling and min/max of the dependent variables


  Commit: 24be34a5c69ff149a560999f823643c7b0792349
      https://github.com/ehb54/ultrascan3/commit/24be34a5c69ff149a560999f823643c7b0792349
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: finishe curve fitting and data plotting


  Commit: 9400854e36aec49322a546bb77d2b71df01a6ab3
      https://github.com/ehb54/ultrascan3/commit/9400854e36aec49322a546bb77d2b71df01a6ab3
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  s_grid_editor: correct plot min/max. rename min and max labels of the z-axis


  Commit: 43b41962e22e4af8e1616b048ce38b8c3714aafa
      https://github.com/ehb54/ultrascan3/commit/43b41962e22e4af8e1616b048ce38b8c3714aafa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-08 (Fri, 08 Aug 2025)

  Changed paths:
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge pull request #250 from ehb54/master

Bring the branch into up-to-date state with the master


  Commit: d4427c298c0021926269eced3660ad13ddb57da1
      https://github.com/ehb54/ultrascan3/commit/d4427c298c0021926269eced3660ad13ddb57da1
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-08 (Fri, 08 Aug 2025)

  Changed paths:
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M utils/us_model.cpp
    M utils/us_model.h

  Log Message:
  -----------
  completed US_Grid_ZFunction and add functions to parse z expression


  Commit: b28b060a27873c104daa81b246b10d28c06719a7
      https://github.com/ehb54/ultrascan3/commit/b28b060a27873c104daa81b246b10d28c06719a7
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

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

  Log Message:
  -----------
  renamed some of slots. set z-value function is merged to the main program.


  Commit: 9502025efbe734d0d076441a4ce57152c1cb5be1
      https://github.com/ehb54/ultrascan3/commit/9502025efbe734d0d076441a4ce57152c1cb5be1
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

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

  Log Message:
  -----------
  update some variable name and pick a new sorting approach


  Commit: 82dba023d20a191fd66a944d637a5c2ad2b16a87
      https://github.com/ehb54/ultrascan3/commit/82dba023d20a191fd66a944d637a5c2ad2b16a87
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

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

  Log Message:
  -----------
  completed import/export the model file


  Commit: 6c42a3106a9fc648137eb52b102fd9906fd2e1dc
      https://github.com/ehb54/ultrascan3/commit/6c42a3106a9fc648137eb52b102fd9906fd2e1dc
  Author: SophiaBird95 <135044923+SophiaBird95 at users.noreply.github.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Merge pull request #243 from ehb54/alexey-dev-issue529

GMP | R&D -- MWL exp.: remove lambda-start/end buttons as spurious user intractions


  Commit: a467c94674c461b9cdf1bf4861ff3b0d826153c4
      https://github.com/ehb54/ultrascan3/commit/a467c94674c461b9cdf1bf4861ff3b0d826153c4
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

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

  Log Message:
  -----------
  parse parameters that already set up in the set-function widget


  Commit: f11e93fa0fdafa964feeb508673735618375692c
      https://github.com/ehb54/ultrascan3/commit/f11e93fa0fdafa964feeb508673735618375692c
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: put comments in the header file.


  Commit: 1d528556d364d7b6609e4bd1bdd42e511a7de5a7
      https://github.com/ehb54/ultrascan3/commit/1d528556d364d7b6609e4bd1bdd42e511a7de5a7
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/master' into issue_532


  Commit: d3d86f69dd9b0447a7a21aa29b0b9fccab83f8fa
      https://github.com/ehb54/ultrascan3/commit/d3d86f69dd9b0447a7a21aa29b0b9fccab83f8fa
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    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
    M us_somo/somo/doc/manual/somo/somo_cluster_config.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html

  Log Message:
  -----------
  somo doc updates


  Commit: a2305a2a45f9bc2b4172267de5ac724cd8ffc3d7
      https://github.com/ehb54/ultrascan3/commit/a2305a2a45f9bc2b4172267de5ac724cd8ffc3d7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    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
    A us_somo/develop/include/us_revision.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/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.cpp
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_dirhist.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_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_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

  Log Message:
  -----------
  somo updates


  Commit: 535c6595f0301d0e1fd51fde59f6be1526723374
      https://github.com/ehb54/ultrascan3/commit/535c6595f0301d0e1fd51fde59f6be1526723374
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp

  Log Message:
  -----------
  widen zeno hydro window


  Commit: 067234bbefc26d45806d7b7158a217a02a231acc
      https://github.com/ehb54/ultrascan3/commit/067234bbefc26d45806d7b7158a217a02a231acc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h

  Log Message:
  -----------
  review updates


  Commit: 010cbe3ff2174263913aa0739e19022fba47b4e5
      https://github.com/ehb54/ultrascan3/commit/010cbe3ff2174263913aa0739e19022fba47b4e5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_config.cpp

  Log Message:
  -----------
  review updates


  Commit: 7c8812172d1813b891f93df82d27f1cb5a9e5540
      https://github.com/ehb54/ultrascan3/commit/7c8812172d1813b891f93df82d27f1cb5a9e5540
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_config.cpp

  Log Message:
  -----------
  review updates


  Commit: f767720f6aacfc70d69615a82f364cb9e31e4d06
      https://github.com/ehb54/ultrascan3/commit/f767720f6aacfc70d69615a82f364cb9e31e4d06
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_config.cpp

  Log Message:
  -----------
  review updates


  Commit: bdd0264a5a222af75694013a39418b3df8caaf62
      https://github.com/ehb54/ultrascan3/commit/bdd0264a5a222af75694013a39418b3df8caaf62
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp

  Log Message:
  -----------
  review updates


  Commit: 46e6d45623e94e8ee5f4caee294f0d4f725cf040
      https://github.com/ehb54/ultrascan3/commit/46e6d45623e94e8ee5f4caee294f0d4f725cf040
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp

  Log Message:
  -----------
  review updates


  Commit: f7f4c399680fe23d645fa3995b1d2666f48a0d05
      https://github.com/ehb54/ultrascan3/commit/f7f4c399680fe23d645fa3995b1d2666f48a0d05
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_util.cpp

  Log Message:
  -----------
  review updates


  Commit: 15b11afbf5ab46b92562c790b64ab027ad3a4a81
      https://github.com/ehb54/ultrascan3/commit/15b11afbf5ab46b92562c790b64ab027ad3a4a81
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M utils/us_model.cpp
    M utils/us_model.h

  Log Message:
  -----------
  Merge pull request #251 from samo38/issue_532

Ticket 532: Custom Grid Enhancement


  Commit: c488e35264600c64881f4e2b9a64eda47383e724
      https://github.com/ehb54/ultrascan3/commit/c488e35264600c64881f4e2b9a64eda47383e724
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-15 (Fri, 15 Aug 2025)

  Changed paths:
    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
    A us_somo/develop/include/us_revision.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/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_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_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_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
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    A us_somo/develop/src/us_hydrodyn_saxs_buffer_fit.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_buffer_gui.cpp
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    A us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
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    M us_somo/develop/src/us_saxs_util_iqq.cpp
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    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
    M us_somo/somo/doc/manual/somo/somo_cluster_config.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html

  Log Message:
  -----------
  Merge pull request #253 from ehb54/somo-pre-auc2025

Somo pre auc2025


  Commit: f57e5fb621d9deecb494bea705f4921181d75d2f
      https://github.com/ehb54/ultrascan3/commit/f57e5fb621d9deecb494bea705f4921181d75d2f
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-15 (Fri, 15 Aug 2025)

  Changed paths:
    R us_somo/develop/include/us_revision.h

  Log Message:
  -----------
  Delete us_somo/develop/include/us_revision.h

File should not be in the master branch


  Commit: b3e7a2ce827a2aa01fc3ea379e3f7d31f3ae2041
      https://github.com/ehb54/ultrascan3/commit/b3e7a2ce827a2aa01fc3ea379e3f7d31f3ae2041
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-15 (Fri, 15 Aug 2025)

  Changed paths:
    R us_somo/develop/include/us_revision.h

  Log Message:
  -----------
  Merge pull request #254 from ehb54/ehb54-issue-538-1

Delete us_somo/develop/include/us_revision.h


  Commit: e6f85d995a07a80e2f9d856998eae8b128628daa
      https://github.com/ehb54/ultrascan3/commit/e6f85d995a07a80e2f9d856998eae8b128628daa
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-16 (Sat, 16 Aug 2025)

  Changed paths:
    A us_somo/somo/doc/manual/somo/somo_ZENO_correction_warning.png

  Log Message:
  -----------
  missing manual page


  Commit: 2c7eb240d79827f5dfff035736fdf12f190e0cba
      https://github.com/ehb54/ultrascan3/commit/2c7eb240d79827f5dfff035736fdf12f190e0cba
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-16 (Sat, 16 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us3_defines.h
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  somo - fix for windows unicode


  Commit: b6169ad5a2b7f4daab15c47ac7732818cc7c68f2
      https://github.com/ehb54/ultrascan3/commit/b6169ad5a2b7f4daab15c47ac7732818cc7c68f2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-16 (Sat, 16 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  additional comment line


  Commit: b43e6bb7fdc3a74faaf03cdc5edf23c76875b783
      https://github.com/ehb54/ultrascan3/commit/b43e6bb7fdc3a74faaf03cdc5edf23c76875b783
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-17 (Sun, 17 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us3_defines.h
    M us_somo/develop/src/us_saxs_util_static.cpp
    A us_somo/somo/doc/manual/somo/somo_ZENO_correction_warning.png

  Log Message:
  -----------
  Merge pull request #255 from ehb54/ehb54-issue-538-2

missing manual page, special character issue on windows


  Commit: d1d54f83278fbf935b3d77dd5369947ee304a9f8
      https://github.com/ehb54/ultrascan3/commit/d1d54f83278fbf935b3d77dd5369947ee304a9f8
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-08-19 (Tue, 19 Aug 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
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  FIX: Adjust the calculation of the standard deviation for the weights


  Commit: 42cef0425363b1b72f8c2a1d0d9346f1f00773b0
      https://github.com/ehb54/ultrascan3/commit/42cef0425363b1b72f8c2a1d0d9346f1f00773b0
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-08-19 (Tue, 19 Aug 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge pull request #256 from ehb54/lukas/us_ga_init_stddev

FIX: Adjust the calculation of the standard deviation for the weights


  Commit: 76e2cf6ae4e764993cbd9d37d1bd086413514e3d
      https://github.com/ehb54/ultrascan3/commit/76e2cf6ae4e764993cbd9d37d1bd086413514e3d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .gitignore
    M test-docker.sh
    A test/README
    R test/README.md
    M test/utils/test_us_ana_profile.cpp
    M test/utils/test_us_analyte.cpp
    M test/utils/test_us_astfem_math.cpp
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_crypto.cpp
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_math2.cpp
    M test/utils/test_us_matrix.cpp
    M test/utils/test_us_memory.cpp
    M test/utils/test_us_model.cpp
    M test/utils/test_us_project.cpp
    M test/utils/test_us_settings.cpp
    M test/utils/test_us_stiffbase.cpp
    M test/utils/test_us_time_state.cpp
    M test/utils/test_us_util.cpp

  Log Message:
  -----------
  working set of util unit tests


  Commit: 3a4240895ec21be113a64f6d852aa70cdc0f9455
      https://github.com/ehb54/ultrascan3/commit/3a4240895ec21be113a64f6d852aa70cdc0f9455
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_tmst_plot.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils

# Conflicts:
#	utils/us_simparms.cpp


  Commit: eb5398d2831269197d566f36400b5f80c87ac2b1
      https://github.com/ehb54/ultrascan3/commit/eb5398d2831269197d566f36400b5f80c87ac2b1
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.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/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_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_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_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
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    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
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    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
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    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
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    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
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    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
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    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/us_model.cpp
    M utils/us_model.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 6c17ff96ca055f6cc43eeb2532d0eceab53580b3
      https://github.com/ehb54/ultrascan3/commit/6c17ff96ca055f6cc43eeb2532d0eceab53580b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_solution.cpp

  Log Message:
  -----------
  set to lowercase ius_db2.h


  Commit: 483c6d095b00b75710d4feeb2d9b996f0a4bd213
      https://github.com/ehb54/ultrascan3/commit/483c6d095b00b75710d4feeb2d9b996f0a4bd213
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M test-docker.sh

  Log Message:
  -----------
  add cmake hint file


  Commit: 76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
      https://github.com/ehb54/ultrascan3/commit/76997c2b070b1a6fdab90be7c72e7ae8d8e7271f
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M utils/us_simparms.cpp

  Log Message:
  -----------
  iusdb changes


  Commit: 295b4c9f222964264a4f4f2c9890d5b9f9d61f24
      https://github.com/ehb54/ultrascan3/commit/295b4c9f222964264a4f4f2c9890d5b9f9d61f24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M utils/ius_db2.h

  Log Message:
  -----------
  iusdb add qstring constuctor, turn off static analysis, move safe directory config


  Commit: 4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
      https://github.com/ehb54/ultrascan3/commit/4ba0f871fcfc325f8d6405a2a94f8ffdca1b09e3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-27 (Wed, 27 Aug 2025)

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

  Log Message:
  -----------
  error in gui build related to iusdb2


  Commit: 44bab627dcc91b01e021d5332de8d038b7bc3de4
      https://github.com/ehb54/ultrascan3/commit/44bab627dcc91b01e021d5332de8d038b7bc3de4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-28 (Thu, 28 Aug 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  GMP | R&D: 2. LIVE_UPDATE -- potential fixes for dropped usiab-to-optima connection during various live update stages...


  Commit: 54c57691b594fde24dc40f2e99e4c3f485207899
      https://github.com/ehb54/ultrascan3/commit/54c57691b594fde24dc40f2e99e4c3f485207899
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-28 (Thu, 28 Aug 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  [1]GMP | R&D: 2. LIVE_UPDATE -- potential fixes for dropped usiab-to-optima connection during various live update stages...


  Commit: 6eb23eb217129f6cfa083e4c2d132b81eeb79449
      https://github.com/ehb54/ultrascan3/commit/6eb23eb217129f6cfa083e4c2d132b81eeb79449
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-28 (Thu, 28 Aug 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  [2]GMP | R&D: 2. LIVE_UPDATE -- potential fixes for dropped usiab-to-optima connection during various live update stages...


  Commit: b8424a8bc274fff5f4fb289c552e31023d1ec512
      https://github.com/ehb54/ultrascan3/commit/b8424a8bc274fff5f4fb289c552e31023d1ec512
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-28 (Thu, 28 Aug 2025)

  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: Run MANAGER -- fix for the wrong event on refreshig Optima Runs Statuses causing forced setting new experiment upon attemt to re-attach...


  Commit: a6089455c047284229de979dc3cff6160bedc1e0
      https://github.com/ehb54/ultrascan3/commit/a6089455c047284229de979dc3cff6160bedc1e0
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-08-29 (Fri, 29 Aug 2025)

  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 #258 from ehb54/alexey-dev-issue545

GMP | R&D: Run MANAGER -- fix for the wrong event on refreshig Optima?


  Commit: 55c201891699765e68d8771a3dd08daf89b25169
      https://github.com/ehb54/ultrascan3/commit/55c201891699765e68d8771a3dd08daf89b25169
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-08-29 (Fri, 29 Aug 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Merge pull request #257 from ehb54/alexey-dev-issue544

GMP | R&D: 2. LIVE_UPDATE -- potential fixes for dropped usiab-to-optima


  Commit: 217485a90c5e92e0e810e5e3dfe2dac0177b8b35
      https://github.com/ehb54/ultrascan3/commit/217485a90c5e92e0e810e5e3dfe2dac0177b8b35
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    R admin/test/cmake/hints.cmake
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakelists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_convert/us_select_triples.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
    A programs/us_experiment/CMakeLists.txt
    A programs/us_fematch/CMakeLists.txt
    A programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_pcsa/us_pcsa.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    A programs/us_query_rmsd/CMakeLists.txt
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_astfem_rsa.cpp
    M test/utils/test_us_buffer.cpp
    M test/utils/test_us_db2.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  error in build related to iusdb2, cmake build for programs, and working unit tests


  Commit: 8401655782f10eb593ea8537ea59378e3da8f03b
      https://github.com/ehb54/ultrascan3/commit/8401655782f10eb593ea8537ea59378e3da8f03b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  move unit tests trigger to separate file


  Commit: 73021e71e98437f3583fc6edcaf0fe2faf72d5fd
      https://github.com/ehb54/ultrascan3/commit/73021e71e98437f3583fc6edcaf0fe2faf72d5fd
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    M programs/us_com_project/CMakelists.txt
    A qwtplot3d/CMakeLists.txt

  Log Message:
  -----------
  add us_com_project cmakelists


  Commit: c9030ec25f5d2ce4547c140beaf0d06baa785f4a
      https://github.com/ehb54/ultrascan3/commit/c9030ec25f5d2ce4547c140beaf0d06baa785f4a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

  Changed paths:
    A programs/us_com_project/CMakeLists.txt
    R programs/us_com_project/CMakelists.txt

  Log Message:
  -----------
  fix us_com_project cmakelists had lowercase l in name


  Commit: 7edcb7cb1815454a3c1517671b8f46ba157b7fd5
      https://github.com/ehb54/ultrascan3/commit/7edcb7cb1815454a3c1517671b8f46ba157b7fd5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml should not run and not send email


  Commit: a414cfc8f6a9b899f987a41925b89b2a948b954a
      https://github.com/ehb54/ultrascan3/commit/a414cfc8f6a9b899f987a41925b89b2a948b954a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml running but non-failing


  Commit: 09d7e2075e6ba517445079e50e2410866d36ef05
      https://github.com/ehb54/ultrascan3/commit/09d7e2075e6ba517445079e50e2410866d36ef05
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml install libqwt-qt5-dev


  Commit: 6014d3b78be1f58f196982b8e963eb9a1fd10650
      https://github.com/ehb54/ultrascan3/commit/6014d3b78be1f58f196982b8e963eb9a1fd10650
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 86802e7c8b63d5dafae200d92ab4edd449a76122
      https://github.com/ehb54/ultrascan3/commit/86802e7c8b63d5dafae200d92ab4edd449a76122
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml use cmake


  Commit: 1c1fe3aebbc7885934e26733499fdc6e3443cd25
      https://github.com/ehb54/ultrascan3/commit/1c1fe3aebbc7885934e26733499fdc6e3443cd25
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-01 (Mon, 01 Sep 2025)

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

  Log Message:
  -----------
  modifed static-analysis.yml remove format check


  Commit: 545dd0c591ceb5f40b85403fe9d72a8dc2079608
      https://github.com/ehb54/ultrascan3/commit/545dd0c591ceb5f40b85403fe9d72a8dc2079608
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml only check changed files


  Commit: ff38446e4155e613f61b9ccfdadc5141796dba1d
      https://github.com/ehb54/ultrascan3/commit/ff38446e4155e613f61b9ccfdadc5141796dba1d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: 44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
      https://github.com/ehb54/ultrascan3/commit/44dc6b5ad0d3a3b1288a71a6096e71bcf767d2fb
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  fix static-analysis.yml env variable handling


  Commit: ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
      https://github.com/ehb54/ultrascan3/commit/ef4c4e8e42954ff80a0ef6df92e9b990b7edaa68
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  mod workflow triggers to push or pr on master only


  Commit: befe3e2ed9031970d5d93eb3b0080c35868d586b
      https://github.com/ehb54/ultrascan3/commit/befe3e2ed9031970d5d93eb3b0080c35868d586b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

  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.: 8.Aprofile -- custom grid implementation...


  Commit: a757689d32acc3aff80b1e0c9b5d4f580c01ffc9
      https://github.com/ehb54/ultrascan3/commit/a757689d32acc3aff80b1e0c9b5d4f580c01ffc9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  [2]GMP | 1. EXP.: 8.Aprofile -- custom grid implementation...


  Commit: 6f9f6d81148a6128933c1a30c8960fc7b0ca9b18
      https://github.com/ehb54/ultrascan3/commit/6f9f6d81148a6128933c1a30c8960fc7b0ca9b18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

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

  Log Message:
  -----------
  [3]GMP | 1. EXP.: 8.Aprofile -- custom grid implementation...


  Commit: 826cea37317d3d85e5a6c1e9f49a6f11a4456568
      https://github.com/ehb54/ultrascan3/commit/826cea37317d3d85e5a6c1e9f49a6f11a4456568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  [4]GMP | 1. EXP.: 8.Aprofile -- custom grid implementation...


  Commit: f1864dd5785437638d1fe97073331b90c06e7c22
      https://github.com/ehb54/ultrascan3/commit/f1864dd5785437638d1fe97073331b90c06e7c22
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  [5]GMP | 1. EXP.: 8.Aprofile -- custom grid implementation...


  Commit: 71f24752c7eede2c90f377adda0d7a22bdacb0a5
      https://github.com/ehb54/ultrascan3/commit/71f24752c7eede2c90f377adda0d7a22bdacb0a5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  [6]GMP | 1. EXP.: 8.Aprofile -- custom grid implementation...


  Commit: b3affb0867414d2529ed378da6d7a56014388ffc
      https://github.com/ehb54/ultrascan3/commit/b3affb0867414d2529ed378da6d7a56014388ffc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-02 (Tue, 02 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP | 6. REPORT -- modify presentaion in case of CG...


  Commit: f254035dd92e63c66f56cf040d8b7a153ccf21c1
      https://github.com/ehb54/ultrascan3/commit/f254035dd92e63c66f56cf040d8b7a153ccf21c1
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #259 from ehb54/alexey-dev-issue543

Alexey dev issue543: Custom Grid in GMP, GUI/protocol/report portions


  Commit: 42e26337f0dd52027b91e41ba3af0f9e1b626a24
      https://github.com/ehb54/ultrascan3/commit/42e26337f0dd52027b91e41ba3af0f9e1b626a24
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .gitignore
    R admin/codeql/custom-queries/cpp/codeql-pack.yml
    R admin/codeql/custom-queries/cpp/find-unused-functions.ql
    M gui/CMakeLists.txt
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_model_editor.cpp
    R gui/us_model_editor.h
    M gui/us_model_gui.cpp
    M gui/us_model_loader.h
    M gui/us_noise_loader.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_edit/us_edit.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  code cleanup before PR review


  Commit: 895bcceea66cf95608da4f456620659d8e9517d5
      https://github.com/ehb54/ultrascan3/commit/895bcceea66cf95608da4f456620659d8e9517d5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-04 (Thu, 04 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #260 from ehb54/master

commit update


  Commit: 19e27c3ec7093c10f143441101c85d0af09b12ac
      https://github.com/ehb54/ultrascan3/commit/19e27c3ec7093c10f143441101c85d0af09b12ac
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: better reporting of critical issues


  Commit: 3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
      https://github.com/ehb54/ultrascan3/commit/3d25a66f7dcdd4e3a849f5ea31ae253f22c303be
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/aaron-dev-test-utils' into aaron-dev-test-utils


  Commit: eaf7d5bc8dae71e71e890cbec10deb318fe0862c
      https://github.com/ehb54/ultrascan3/commit/eaf7d5bc8dae71e71e890cbec10deb318fe0862c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-05 (Fri, 05 Sep 2025)

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

  Log Message:
  -----------
  mod: artifact upload fix


  Commit: f04888d7116e9c5498dd5a316307e9f4dc238d40
      https://github.com/ehb54/ultrascan3/commit/f04888d7116e9c5498dd5a316307e9f4dc238d40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

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

  Log Message:
  -----------
  fix: critical static analysis only


  Commit: d9ed24af5742fb54910d7c1d9873b57c528b4661
      https://github.com/ehb54/ultrascan3/commit/d9ed24af5742fb54910d7c1d9873b57c528b4661
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-06 (Sat, 06 Sep 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/FindQwt.cmake
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/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
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_settings.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: address review comments


  Commit: 52d2e12f19167416a58de29b71876a11edd2caf6
      https://github.com/ehb54/ultrascan3/commit/52d2e12f19167416a58de29b71876a11edd2caf6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-12 (Fri, 12 Sep 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  GMP | 1. EXP.: 8.Aprofile -- [Add model ID to framework]custom grid implementation...


  Commit: 5c1814ae911784afd312e835594b931008d8bed4
      https://github.com/ehb54/ultrascan3/commit/5c1814ae911784afd312e835594b931008d8bed4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-12 (Fri, 12 Sep 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.: 8.Aprofile -- [Add model ID to framework]custom grid implementation...


  Commit: 4e5d8b4cc07c2a5c5065886cf61e61c76fafffad
      https://github.com/ehb54/ultrascan3/commit/4e5d8b4cc07c2a5c5065886cf61e61c76fafffad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-14 (Sun, 14 Sep 2025)

  Changed paths:
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  [2]GMP | 1. EXP.: 8.Aprofile -- [Add model ID to framework]custom grid implementation...ush


  Commit: 747e42f7732dc906533cbd0cd954e81e3e565d98
      https://github.com/ehb54/ultrascan3/commit/747e42f7732dc906533cbd0cd954e81e3e565d98
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

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

  Log Message:
  -----------
  GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: 0337b97ebfe25072971b60c29b4a2d390667da17
      https://github.com/ehb54/ultrascan3/commit/0337b97ebfe25072971b60c29b4a2d390667da17
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp

  Log Message:
  -----------
  [test1]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: 77987890dfd45f62499deda691795b2e88ed4c26
      https://github.com/ehb54/ultrascan3/commit/77987890dfd45f62499deda691795b2e88ed4c26
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp

  Log Message:
  -----------
  [test2]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: f0d642fb0b9364e641fb3119b5eb5f3d9a70d908
      https://github.com/ehb54/ultrascan3/commit/f0d642fb0b9364e641fb3119b5eb5f3d9a70d908
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

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

  Log Message:
  -----------
  [test4]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: cabec77d85cef315e34c7a7362b56b19524d3972
      https://github.com/ehb54/ultrascan3/commit/cabec77d85cef315e34c7a7362b56b19524d3972
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [test5]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: ffb3fb9dc2da42d44a60eaefd9a678aea956a204
      https://github.com/ehb54/ultrascan3/commit/ffb3fb9dc2da42d44a60eaefd9a678aea956a204
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-15 (Mon, 15 Sep 2025)

  Changed paths:
    M gui/us_model_loader.cpp

  Log Message:
  -----------
  [test6]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: 8373d17ba7f453a11426f8935218990b8e317f51
      https://github.com/ehb54/ultrascan3/commit/8373d17ba7f453a11426f8935218990b8e317f51
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [test77]GMP | 5. ANALYSIS -- fix for false 'no -FM data' message triggering for the newly developed custom grid analysis...


  Commit: d29359d571538fdcdba340546c1ace762f2585f7
      https://github.com/ehb54/ultrascan3/commit/d29359d571538fdcdba340546c1ace762f2585f7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

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

  Log Message:
  -----------
  Add function to check acceleration rate and first scan validity

Introduced `check_acceleration()` in `US_AstfemMath` to validate acceleration rates and detect potential issues with first scan timing. Enhanced error reporting for experiments with low acceleration or scans during acceleration phase. Updated header file accordingly.


  Commit: 00b9132e2f4a788b4b056a3277c0b52a4f0adec4
      https://github.com/ehb54/ultrascan3/commit/00b9132e2f4a788b4b056a3277c0b52a4f0adec4
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp

  Log Message:
  -----------
  Refactor speed step validation logic and integrate `check_acceleration()`

Replaced manual speed step validation with the `check_acceleration()` function from `US_AstfemMath`, improving modularity and error detection. Enhanced message box handling for better user feedback on scan timing and acceleration issues.


  Commit: b3b5449d21badd09a6c72964db5f09a1c6ac22ab
      https://github.com/ehb54/ultrascan3/commit/b3b5449d21badd09a6c72964db5f09a1c6ac22ab
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Replace manual acceleration checks with `check_acceleration()` helper

Streamlined acceleration validation using `US_AstfemMath::check_acceleration()` for improved modularity, reduced code redundancy, and enhanced error handling. Updated message box logic to display detailed user feedback when issues are detected.


  Commit: e7990f3902c576ee20053e446ae508e1d193ef29
      https://github.com/ehb54/ultrascan3/commit/e7990f3902c576ee20053e446ae508e1d193ef29
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Refactor message box logic and integrate updated `check_acceleration()` validation

Simplified acceleration validation by utilizing `US_AstfemMath::check_acceleration()`. Streamlined message box handling to improve readability and user feedback for experiments with acceleration issues.


  Commit: 31e99caf2928581de4943b1119be73a9436d1447
      https://github.com/ehb54/ultrascan3/commit/31e99caf2928581de4943b1119be73a9436d1447
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Remove obsolete low acceleration check and associated UI logic

Eliminated redundant low acceleration validation and message box logic from `us_experiment_gui_optima.cpp`, simplifying the code and improving maintainability.


  Commit: 91d63509d1f79d315225eff1b2d7fb5b6115ecc3
      https://github.com/ehb54/ultrascan3/commit/91d63509d1f79d315225eff1b2d7fb5b6115ecc3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_fematch/us_fematch.cpp

  Log Message:
  -----------
  Replace manual acceleration UI logic with `check_acceleration()` integration

Streamlined acceleration validation by utilizing `US_AstfemMath::check_acceleration()`. Removed redundant manual checks and simplified message box handling for improved user feedback and code maintainability.


  Commit: a460bef08c775745062f6fe891f2893e2002d117
      https://github.com/ehb54/ultrascan3/commit/a460bef08c775745062f6fe891f2893e2002d117
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp

  Log Message:
  -----------
  Replace manual acceleration UI logic with `check_acceleration()` integration

Streamlined acceleration validation by utilizing `US_AstfemMath::check_acceleration()`. Removed redundant manual checks and simplified message box handling for improved user feedback and code maintainability.


  Commit: 009aba4948371da1e6e6f05f46f5a11c092b324c
      https://github.com/ehb54/ultrascan3/commit/009aba4948371da1e6e6f05f46f5a11c092b324c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_reporter_gmp.cpp`

Replaced manual acceleration checks with `US_AstfemMath::check_acceleration()`, streamlining validation and improving error reporting with enhanced message box logic. Removed redundant code for better maintainability.


  Commit: bee67ad94ebbc7c9821dc0aad18e6bce737b4568
      https://github.com/ehb54/ultrascan3/commit/bee67ad94ebbc7c9821dc0aad18e6bce737b4568
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

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

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: 227d32eb57b85946a3d39e4643719738eeddabb5
      https://github.com/ehb54/ultrascan3/commit/227d32eb57b85946a3d39e4643719738eeddabb5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

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

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: fa44532656ec9a8863fe76d5878356f412f827fb
      https://github.com/ehb54/ultrascan3/commit/fa44532656ec9a8863fe76d5878356f412f827fb
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_vhw_enhanced.cpp`

Added validation for acceleration profiles using `US_AstfemMath::check_acceleration()`. Enhanced message box logic for user feedback and streamlined error handling for scan data issues.


  Commit: 3b4ade0ff450252975099029f53fae26589346a6
      https://github.com/ehb54/ultrascan3/commit/3b4ade0ff450252975099029f53fae26589346a6
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_analysis_base2.cpp` in order to add it to us_second_moment, us_dcdt, us_pcsa

Added acceleration validation leveraging `US_AstfemMath::check_acceleration()`. Enhanced message box logic for user feedback and streamlined error handling for scan data issues.


  Commit: 9fb462a87d5cfef990e583e0aa8dda091841052b
      https://github.com/ehb54/ultrascan3/commit/9fb462a87d5cfef990e583e0aa8dda091841052b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_fematch/us_resplot_fem.cpp

  Log Message:
  -----------
  [debug]GMP | 6. REPORT: CG -- ...


  Commit: 42982afb88ddce0d00ece507d399d59735905d72
      https://github.com/ehb54/ultrascan3/commit/42982afb88ddce0d00ece507d399d59735905d72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug1]GMP | 6. REPORT: CG -- ...


  Commit: 493798b230e227ab68985ca50882c28058efd160
      https://github.com/ehb54/ultrascan3/commit/493798b230e227ab68985ca50882c28058efd160
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug2]GMP | 6. REPORT: CG -- ...


  Commit: a468cc16f534c3769ca2b90b209848d226d596fc
      https://github.com/ehb54/ultrascan3/commit/a468cc16f534c3769ca2b90b209848d226d596fc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug3]GMP | 6. REPORT: CG -- ...


  Commit: 35851638d1fc647e0bd2dd3861e329898ac2fec1
      https://github.com/ehb54/ultrascan3/commit/35851638d1fc647e0bd2dd3861e329898ac2fec1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug4]GMP | 6. REPORT: CG -- ...


  Commit: 8de77f30a55f3d955960b24d9fc654f85a643da1
      https://github.com/ehb54/ultrascan3/commit/8de77f30a55f3d955960b24d9fc654f85a643da1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug5]GMP | 6. REPORT: CG -- ...


  Commit: 116f06f0e3cb97e592455a896ea074987b1d687d
      https://github.com/ehb54/ultrascan3/commit/116f06f0e3cb97e592455a896ea074987b1d687d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug5]GMP | 6. REPORT: CG -- ...


  Commit: ada9fc194b6107aa9234582f328928f990f49ab8
      https://github.com/ehb54/ultrascan3/commit/ada9fc194b6107aa9234582f328928f990f49ab8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-16 (Tue, 16 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [debug7]GMP | 6. REPORT: CG -- ...


  Commit: 32bb4b7a5dc2070311763e159ad64dab3cc648d4
      https://github.com/ehb54/ultrascan3/commit/32bb4b7a5dc2070311763e159ad64dab3cc648d4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Enhance advanced_config documentation with new flags

Added detailed descriptions for various configuration flags related to debugging and speed settings.


  Commit: b52f75b2a6792fda0bab5a3eb02250629eed0b4a
      https://github.com/ehb54/ultrascan3/commit/b52f75b2a6792fda0bab5a3eb02250629eed0b4a
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Update wording

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>


  Commit: 62d4ea94709d6f723457f2bc6436f79c5486ddae
      https://github.com/ehb54/ultrascan3/commit/62d4ea94709d6f723457f2bc6436f79c5486ddae
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Update hsclogo description in advanced_config


  Commit: 803cac4e0551cf55251878109066602030536089
      https://github.com/ehb54/ultrascan3/commit/803cac4e0551cf55251878109066602030536089
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M programs/us_fematch/us_fematch.cpp

  Log Message:
  -----------
  Integrate `check_acceleration()` in `us_fematch.cpp`

Replaced manual acceleration validation with `US_AstfemMath::check_acceleration()`. Improved error handling and message box logic to provide better user feedback for scan data issues.


  Commit: 6147e952e75e949c7809a98a21beb2107f87e395
      https://github.com/ehb54/ultrascan3/commit/6147e952e75e949c7809a98a21beb2107f87e395
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Clarify `check_acceleration()` documentation for return format and behavior


  Commit: d976a8685de0adc6d272b35cec81016a34e4a38e
      https://github.com/ehb54/ultrascan3/commit/d976a8685de0adc6d272b35cec81016a34e4a38e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

  Log Message:
  -----------
  Refactor `check_acceleration()` logic for improved readability and robustness

Simplified variable naming, added guards for edge cases, and clarified acceleration rate and time checks. Enhanced error messages to provide more detailed user feedback.


  Commit: 6c6ba45b05dacb1c10cf803c959c2b9b4bdbe14c
      https://github.com/ehb54/ultrascan3/commit/6c6ba45b05dacb1c10cf803c959c2b9b4bdbe14c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Fix incorrect dereference of `edata` in `check_acceleration()` call


  Commit: 103683b0b42e6d3ee23a86bb3749b3cc0aa08e11
      https://github.com/ehb54/ultrascan3/commit/103683b0b42e6d3ee23a86bb3749b3cc0aa08e11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Fix incorrect dereference of `edata` in `check_acceleration()` call within `us_reporter_gmp.cpp`


  Commit: 347ef44a538b0dfd5dd64c49aa7d9baecf6f1c03
      https://github.com/ehb54/ultrascan3/commit/347ef44a538b0dfd5dd64c49aa7d9baecf6f1c03
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-18 (Thu, 18 Sep 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Merge pull request #263 from ehb54/lukas/debug_text_docs

Document advanced settings debug text values/flags


  Commit: 9d51aa93fbdb6f1a84076e3ddd128210f701d29d
      https://github.com/ehb54/ultrascan3/commit/9d51aa93fbdb6f1a84076e3ddd128210f701d29d
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp

  Log Message:
  -----------
  Refactor speed profile and time state handling in `us_analysis_base2.cpp`

Refactored speed profile processing to improve clarity and maintainability. Added enhanced logic to handle time state files and initialization of simulation parameters. Simplified acceleration checks using `US_AstfemMath::check_acceleration()`.


  Commit: 1f7336dfecb15d81c71c88e6922196f0137c6431
      https://github.com/ehb54/ultrascan3/commit/1f7336dfecb15d81c71c88e6922196f0137c6431
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M utils/us_astfem_math.cpp

  Log Message:
  -----------
  Adjust `kT1Factor` initialization and format specifiers in error messages

Revised `kT1Factor` to use explicit calculation for enhanced clarity. Updated float formatting in error messages from 'g' to 'f' for consistent precision in user feedback.


  Commit: b29fc424db0d4aa7e5e60d830be2fbadb73666e1
      https://github.com/ehb54/ultrascan3/commit/b29fc424db0d4aa7e5e60d830be2fbadb73666e1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp

  Log Message:
  -----------
  Remove manual `check_acceleration()` validation in `us_2dsa.cpp`

Eliminated redundant acceleration validation logic and message box handling. Streamlined by removing unused `US_AstfemMath::check_acceleration()` integration.


  Commit: 626668c35b1cdd774c6ba744a7cd473feb548602
      https://github.com/ehb54/ultrascan3/commit/626668c35b1cdd774c6ba744a7cd473feb548602
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Simplify `check_results` bounds checks in message box handling across programs


  Commit: b21a559ee9e33fed395a785dbaa8f14fe58e9831
      https://github.com/ehb54/ultrascan3/commit/b21a559ee9e33fed395a785dbaa8f14fe58e9831
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-19 (Fri, 19 Sep 2025)

  Changed paths:
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp

  Log Message:
  -----------
  Remove unused `check_acceleration` logic and disable `update(0)` call in `us_vhw_enhanced.cpp` to prevent unnecessary update cycle


  Commit: a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
      https://github.com/ehb54/ultrascan3/commit/a4fcd0c5999879b9af70342cbf2a4d40b9d2b803
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-21 (Sun, 21 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: e49834c3a05a6ffbc730f24be564d3c319a06d2a
      https://github.com/ehb54/ultrascan3/commit/e49834c3a05a6ffbc730f24be564d3c319a06d2a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

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

  Log Message:
  -----------
  Add `calc_omega2t` functionality to `US_AstfemMath` for omega2t calculations

Introduced a new method `calc_omega2t` in `US_AstfemMath` to calculate omega2t values based on speed profiles, acceleration rates, and time parameters. Enhanced flexibility for processing speed step data.


  Commit: 046484c8433d54042b223de7aebd2b793424b6a9
      https://github.com/ehb54/ultrascan3/commit/046484c8433d54042b223de7aebd2b793424b6a9
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Refactor speed step simulation logic in `us_astfem_sim.cpp`

Streamlined speed profile processing by removing redundant legacy logic and incorporating `calc_omega2t` for precise omega2t and time grid calculations. Enhanced clarity and maintainability of simulation loop.


  Commit: 1246e6e3724e8a382585cc65e0208d3008bfbeeb
      https://github.com/ehb54/ultrascan3/commit/1246e6e3724e8a382585cc65e0208d3008bfbeeb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

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

  Log Message:
  -----------
  [1a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5e6c7f858d8e6163099c500c970c02e54801243b
      https://github.com/ehb54/ultrascan3/commit/5e6c7f858d8e6163099c500c970c02e54801243b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
      https://github.com/ehb54/ultrascan3/commit/5c98f81ac04ec7e465bdc36d6c858c27e3f146a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 5edb9ce91335769271fb5f593482a97dc4233059
      https://github.com/ehb54/ultrascan3/commit/5edb9ce91335769271fb5f593482a97dc4233059
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [4]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 9aff495b37873080961f8c231a3ce673377f80d3
      https://github.com/ehb54/ultrascan3/commit/9aff495b37873080961f8c231a3ce673377f80d3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
      https://github.com/ehb54/ultrascan3/commit/1351f83ecb06b104ec53c3eac4dfa8e1deb9e008
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [5a]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 321a8cba345ec3c3f2187e0ba10f28376fd49a3e
      https://github.com/ehb54/ultrascan3/commit/321a8cba345ec3c3f2187e0ba10f28376fd49a3e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [5b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 373ac0ac501856ea0df8f4f579f953d89ec810b0
      https://github.com/ehb54/ultrascan3/commit/373ac0ac501856ea0df8f4f579f953d89ec810b0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [6b-TEST]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ea3905ba9097c5eed14e034d6656fd0c84dff988
      https://github.com/ehb54/ultrascan3/commit/ea3905ba9097c5eed14e034d6656fd0c84dff988
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [6b-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
      https://github.com/ehb54/ultrascan3/commit/ed8dbfb27ca0afd51e92c0717d6e05536217b8b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [7-TEST- restore]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: df769b270aea86fedc2fb0da2875e71741354606
      https://github.com/ehb54/ultrascan3/commit/df769b270aea86fedc2fb0da2875e71741354606
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-22 (Mon, 22 Sep 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge pull request #262 from ehb54/lukas/bad-timestate

Bad timestate warnings


  Commit: 021924be498aba94508063128ff7d169d1d6c80c
      https://github.com/ehb54/ultrascan3/commit/021924be498aba94508063128ff7d169d1d6c80c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-23 (Tue, 23 Sep 2025)

  Changed paths:
    M gui/us_model_loader.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  Merge pull request #261 from ehb54/alexey-dev-issue553

Alexey dev issue553: GMP-Custom grid: pass also CG-modelID throught the framework


  Commit: 905f41462ec9dab9667e915d639af2970e21a7a4
      https://github.com/ehb54/ultrascan3/commit/905f41462ec9dab9667e915d639af2970e21a7a4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [proper settings of min/max for scan_beg|nth|end for different optics systems] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 671b8e4d0e4951014a52280942d6a6c9712f14fa
      https://github.com/ehb54/ultrascan3/commit/671b8e4d0e4951014a52280942d6a6c9712f14fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: d584fa48438a0f9d744b750a6abe23533cc48b52
      https://github.com/ehb54/ultrascan3/commit/d584fa48438a0f9d744b750a6abe23533cc48b52
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- [RESTORE--UNIT TEST for multi-channel run] init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 84f86b86f77bbcd33e113217d09cbda59701b58b
      https://github.com/ehb54/ultrascan3/commit/84f86b86f77bbcd33e113217d09cbda59701b58b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 8ecca10f20a347fd906905b16f8e85ef5afff22a
      https://github.com/ehb54/ultrascan3/commit/8ecca10f20a347fd906905b16f8e85ef5afff22a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: fe9b9031b3af683efa02792cf18ca46a51d376d8
      https://github.com/ehb54/ultrascan3/commit/fe9b9031b3af683efa02792cf18ca46a51d376d8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2 DEBUGS]GMP | 1. EXP.: AProfile && 4. EDIT -- init. steps and tests for configuring scans exclusion (every nth to be inscluded), saving && passing for downstream analysis and eporting...


  Commit: 4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
      https://github.com/ehb54/ultrascan3/commit/4c16cc30bec6d2d9ea234a0ad826339c18f1dc27
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP | 1. EXP.: AProfile && 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: dd3e9be9669f28156c33235c7e73db3040c614a5
      https://github.com/ehb54/ultrascan3/commit/dd3e9be9669f28156c33235c7e73db3040c614a5
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: 93c11d987df52db6a1d9484f4f49a7acb54bd4dc
      https://github.com/ehb54/ultrascan3/commit/93c11d987df52db6a1d9484f4f49a7acb54bd4dc
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Update CMakeLists.txt

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


  Commit: ea99232fad84d9c9e2e785ee18794694bb22b883
      https://github.com/ehb54/ultrascan3/commit/ea99232fad84d9c9e2e785ee18794694bb22b883
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M utils/CMakeLists.txt

  Log Message:
  -----------
  Update utils/CMakeLists.txt

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


  Commit: a1344544e53b2158a855ac3ddb3296bbb15d21e0
      https://github.com/ehb54/ultrascan3/commit/a1344544e53b2158a855ac3ddb3296bbb15d21e0
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Update gui/CMakeLists.txt

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


  Commit: 6115f78b236f317ecc7ce852c9541d8ac10084e4
      https://github.com/ehb54/ultrascan3/commit/6115f78b236f317ecc7ce852c9541d8ac10084e4
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-24 (Wed, 24 Sep 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  Update test/utils/CMakeLists.txt

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


  Commit: b1ff389cba607cd5f34556fb6945f050ad099ff8
      https://github.com/ehb54/ultrascan3/commit/b1ff389cba607cd5f34556fb6945f050ad099ff8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: b557af349d02a148cef58c38976319f129cf4afa
      https://github.com/ehb54/ultrascan3/commit/b557af349d02a148cef58c38976319f129cf4afa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

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

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
      https://github.com/ehb54/ultrascan3/commit/57f3b61a10ffe0edcfdee555dbf12a7a6d15dc11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
      https://github.com/ehb54/ultrascan3/commit/825febd6fda9e31b55b9c0e13a0f2af701b3c6e0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: 4f9217705b688c38c3e420a609c2692c23a7e160
      https://github.com/ehb54/ultrascan3/commit/4f9217705b688c38c3e420a609c2692c23a7e160
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [4]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: f8379662ac83a104ca49b29cc3b5a7f830944d05
      https://github.com/ehb54/ultrascan3/commit/f8379662ac83a104ca49b29cc3b5a7f830944d05
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [5]GMP | 6. REPORT -- display scan exclusion settings beg|nth|end|remaining in Scan section...


  Commit: e87ab944bf93815dda5842e3dadee3249c11a52c
      https://github.com/ehb54/ultrascan3/commit/e87ab944bf93815dda5842e3dadee3249c11a52c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_vector.cpp

  Log Message:
  -----------
  fix: cmake collision during build


  Commit: 4a401e5be566119b5510674930f3b4365211a052
      https://github.com/ehb54/ultrascan3/commit/4a401e5be566119b5510674930f3b4365211a052
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-09-25 (Thu, 25 Sep 2025)

  Changed paths:
    M programs/CMakeLists.txt

  Log Message:
  -----------
  fix: add QWT to us_program_common


  Commit: 036113902d7405af0d641ad3afb98b2010cef02f
      https://github.com/ehb54/ultrascan3/commit/036113902d7405af0d641ad3afb98b2010cef02f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 2e456f0922765ab66ffb5844fc6ef570a37ce431
      https://github.com/ehb54/ultrascan3/commit/2e456f0922765ab66ffb5844fc6ef570a37ce431
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    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

  Log Message:
  -----------
  Merge pull request #225 from ehb54/ehb54-issue-496

PAM for linux password for php


  Commit: 0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
      https://github.com/ehb54/ultrascan3/commit/0fa81d8ac6c3fc80cbfb121038e9a6a0cde634bf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_main.cpp

  Log Message:
  -----------
  [REstore form -- unit test for multi-channel case] GMP | 4. EDIT -- treat scan exclusion differently for ABDE vs. VELOCITY types (ABDE - usually only last scan remains for each triple, ensured manually; VEL. - based on AProfile's settings beg|nth|end)...


  Commit: 154500215bfe391bf9dd7fda43456fe170c3c834
      https://github.com/ehb54/ultrascan3/commit/154500215bfe391bf9dd7fda43456fe170c3c834
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

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

  Log Message:
  -----------
  us_grid_editor: update the program GUI to get the cusotm grid from the users


  Commit: 42b30b23222d6e9b070861a382ebe34ad77611ab
      https://github.com/ehb54/ultrascan3/commit/42b30b23222d6e9b070861a382ebe34ad77611ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP | 6. REPORT -- do not display scan exclusion settings Scan section if optics type not used...


  Commit: 9f8fa54c2859fc4a8c4f996ef37443963f0e4ab2
      https://github.com/ehb54/ultrascan3/commit/9f8fa54c2859fc4a8c4f996ef37443963f0e4ab2
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

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

  Log Message:
  -----------
  us_grid_editor: add function to parse a grid file


  Commit: f6b215b4f73633db8bee542cefd88da89761620b
      https://github.com/ehb54/ultrascan3/commit/f6b215b4f73633db8bee542cefd88da89761620b
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-26 (Fri, 26 Sep 2025)

  Changed paths:
    M programs/us_grid_editor/us_grid_editor.cpp

  Log Message:
  -----------
  us_grid_editor: save the user grid model locally and on DB


  Commit: 4ec94c4a344d53369ca022d39c166df3b0859490
      https://github.com/ehb54/ultrascan3/commit/4ec94c4a344d53369ca022d39c166df3b0859490
  Author: saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-09-27 (Sat, 27 Sep 2025)

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

  Log Message:
  -----------
  fixed the issue with resetting to the default after pasrsing the CSV file. Refine the functions to reload the model from DB and local drive


  Commit: f286c4ffff8050ccb898b5446f3915031c6b7585
      https://github.com/ehb54/ultrascan3/commit/f286c4ffff8050ccb898b5446f3915031c6b7585
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-09-27 (Sat, 27 Sep 2025)

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

  Log Message:
  -----------
  Merge pull request #264 from samo38/issue_563

Issue 563: Custom Grid Program


  Commit: e3282fcfa778c046776d3abf2a718a9617230b4d
      https://github.com/ehb54/ultrascan3/commit/e3282fcfa778c046776d3abf2a718a9617230b4d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  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 -- do not specify details on Scan exlusions of there were no any...


  Commit: 8a112ba9e5ae7859d58f117c486f2e52cbba2899
      https://github.com/ehb54/ultrascan3/commit/8a112ba9e5ae7859d58f117c486f2e52cbba2899
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [1]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d1287da6bdde6dcb79acc019617ea24b5d93d410
      https://github.com/ehb54/ultrascan3/commit/d1287da6bdde6dcb79acc019617ea24b5d93d410
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

  Changed paths:
    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 gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    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_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge pull request #265 from ehb54/master

add master


  Commit: 8dff3550c25c2827799de8e3f245f1f34a9044ab
      https://github.com/ehb54/ultrascan3/commit/8dff3550c25c2827799de8e3f245f1f34a9044ab
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-29 (Mon, 29 Sep 2025)

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

  Log Message:
  -----------
  [2]GMP | 6. REPORT -- do not specify details on Scan exlusions of there were no any...


  Commit: d927f1c7acffd7436189c83726111d960cbd1e2d
      https://github.com/ehb54/ultrascan3/commit/d927f1c7acffd7436189c83726111d960cbd1e2d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 4c3a97f136b46591a7381b85fb726ea2fb87f7f2
      https://github.com/ehb54/ultrascan3/commit/4c3a97f136b46591a7381b85fb726ea2fb87f7f2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

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

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
      https://github.com/ehb54/ultrascan3/commit/7c65e196caeaf47f46d74fe305d0dec5c3f6f4e1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- [Modified logic for--] do not allow remainig scans to be less than 3 per channel;restore otherwise...


  Commit: 07f7d5c89032aa8dac1c13fe611e51d8e076cfde
      https://github.com/ehb54/ultrascan3/commit/07f7d5c89032aa8dac1c13fe611e51d8e076cfde
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 232008ddbb42fa37d28890542961579241726f13
      https://github.com/ehb54/ultrascan3/commit/232008ddbb42fa37d28890542961579241726f13
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-09-30 (Tue, 30 Sep 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  [1]GMP | 1. EXP.:APorile:ScanExcls. -- backward compatibility with older protocols with no nth scan excl. settings...


  Commit: 3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
      https://github.com/ehb54/ultrascan3/commit/3eb9ae51c6a5f7fc763508aa6e322281d3540f3b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M test/utils/CMakeLists.txt

  Log Message:
  -----------
  fix: duplicate include removed


  Commit: 003fcead31be5da3e4a5744bd8b5a9a3adb9686d
      https://github.com/ehb54/ultrascan3/commit/003fcead31be5da3e4a5744bd8b5a9a3adb9686d
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h

  Log Message:
  -----------
  Merge pull request #267 from ehb54/alexey-dev-issue556

Alexey dev issue556: Scan Exclusion Profile Editor for AProfile in GMP #556


  Commit: 9b2e06a5e4a371044a913065222c7d91603e0085
      https://github.com/ehb54/ultrascan3/commit/9b2e06a5e4a371044a913065222c7d91603e0085
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intargal -- avoid loading editProfiles...


  Commit: abfa96706807a26b5b0642ed078a97acf01a3e18
      https://github.com/ehb54/ultrascan3/commit/abfa96706807a26b5b0642ed078a97acf01a3e18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  US_intergal -- restore editProfiles read; add debugs...


  Commit: d712bbbb0ceb306e036f428d4245c0e3b87c097b
      https://github.com/ehb54/ultrascan3/commit/d712bbbb0ceb306e036f428d4245c0e3b87c097b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [1]US_intergal -- restore editProfiles read; add debugs...


  Commit: 088595bbbb4e35e890cb8d2bf308945e0333f3f1
      https://github.com/ehb54/ultrascan3/commit/088595bbbb4e35e890cb8d2bf308945e0333f3f1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [2]US_intergal -- restore editProfiles read; add debugs...


  Commit: 15343601bc0774d196184c33adbddefab8430a11
      https://github.com/ehb54/ultrascan3/commit/15343601bc0774d196184c33adbddefab8430a11
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-02 (Thu, 02 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  [3]US_intergal -- create curves' labels from the model's desc...


  Commit: d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
      https://github.com/ehb54/ultrascan3/commit/d62e7b57ef0ea16676a289087f4e4ba7a92ef3f8
  Author: HabGab <gabirh at myumanitoba.ca>
  Date:   2025-10-03 (Fri, 03 Oct 2025)

  Changed paths:
    M programs/us_integral/us_integral.cpp

  Log Message:
  -----------
  Merge pull request #268 from ehb54/alexey-dev-issue562

Alexey dev issue562: Enable plotting CG-SG integral distr.


  Commit: 399d845e5667346225803b9ac45b753c7676e39d
      https://github.com/ehb54/ultrascan3/commit/399d845e5667346225803b9ac45b753c7676e39d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_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_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: f924d79f3ecf67db15ced074ac2b50a4cafc9c72
      https://github.com/ehb54/ultrascan3/commit/f924d79f3ecf67db15ced074ac2b50a4cafc9c72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [1] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
      https://github.com/ehb54/ultrascan3/commit/a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: 8f9f1257b799c491fa5629c912071eabb435388f
      https://github.com/ehb54/ultrascan3/commit/8f9f1257b799c491fa5629c912071eabb435388f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: c3a261985e7e3979e7a9a11fcad5c851e739f41b
      https://github.com/ehb54/ultrascan3/commit/c3a261985e7e3979e7a9a11fcad5c851e739f41b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: 3ad35587a1da03cc9926344ac40bb3d364a32d24
      https://github.com/ehb54/ultrascan3/commit/3ad35587a1da03cc9926344ac40bb3d364a32d24
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: d6a4a469c86320252916565b3bd860c07cab4b1f
      https://github.com/ehb54/ultrascan3/commit/d6a4a469c86320252916565b3bd860c07cab4b1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: d3528cb233647917b4f76c9423f9deae1983f2bd
      https://github.com/ehb54/ultrascan3/commit/d3528cb233647917b4f76c9423f9deae1983f2bd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: 8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
      https://github.com/ehb54/ultrascan3/commit/8b4d2dc93db3c9ce00f4cfcebac25a50f25ce7f2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-07 (Tue, 07 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M test/utils/test_us_astfem_math.cpp
    R test/utils/test_us_astfem_rsa.cpp

  Log Message:
  -----------
  Consolidated commit after cleanup


  Commit: 934f494e4683d95677c5a7051705426df529cf13
      https://github.com/ehb54/ultrascan3/commit/934f494e4683d95677c5a7051705426df529cf13
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-08 (Wed, 08 Oct 2025)

  Changed paths:
    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 doc/manual/advanced_config.body
    M gui/us_analysis_base2.cpp
    M gui/us_model_loader.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.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_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    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_vhw_enhanced/us_vhw_enhanced.cpp
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into aaron-dev-test-utils


  Commit: 4e54cb0bd0e5eda0aebea648780b89b67b47d482
      https://github.com/ehb54/ultrascan3/commit/4e54cb0bd0e5eda0aebea648780b89b67b47d482
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #234 from ehb54/aaron-dev-test-utils

Add: google mock framework, static code analysis


  Commit: 6dc67538e4d0efedcf66715d9f44781f3f8e27e4
      https://github.com/ehb54/ultrascan3/commit/6dc67538e4d0efedcf66715d9f44781f3f8e27e4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #269 from ehb54/master

Bring this branch to the latest master state


  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...


  Commit: 8d1c1b4dcbf1b2c698688d5aad236d07578858d5
      https://github.com/ehb54/ultrascan3/commit/8d1c1b4dcbf1b2c698688d5aad236d07578858d5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  GMP: 5. ANALYSIS: FITMEN -- disable update btn right after it's clicked...


  Commit: 34e1993274025890c5cceda224c19973aa5b2ae2
      https://github.com/ehb54/ultrascan3/commit/34e1993274025890c5cceda224c19973aa5b2ae2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #271 from ehb54/alexey-dev-issue576

GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise..


  Commit: bdba96a7dc97bb081790098cfb3d72bc10a32c18
      https://github.com/ehb54/ultrascan3/commit/bdba96a7dc97bb081790098cfb3d72bc10a32c18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #274 from ehb54/master

Bring to the current master state


  Commit: 7c722f2fc3f2a82a9d5063fe4aecc128f465873d
      https://github.com/ehb54/ultrascan3/commit/7c722f2fc3f2a82a9d5063fe4aecc128f465873d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #275 from ehb54/master

Bring to current master state


  Commit: 236ab6f7717916a81de574fbe27299f18683a06c
      https://github.com/ehb54/ultrascan3/commit/236ab6f7717916a81de574fbe27299f18683a06c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Prevent early exit when saving a new buffer to database


  Commit: 3edada407972c86d03c8f30822ebf6a3c1166357
      https://github.com/ehb54/ultrascan3/commit/3edada407972c86d03c8f30822ebf6a3c1166357
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Include *.ui and *.qrc in gui build to ensure all resources and forms are available


  Commit: 427e601f770f5eb39efb249bca9eb81b557561ae
      https://github.com/ehb54/ultrascan3/commit/427e601f770f5eb39efb249bca9eb81b557561ae
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Clean up debug statements and enhance comments

Removed commented debug statements and added clarifying comments for variable assignments.


  Commit: 0bd193389e5967e65d03d34b4ce6dcf0f3817f84
      https://github.com/ehb54/ultrascan3/commit/0bd193389e5967e65d03d34b4ce6dcf0f3817f84
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Merge pull request #280 from ehb54/lukas/cmake-gui-resources

Include *.ui and *.qrc in us_gui library


  Commit: 72ff576e489d378f03adc4296b68bd001b1c649e
      https://github.com/ehb54/ultrascan3/commit/72ff576e489d378f03adc4296b68bd001b1c649e
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.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_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #273 from ehb54/alexey-dev-issue567

Alexey dev issue567: Deal with dataDisk Pseudoabsorbance type && correct GUI representaitons of US_Edit scenarios


  Commit: eb8022621705540d2e5a0010b5141f3bd1620591
      https://github.com/ehb54/ultrascan3/commit/eb8022621705540d2e5a0010b5141f3bd1620591
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  Merge pull request #272 from ehb54/alexey-dev-issue575

GMP: 5. ANALYSIS: FITMEN -- disable update btn right after it's clicked..


  Commit: 18b990073be39e32a749536729cba62d576e6c98
      https://github.com/ehb54/ultrascan3/commit/18b990073be39e32a749536729cba62d576e6c98
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_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 #237 from ehb54/alexey-dev-issue521

Alexey dev issue521: Correct and read-only exp. time in channels reports, qspinboxes instead of qwtcounters to control input


  Commit: d131cbbccf4b88f4a39d285fb99a84ccfaacb536
      https://github.com/ehb54/ultrascan3/commit/d131cbbccf4b88f4a39d285fb99a84ccfaacb536
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 567202c3572f02c0b782f92791cac022e863829c
      https://github.com/ehb54/ultrascan3/commit/567202c3572f02c0b782f92791cac022e863829c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Merge pull request #278 from ehb54/lukas/us_buffer_saveToDB

Prevent early exit when saving a new buffer to database


  Commit: 2d1d5599a18b1105dd622fb570a284c2af9b3027
      https://github.com/ehb54/ultrascan3/commit/2d1d5599a18b1105dd622fb570a284c2af9b3027
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  us_astfem_sim: save TI, RI noises in the result directory


  Commit: 52692bf1ec74f08f07f036d50913983f0cb4902c
      https://github.com/ehb54/ultrascan3/commit/52692bf1ec74f08f07f036d50913983f0cb4902c
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  us_astfem_sim.cpp: fix writing the RI csv profile for multi-speed experiments


  Commit: 2bb6c53d1c011cceb17b9ebabc3e0700fea48879
      https://github.com/ehb54/ultrascan3/commit/2bb6c53d1c011cceb17b9ebabc3e0700fea48879
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
      https://github.com/ehb54/ultrascan3/commit/2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [[1]debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 5d05e1a2439de5fa9adb431619c350ae188fcf31
      https://github.com/ehb54/ultrascan3/commit/5d05e1a2439de5fa9adb431619c350ae188fcf31
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

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

  Log Message:
  -----------
  us_astfem_sim: save TI,RI noise profiles into the outout directory


  Commit: 883d73df2ac05d1717a2f924737d36a6ddda5a49
      https://github.com/ehb54/ultrascan3/commit/883d73df2ac05d1717a2f924737d36a6ddda5a49
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge pull request #282 from ehb54/alexey-dev-issue577

GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 1de51a8c4fb82a5cbb3cf09653f9e235a54c327c
      https://github.com/ehb54/ultrascan3/commit/1de51a8c4fb82a5cbb3cf09653f9e235a54c327c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

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

  Log Message:
  -----------
  Merge pull request #281 from samo38/issue_587

us_astfem_sim: save TI, RI noises in the result directory


  Commit: ecfbe0af9e3b7e855a5d67f491614c06b26261f1
      https://github.com/ehb54/ultrascan3/commit/ecfbe0af9e3b7e855a5d67f491614c06b26261f1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-15 (Wed, 15 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    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
    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_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.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
    A programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    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_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    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
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.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_solutedata.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.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_vhw_enhanced/us_vhw_enhanced.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
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/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_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_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_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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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.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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  merge master into ehb54-issue-553, conflicts manually resolved


Compare: https://github.com/ehb54/ultrascan3/compare/3fd01182e1ee...ecfbe0af9e3b

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From noreply at github.com  Wed Oct 15 14:19:05 2025
From: noreply at github.com (ehb54)
Date: Wed, 15 Oct 2025 13:19:05 -0700
Subject: [us-commits] [ehb54/ultrascan3] d19407: merge master into
 ehb54-issue-553, conflicts manua...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-533/ecfbe0-d19407@github.com>

  Branch: refs/heads/ehb54-issue-533
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d19407a738880744130ad2ac275bcd672ace631d
      https://github.com/ehb54/ultrascan3/commit/d19407a738880744130ad2ac275bcd672ace631d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  merge master into ehb54-issue-553, conflicts manually resolved



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From noreply at github.com  Wed Oct 15 18:13:14 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 15 Oct 2025 17:13:14 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-533/d19407-000000@github.com>

  Branch: refs/heads/ehb54-issue-533
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Oct 15 18:13:07 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 15 Oct 2025 17:13:07 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0fc8fc: issue 533 : convert
 QString::sprintf to asprintf i...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/1de51a-b94b4a@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0fc8fc48c10614b999f6720cdcc5ffeb354dd28f
      https://github.com/ehb54/ultrascan3/commit/0fc8fc48c10614b999f6720cdcc5ffeb354dd28f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_run_details2.cpp
    M gui/us_tmst_plot.cpp
    M gui/us_window_message.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.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_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    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_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.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_pcsa.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_vhw_combine.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

  Log Message:
  -----------
  issue 533 : convert QString::sprintf to asprintf in gui & programs


  Commit: 54079b9265341294439c9ae4167fc5a6cadad909
      https://github.com/ehb54/ultrascan3/commit/54079b9265341294439c9ae4167fc5a6cadad909
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M gui/us_extinctfitter_gui.cpp
    M gui/us_minimize.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_config/us_color.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  issue 533 : convert QString - varname.sprintf to varname = asprintf in gui & programs


  Commit: b31ecaceddee2236fab9e0fb4465885db648a952
      https://github.com/ehb54/ultrascan3/commit/b31ecaceddee2236fab9e0fb4465885db648a952
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_minimize.cpp
    M gui/us_run_details2.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_solutedata.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/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp

  Log Message:
  -----------
  issue 533 : convert QString - the last of sprintf in gui & programs


  Commit: 3fd01182e1ee82fcbf4e2dfc5710d5bf9bd99207
      https://github.com/ehb54/ultrascan3/commit/3fd01182e1ee82fcbf4e2dfc5710d5bf9bd99207
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp

  Log Message:
  -----------
  issue 533 : convert QString - the last of sprintf in gui & programs


  Commit: ecfbe0af9e3b7e855a5d67f491614c06b26261f1
      https://github.com/ehb54/ultrascan3/commit/ecfbe0af9e3b7e855a5d67f491614c06b26261f1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-15 (Wed, 15 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    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
    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_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_scan_excl_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.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
    A programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    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_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    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
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.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_solutedata.cpp
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_integral/us_integral.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.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_vhw_enhanced/us_vhw_enhanced.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
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/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_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_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_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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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.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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  merge master into ehb54-issue-553, conflicts manually resolved


  Commit: d19407a738880744130ad2ac275bcd672ace631d
      https://github.com/ehb54/ultrascan3/commit/d19407a738880744130ad2ac275bcd672ace631d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  merge master into ehb54-issue-553, conflicts manually resolved


  Commit: b94b4a3819d4ec6a71a8d0f0fbfac37d57b8299e
      https://github.com/ehb54/ultrascan3/commit/b94b4a3819d4ec6a71a8d0f0fbfac37d57b8299e
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_minimize.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_run_details2.cpp
    M gui/us_tmst_plot.cpp
    M gui/us_window_message.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_mpi_analysis/2dsa_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/pcsa_master.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_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_vhw_combine.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_viewer_gui.cpp
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #246 from ehb54/ehb54-issue-533

issue 533 : convert QString::sprintf to asprintf in gui & programs


Compare: https://github.com/ehb54/ultrascan3/compare/1de51a8c4fb8...b94b4a3819d4

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From noreply at github.com  Wed Oct 15 20:57:42 2025
From: noreply at github.com (HabGab)
Date: Wed, 15 Oct 2025 19:57:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0e9777: Octi 15
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/484daa-4d7446@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0e9777e91c2741b689d004a723d50a1fe076c54c
      https://github.com/ehb54/ultrascan3/commit/0e9777e91c2741b689d004a723d50a1fe076c54c
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M doc/manual/source/2dsa.rst
    A doc/manual/source/2dsa_analys.rst
    R doc/manual/source/2dsa_simulate.rst
    M doc/manual/source/_static/images/2dsa_analvv.png
    M doc/manual/source/_static/images/buffer_new.png
    A doc/manual/source/_static/images/buffer_new_spectrum.png
    A doc/manual/source/_static/images/buffer_spectrum.png
    A doc/manual/source/_static/images/edit_buffer_spec_menu.png
    A doc/manual/source/_static/images/sw_spectrum.png
    M doc/manual/source/_static/images/usfont-1.png
    R doc/manual/source/buffer.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
    M doc/manual/source/config.rst
    R doc/manual/source/fe_match.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
    R doc/manual/source/fe_match_simulate.rst
    M doc/manual/source/index.rst
    R doc/manual/source/index_index.rst
    M doc/manual/source/pcsa.rst
    M doc/manual/source/pcsa_analys.rst

  Log Message:
  -----------
  Octi 15


  Commit: 4d744647e9e7b10862d2d0e9354d81f1e07627b2
      https://github.com/ehb54/ultrascan3/commit/4d744647e9e7b10862d2d0e9354d81f1e07627b2
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    R doc/manual/source/2dsa.rst
    A doc/manual/source/2dsa/2dsa_adv.rst
    A doc/manual/source/2dsa/2dsa_analys.rst
    A doc/manual/source/2dsa/2dsa_main.rst
    A doc/manual/source/2dsa/index.rst
    R doc/manual/source/2dsa_analys.rst
    M doc/manual/source/_static/images/2dsa_resplot.png
    A doc/manual/source/_static/images/norm_gridplot.png
    R doc/manual/source/analyte.rst
    A doc/manual/source/analyte/analyte.rst
    A doc/manual/source/analyte/index.rst
    A doc/manual/source/experiment/index.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
    R doc/manual/source/gmp.rst
    A doc/manual/source/gmp/gmp.rst
    A doc/manual/source/gmp/index.rst
    M doc/manual/source/index.rst
    R doc/manual/source/pcsa.rst
    A doc/manual/source/pcsa/index.rst
    A doc/manual/source/pcsa/pcsa.rst
    A doc/manual/source/pcsa/pcsa_analys.rst
    A doc/manual/source/pcsa/pcsa_results.rst
    R doc/manual/source/pcsa_analys.rst
    R doc/manual/source/pcsa_results.rst
    A doc/manual/source/projects/index.rst
    A doc/manual/source/solutions/index.rst

  Log Message:
  -----------
  octo 15


Compare: https://github.com/ehb54/ultrascan3/compare/484daa758711...4d744647e9e7

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From noreply at github.com  Thu Oct 16 08:31:21 2025
From: noreply at github.com (ehb54)
Date: Thu, 16 Oct 2025 07:31:21 -0700
Subject: [us-commits] [ehb54/ultrascan3] 02cbec: us_gzip.cpp - remove
 useless deprecreated 'registe...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-591/000000-02cbec@github.com>

  Branch: refs/heads/ehb54-issue-591
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 02cbecf79d8b693a2499249cfce28aa7d58abf6b
      https://github.com/ehb54/ultrascan3/commit/02cbecf79d8b693a2499249cfce28aa7d58abf6b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-16 (Thu, 16 Oct 2025)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  us_gzip.cpp - remove useless deprecreated 'register' keyword



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From noreply at github.com  Thu Oct 16 23:17:48 2025
From: noreply at github.com (alexsav815)
Date: Thu, 16 Oct 2025 22:17:48 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue592/000000-b94b4a@github.com>

  Branch: refs/heads/alexey-dev-issue592
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Oct 16 23:39:33 2025
From: noreply at github.com (alexsav815)
Date: Thu, 16 Oct 2025 22:39:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] bb1099: GMP | R&D: 1. EXP.=> Speeds
 -- change signals/slot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue592/b94b4a-bb1099@github.com>

  Branch: refs/heads/alexey-dev-issue592
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bb10991bf7c251763f2aa53737e6574537102d34
      https://github.com/ehb54/ultrascan3/commit/bb10991bf7c251763f2aa53737e6574537102d34
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

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

  Log Message:
  -----------
  GMP | R&D: 1. EXP.=> Speeds -- change signals/slot sigs. in spinboxes for speed & acceler....



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From noreply at github.com  Fri Oct 17 06:02:48 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 17 Oct 2025 05:02:48 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue592/bb1099-000000@github.com>

  Branch: refs/heads/alexey-dev-issue592
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Oct 17 06:02:44 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 17 Oct 2025 05:02:44 -0700
Subject: [us-commits] [ehb54/ultrascan3] bb1099: GMP | R&D: 1. EXP.=> Speeds
 -- change signals/slot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/b94b4a-b59631@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bb10991bf7c251763f2aa53737e6574537102d34
      https://github.com/ehb54/ultrascan3/commit/bb10991bf7c251763f2aa53737e6574537102d34
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

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

  Log Message:
  -----------
  GMP | R&D: 1. EXP.=> Speeds -- change signals/slot sigs. in spinboxes for speed & acceler....


  Commit: b5963153ad855cd97a12fb72e6597d2f2684f421
      https://github.com/ehb54/ultrascan3/commit/b5963153ad855cd97a12fb72e6597d2f2684f421
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

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

  Log Message:
  -----------
  Merge pull request #284 from ehb54/alexey-dev-issue592

GMP | R&D: 1. EXP.=> Speeds -- change signals/slot sigs. in spinboxes?


Compare: https://github.com/ehb54/ultrascan3/compare/b94b4a3819d4...b5963153ad85

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From noreply at github.com  Fri Oct 17 06:31:31 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 05:31:31 -0700
Subject: [us-commits] [ehb54/ultrascan3] daee08: Refactor constructor
 initialization to replace nul...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QFlags/000000-daee08@github.com>

  Branch: refs/heads/lukas/qt6-QFlags
  Home:   https://github.com/ehb54/ultrascan3
  Commit: daee08ef80606ac9f5b82e6e92d3c3319d784081
      https://github.com/ehb54/ultrascan3/commit/daee08ef80606ac9f5b82e6e92d3c3319d784081
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_abstractrotor_gui.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_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.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_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.h
    M programs/us/us.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_astfem_sim/us_clipdata.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    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_ddist_combine/us_select_rundd.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_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_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_ga_init/us_ga_init.cpp
    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_globalequil.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_integral/us_delete_models.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_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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    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_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.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
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp

  Log Message:
  -----------
  Refactor constructor initialization to replace null pointers `(0, 0)` with `nullptr` and explicit `Qt::WindowFlags()` for improved code clarity and modern C++ standards compliance.



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From noreply at github.com  Fri Oct 17 06:49:53 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 05:49:53 -0700
Subject: [us-commits] [ehb54/ultrascan3] 31ff64: Replace deprecated
 `QFontMetrics::width()` with `Q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-width/000000-31ff64@github.com>

  Branch: refs/heads/lukas/qt6-width
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 31ff647d5d67c493fd31589da76c247dae579e47
      https://github.com/ehb54/ultrascan3/commit/31ff647d5d67c493fd31589da76c247dae579e47
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_widgets.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_ddist_combine/us_select_rundd.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_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_integral/us_delete_models.cpp
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp

  Log Message:
  -----------
  Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` across all affected files for compatibility with Qt 5.11 and above. Streamlines text measurement handling and ensures future proofing.



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From noreply at github.com  Fri Oct 17 07:01:25 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 06:01:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] d86efe: Initialize `koligo` to 0 in
 `us_associations_gui.c...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QFlags/daee08-d86efe@github.com>

  Branch: refs/heads/lukas/qt6-QFlags
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d86efe4f3b328918793421ae448d2eb5841785cc
      https://github.com/ehb54/ultrascan3/commit/d86efe4f3b328918793421ae448d2eb5841785cc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_associations_gui.cpp

  Log Message:
  -----------
  Initialize `koligo` to 0 in `us_associations_gui.cpp` to prevent potential usage of an uninitialized variable.



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From noreply at github.com  Fri Oct 17 08:33:26 2025
From: noreply at github.com (ehb54)
Date: Fri, 17 Oct 2025 07:33:26 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-591/02cbec-000000@github.com>

  Branch: refs/heads/ehb54-issue-591
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Oct 17 08:33:23 2025
From: noreply at github.com (ehb54)
Date: Fri, 17 Oct 2025 07:33:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] 02cbec: us_gzip.cpp - remove
 useless deprecreated 'registe...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/b59631-7e8e1a@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 02cbecf79d8b693a2499249cfce28aa7d58abf6b
      https://github.com/ehb54/ultrascan3/commit/02cbecf79d8b693a2499249cfce28aa7d58abf6b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-16 (Thu, 16 Oct 2025)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  us_gzip.cpp - remove useless deprecreated 'register' keyword


  Commit: 7e8e1a176e3f0215069784cf407c928c4c336793
      https://github.com/ehb54/ultrascan3/commit/7e8e1a176e3f0215069784cf407c928c4c336793
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  Merge pull request #283 from ehb54/ehb54-issue-591

us_gzip.cpp - remove useless deprecreated 'register' keyword


Compare: https://github.com/ehb54/ultrascan3/compare/b5963153ad85...7e8e1a176e3f

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From noreply at github.com  Fri Oct 17 09:24:20 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 08:24:20 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QFlags/d86efe-000000@github.com>

  Branch: refs/heads/lukas/qt6-QFlags
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Oct 17 09:24:18 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 08:24:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] daee08: Refactor constructor
 initialization to replace nul...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/7e8e1a-233334@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: daee08ef80606ac9f5b82e6e92d3c3319d784081
      https://github.com/ehb54/ultrascan3/commit/daee08ef80606ac9f5b82e6e92d3c3319d784081
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_abstractrotor_gui.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_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.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_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.h
    M programs/us/us.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_astfem_sim/us_clipdata.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    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_ddist_combine/us_select_rundd.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_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_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_ga_init/us_ga_init.cpp
    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_globalequil.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_integral/us_delete_models.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_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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    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_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.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
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp

  Log Message:
  -----------
  Refactor constructor initialization to replace null pointers `(0, 0)` with `nullptr` and explicit `Qt::WindowFlags()` for improved code clarity and modern C++ standards compliance.


  Commit: d86efe4f3b328918793421ae448d2eb5841785cc
      https://github.com/ehb54/ultrascan3/commit/d86efe4f3b328918793421ae448d2eb5841785cc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_associations_gui.cpp

  Log Message:
  -----------
  Initialize `koligo` to 0 in `us_associations_gui.cpp` to prevent potential usage of an uninitialized variable.


  Commit: 233334757bf486df06d554277c1ec4cf0d0310d2
      https://github.com/ehb54/ultrascan3/commit/233334757bf486df06d554277c1ec4cf0d0310d2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_abstractrotor_gui.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_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.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_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.h
    M programs/us/us.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_astfem_sim/us_clipdata.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    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_ddist_combine/us_select_rundd.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_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_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_ga_init/us_ga_init.cpp
    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_globalequil.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_integral/us_delete_models.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_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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    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_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.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
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp

  Log Message:
  -----------
  Merge pull request #285 from ehb54/lukas/qt6-QFlags

Deal with deprecated QFlags prior Qt6 migration


Compare: https://github.com/ehb54/ultrascan3/compare/7e8e1a176e3f...233334757bf4

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From noreply at github.com  Fri Oct 17 09:25:03 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 08:25:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] 31ff64: Replace deprecated
 `QFontMetrics::width()` with `Q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/233334-03ea18@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 31ff647d5d67c493fd31589da76c247dae579e47
      https://github.com/ehb54/ultrascan3/commit/31ff647d5d67c493fd31589da76c247dae579e47
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_widgets.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_ddist_combine/us_select_rundd.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_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_integral/us_delete_models.cpp
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp

  Log Message:
  -----------
  Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` across all affected files for compatibility with Qt 5.11 and above. Streamlines text measurement handling and ensures future proofing.


  Commit: 03ea185a14d6a79954e1b261b128dee91df5aeec
      https://github.com/ehb54/ultrascan3/commit/03ea185a14d6a79954e1b261b128dee91df5aeec
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_widgets.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_ddist_combine/us_select_rundd.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_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_integral/us_delete_models.cpp
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp

  Log Message:
  -----------
  Merge pull request #286 from ehb54/lukas/qt6-width

Replace deprecated QFontMetrics::width() with horizontalAdvance()


Compare: https://github.com/ehb54/ultrascan3/compare/233334757bf4...03ea185a14d6

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From noreply at github.com  Fri Oct 17 09:25:06 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 08:25:06 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-width/31ff64-000000@github.com>

  Branch: refs/heads/lukas/qt6-width
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Oct 17 09:40:58 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 08:40:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 738825: Add null checks before
 adding child items to make ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/03ea18-956516@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7388255d2bb422f8dca061365e459ac69e9267a4
      https://github.com/ehb54/ultrascan3/commit/7388255d2bb422f8dca061365e459ac69e9267a4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Add null checks before adding child items to make static analysis happy


  Commit: f3022f734322210c7a6d74c4d72f7d5871d7f9c2
      https://github.com/ehb54/ultrascan3/commit/f3022f734322210c7a6d74c4d72f7d5871d7f9c2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Fix formatting in us_data_loader.cpp


  Commit: 956516318c816bd92b269c913872f6eb9d952d91
      https://github.com/ehb54/ultrascan3/commit/956516318c816bd92b269c913872f6eb9d952d91
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Merge pull request #279 from ehb54/lukas/static_analysis_warnings

Add null checks before adding child items to make static analysis happy


Compare: https://github.com/ehb54/ultrascan3/compare/03ea185a14d6...956516318c81

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From noreply at github.com  Fri Oct 17 09:41:02 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 17 Oct 2025 08:41:02 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/static_analysis_warnings/f3022f-000000@github.com>

  Branch: refs/heads/lukas/static_analysis_warnings
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Oct 17 13:01:05 2025
From: noreply at github.com (ehb54)
Date: Fri, 17 Oct 2025 12:01:05 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8e2b7b: somo saxs hplc expose
 gaussian ampl min
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/aa99fd-8e2b7b@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8e2b7b02a84be80db618110bc48d42adfcf9af6c
      https://github.com/ehb54/ultrascan3/commit/8e2b7b02a84be80db618110bc48d42adfcf9af6c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    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/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp

  Log Message:
  -----------
  somo saxs hplc expose gaussian ampl min



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From noreply at github.com  Sat Oct 18 10:50:56 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Oct 2025 09:50:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] cefb4f: add: cmake build update
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/4e54cb-cefb4f@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cefb4f09592f41675136902739310639b3013aca
      https://github.com/ehb54/ultrascan3/commit/cefb4f09592f41675136902739310639b3013aca
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    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
    M gui/CMakeLists.txt
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    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
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_fit_meniscus/CMakeLists.txt
    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
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/bootstrap.sh
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt
    M utils/us_defines.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  add: cmake build update



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From noreply at github.com  Sat Oct 18 10:51:20 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Oct 2025 09:51:20 -0700
Subject: [us-commits] [ehb54/ultrascan3] aaeaad: add: vcpkg submodule
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/cefb4f-aaeaad@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: aaeaad6c02761cee619ff74a0115ebbed284238d
      https://github.com/ehb54/ultrascan3/commit/aaeaad6c02761cee619ff74a0115ebbed284238d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    A .gitmodules

  Log Message:
  -----------
  add: vcpkg submodule



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From noreply at github.com  Sat Oct 18 11:19:02 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Oct 2025 10:19:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] ea0b94: 8. AProfile: Report -- a
 sublte bug fixed for corr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/aaeaad-752239@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ea0b94a1f952fafffb14e048ef59ac09de4dae31
      https://github.com/ehb54/ultrascan3/commit/ea0b94a1f952fafffb14e048ef59ac09de4dae31
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-09 (Wed, 09 Jul 2025)

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

  Log Message:
  -----------
  8. AProfile: Report -- a sublte bug fixed for correctly inheriting exp. duration timefrom the main protocol into AProfile's->reports when setting protocol from scratch for the first time; also make exp. dur. fileds read-only ...


  Commit: 5ea9fa1c7dd4d0508386d70cc3f96d2f33275adf
      https://github.com/ehb54/ultrascan3/commit/5ea9fa1c7dd4d0508386d70cc3f96d2f33275adf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-10 (Thu, 10 Jul 2025)

  Changed paths:
    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:
  -----------
  GMP | R&D -- replace all QwtCounters with QSpinBoxes, to better control and validate inputs ...


  Commit: f8117c1eed92f953f483005cb49d40818b971cc9
      https://github.com/ehb54/ultrascan3/commit/f8117c1eed92f953f483005cb49d40818b971cc9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-28 (Mon, 28 Jul 2025)

  Changed paths:
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp

  Log Message:
  -----------
  GMP | R&D -- change ranges for dd-hh-mm-ss QSpinBoxes in 1. EXP.: 3. Speeds...


  Commit: 0fc8fc48c10614b999f6720cdcc5ffeb354dd28f
      https://github.com/ehb54/ultrascan3/commit/0fc8fc48c10614b999f6720cdcc5ffeb354dd28f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_run_details2.cpp
    M gui/us_tmst_plot.cpp
    M gui/us_window_message.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.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_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    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_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.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_pcsa.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_vhw_combine.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

  Log Message:
  -----------
  issue 533 : convert QString::sprintf to asprintf in gui & programs


  Commit: 54079b9265341294439c9ae4167fc5a6cadad909
      https://github.com/ehb54/ultrascan3/commit/54079b9265341294439c9ae4167fc5a6cadad909
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M gui/us_extinctfitter_gui.cpp
    M gui/us_minimize.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_config/us_color.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_spectrum/us_spectrum.cpp

  Log Message:
  -----------
  issue 533 : convert QString - varname.sprintf to varname = asprintf in gui & programs


  Commit: b31ecaceddee2236fab9e0fb4465885db648a952
      https://github.com/ehb54/ultrascan3/commit/b31ecaceddee2236fab9e0fb4465885db648a952
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_minimize.cpp
    M gui/us_run_details2.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_ga_init/us_solutedata.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/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp

  Log Message:
  -----------
  issue 533 : convert QString - the last of sprintf in gui & programs


  Commit: 3fd01182e1ee82fcbf4e2dfc5710d5bf9bd99207
      https://github.com/ehb54/ultrascan3/commit/3fd01182e1ee82fcbf4e2dfc5710d5bf9bd99207
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp

  Log Message:
  -----------
  issue 533 : convert QString - the last of sprintf in gui & programs


  Commit: 399d845e5667346225803b9ac45b753c7676e39d
      https://github.com/ehb54/ultrascan3/commit/399d845e5667346225803b9ac45b753c7676e39d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_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_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: f924d79f3ecf67db15ced074ac2b50a4cafc9c72
      https://github.com/ehb54/ultrascan3/commit/f924d79f3ecf67db15ced074ac2b50a4cafc9c72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [1] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
      https://github.com/ehb54/ultrascan3/commit/a95afc6b2d4b4b118c7e84a6e1258fbf85076bf0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: 8f9f1257b799c491fa5629c912071eabb435388f
      https://github.com/ehb54/ultrascan3/commit/8f9f1257b799c491fa5629c912071eabb435388f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ...


  Commit: c3a261985e7e3979e7a9a11fcad5c851e739f41b
      https://github.com/ehb54/ultrascan3/commit/c3a261985e7e3979e7a9a11fcad5c851e739f41b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: 3ad35587a1da03cc9926344ac40bb3d364a32d24
      https://github.com/ehb54/ultrascan3/commit/3ad35587a1da03cc9926344ac40bb3d364a32d24
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [1]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: d6a4a469c86320252916565b3bd860c07cab4b1f
      https://github.com/ehb54/ultrascan3/commit/d6a4a469c86320252916565b3bd860c07cab4b1f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [2]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: d3528cb233647917b4f76c9423f9deae1983f2bd
      https://github.com/ehb54/ultrascan3/commit/d3528cb233647917b4f76c9423f9deae1983f2bd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [3]Us_Edit -- address non-hidden widgets in different constructors && scenarios ...


  Commit: 6dc67538e4d0efedcf66715d9f44781f3f8e27e4
      https://github.com/ehb54/ultrascan3/commit/6dc67538e4d0efedcf66715d9f44781f3f8e27e4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-08 (Wed, 08 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
    A admin/cmake/FindQwt.cmake
    A admin/cmake/us_version.h.in
    A admin/test/docker/Dockerfile
    R doc/manual/README
    A doc/manual/README.md
    A gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.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_project_gui.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_solution_gui.cpp
    A programs/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    A programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_com_project/CMakeLists.txt
    A programs/us_com_project_academic/CMakeLists.txt
    M programs/us_config/us_database.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_select_triples.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_edit/us_edit.h
    A programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment_gui_optima.cpp
    A programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    A programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_manage_data.cpp
    A programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.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_rpscan.cpp
    A programs/us_protocol_dev/CMakeLists.txt
    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_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    A programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    A qwtplot3d/CMakeLists.txt
    A test-docker.sh
    A test/README
    A test/common/qt_test_base.cpp
    A test/common/qt_test_base.h
    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/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M utils/CMakeLists.txt
    A utils/ius_db2.h
    M utils/us_ana_profile.cpp
    M utils/us_analyte.cpp
    M utils/us_analyte.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_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_hardware.cpp
    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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_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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  Merge pull request #269 from ehb54/master

Bring this branch to the latest master state


  Commit: af2045563aa019e69852ce42d22235076e6d33f7
      https://github.com/ehb54/ultrascan3/commit/af2045563aa019e69852ce42d22235076e6d33f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise...


  Commit: 8d1c1b4dcbf1b2c698688d5aad236d07578858d5
      https://github.com/ehb54/ultrascan3/commit/8d1c1b4dcbf1b2c698688d5aad236d07578858d5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  GMP: 5. ANALYSIS: FITMEN -- disable update btn right after it's clicked...


  Commit: 34e1993274025890c5cceda224c19973aa5b2ae2
      https://github.com/ehb54/ultrascan3/commit/34e1993274025890c5cceda224c19973aa5b2ae2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #271 from ehb54/alexey-dev-issue576

GMP: 1. EXP. -- for dataDisk option, do not block submission due to disconnected Optima; block otherwise..


  Commit: bdba96a7dc97bb081790098cfb3d72bc10a32c18
      https://github.com/ehb54/ultrascan3/commit/bdba96a7dc97bb081790098cfb3d72bc10a32c18
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #274 from ehb54/master

Bring to the current master state


  Commit: 7c722f2fc3f2a82a9d5063fe4aecc128f465873d
      https://github.com/ehb54/ultrascan3/commit/7c722f2fc3f2a82a9d5063fe4aecc128f465873d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #275 from ehb54/master

Bring to current master state


  Commit: 236ab6f7717916a81de574fbe27299f18683a06c
      https://github.com/ehb54/ultrascan3/commit/236ab6f7717916a81de574fbe27299f18683a06c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Prevent early exit when saving a new buffer to database


  Commit: 7388255d2bb422f8dca061365e459ac69e9267a4
      https://github.com/ehb54/ultrascan3/commit/7388255d2bb422f8dca061365e459ac69e9267a4
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Add null checks before adding child items to make static analysis happy


  Commit: f3022f734322210c7a6d74c4d72f7d5871d7f9c2
      https://github.com/ehb54/ultrascan3/commit/f3022f734322210c7a6d74c4d72f7d5871d7f9c2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-11 (Sat, 11 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Fix formatting in us_data_loader.cpp


  Commit: 3edada407972c86d03c8f30822ebf6a3c1166357
      https://github.com/ehb54/ultrascan3/commit/3edada407972c86d03c8f30822ebf6a3c1166357
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Include *.ui and *.qrc in gui build to ensure all resources and forms are available


  Commit: 427e601f770f5eb39efb249bca9eb81b557561ae
      https://github.com/ehb54/ultrascan3/commit/427e601f770f5eb39efb249bca9eb81b557561ae
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Clean up debug statements and enhance comments

Removed commented debug statements and added clarifying comments for variable assignments.


  Commit: 0bd193389e5967e65d03d34b4ce6dcf0f3817f84
      https://github.com/ehb54/ultrascan3/commit/0bd193389e5967e65d03d34b4ce6dcf0f3817f84
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt

  Log Message:
  -----------
  Merge pull request #280 from ehb54/lukas/cmake-gui-resources

Include *.ui and *.qrc in us_gui library


  Commit: 72ff576e489d378f03adc4296b68bd001b1c649e
      https://github.com/ehb54/ultrascan3/commit/72ff576e489d378f03adc4296b68bd001b1c649e
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_edit/us_edit.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_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #273 from ehb54/alexey-dev-issue567

Alexey dev issue567: Deal with dataDisk Pseudoabsorbance type && correct GUI representaitons of US_Edit scenarios


  Commit: eb8022621705540d2e5a0010b5141f3bd1620591
      https://github.com/ehb54/ultrascan3/commit/eb8022621705540d2e5a0010b5141f3bd1620591
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  Merge pull request #272 from ehb54/alexey-dev-issue575

GMP: 5. ANALYSIS: FITMEN -- disable update btn right after it's clicked..


  Commit: 18b990073be39e32a749536729cba62d576e6c98
      https://github.com/ehb54/ultrascan3/commit/18b990073be39e32a749536729cba62d576e6c98
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-13 (Mon, 13 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_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 #237 from ehb54/alexey-dev-issue521

Alexey dev issue521: Correct and read-only exp. time in channels reports, qspinboxes instead of qwtcounters to control input


  Commit: d131cbbccf4b88f4a39d285fb99a84ccfaacb536
      https://github.com/ehb54/ultrascan3/commit/d131cbbccf4b88f4a39d285fb99a84ccfaacb536
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 567202c3572f02c0b782f92791cac022e863829c
      https://github.com/ehb54/ultrascan3/commit/567202c3572f02c0b782f92791cac022e863829c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M utils/us_buffer.cpp

  Log Message:
  -----------
  Merge pull request #278 from ehb54/lukas/us_buffer_saveToDB

Prevent early exit when saving a new buffer to database


  Commit: 2d1d5599a18b1105dd622fb570a284c2af9b3027
      https://github.com/ehb54/ultrascan3/commit/2d1d5599a18b1105dd622fb570a284c2af9b3027
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  us_astfem_sim: save TI, RI noises in the result directory


  Commit: 52692bf1ec74f08f07f036d50913983f0cb4902c
      https://github.com/ehb54/ultrascan3/commit/52692bf1ec74f08f07f036d50913983f0cb4902c
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  us_astfem_sim.cpp: fix writing the RI csv profile for multi-speed experiments


  Commit: 2bb6c53d1c011cceb17b9ebabc3e0700fea48879
      https://github.com/ehb54/ultrascan3/commit/2bb6c53d1c011cceb17b9ebabc3e0700fea48879
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
      https://github.com/ehb54/ultrascan3/commit/2dfbe74efa5e6ca4ebd7b4acb23c8198c6eea001
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [[1]debug version, stops at XML write]GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 5d05e1a2439de5fa9adb431619c350ae188fcf31
      https://github.com/ehb54/ultrascan3/commit/5d05e1a2439de5fa9adb431619c350ae188fcf31
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

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

  Log Message:
  -----------
  us_astfem_sim: save TI,RI noise profiles into the outout directory


  Commit: 883d73df2ac05d1717a2f924737d36a6ddda5a49
      https://github.com/ehb54/ultrascan3/commit/883d73df2ac05d1717a2f924737d36a6ddda5a49
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge pull request #282 from ehb54/alexey-dev-issue577

GMP: 4. EDIT -- add rotor stretch to bottom in edit profiles...


  Commit: 1de51a8c4fb82a5cbb3cf09653f9e235a54c327c
      https://github.com/ehb54/ultrascan3/commit/1de51a8c4fb82a5cbb3cf09653f9e235a54c327c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-14 (Tue, 14 Oct 2025)

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

  Log Message:
  -----------
  Merge pull request #281 from samo38/issue_587

us_astfem_sim: save TI, RI noises in the result directory


  Commit: ecfbe0af9e3b7e855a5d67f491614c06b26261f1
      https://github.com/ehb54/ultrascan3/commit/ecfbe0af9e3b7e855a5d67f491614c06b26261f1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

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    A qwtplot3d/CMakeLists.txt
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    R test/utils/test_us_datafiles.h
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    M utils/us_hardware.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    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.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_time_state.cpp
    M utils/us_time_state.h

  Log Message:
  -----------
  merge master into ehb54-issue-553, conflicts manually resolved


  Commit: d19407a738880744130ad2ac275bcd672ace631d
      https://github.com/ehb54/ultrascan3/commit/d19407a738880744130ad2ac275bcd672ace631d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  merge master into ehb54-issue-553, conflicts manually resolved


  Commit: b94b4a3819d4ec6a71a8d0f0fbfac37d57b8299e
      https://github.com/ehb54/ultrascan3/commit/b94b4a3819d4ec6a71a8d0f0fbfac37d57b8299e
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-10-15 (Wed, 15 Oct 2025)

  Changed paths:
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_minimize.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_run_details2.cpp
    M gui/us_tmst_plot.cpp
    M gui/us_window_message.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_mpi_analysis/2dsa_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/pcsa_master.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_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_vhw_combine.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_viewer_gui.cpp
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #246 from ehb54/ehb54-issue-533

issue 533 : convert QString::sprintf to asprintf in gui & programs


  Commit: 02cbecf79d8b693a2499249cfce28aa7d58abf6b
      https://github.com/ehb54/ultrascan3/commit/02cbecf79d8b693a2499249cfce28aa7d58abf6b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-16 (Thu, 16 Oct 2025)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  us_gzip.cpp - remove useless deprecreated 'register' keyword


  Commit: bb10991bf7c251763f2aa53737e6574537102d34
      https://github.com/ehb54/ultrascan3/commit/bb10991bf7c251763f2aa53737e6574537102d34
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

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

  Log Message:
  -----------
  GMP | R&D: 1. EXP.=> Speeds -- change signals/slot sigs. in spinboxes for speed & acceler....


  Commit: b5963153ad855cd97a12fb72e6597d2f2684f421
      https://github.com/ehb54/ultrascan3/commit/b5963153ad855cd97a12fb72e6597d2f2684f421
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

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

  Log Message:
  -----------
  Merge pull request #284 from ehb54/alexey-dev-issue592

GMP | R&D: 1. EXP.=> Speeds -- change signals/slot sigs. in spinboxes?


  Commit: daee08ef80606ac9f5b82e6e92d3c3319d784081
      https://github.com/ehb54/ultrascan3/commit/daee08ef80606ac9f5b82e6e92d3c3319d784081
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_abstractrotor_gui.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_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.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_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.h
    M programs/us/us.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_astfem_sim/us_clipdata.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    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_ddist_combine/us_select_rundd.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_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_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_ga_init/us_ga_init.cpp
    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_globalequil.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_integral/us_delete_models.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_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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    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_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.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
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp

  Log Message:
  -----------
  Refactor constructor initialization to replace null pointers `(0, 0)` with `nullptr` and explicit `Qt::WindowFlags()` for improved code clarity and modern C++ standards compliance.


  Commit: 31ff647d5d67c493fd31589da76c247dae579e47
      https://github.com/ehb54/ultrascan3/commit/31ff647d5d67c493fd31589da76c247dae579e47
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_widgets.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_ddist_combine/us_select_rundd.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_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_integral/us_delete_models.cpp
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp

  Log Message:
  -----------
  Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` across all affected files for compatibility with Qt 5.11 and above. Streamlines text measurement handling and ensures future proofing.


  Commit: d86efe4f3b328918793421ae448d2eb5841785cc
      https://github.com/ehb54/ultrascan3/commit/d86efe4f3b328918793421ae448d2eb5841785cc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_associations_gui.cpp

  Log Message:
  -----------
  Initialize `koligo` to 0 in `us_associations_gui.cpp` to prevent potential usage of an uninitialized variable.


  Commit: 7e8e1a176e3f0215069784cf407c928c4c336793
      https://github.com/ehb54/ultrascan3/commit/7e8e1a176e3f0215069784cf407c928c4c336793
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M utils/us_gzip.cpp

  Log Message:
  -----------
  Merge pull request #283 from ehb54/ehb54-issue-591

us_gzip.cpp - remove useless deprecreated 'register' keyword


  Commit: 233334757bf486df06d554277c1ec4cf0d0310d2
      https://github.com/ehb54/ultrascan3/commit/233334757bf486df06d554277c1ec4cf0d0310d2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_abstractrotor_gui.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_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.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_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.h
    M programs/us/us.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_astfem_sim/us_clipdata.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    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_ddist_combine/us_select_rundd.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_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_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_ga_init/us_ga_init.cpp
    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_globalequil.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_integral/us_delete_models.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_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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    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_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.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
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp

  Log Message:
  -----------
  Merge pull request #285 from ehb54/lukas/qt6-QFlags

Deal with deprecated QFlags prior Qt6 migration


  Commit: 03ea185a14d6a79954e1b261b128dee91df5aeec
      https://github.com/ehb54/ultrascan3/commit/03ea185a14d6a79954e1b261b128dee91df5aeec
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_widgets.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_ddist_combine/us_select_rundd.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_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_integral/us_delete_models.cpp
    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_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_select_runid.cpp

  Log Message:
  -----------
  Merge pull request #286 from ehb54/lukas/qt6-width

Replace deprecated QFontMetrics::width() with horizontalAdvance()


  Commit: 956516318c816bd92b269c913872f6eb9d952d91
      https://github.com/ehb54/ultrascan3/commit/956516318c816bd92b269c913872f6eb9d952d91
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    M gui/us_data_loader.cpp

  Log Message:
  -----------
  Merge pull request #279 from ehb54/lukas/static_analysis_warnings

Add null checks before adding child items to make static analysis happy


  Commit: 752239a4b3601d73dc40a986b5616f860208f51e
      https://github.com/ehb54/ultrascan3/commit/752239a4b3601d73dc40a986b5616f860208f51e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M 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_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_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.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.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.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 programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    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_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
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    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.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    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_ddist_combine/us_ddist_combine.cpp
    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_edit/us_edit.cpp
    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
    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_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.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
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    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_globalequil.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_integral/us_delete_models.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_mpi_analysis/2dsa_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/pcsa_master.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_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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    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_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_rotor_calibration/us_get_dbexp.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
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp
    M utils/us_buffer.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_pcsa_modelrec.cpp
    M utils/us_project.cpp
    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_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into 534-enhancement-version-upgrade

# Conflicts:
#	gui/us_window_message.cpp
#	programs/us_rasmol_control/us_rasmol_control.cpp


Compare: https://github.com/ehb54/ultrascan3/compare/aaeaad6c0276...752239a4b360

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From noreply at github.com  Sun Oct 19 00:38:12 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 18 Oct 2025 23:38:12 -0700
Subject: [us-commits] [ehb54/ultrascan3] aa011c: add: version to splash
 screen
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/752239-aa011c@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
      https://github.com/ehb54/ultrascan3/commit/aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-19 (Sun, 19 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    M etc/us3-splash.png
    M gui/CMakeLists.txt
    M gui/images/us3-splash.png
    M programs/CMakeLists.txt
    M programs/us/us.cpp
    M utils/us_defines.h

  Log Message:
  -----------
  add: version to splash screen



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From noreply at github.com  Sun Oct 19 23:20:24 2025
From: noreply at github.com (aaron-auc)
Date: Sun, 19 Oct 2025 22:20:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7f79da: mod: color palette
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/aa011c-7f79da@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7f79da6635b8554a946f428c516d36f3cc0025cf
      https://github.com/ehb54/ultrascan3/commit/7f79da6635b8554a946f428c516d36f3cc0025cf
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A doc/manual/CMakeLists.txt
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h

  Log Message:
  -----------
  mod: color palette



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From noreply at github.com  Mon Oct 20 01:52:52 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 00:52:52 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qsort/000000-956516@github.com>

  Branch: refs/heads/lukas/qt6-qsort
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 20 02:42:10 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 01:42:10 -0700
Subject: [us-commits] [ehb54/ultrascan3] 18e782: Replace deprecated
 `QFontMetrics::width()` with `Q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qsort/956516-ca79ad@github.com>

  Branch: refs/heads/lukas/qt6-qsort
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 18e782f4b6d425c0b62bd705031dd46f8093e5ee
      https://github.com/ehb54/ultrascan3/commit/18e782f4b6d425c0b62bd705031dd46f8093e5ee
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_passwd.cpp

  Log Message:
  -----------
  Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_passwd.cpp` for compatibility with Qt 5.11+.


  Commit: 8806efdebcd11f54118dd57aecd06d8d7aae7f4c
      https://github.com/ehb54/ultrascan3/commit/8806efdebcd11f54118dd57aecd06d8d7aae7f4c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_scan_excl_gui.cpp

  Log Message:
  -----------
  Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_scan_excl_gui.cpp` for Qt 5.11+ compatibility.


  Commit: 22790d4f2a17da1e6a69915e7086c1b4d31def49
      https://github.com/ehb54/ultrascan3/commit/22790d4f2a17da1e6a69915e7086c1b4d31def49
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_widgets_dialog.cpp

  Log Message:
  -----------
  Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_widgets_dialog.cpp` for Qt 5.11+ compatibility.


  Commit: ca79adf4a6eb5fcd7fe326ca3094d0c5788f7fc0
      https://github.com/ehb54/ultrascan3/commit/ca79adf4a6eb5fcd7fe326ca3094d0c5788f7fc0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_table.cpp
    M programs/us_2dsa/us_2dsa_process.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.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_eqreporter.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_integral/us_integral.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_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M utils/us_hardware.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Replace `qSort` with `std::sort` across all files for consistency and modern C++ standards compliance. Updated related comments to reflect changes.


Compare: https://github.com/ehb54/ultrascan3/compare/956516318c81...ca79adf4a6eb

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From noreply at github.com  Mon Oct 20 02:42:19 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 01:42:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] f81ff5: Fix typo in header guard
 macro name in `us_hydrosi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qsort/ca79ad-f81ff5@github.com>

  Branch: refs/heads/lukas/qt6-qsort
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f81ff5c5926cc4958ab0010cef4f6cc40a411672
      https://github.com/ehb54/ultrascan3/commit/f81ff5c5926cc4958ab0010cef4f6cc40a411672
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M utils/us_hydrosim.h

  Log Message:
  -----------
  Fix typo in header guard macro name in `us_hydrosim.h`



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From noreply at github.com  Mon Oct 20 07:07:18 2025
From: noreply at github.com (ehb54)
Date: Mon, 20 Oct 2025 06:07:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] f7cc6c: fix typo in global gaussian
 reported p-value results
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/8e2b7b-f7cc6c@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f7cc6cff857c4b88f243c7d4be63e776992386d7
      https://github.com/ehb54/ultrascan3/commit/f7cc6cff857c4b88f243c7d4be63e776992386d7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-19 (Sun, 19 Oct 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp

  Log Message:
  -----------
  fix typo in global gaussian reported p-value results



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From noreply at github.com  Mon Oct 20 07:50:20 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 06:50:20 -0700
Subject: [us-commits] [ehb54/ultrascan3] 019da7: Lukas/qt6 qsort (#288)
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/956516-019da7@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 019da7c3ca727d8f5109dca514e5dcd42ce124dd
      https://github.com/ehb54/ultrascan3/commit/019da7c3ca727d8f5109dca514e5dcd42ce124dd
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_passwd.cpp
    M gui/us_run_details2.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_table.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dsa/us_2dsa_process.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.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_eqreporter.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_integral/us_integral.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_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Lukas/qt6 qsort (#288)

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_passwd.cpp` for compatibility with Qt 5.11+.

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_scan_excl_gui.cpp` for Qt 5.11+ compatibility.

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_widgets_dialog.cpp` for Qt 5.11+ compatibility.

* Replace `qSort` with `std::sort` across all files for consistency and modern C++ standards compliance. Updated related comments to reflect changes.

* Fix typo in header guard macro name in `us_hydrosim.h`



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From noreply at github.com  Mon Oct 20 07:50:24 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 06:50:24 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qsort/f81ff5-000000@github.com>

  Branch: refs/heads/lukas/qt6-qsort
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From noreply at github.com  Mon Oct 20 07:51:43 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 06:51:43 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QTime/000000-019da7@github.com>

  Branch: refs/heads/lukas/qt6-QTime
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 20 08:11:33 2025
From: noreply at github.com (ehb54)
Date: Mon, 20 Oct 2025 07:11:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] ef4c4a: somo saxs hplc guass marker
 change inactive color
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/f7cc6c-ef4c4a@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ef4c4a127a06e5e5477542ae51c44e3785b8b046
      https://github.com/ehb54/ultrascan3/commit/ef4c4a127a06e5e5477542ae51c44e3785b8b046
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp

  Log Message:
  -----------
  somo saxs hplc guass marker change inactive color



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From noreply at github.com  Mon Oct 20 09:42:15 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 08:42:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8717af: Replace `QTime` with
 `QElapsedTimer` across multip...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QTime/019da7-8717af@github.com>

  Branch: refs/heads/lukas/qt6-QTime
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8717afee7431388f40c8eae1035e14421e0669f4
      https://github.com/ehb54/ultrascan3/commit/8717afee7431388f40c8eae1035e14421e0669f4
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M utils/us_timer.cpp
    M utils/us_timer.h

  Log Message:
  -----------
  Replace `QTime` with `QElapsedTimer` across multiple source files for enhanced timing precision and consistency. Update related method signatures and data structures as needed to align with the new timer implementation.



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From noreply at github.com  Mon Oct 20 09:44:06 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 08:44:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] b24591: Replace deprecated
 `QFontMetrics::width()` with `Q...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QTime/8717af-b24591@github.com>

  Branch: refs/heads/lukas/qt6-QTime
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b24591e4162304c28b4a579586fe917a9e772918
      https://github.com/ehb54/ultrascan3/commit/b24591e4162304c28b4a579586fe917a9e772918
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us_config/us_config.cpp

  Log Message:
  -----------
  Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_config.cpp` for Qt 5.11+ compatibility and better text measurement handling.



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From noreply at github.com  Mon Oct 20 12:01:56 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Oct 2025 11:01:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] d39673: mod: get version
 description for build from us_def...
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/7f79da-d39673@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d396732b1811c44b0e9b297acf9dbb04b42f5b9e
      https://github.com/ehb54/ultrascan3/commit/d396732b1811c44b0e9b297acf9dbb04b42f5b9e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/UsDefinesParser.cmake
    M utils/us_defines.h

  Log Message:
  -----------
  mod: get version description for build from us_defines



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From noreply at github.com  Mon Oct 20 12:14:20 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Oct 2025 11:14:20 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0c3758: mod: remove OS from splash
 screen
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/d39673-0c3758@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0c3758833374f0f823c94711990117ec205ab239
      https://github.com/ehb54/ultrascan3/commit/0c3758833374f0f823c94711990117ec205ab239
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: remove OS from splash screen



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From noreply at github.com  Mon Oct 20 14:46:46 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Oct 2025 13:46:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 11bbb0: mod: better font handling
 improved image
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/0c3758-11bbb0@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 11bbb002a0e60f0eae185c97adcae193b1ad6b40
      https://github.com/ehb54/ultrascan3/commit/11bbb002a0e60f0eae185c97adcae193b1ad6b40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/images/us3-splash.png
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: better font handling improved image



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From noreply at github.com  Mon Oct 20 19:36:39 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Oct 2025 18:36:39 -0700
Subject: [us-commits] [ehb54/us3lims_common]
Message-ID: <ehb54/us3lims_common/push/refs/heads/versioning/000000-e0be1c@github.com>

  Branch: refs/heads/versioning
  Home:   https://github.com/ehb54/us3lims_common

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From noreply at github.com  Mon Oct 20 19:37:08 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Oct 2025 18:37:08 -0700
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/versioning/000000-6ffbfa@github.com>

  Branch: refs/heads/versioning
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From noreply at github.com  Mon Oct 20 19:38:53 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Oct 2025 18:38:53 -0700
Subject: [us-commits] [ehb54/us3lims_newinst]
Message-ID: <ehb54/us3lims_newinst/push/refs/heads/versioning/000000-813b44@github.com>

  Branch: refs/heads/versioning
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From noreply at github.com  Mon Oct 20 19:41:42 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 20 Oct 2025 18:41:42 -0700
Subject: [us-commits] [ehb54/us3lims_gridctl]
Message-ID: <ehb54/us3lims_gridctl/push/refs/heads/versioning/000000-ef171b@github.com>

  Branch: refs/heads/versioning
  Home:   https://github.com/ehb54/us3lims_gridctl

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From noreply at github.com  Mon Oct 20 20:18:13 2025
From: noreply at github.com (alexsav815)
Date: Mon, 20 Oct 2025 19:18:13 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/000000-019da7@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Oct 20 20:36:03 2025
From: noreply at github.com (alexsav815)
Date: Mon, 20 Oct 2025 19:36:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] 989b56: GMP Reporter -- ind.
 combined plots in loop....
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/019da7-989b56@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 989b56b797288947df2fec2506b18a7244f9bc06
      https://github.com/ehb54/ultrascan3/commit/989b56b797288947df2fec2506b18a7244f9bc06
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP Reporter -- ind. combined plots in loop....



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From noreply at github.com  Mon Oct 20 20:52:25 2025
From: noreply at github.com (alexsav815)
Date: Mon, 20 Oct 2025 19:52:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 16ab6c: GMP: 8. AProfile:
 ReportItems -- allow for scienct...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/989b56-16ab6c@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 16ab6ce8ca660172b0ac78c0e8309df85225253e
      https://github.com/ehb54/ultrascan3/commit/16ab6ce8ca660172b0ac78c0e8309df85225253e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  GMP: 8. AProfile: ReportItems -- allow for scienctific notations....



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From noreply at github.com  Mon Oct 20 21:02:44 2025
From: noreply at github.com (alexsav815)
Date: Mon, 20 Oct 2025 20:02:44 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3f73b4: [1]GMP: 8. AProfile:
 ReportItems -- allow for scie...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/16ab6c-3f73b4@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3f73b4091ff487ed34f20940b3848f81fa05c856
      https://github.com/ehb54/ultrascan3/commit/3f73b4091ff487ed34f20940b3848f81fa05c856
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....



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From noreply at github.com  Mon Oct 20 21:14:27 2025
From: noreply at github.com (alexsav815)
Date: Mon, 20 Oct 2025 20:14:27 -0700
Subject: [us-commits] [ehb54/ultrascan3] 23642c: [2]GMP: 8. AProfile:
 ReportItems -- allow for scie...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/3f73b4-23642c@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 23642c68a2458e32859565ace8c19acc79c81f79
      https://github.com/ehb54/ultrascan3/commit/23642c68a2458e32859565ace8c19acc79c81f79
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [2]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....ush



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From noreply at github.com  Mon Oct 20 22:23:58 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 20 Oct 2025 21:23:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2c6055: Lukas/qt6 q time (#289)
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/019da7-2c6055@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2c6055c8e24ad4e4f308aba6baa316732c199ac6
      https://github.com/ehb54/ultrascan3/commit/2c6055c8e24ad4e4f308aba6baa316732c199ac6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_config/us_config.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M utils/us_timer.cpp
    M utils/us_timer.h

  Log Message:
  -----------
  Lukas/qt6 q time (#289)

* Replace `QTime` with `QElapsedTimer` across multiple source files for enhanced timing precision and consistency. Update related method signatures and data structures as needed to align with the new timer implementation.

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_config.cpp` for Qt 5.11+ compatibility and better text measurement handling.



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From noreply at github.com  Tue Oct 21 01:09:23 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 00:09:23 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QPrinter/000000-2c6055@github.com>

  Branch: refs/heads/lukas/qt6-QPrinter
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Oct 21 02:05:38 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 01:05:38 -0700
Subject: [us-commits] [ehb54/ultrascan3] 045f26: Update deprecated Qt APIs
 in `us_plot.cpp` and `US...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QPrinter/2c6055-ac7602@github.com>

  Branch: refs/heads/lukas/qt6-QPrinter
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 045f261a9a7da2a5d07412dcaf94406e6d7eb25a
      https://github.com/ehb54/ultrascan3/commit/045f261a9a7da2a5d07412dcaf94406e6d7eb25a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Update deprecated Qt APIs in `us_plot.cpp` and `US_PlotPicker`

Replaced `QPrinter::setOrientation()` with `QPrinter::setPageOrientation()` and migrated from `QTime` to `QElapsedTimer` for mouse event handling. Improves compatibility with modern Qt versions and enhances code consistency.


  Commit: d7d5acb16cf08470fc0fb3e9d919cda4fe58d00e
      https://github.com/ehb54/ultrascan3/commit/d7d5acb16cf08470fc0fb3e9d919cda4fe58d00e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_2dsa/us_2dsa_process.h

  Log Message:
  -----------
  Migrate `QTime` to `QElapsedTimer` in `us_2dsa_process.h` for modern Qt compatibility and improved timing accuracy.


  Commit: 26edf0996572268569a5979a221306bc289b6916
      https://github.com/ehb54/ultrascan3/commit/26edf0996572268569a5979a221306bc289b6916
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_pcsa/us_pcsa_process.h

  Log Message:
  -----------
  Migrate `QTime` to `QElapsedTimer` in `us_pcsa_process.h` for modern Qt compatibility and improved timing precision.


  Commit: ac760208f3f700426a726ff212ee3165f77ac2a2
      https://github.com/ehb54/ultrascan3/commit/ac760208f3f700426a726ff212ee3165f77ac2a2
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_reporter/us_reporter.cpp

  Log Message:
  -----------
  Replace deprecated `QPrinter` methods with modern equivalents for improved Qt compatibility.


Compare: https://github.com/ehb54/ultrascan3/compare/2c6055c8e24a...ac760208f3f7

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From noreply at github.com  Tue Oct 21 02:21:20 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 01:21:20 -0700
Subject: [us-commits] [ehb54/ultrascan3] 11359a: Replace deprecated
 `QPrinter` methods with modern ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QPrinter/ac7602-11359a@github.com>

  Branch: refs/heads/lukas/qt6-QPrinter
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 11359a717db20fdc27992657a73d2475a0984894
      https://github.com/ehb54/ultrascan3/commit/11359a717db20fdc27992657a73d2475a0984894
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Replace deprecated `QPrinter` methods with modern `QPageSize` and `QPageLayout` equivalents for improved Qt compatibility.



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From noreply at github.com  Tue Oct 21 08:11:37 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 07:11:37 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8a0e36: Replace
 `QPrinter::setPageSize(QPrinter::Letter)` ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QPrinter/11359a-8a0e36@github.com>

  Branch: refs/heads/lukas/qt6-QPrinter
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8a0e362b7fa46907fb016106cea57b097b08c6d5
      https://github.com/ehb54/ultrascan3/commit/8a0e362b7fa46907fb016106cea57b097b08c6d5
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_hydrodyn.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_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp

  Log Message:
  -----------
  Replace `QPrinter::setPageSize(QPrinter::Letter)` with `QPrinter::setPageSize(QPageSize(QPageSize::Letter))` across multiple files for improved Qt compatibility.



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From noreply at github.com  Tue Oct 21 08:24:06 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 07:24:06 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QTime/b24591-000000@github.com>

  Branch: refs/heads/lukas/qt6-QTime
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Oct 21 08:24:29 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 07:24:29 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/000000-2c6055@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Oct 21 08:51:18 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 07:51:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] e6aa2f: Add empty argument list to
 `process->start` for co...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/2c6055-ed1181@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e6aa2f804e8dd030d6b6e232b470897465d70b86
      https://github.com/ehb54/ultrascan3/commit/e6aa2f804e8dd030d6b6e232b470897465d70b86
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  Add empty argument list to `process->start` for consistency and compatibility


  Commit: 731bde9db6982ff6f770bc768e6552a83ffb9a09
      https://github.com/ehb54/ultrascan3/commit/731bde9db6982ff6f770bc768e6552a83ffb9a09
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_sassoc.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp

  Log Message:
  -----------
  Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` for compatibility with modern Qt versions across all affected files.


  Commit: 344b388797ce0f9c6ba8bf1d689d06d00ea26905
      https://github.com/ehb54/ultrascan3/commit/344b388797ce0f9c6ba8bf1d689d06d00ea26905
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M test/modelbuilder/us_modelbuilder.cpp

  Log Message:
  -----------
  Replace `endl` with `Qt::endl` in `us_modelbuilder.cpp` for compatibility with Qt's modern streaming API.


  Commit: ed11814227bf2456f862317c9d70dda10c2322cc
      https://github.com/ehb54/ultrascan3/commit/ed11814227bf2456f862317c9d70dda10c2322cc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  Replace `QColor::light()` with `QColor::lighter()` in `us_xpn_viewer_gui.cpp` for compatibility with modern Qt API.


Compare: https://github.com/ehb54/ultrascan3/compare/2c6055c8e24a...ed11814227bf

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From noreply at github.com  Tue Oct 21 09:37:39 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 08:37:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8b6da2: Replace deprecated use of
 `QPixmap*` with modern `...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/ed1181-8964f6@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8b6da20a28c8ac39453a3e769da06670f40e8946
      https://github.com/ehb54/ultrascan3/commit/8b6da20a28c8ac39453a3e769da06670f40e8946
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_colorgradient/us_colorgradient.cpp

  Log Message:
  -----------
  Replace deprecated use of `QPixmap*` with modern `QPixmap` by value in `us_colorgradient.cpp` for compatibility with updated Qt API.


  Commit: 0e2fc963eada627cdb9ba36ea2293b81c563072b
      https://github.com/ehb54/ultrascan3/commit/0e2fc963eada627cdb9ba36ea2293b81c563072b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_ramp/us_ramp_gui.cpp

  Log Message:
  -----------
  Replace deprecated `swap()` with `swapItemsAt()` across all affected files for compatibility with modern Qt API.


  Commit: 72964814e9754f0d36a63f093fc3ff7b387a87e7
      https://github.com/ehb54/ultrascan3/commit/72964814e9754f0d36a63f093fc3ff7b387a87e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Replace deprecated `mysql_ssl_set()` with `mysql_optionsv()` for SSL configuration in `us_db2.cpp` to align with modern MySQL API.


  Commit: 8ce1794b08ae15b9494ee771e83dac45807385c5
      https://github.com/ehb54/ultrascan3/commit/8ce1794b08ae15b9494ee771e83dac45807385c5
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Disable `MYSQL_OPT_SSL_VERIFY_SERVER_CERT` in `us_db2.cpp` for improved compatibility with specific MySQL setups.


  Commit: 09b3a3b043b6d63141c2a857edc89c5142717086
      https://github.com/ehb54/ultrascan3/commit/09b3a3b043b6d63141c2a857edc89c5142717086
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M doc/manual/advanced_config.body

  Log Message:
  -----------
  Document `MYSQL_OPT_SSL_VERIFY_SERVER_CERT` flag in advanced configuration manual.


  Commit: 8964f638fccad8ea60f2d2a925ee709cf1635947
      https://github.com/ehb54/ultrascan3/commit/8964f638fccad8ea60f2d2a925ee709cf1635947
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Replace deprecated `qsrand()` and `qrand()` with `QRandomGenerator` in `us_crypto.cpp` for compatibility with modern Qt API.


Compare: https://github.com/ehb54/ultrascan3/compare/ed11814227bf...8964f638fcca

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From noreply at github.com  Tue Oct 21 09:39:43 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 08:39:43 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0ad65c: Replace deprecated
 `QPrinter::setPageSize()` usage...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QPrinter/8a0e36-0ad65c@github.com>

  Branch: refs/heads/lukas/qt6-QPrinter
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0ad65cca9ce68b0dfb5456ad38c77b03d342d573
      https://github.com/ehb54/ultrascan3/commit/0ad65cca9ce68b0dfb5456ad38c77b03d342d573
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_reporter/us_reporter.cpp

  Log Message:
  -----------
  Replace deprecated `QPrinter::setPageSize()` usage with `QPageSize` constructor for compatibility with modern Qt versions.



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From noreply at github.com  Tue Oct 21 09:53:54 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 08:53:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] c0c7ad: Replace deprecated
 `mysql_optionsv()` with `mysql_...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/8964f6-c0c7ad@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c0c7ad8982c0d5fba89d1bcfa0fced005eb28187
      https://github.com/ehb54/ultrascan3/commit/c0c7ad8982c0d5fba89d1bcfa0fced005eb28187
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Replace deprecated `mysql_optionsv()` with `mysql_options()` for SSL configuration in `us_db2.cpp` to align with modern MySQL API.



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From noreply at github.com  Tue Oct 21 10:15:42 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 09:15:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] 40fc3c: Add support for
 `MYSQL_OPT_SSL_MODE` in `us_db2.cp...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/c0c7ad-297596@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 40fc3cc74c3f2e6a20d6a7c51854df49fab77b03
      https://github.com/ehb54/ultrascan3/commit/40fc3cc74c3f2e6a20d6a7c51854df49fab77b03
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M utils/us_db2.cpp

  Log Message:
  -----------
  Add support for `MYSQL_OPT_SSL_MODE` in `us_db2.cpp` to handle SSL configuration on modern MySQL versions while retaining compatibility with legacy `MYSQL_OPT_SSL_VERIFY_SERVER_CERT`.


  Commit: 2975966d200cc898e0f46c0e80a32a2d70a73564
      https://github.com/ehb54/ultrascan3/commit/2975966d200cc898e0f46c0e80a32a2d70a73564
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp

  Log Message:
  -----------
  Replace deprecated `Qt::MidButton` with `Qt::MiddleButton` for compatibility with modern Qt API.


Compare: https://github.com/ehb54/ultrascan3/compare/c0c7ad8982c0...2975966d200c

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From noreply at github.com  Tue Oct 21 10:21:37 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 09:21:37 -0700
Subject: [us-commits] [ehb54/ultrascan3] f85794: Replace deprecated
 `QFileDialog::DirectoryOnly` wi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/297596-f85794@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f85794694bd8132bf52447d07585b0d757130e23
      https://github.com/ehb54/ultrascan3/commit/f85794694bd8132bf52447d07585b0d757130e23
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_pseudo_absorbance/us_add_refScan.cpp

  Log Message:
  -----------
  Replace deprecated `QFileDialog::DirectoryOnly` with `QFileDialog::ShowDirsOnly` for compatibility with modern Qt API.



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From noreply at github.com  Tue Oct 21 10:56:58 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 09:56:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 955dd7: Use
 `QRandomGenerator::securelySeeded()` in `us_cr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/f85794-955dd7@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 955dd7b9e5d5fed7be2b1826e776c86245c9f94e
      https://github.com/ehb54/ultrascan3/commit/955dd7b9e5d5fed7be2b1826e776c86245c9f94e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M utils/us_crypto.cpp

  Log Message:
  -----------
  Use `QRandomGenerator::securelySeeded()` in `us_crypto.cpp` for improved security and modern Qt API compliance.



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From noreply at github.com  Tue Oct 21 11:11:55 2025
From: noreply at github.com (SophiaBird95)
Date: Tue, 21 Oct 2025 10:11:55 -0700
Subject: [us-commits] [ehb54/ultrascan3] 72add4: GMP-ABDE: 5. ANALYSIS --
 honor AProfile's setting ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/2c6055-dbda7b@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 72add4bba839a101a1cd875f5ff266fa9a91ccc9
      https://github.com/ehb54/ultrascan3/commit/72add4bba839a101a1cd875f5ff266fa9a91ccc9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  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:
  -----------
  GMP-ABDE: 5. ANALYSIS -- honor AProfile's setting (channels selection) in MWL-species fit and normalization...


  Commit: 60b0a4d52d2f57ac00206f32b33f7a01c943bf8e
      https://github.com/ehb54/ultrascan3/commit/60b0a4d52d2f57ac00206f32b33f7a01c943bf8e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #276 from ehb54/master

Bring to current master


  Commit: dbda7b82c9f80e4698a98012037116cfabaaa824
      https://github.com/ehb54/ultrascan3/commit/dbda7b82c9f80e4698a98012037116cfabaaa824
  Author: SophiaBird95 <135044923+SophiaBird95 at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  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:
  -----------
  Merge pull request #270 from ehb54/alexey-dev-issue574

GMP-ABDE: 5. ANALYSIS -- honor AProfile's setting (channels selection) for ANALYSIS && REPORT stages


Compare: https://github.com/ehb54/ultrascan3/compare/2c6055c8e24a...dbda7b82c9f8

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From noreply at github.com  Tue Oct 21 11:54:21 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 10:54:21 -0700
Subject: [us-commits] [ehb54/ultrascan3] 83a8bb: Lukas/qt6 q printer (#290)
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/dbda7b-83a8bb@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 83a8bbdce557a43ae4881196a8b7e72d19bd2de8
      https://github.com/ehb54/ultrascan3/commit/83a8bbdce557a43ae4881196a8b7e72d19bd2de8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_2dsa_process.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_hydrodyn.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_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp

  Log Message:
  -----------
  Lukas/qt6 q printer (#290)

* Update deprecated Qt APIs in `us_plot.cpp` and `US_PlotPicker`

Replaced `QPrinter::setOrientation()` with `QPrinter::setPageOrientation()` and migrated from `QTime` to `QElapsedTimer` for mouse event handling. Improves compatibility with modern Qt versions and enhances code consistency.

* Migrate `QTime` to `QElapsedTimer` in `us_2dsa_process.h` for modern Qt compatibility and improved timing accuracy.

* Migrate `QTime` to `QElapsedTimer` in `us_pcsa_process.h` for modern Qt compatibility and improved timing precision.

* Replace deprecated `QPrinter` methods with modern equivalents for improved Qt compatibility.

* Replace deprecated `QPrinter` methods with modern `QPageSize` and `QPageLayout` equivalents for improved Qt compatibility.

* Replace `QPrinter::setPageSize(QPrinter::Letter)` with `QPrinter::setPageSize(QPageSize(QPageSize::Letter))` across multiple files for improved Qt compatibility.

* Replace deprecated `QPrinter::setPageSize()` usage with `QPageSize` constructor for compatibility with modern Qt versions.



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From noreply at github.com  Tue Oct 21 11:55:01 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 10:55:01 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-QPrinter/0ad65c-000000@github.com>

  Branch: refs/heads/lukas/qt6-QPrinter
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Oct 21 14:38:54 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 13:38:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] b33cd8: Lukas/qt6 qendl qstring
 qcolor::light qproccess::s...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/83a8bb-b33cd8@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b33cd87e51169ea4a1a8b4eb21dc602abbc56988
      https://github.com/ehb54/ultrascan3/commit/b33cd87e51169ea4a1a8b4eb21dc602abbc56988
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M doc/manual/advanced_config.body
    M gui/us_analyte_gui.cpp
    M gui/us_plot.cpp
    M gui/us_sassoc.cpp
    M programs/us/us.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M utils/us_crypto.cpp
    M utils/us_db2.cpp

  Log Message:
  -----------
  Lukas/qt6 qendl qstring qcolor::light qproccess::start (#291)

* Add empty argument list to `process->start` for consistency and compatibility

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` for compatibility with modern Qt versions across all affected files.

* Replace `endl` with `Qt::endl` in `us_modelbuilder.cpp` for compatibility with Qt's modern streaming API.

* Replace `QColor::light()` with `QColor::lighter()` in `us_xpn_viewer_gui.cpp` for compatibility with modern Qt API.

* Replace deprecated use of `QPixmap*` with modern `QPixmap` by value in `us_colorgradient.cpp` for compatibility with updated Qt API.

* Replace deprecated `swap()` with `swapItemsAt()` across all affected files for compatibility with modern Qt API.

* Replace deprecated `mysql_ssl_set()` with `mysql_optionsv()` for SSL configuration in `us_db2.cpp` to align with modern MySQL API.

* Disable `MYSQL_OPT_SSL_VERIFY_SERVER_CERT` in `us_db2.cpp` for improved compatibility with specific MySQL setups.

* Document `MYSQL_OPT_SSL_VERIFY_SERVER_CERT` flag in advanced configuration manual.

* Replace deprecated `qsrand()` and `qrand()` with `QRandomGenerator` in `us_crypto.cpp` for compatibility with modern Qt API.

* Replace deprecated `mysql_optionsv()` with `mysql_options()` for SSL configuration in `us_db2.cpp` to align with modern MySQL API.

* Add support for `MYSQL_OPT_SSL_MODE` in `us_db2.cpp` to handle SSL configuration on modern MySQL versions while retaining compatibility with legacy `MYSQL_OPT_SSL_VERIFY_SERVER_CERT`.

* Replace deprecated `Qt::MidButton` with `Qt::MiddleButton` for compatibility with modern Qt API.

* Replace deprecated `QFileDialog::DirectoryOnly` with `QFileDialog::ShowDirsOnly` for compatibility with modern Qt API.

* Use `QRandomGenerator::securelySeeded()` in `us_crypto.cpp` for improved security and modern Qt API compliance.



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From noreply at github.com  Tue Oct 21 14:39:05 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 21 Oct 2025 13:39:05 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-qendl-qstring/955dd7-000000@github.com>

  Branch: refs/heads/lukas/qt6-qendl-qstring
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Oct 21 14:42:38 2025
From: noreply at github.com (alexsav815)
Date: Tue, 21 Oct 2025 13:42:38 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1a03ab: [unit conv.]GMP Reporter --
 ind. combined plots in...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/23642c-1a03ab@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1a03ab20cc40456ca64dde16388dff6b7868db64
      https://github.com/ehb54/ultrascan3/commit/1a03ab20cc40456ca64dde16388dff6b7868db64
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop....



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From noreply at github.com  Tue Oct 21 15:37:14 2025
From: noreply at github.com (alexsav815)
Date: Tue, 21 Oct 2025 14:37:14 -0700
Subject: [us-commits] [ehb54/ultrascan3] 8e826a: [unit conv.]GMP Reporter --
 ind. combined plots in...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/1a03ab-8e826a@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
      https://github.com/ehb54/ultrascan3/commit/8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop: convert units for D, MW properly to display integration ranges; add units memo in ReportItems && Global settings for combined plots guis....



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From noreply at github.com  Wed Oct 22 02:33:13 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 01:33:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] ff0221: Fix incorrect bitwise
 operator in `setFrameStyle` ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-final-touches/000000-edd8b4@github.com>

  Branch: refs/heads/lukas/qt6-final-touches
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ff0221d9261f8caeee809e8f44f504ec6b272058
      https://github.com/ehb54/ultrascan3/commit/ff0221d9261f8caeee809e8f44f504ec6b272058
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_globalequil/us_long_messagebox.cpp

  Log Message:
  -----------
  Fix incorrect bitwise operator in `setFrameStyle` for message box

Corrected `||` to `|` in `setFrameStyle` to ensure proper combination of frame style flags.


  Commit: 18fc7ab086a1a31029ac2150a1e1f3f34ec00358
      https://github.com/ehb54/ultrascan3/commit/18fc7ab086a1a31029ac2150a1e1f3f34ec00358
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

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

  Log Message:
  -----------
  Replace `qrand`/`qsrand` usage with `QRandomGenerator` in `US_Math2` for improved random number generation and modern standards compliance.


  Commit: 489873396379c3eac678c80a5da334c2519d9dfd
      https://github.com/ehb54/ultrascan3/commit/489873396379c3eac678c80a5da334c2519d9dfd
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp

  Log Message:
  -----------
  Replace deprecated `QWheelEvent::delta()` with `QWheelEvent::angleDelta().y()` to ensure compatibility with modern Qt versions.


  Commit: 98acbca309246209738f9b6e7d79e9ce6eaf1746
      https://github.com/ehb54/ultrascan3/commit/98acbca309246209738f9b6e7d79e9ce6eaf1746
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_plot.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_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M utils/us_link_ssl.cpp

  Log Message:
  -----------
  Refactor `.simplified()` usage to assign returned value explicitly across multiple files for improved readability and consistency.


  Commit: 262b55f449a7584ec3596e84d922228a11b4b2f4
      https://github.com/ehb54/ultrascan3/commit/262b55f449a7584ec3596e84d922228a11b4b2f4
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  Fix missing brackets in conditional check for `pb_scan_excl` visibility

Ensure proper scoping by adding brackets to the conditional block, improving code readability and correctness.


  Commit: 2170fd89b00c28e65f51d2957500296e8347f07e
      https://github.com/ehb54/ultrascan3/commit/2170fd89b00c28e65f51d2957500296e8347f07e
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M CMakeLists.txt

  Log Message:
  -----------
  Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.10 and earlier.


  Commit: 36e065b119732fd5f10f06fb26199a7d6c55ecc8
      https://github.com/ehb54/ultrascan3/commit/36e065b119732fd5f10f06fb26199a7d6c55ecc8
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Enable deprecation warnings as errors and define `QT_DISABLE_DEPRECATED_UP_TO` for consistent handling of deprecated functionality across builds.


  Commit: edd8b43cec3541a9eb52e20ca327a30f9c50c259
      https://github.com/ehb54/ultrascan3/commit/edd8b43cec3541a9eb52e20ca327a30f9c50c259
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M qwtplot3d/qwtplot3d.pro

  Log Message:
  -----------
  Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.9 and earlier.


Compare: https://github.com/ehb54/ultrascan3/compare/ff0221d9261f%5E...edd8b43cec35

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From noreply at github.com  Wed Oct 22 05:43:56 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 04:43:56 -0700
Subject: [us-commits] [ehb54/ultrascan3] d5235a: Replace deprecated
 `QString::SkipEmptyParts` with ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-final-touches/edd8b4-d5235a@github.com>

  Branch: refs/heads/lukas/qt6-final-touches
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d5235a1eb173141dcb66d599172f81b326af929b
      https://github.com/ehb54/ultrascan3/commit/d5235a1eb173141dcb66d599172f81b326af929b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_parse.cpp

  Log Message:
  -----------
  Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.



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From noreply at github.com  Wed Oct 22 06:36:50 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 05:36:50 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9c5730: Replace deprecated
 `QString::SkipEmptyParts` with ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-final-touches/d5235a-9c5730@github.com>

  Branch: refs/heads/lukas/qt6-final-touches
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9c573005957c0603f3696a59b248478383d12e9b
      https://github.com/ehb54/ultrascan3/commit/9c573005957c0603f3696a59b248478383d12e9b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M us_somo/develop/src/us_dirhist.cpp

  Log Message:
  -----------
  Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.



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From noreply at github.com  Wed Oct 22 09:58:15 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 08:58:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] ba42be: qt6 migration - final
 touches (#293)
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/b33cd8-ba42be@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ba42be34c9a7147dfdd18b0f1487beade68f6d39
      https://github.com/ehb54/ultrascan3/commit/ba42be34c9a7147dfdd18b0f1487beade68f6d39
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_plot.cpp
    M programs/us_analysis_profile/us_analysis_profile.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_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 qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h

  Log Message:
  -----------
  qt6 migration - final touches (#293)

* Fix incorrect bitwise operator in `setFrameStyle` for message box

Corrected `||` to `|` in `setFrameStyle` to ensure proper combination of frame style flags.

* Replace `qrand`/`qsrand` usage with `QRandomGenerator` in `US_Math2` for improved random number generation and modern standards compliance.

* Replace deprecated `QWheelEvent::delta()` with `QWheelEvent::angleDelta().y()` to ensure compatibility with modern Qt versions.

* Refactor `.simplified()` usage to assign returned value explicitly across multiple files for improved readability and consistency.

* Fix missing brackets in conditional check for `pb_scan_excl` visibility

Ensure proper scoping by adding brackets to the conditional block, improving code readability and correctness.

* Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.10 and earlier.

* Enable deprecation warnings as errors and define `QT_DISABLE_DEPRECATED_UP_TO` for consistent handling of deprecated functionality across builds.

* Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.9 and earlier.

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.



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From noreply at github.com  Wed Oct 22 09:58:20 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 08:58:20 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-final-touches/9c5730-000000@github.com>

  Branch: refs/heads/lukas/qt6-final-touches
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Oct 22 10:09:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 09:09:59 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_astfem_sim_saving/000000-ba42be@github.com>

  Branch: refs/heads/lukas/us_astfem_sim_saving
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Oct 22 10:12:15 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 09:12:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] f0b2ee: Enhance directory handling
 and noise saving logic
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_astfem_sim_saving/ba42be-f0b2ee@github.com>

  Branch: refs/heads/lukas/us_astfem_sim_saving
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
      https://github.com/ehb54/ultrascan3/commit/f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Enhance directory handling and noise saving logic

Added checks to prevent overwriting existing directories and prompt user for confirmation. Updated saving logic for TI and RI noises.



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From noreply at github.com  Wed Oct 22 11:33:09 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 22 Oct 2025 10:33:09 -0700
Subject: [us-commits] [ehb54/ultrascan3] 74cf8f: Remove disabling of save
 button after simulation w...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_astfem_sim_saving/f0b2ee-74cf8f@github.com>

  Branch: refs/heads/lukas/us_astfem_sim_saving
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 74cf8fef407532cec7439f4b6fce957a30e11b7f
      https://github.com/ehb54/ultrascan3/commit/74cf8fef407532cec7439f4b6fce957a30e11b7f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Remove disabling of save button after simulation was saved



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From noreply at github.com  Wed Oct 22 12:11:10 2025
From: noreply at github.com (alexsav815)
Date: Wed, 22 Oct 2025 11:11:10 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue611/000000-ba42be@github.com>

  Branch: refs/heads/alexey-dev-issue611
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Oct 22 12:30:25 2025
From: noreply at github.com (ehb54)
Date: Wed, 22 Oct 2025 11:30:25 -0700
Subject: [us-commits] [ehb54/us3lims_common]
Message-ID: <ehb54/us3lims_common/push/refs/heads/master/e0be1c-000000@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/us3lims_common

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From noreply at github.com  Wed Oct 22 12:30:56 2025
From: noreply at github.com (ehb54)
Date: Wed, 22 Oct 2025 11:30:56 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo]
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/main/000000-a32b24@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3lims_webinfo

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From noreply at github.com  Wed Oct 22 12:30:24 2025
From: noreply at github.com (ehb54)
Date: Wed, 22 Oct 2025 11:30:24 -0700
Subject: [us-commits] [ehb54/us3lims_common]
Message-ID: <ehb54/us3lims_common/push/refs/heads/main/000000-e0be1c@github.com>

  Branch: refs/heads/main
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From noreply at github.com  Wed Oct 22 12:32:16 2025
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Subject: [us-commits] [ehb54/us3lims_newinst]
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From noreply at github.com  Wed Oct 22 12:33:13 2025
From: noreply at github.com (alexsav815)
Date: Wed, 22 Oct 2025 11:33:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] 25a781: 1. EXP: 8.Aprof. -- Apply
 to all extends to run an...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue611/ba42be-25a781@github.com>

  Branch: refs/heads/alexey-dev-issue611
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 25a7817f58968e8b726b1ae341570a6868b2d0c8
      https://github.com/ehb54/ultrascan3/commit/25a7817f58968e8b726b1ae341570a6868b2d0c8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

  Log Message:
  -----------
  1. EXP: 8.Aprof. -- Apply to all extends to run ana/reports....



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Subject: [us-commits] [ehb54/us3lims_gridctl]
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From noreply at github.com  Wed Oct 22 12:33:38 2025
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Date: Wed, 22 Oct 2025 11:33:38 -0700
Subject: [us-commits] [ehb54/ultrascan3]
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From noreply at github.com  Wed Oct 22 12:33:39 2025
From: noreply at github.com (ehb54)
Date: Wed, 22 Oct 2025 11:33:39 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/ba42be-000000@github.com>

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From noreply at github.com  Wed Oct 22 13:26:06 2025
From: noreply at github.com (Borries Demeler)
Date: Wed, 22 Oct 2025 12:26:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] f0b2ee: Enhance directory handling
 and noise saving logic
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/ba42be-dc9e65@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
      https://github.com/ehb54/ultrascan3/commit/f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Enhance directory handling and noise saving logic

Added checks to prevent overwriting existing directories and prompt user for confirmation. Updated saving logic for TI and RI noises.


  Commit: 74cf8fef407532cec7439f4b6fce957a30e11b7f
      https://github.com/ehb54/ultrascan3/commit/74cf8fef407532cec7439f4b6fce957a30e11b7f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Remove disabling of save button after simulation was saved


  Commit: dc9e6549f27c2f12e35a41d74a9519fac652a318
      https://github.com/ehb54/ultrascan3/commit/dc9e6549f27c2f12e35a41d74a9519fac652a318
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Merge pull request #294 from ehb54/lukas/us_astfem_sim_saving

Enhance directory handling and noise saving logic


Compare: https://github.com/ehb54/ultrascan3/compare/ba42be34c9a7...dc9e6549f27c

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From noreply at github.com  Wed Oct 22 13:26:09 2025
From: noreply at github.com (Borries Demeler)
Date: Wed, 22 Oct 2025 12:26:09 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_astfem_sim_saving/74cf8f-000000@github.com>

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From noreply at github.com  Wed Oct 22 14:37:54 2025
From: noreply at github.com (HabGab)
Date: Wed, 22 Oct 2025 13:37:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 496340: oct 17
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/4d7446-1fb3a2@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 496340a36b16db89f83310cb92e7562703bbb809
      https://github.com/ehb54/ultrascan3/commit/496340a36b16db89f83310cb92e7562703bbb809
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    A doc/manual/source/analyte/analyte_edit.rst

  Log Message:
  -----------
  oct 17


  Commit: e29a1d95a7bc8428bb0acdce04f78660cf647c5a
      https://github.com/ehb54/ultrascan3/commit/e29a1d95a7bc8428bb0acdce04f78660cf647c5a
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    A doc/manual/source/analyte/analyte_new.rst

  Log Message:
  -----------
  oct172


  Commit: db730c8863cbbcae6152e116586c2dd72f0c8663
      https://github.com/ehb54/ultrascan3/commit/db730c8863cbbcae6152e116586c2dd72f0c8663
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-17 (Fri, 17 Oct 2025)

  Changed paths:
    R doc/manual/source/analyte/analyte.rst
    A doc/manual/source/analyte/analyte_select.rst
    A doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/analyte/index.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

  Log Message:
  -----------
  nvm


  Commit: 1fb3a2560b707b5816e619d910a2098133d2f4ec
      https://github.com/ehb54/ultrascan3/commit/1fb3a2560b707b5816e619d910a2098133d2f4ec
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    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/buffer/buffer_edit.rst

  Log Message:
  -----------
  oct22


Compare: https://github.com/ehb54/ultrascan3/compare/4d744647e9e7...1fb3a2560b70

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From noreply at github.com  Wed Oct 22 18:12:33 2025
From: noreply at github.com (alexsav815)
Date: Wed, 22 Oct 2025 17:12:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3439e7: [unit conv.]GMP Reporter --
 debug stats; MW & D....
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/8e826a-3439e7@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
      https://github.com/ehb54/ultrascan3/commit/3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- debug stats; MW & D....



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From noreply at github.com  Wed Oct 22 19:19:54 2025
From: noreply at github.com (alexsav815)
Date: Wed, 22 Oct 2025 18:19:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1eb76f: [11unit conv.]GMP Reporter
 -- debug stats; MW & D....
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/3439e7-1eb76f@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1eb76f7674fa95820ac254061b4539a1ba0b4dc2
      https://github.com/ehb54/ultrascan3/commit/1eb76f7674fa95820ac254061b4539a1ba0b4dc2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

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

  Log Message:
  -----------
  [11unit conv.]GMP Reporter -- debug stats; MW & D....



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From noreply at github.com  Thu Oct 23 13:50:28 2025
From: noreply at github.com (alexsav815)
Date: Thu, 23 Oct 2025 12:50:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] e519d6: GMP Reporter -- units conv.
 for s, D20W, MW & D in...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/1eb76f-e519d6@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
      https://github.com/ehb54/ultrascan3/commit/e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_report_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....



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From noreply at github.com  Thu Oct 23 16:28:19 2025
From: noreply at github.com (HabGab)
Date: Thu, 23 Oct 2025 15:28:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4e28e4: Oct 23
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/1fb3a2-4e28e4@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4e28e490dfb60059cdf82104460a0557f1f81f0a
      https://github.com/ehb54/ultrascan3/commit/4e28e490dfb60059cdf82104460a0557f1f81f0a
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M doc/manual/source/_static/images/analyte_details.png
    A doc/manual/source/_static/images/analyte_edit.png
    A doc/manual/source/_static/images/analyte_edit_spec.png
    A doc/manual/source/_static/images/analyte_new_sequence.png
    A doc/manual/source/_static/images/analyte_newc.png
    A doc/manual/source/_static/images/analyte_newd.png
    A doc/manual/source/_static/images/analyte_newp.png
    A doc/manual/source/_static/images/analyte_selectc.png
    A doc/manual/source/_static/images/analyte_selectd.png
    A doc/manual/source/_static/images/analyte_selectp.png
    A doc/manual/source/_static/images/analyte_sequence.png
    A doc/manual/source/_static/images/analyte_settings.png
    A doc/manual/source/_static/images/analyte_spec-gui.png
    A doc/manual/source/_static/images/analyte_specmenu.png
    A doc/manual/source/_static/images/analyte_spectrum.png
    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/buffer/buffer_edit.rst
    M doc/manual/source/buffer/buffer_select.rst

  Log Message:
  -----------
  Oct 23



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From noreply at github.com  Thu Oct 23 18:03:25 2025
From: noreply at github.com (alexsav815)
Date: Thu, 23 Oct 2025 17:03:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] d351cf: [1]GMP Reporter -- units
 conv. for s, D20W, MW & D...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/e519d6-d351cf@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d351cf7e1466b360b85fb0cac36fe7ec8efa445f
      https://github.com/ehb54/ultrascan3/commit/d351cf7e1466b360b85fb0cac36fe7ec8efa445f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....



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From noreply at github.com  Thu Oct 23 19:56:48 2025
From: noreply at github.com (Borries Demeler)
Date: Thu, 23 Oct 2025 18:56:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] 989b56: GMP Reporter -- ind.
 combined plots in loop....
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/dc9e65-4a6823@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 989b56b797288947df2fec2506b18a7244f9bc06
      https://github.com/ehb54/ultrascan3/commit/989b56b797288947df2fec2506b18a7244f9bc06
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP Reporter -- ind. combined plots in loop....


  Commit: 16ab6ce8ca660172b0ac78c0e8309df85225253e
      https://github.com/ehb54/ultrascan3/commit/16ab6ce8ca660172b0ac78c0e8309df85225253e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  GMP: 8. AProfile: ReportItems -- allow for scienctific notations....


  Commit: 3f73b4091ff487ed34f20940b3848f81fa05c856
      https://github.com/ehb54/ultrascan3/commit/3f73b4091ff487ed34f20940b3848f81fa05c856
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....


  Commit: 23642c68a2458e32859565ace8c19acc79c81f79
      https://github.com/ehb54/ultrascan3/commit/23642c68a2458e32859565ace8c19acc79c81f79
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [2]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....ush


  Commit: 1a03ab20cc40456ca64dde16388dff6b7868db64
      https://github.com/ehb54/ultrascan3/commit/1a03ab20cc40456ca64dde16388dff6b7868db64
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop....


  Commit: 8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
      https://github.com/ehb54/ultrascan3/commit/8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop: convert units for D, MW properly to display integration ranges; add units memo in ReportItems && Global settings for combined plots guis....


  Commit: 3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
      https://github.com/ehb54/ultrascan3/commit/3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- debug stats; MW & D....


  Commit: 1eb76f7674fa95820ac254061b4539a1ba0b4dc2
      https://github.com/ehb54/ultrascan3/commit/1eb76f7674fa95820ac254061b4539a1ba0b4dc2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

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

  Log Message:
  -----------
  [11unit conv.]GMP Reporter -- debug stats; MW & D....


  Commit: e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
      https://github.com/ehb54/ultrascan3/commit/e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_report_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....


  Commit: d351cf7e1466b360b85fb0cac36fe7ec8efa445f
      https://github.com/ehb54/ultrascan3/commit/d351cf7e1466b360b85fb0cac36fe7ec8efa445f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....


  Commit: 4a68235cf595a6ec04a0deb90dd29b8aaaf6f673
      https://github.com/ehb54/ultrascan3/commit/4a68235cf595a6ec04a0deb90dd29b8aaaf6f673
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_report_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #292 from ehb54/alexey-dev-issue604

Alexey dev issue604: Report for ind. comb. && Units for [s,D,MW] conversion and memo


Compare: https://github.com/ehb54/ultrascan3/compare/dc9e6549f27c...4a68235cf595

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From noreply at github.com  Thu Oct 23 19:56:52 2025
From: noreply at github.com (Borries Demeler)
Date: Thu, 23 Oct 2025 18:56:52 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue604/d351cf-000000@github.com>

  Branch: refs/heads/alexey-dev-issue604
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Oct 24 08:28:39 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 24 Oct 2025 07:28:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7fad8e: Update branch references
 from `master` to `main` a...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/master2main-usglobal/000000-781dbd@github.com>

  Branch: refs/heads/lukas/master2main-usglobal
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7fad8eee6a232dc059f07270c6c9abf40dbb6b65
      https://github.com/ehb54/ultrascan3/commit/7fad8eee6a232dc059f07270c6c9abf40dbb6b65
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-24 (Fri, 24 Oct 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M README.md
    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

  Log Message:
  -----------
  Update branch references from `master` to `main` across workflows, documentation, and build scripts. Add conditional triggers to workflows for targeted file-path changes, improving efficiency.


  Commit: 781dbde5fee6a935af354380bac2cdfba5d22274
      https://github.com/ehb54/ultrascan3/commit/781dbde5fee6a935af354380bac2cdfba5d22274
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-24 (Fri, 24 Oct 2025)

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

  Log Message:
  -----------
  Move user-level synchronization logic to `US_Win::update_user_level()` to ensure master password has only to be entered once


Compare: https://github.com/ehb54/ultrascan3/compare/7fad8eee6a23%5E...781dbde5fee6

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From noreply at github.com  Fri Oct 24 08:34:27 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 24 Oct 2025 07:34:27 -0700
Subject: [us-commits] [ehb54/ultrascan3] 56e246: Let codeql-analysis run no
 matter the changes
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/master2main-usglobal/781dbd-56e246@github.com>

  Branch: refs/heads/lukas/master2main-usglobal
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 56e2466de7ed5d2716f23bab264227bb096a5787
      https://github.com/ehb54/ultrascan3/commit/56e2466de7ed5d2716f23bab264227bb096a5787
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-24 (Fri, 24 Oct 2025)

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

  Log Message:
  -----------
  Let codeql-analysis run no matter the changes



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From noreply at github.com  Fri Oct 24 09:49:30 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 24 Oct 2025 08:49:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] ab401b: Implement optional
 auto-positioning based on `US_S...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/master2main-usglobal/56e246-ab401b@github.com>

  Branch: refs/heads/lukas/master2main-usglobal
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ab401b18a15fef4dda7d929ba1cdbb521ca9c659
      https://github.com/ehb54/ultrascan3/commit/ab401b18a15fef4dda7d929ba1cdbb521ca9c659
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-24 (Fri, 24 Oct 2025)

  Changed paths:
    M doc/manual/advanced_config.body
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_second_moment/us_second_moment.cpp

  Log Message:
  -----------
  Implement optional auto-positioning based on `US_Settings::debug_value("auto_positioning")`.

Modified multiple modules to conditionally apply global positioning logic when "auto_positioning" is enabled. Refactored `US_Widgets` to include a `global_positioning` flag and adjusted widget geometry initialization accordingly.



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From noreply at github.com  Fri Oct 24 10:01:25 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 24 Oct 2025 09:01:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0c3499: Update gui/us_widgets.h
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/master2main-usglobal/ab401b-0c3499@github.com>

  Branch: refs/heads/lukas/master2main-usglobal
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0c349995730c981373ffa617027658fc717d395c
      https://github.com/ehb54/ultrascan3/commit/0c349995730c981373ffa617027658fc717d395c
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-24 (Fri, 24 Oct 2025)

  Changed paths:
    M gui/us_widgets.h

  Log Message:
  -----------
  Update gui/us_widgets.h

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>



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From noreply at github.com  Fri Oct 24 10:01:33 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 24 Oct 2025 09:01:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3d5078: Update
 programs/us_mwl_species_fit/us_mwl_species_...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/master2main-usglobal/0c3499-3d5078@github.com>

  Branch: refs/heads/lukas/master2main-usglobal
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3d5078866027e3f410fb76fd832c2c4d93fd2aab
      https://github.com/ehb54/ultrascan3/commit/3d5078866027e3f410fb76fd832c2c4d93fd2aab
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-24 (Fri, 24 Oct 2025)

  Changed paths:
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp

  Log Message:
  -----------
  Update programs/us_mwl_species_fit/us_mwl_species_fit.cpp

Co-authored-by: Copilot <175728472+Copilot at users.noreply.github.com>



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From noreply at github.com  Fri Oct 24 12:32:51 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 24 Oct 2025 11:32:51 -0700
Subject: [us-commits] [ehb54/ultrascan3] 08bd6d: Lukas/master2main usglobal
 (#297)
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/4a6823-08bd6d@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 08bd6d595eb6426644151df1b6004aa0fd8c2948
      https://github.com/ehb54/ultrascan3/commit/08bd6d595eb6426644151df1b6004aa0fd8c2948
  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
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M README.md
    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_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_dcdt/us_dcdt.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_second_moment/us_second_moment.cpp

  Log Message:
  -----------
  Lukas/master2main usglobal (#297)

* Update branch references from `master` to `main` across workflows, documentation, and build scripts. Add conditional triggers to workflows for targeted file-path changes, improving efficiency.

* Move user-level synchronization logic to `US_Win::update_user_level()` to ensure master password has only to be entered once

* Let codeql-analysis run no matter the changes

* Implement optional auto-positioning based on `US_Settings::debug_value("auto_positioning")`.

Modified multiple modules to conditionally apply global positioning logic when "auto_positioning" is enabled. Refactored `US_Widgets` to include a `global_positioning` flag and adjusted widget geometry initialization accordingly.

* Update gui/us_widgets.h
* Update programs/us_mwl_species_fit/us_mwl_species_fit.cpp



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From noreply at github.com  Fri Oct 24 12:32:57 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 24 Oct 2025 11:32:57 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/master2main-usglobal/3d5078-000000@github.com>

  Branch: refs/heads/lukas/master2main-usglobal
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Oct 26 01:57:34 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 26 Oct 2025 00:57:34 -0700
Subject: [us-commits] [ehb54/ultrascan3] 13f6c5: Standardize Qwt environment
 variable checks and ad...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/000000-13f6c5@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  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.



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From noreply at github.com  Sun Oct 26 02:00:38 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 26 Oct 2025 01:00:38 -0700
Subject: [us-commits] [ehb54/ultrascan3] 989b56: GMP Reporter -- ind.
 combined plots in loop....
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/13f6c5-f6d601@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 989b56b797288947df2fec2506b18a7244f9bc06
      https://github.com/ehb54/ultrascan3/commit/989b56b797288947df2fec2506b18a7244f9bc06
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP Reporter -- ind. combined plots in loop....


  Commit: 16ab6ce8ca660172b0ac78c0e8309df85225253e
      https://github.com/ehb54/ultrascan3/commit/16ab6ce8ca660172b0ac78c0e8309df85225253e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  GMP: 8. AProfile: ReportItems -- allow for scienctific notations....


  Commit: 3f73b4091ff487ed34f20940b3848f81fa05c856
      https://github.com/ehb54/ultrascan3/commit/3f73b4091ff487ed34f20940b3848f81fa05c856
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....


  Commit: 23642c68a2458e32859565ace8c19acc79c81f79
      https://github.com/ehb54/ultrascan3/commit/23642c68a2458e32859565ace8c19acc79c81f79
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [2]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....ush


  Commit: 1a03ab20cc40456ca64dde16388dff6b7868db64
      https://github.com/ehb54/ultrascan3/commit/1a03ab20cc40456ca64dde16388dff6b7868db64
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop....


  Commit: 8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
      https://github.com/ehb54/ultrascan3/commit/8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop: convert units for D, MW properly to display integration ranges; add units memo in ReportItems && Global settings for combined plots guis....


  Commit: ba42be34c9a7147dfdd18b0f1487beade68f6d39
      https://github.com/ehb54/ultrascan3/commit/ba42be34c9a7147dfdd18b0f1487beade68f6d39
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_plot.cpp
    M programs/us_analysis_profile/us_analysis_profile.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_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 qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h

  Log Message:
  -----------
  qt6 migration - final touches (#293)

* Fix incorrect bitwise operator in `setFrameStyle` for message box

Corrected `||` to `|` in `setFrameStyle` to ensure proper combination of frame style flags.

* Replace `qrand`/`qsrand` usage with `QRandomGenerator` in `US_Math2` for improved random number generation and modern standards compliance.

* Replace deprecated `QWheelEvent::delta()` with `QWheelEvent::angleDelta().y()` to ensure compatibility with modern Qt versions.

* Refactor `.simplified()` usage to assign returned value explicitly across multiple files for improved readability and consistency.

* Fix missing brackets in conditional check for `pb_scan_excl` visibility

Ensure proper scoping by adding brackets to the conditional block, improving code readability and correctness.

* Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.10 and earlier.

* Enable deprecation warnings as errors and define `QT_DISABLE_DEPRECATED_UP_TO` for consistent handling of deprecated functionality across builds.

* Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.9 and earlier.

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.


  Commit: f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
      https://github.com/ehb54/ultrascan3/commit/f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Enhance directory handling and noise saving logic

Added checks to prevent overwriting existing directories and prompt user for confirmation. Updated saving logic for TI and RI noises.


  Commit: 74cf8fef407532cec7439f4b6fce957a30e11b7f
      https://github.com/ehb54/ultrascan3/commit/74cf8fef407532cec7439f4b6fce957a30e11b7f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Remove disabling of save button after simulation was saved


  Commit: dc9e6549f27c2f12e35a41d74a9519fac652a318
      https://github.com/ehb54/ultrascan3/commit/dc9e6549f27c2f12e35a41d74a9519fac652a318
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Merge pull request #294 from ehb54/lukas/us_astfem_sim_saving

Enhance directory handling and noise saving logic


  Commit: 3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
      https://github.com/ehb54/ultrascan3/commit/3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- debug stats; MW & D....


  Commit: 1eb76f7674fa95820ac254061b4539a1ba0b4dc2
      https://github.com/ehb54/ultrascan3/commit/1eb76f7674fa95820ac254061b4539a1ba0b4dc2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

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

  Log Message:
  -----------
  [11unit conv.]GMP Reporter -- debug stats; MW & D....


  Commit: e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
      https://github.com/ehb54/ultrascan3/commit/e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_report_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....


  Commit: d351cf7e1466b360b85fb0cac36fe7ec8efa445f
      https://github.com/ehb54/ultrascan3/commit/d351cf7e1466b360b85fb0cac36fe7ec8efa445f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....


  Commit: 4a68235cf595a6ec04a0deb90dd29b8aaaf6f673
      https://github.com/ehb54/ultrascan3/commit/4a68235cf595a6ec04a0deb90dd29b8aaaf6f673
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_report_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #292 from ehb54/alexey-dev-issue604

Alexey dev issue604: Report for ind. comb. && Units for [s,D,MW] conversion and memo


  Commit: 08bd6d595eb6426644151df1b6004aa0fd8c2948
      https://github.com/ehb54/ultrascan3/commit/08bd6d595eb6426644151df1b6004aa0fd8c2948
  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
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M README.md
    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_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_dcdt/us_dcdt.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_second_moment/us_second_moment.cpp

  Log Message:
  -----------
  Lukas/master2main usglobal (#297)

* Update branch references from `master` to `main` across workflows, documentation, and build scripts. Add conditional triggers to workflows for targeted file-path changes, improving efficiency.

* Move user-level synchronization logic to `US_Win::update_user_level()` to ensure master password has only to be entered once

* Let codeql-analysis run no matter the changes

* Implement optional auto-positioning based on `US_Settings::debug_value("auto_positioning")`.

Modified multiple modules to conditionally apply global positioning logic when "auto_positioning" is enabled. Refactored `US_Widgets` to include a `global_positioning` flag and adjusted widget geometry initialization accordingly.

* Update gui/us_widgets.h
* Update programs/us_mwl_species_fit/us_mwl_species_fit.cpp


  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


Compare: https://github.com/ehb54/ultrascan3/compare/13f6c5148d62...f6d6012fbc4f

To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications

From noreply at github.com  Sun Oct 26 02:03:03 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 26 Oct 2025 01:03:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] bcba62: Qt6 no longer supports the
 QString().sprintf() fun...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/f6d601-b50cca@github.com>

  Branch: refs/heads/lukas/qt6-compile
  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: 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


Compare: https://github.com/ehb54/ultrascan3/compare/f6d6012fbc4f...b50cca680591

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From noreply at github.com  Sun Oct 26 07:36:18 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 26 Oct 2025 06:36:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] be440f: Update CMake to support
 optional Qt6 usage and mod...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/b50cca-cdfc55@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  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`.


Compare: https://github.com/ehb54/ultrascan3/compare/b50cca680591...cdfc55c93b1b

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From noreply at github.com  Mon Oct 27 05:19:31 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 27 Oct 2025 04:19:31 -0700
Subject: [us-commits] [ehb54/ultrascan3] b02949: Modernize `FindQwt.cmake`
 for dynamic Qt version d...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/cdfc55-77d601@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  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.


Compare: https://github.com/ehb54/ultrascan3/compare/cdfc55c93b1b...77d60151680d

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From noreply at github.com  Mon Oct 27 07:52:06 2025
From: noreply at github.com (ehb54)
Date: Mon, 27 Oct 2025 06:52:06 -0700
Subject: [us-commits] [ehb54/us3_sql] 5ea073: [SQL for -- ] GMP | R&D :
 dataDisk -- differentiat...
Message-ID: <ehb54/us3_sql/push/refs/heads/main/6ffbfa-f298e4@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3_sql
  Commit: 5ea0736b33b19866bcc11f51efc613f2227cc97c
      https://github.com/ehb54/us3_sql/commit/5ea0736b33b19866bcc11f51efc613f2227cc97c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-06 (Mon, 06 Oct 2025)

  Changed paths:
    M us3.sql

  Log Message:
  -----------
  [SQL for -- ] GMP | R&D : dataDisk -- differentiate between RI-uploaded data to be intensity or pseudo-absorbance; act accordingly in 3. IMPORT; report in REPORT; ......


  Commit: f298e41935d6650bae4e2cfc0bfefa10bbb7c73b
      https://github.com/ehb54/us3_sql/commit/f298e41935d6650bae4e2cfc0bfefa10bbb7c73b
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M us3.sql

  Log Message:
  -----------
  Merge pull request #20 from ehb54/alexey-dev-for-issue567

[SQL for -- ] GMP | R&D : dataDisk -- differentiate between RI-uploaded form Disk vs. Pseudoabsorbance type


Compare: https://github.com/ehb54/us3_sql/compare/6ffbfa7edcdd...f298e41935d6

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From noreply at github.com  Mon Oct 27 07:52:13 2025
From: noreply at github.com (ehb54)
Date: Mon, 27 Oct 2025 06:52:13 -0700
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue567/5ea073-000000@github.com>

  Branch: refs/heads/alexey-dev-for-issue567
  Home:   https://github.com/ehb54/us3_sql

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From noreply at github.com  Mon Oct 27 12:03:12 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 27 Oct 2025 11:03:12 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4375de: mod: update icons
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/11bbb0-4375de@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4375dec9c287500081a412353bd6a8d4b0dbd015
      https://github.com/ehb54/ultrascan3/commit/4375dec9c287500081a412353bd6a8d4b0dbd015
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M 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-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M gui/images/check.png
    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: update icons



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From noreply at github.com  Mon Oct 27 12:04:46 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 27 Oct 2025 11:04:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 515eaa: add: icons for all
 extensions
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/4375de-515eaa@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
      https://github.com/ehb54/ultrascan3/commit/515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    A etc/us3-icon-128x128.xpm
    A etc/us3-icon-32x32.ico

  Log Message:
  -----------
  add: icons for all extensions



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From noreply at github.com  Mon Oct 27 15:44:16 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 27 Oct 2025 14:44:16 -0700
Subject: [us-commits] [ehb54/us3lims_webinfo]
Message-ID: <ehb54/us3lims_webinfo/push/refs/heads/versioning/000000-a32b24@github.com>

  Branch: refs/heads/versioning
  Home:   https://github.com/ehb54/us3lims_webinfo

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From noreply at github.com  Tue Oct 28 11:40:21 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 28 Oct 2025 10:40:21 -0700
Subject: [us-commits] [ehb54/ultrascan3] 1f221d: mod: remove qt4 code
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/515eaa-1f221d@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1f221d2f71c97c26c68d54f94c404ec7a1455bc3
      https://github.com/ehb54/ultrascan3/commit/1f221d2f71c97c26c68d54f94c404ec7a1455bc3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: remove qt4 code



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From noreply at github.com  Tue Oct 28 11:43:59 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 28 Oct 2025 10:43:59 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2db3a5: mod: format code
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/1f221d-2db3a5@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2db3a5f9997a9b2eb153a6af2832c0b693d5e640
      https://github.com/ehb54/ultrascan3/commit/2db3a5f9997a9b2eb153a6af2832c0b693d5e640
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: format code



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From noreply at github.com  Tue Oct 28 11:44:45 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 28 Oct 2025 10:44:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3a9174: add: image readme for image
 conversion
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/2db3a5-3a9174@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3a91742fcd41c424cda2dfa8b85cd80aadc2255b
      https://github.com/ehb54/ultrascan3/commit/3a91742fcd41c424cda2dfa8b85cd80aadc2255b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    A etc/README

  Log Message:
  -----------
  add: image readme for image conversion



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From noreply at github.com  Tue Oct 28 17:46:46 2025
From: noreply at github.com (HabGab)
Date: Tue, 28 Oct 2025 16:46:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] a8ea05: Oct 28th
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/4e28e4-a8ea05@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a8ea05486b2cfed09ae8fdf10c45b2ddafe6d565
      https://github.com/ehb54/ultrascan3/commit/a8ea05486b2cfed09ae8fdf10c45b2ddafe6d565
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_analys.rst
    A doc/manual/source/_static/images/noise_prompt.png
    A doc/manual/source/_static/images/noise_vec_db.png
    M doc/manual/source/analyte/analyte_edit.rst
    M doc/manual/source/analyte/analyte_select.rst
    M doc/manual/source/analyte/analyte_settings.rst
    M doc/manual/source/analyte/index.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/common_dialogs.rst
    M doc/manual/source/conf.py
    M doc/manual/source/config.rst
    M doc/manual/source/ddist_combine.rst
    M doc/manual/source/dens_match.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/fit_meniscus.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/pcsa/index.rst
    M doc/manual/source/pcsa/pcsa.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/second_moment.rst
    M doc/manual/source/solutions/index.rst
    A doc/manual/source/solutions/solution_edit.rst
    A doc/manual/source/solutions/solution_select.rst
    A doc/manual/source/solutions/solution_settings.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_distrib_plot.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
  -----------
  Oct 28th



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From noreply at github.com  Thu Oct 30 13:29:40 2025
From: noreply at github.com (alexsav815)
Date: Thu, 30 Oct 2025 12:29:40 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/000000-08bd6d@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Oct 30 16:51:24 2025
From: noreply at github.com (HabGab)
Date: Thu, 30 Oct 2025 15:51:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] 729897: oct 30
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/a8ea05-729897@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 72989737a24f2d9309bb386bdbc9937c982b9601
      https://github.com/ehb54/ultrascan3/commit/72989737a24f2d9309bb386bdbc9937c982b9601
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-10-30 (Thu, 30 Oct 2025)

  Changed paths:
    M doc/manual/source/2dsa/index.rst
    M doc/manual/source/pcsa/index.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  oct 30



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From noreply at github.com  Fri Oct 31 14:53:03 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 31 Oct 2025 13:53:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] 72add4: GMP-ABDE: 5. ANALYSIS --
 honor AProfile's setting ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/3a9174-102666@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 72add4bba839a101a1cd875f5ff266fa9a91ccc9
      https://github.com/ehb54/ultrascan3/commit/72add4bba839a101a1cd875f5ff266fa9a91ccc9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-09 (Thu, 09 Oct 2025)

  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:
  -----------
  GMP-ABDE: 5. ANALYSIS -- honor AProfile's setting (channels selection) in MWL-species fit and normalization...


  Commit: 60b0a4d52d2f57ac00206f32b33f7a01c943bf8e
      https://github.com/ehb54/ultrascan3/commit/60b0a4d52d2f57ac00206f32b33f7a01c943bf8e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-10 (Fri, 10 Oct 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  Merge pull request #276 from ehb54/master

Bring to current master


  Commit: 019da7c3ca727d8f5109dca514e5dcd42ce124dd
      https://github.com/ehb54/ultrascan3/commit/019da7c3ca727d8f5109dca514e5dcd42ce124dd
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_buffer_gui.cpp
    M gui/us_passwd.cpp
    M gui/us_run_details2.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_table.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dsa/us_2dsa_process.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.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_eqreporter.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_integral/us_integral.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_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Lukas/qt6 qsort (#288)

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_passwd.cpp` for compatibility with Qt 5.11+.

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_scan_excl_gui.cpp` for Qt 5.11+ compatibility.

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_widgets_dialog.cpp` for Qt 5.11+ compatibility.

* Replace `qSort` with `std::sort` across all files for consistency and modern C++ standards compliance. Updated related comments to reflect changes.

* Fix typo in header guard macro name in `us_hydrosim.h`


  Commit: 989b56b797288947df2fec2506b18a7244f9bc06
      https://github.com/ehb54/ultrascan3/commit/989b56b797288947df2fec2506b18a7244f9bc06
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP Reporter -- ind. combined plots in loop....


  Commit: 16ab6ce8ca660172b0ac78c0e8309df85225253e
      https://github.com/ehb54/ultrascan3/commit/16ab6ce8ca660172b0ac78c0e8309df85225253e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  GMP: 8. AProfile: ReportItems -- allow for scienctific notations....


  Commit: 3f73b4091ff487ed34f20940b3848f81fa05c856
      https://github.com/ehb54/ultrascan3/commit/3f73b4091ff487ed34f20940b3848f81fa05c856
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....


  Commit: 23642c68a2458e32859565ace8c19acc79c81f79
      https://github.com/ehb54/ultrascan3/commit/23642c68a2458e32859565ace8c19acc79c81f79
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [2]GMP: 8. AProfile: ReportItems -- allow for scienctific notations....ush


  Commit: 2c6055c8e24ad4e4f308aba6baa316732c199ac6
      https://github.com/ehb54/ultrascan3/commit/2c6055c8e24ad4e4f308aba6baa316732c199ac6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M programs/us_config/us_config.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M utils/us_timer.cpp
    M utils/us_timer.h

  Log Message:
  -----------
  Lukas/qt6 q time (#289)

* Replace `QTime` with `QElapsedTimer` across multiple source files for enhanced timing precision and consistency. Update related method signatures and data structures as needed to align with the new timer implementation.

* Replace deprecated `QFontMetrics::width()` with `QFontMetrics::horizontalAdvance()` in `us_config.cpp` for Qt 5.11+ compatibility and better text measurement handling.


  Commit: dbda7b82c9f80e4698a98012037116cfabaaa824
      https://github.com/ehb54/ultrascan3/commit/dbda7b82c9f80e4698a98012037116cfabaaa824
  Author: SophiaBird95 <135044923+SophiaBird95 at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  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:
  -----------
  Merge pull request #270 from ehb54/alexey-dev-issue574

GMP-ABDE: 5. ANALYSIS -- honor AProfile's setting (channels selection) for ANALYSIS && REPORT stages


  Commit: 83a8bbdce557a43ae4881196a8b7e72d19bd2de8
      https://github.com/ehb54/ultrascan3/commit/83a8bbdce557a43ae4881196a8b7e72d19bd2de8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M gui/us_plot.cpp
    M programs/us_2dsa/us_2dsa_process.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_hydrodyn.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_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp

  Log Message:
  -----------
  Lukas/qt6 q printer (#290)

* Update deprecated Qt APIs in `us_plot.cpp` and `US_PlotPicker`

Replaced `QPrinter::setOrientation()` with `QPrinter::setPageOrientation()` and migrated from `QTime` to `QElapsedTimer` for mouse event handling. Improves compatibility with modern Qt versions and enhances code consistency.

* Migrate `QTime` to `QElapsedTimer` in `us_2dsa_process.h` for modern Qt compatibility and improved timing accuracy.

* Migrate `QTime` to `QElapsedTimer` in `us_pcsa_process.h` for modern Qt compatibility and improved timing precision.

* Replace deprecated `QPrinter` methods with modern equivalents for improved Qt compatibility.

* Replace deprecated `QPrinter` methods with modern `QPageSize` and `QPageLayout` equivalents for improved Qt compatibility.

* Replace `QPrinter::setPageSize(QPrinter::Letter)` with `QPrinter::setPageSize(QPageSize(QPageSize::Letter))` across multiple files for improved Qt compatibility.

* Replace deprecated `QPrinter::setPageSize()` usage with `QPageSize` constructor for compatibility with modern Qt versions.


  Commit: b33cd87e51169ea4a1a8b4eb21dc602abbc56988
      https://github.com/ehb54/ultrascan3/commit/b33cd87e51169ea4a1a8b4eb21dc602abbc56988
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

  Changed paths:
    M doc/manual/advanced_config.body
    M gui/us_analyte_gui.cpp
    M gui/us_plot.cpp
    M gui/us_sassoc.cpp
    M programs/us/us.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M utils/us_crypto.cpp
    M utils/us_db2.cpp

  Log Message:
  -----------
  Lukas/qt6 qendl qstring qcolor::light qproccess::start (#291)

* Add empty argument list to `process->start` for consistency and compatibility

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` for compatibility with modern Qt versions across all affected files.

* Replace `endl` with `Qt::endl` in `us_modelbuilder.cpp` for compatibility with Qt's modern streaming API.

* Replace `QColor::light()` with `QColor::lighter()` in `us_xpn_viewer_gui.cpp` for compatibility with modern Qt API.

* Replace deprecated use of `QPixmap*` with modern `QPixmap` by value in `us_colorgradient.cpp` for compatibility with updated Qt API.

* Replace deprecated `swap()` with `swapItemsAt()` across all affected files for compatibility with modern Qt API.

* Replace deprecated `mysql_ssl_set()` with `mysql_optionsv()` for SSL configuration in `us_db2.cpp` to align with modern MySQL API.

* Disable `MYSQL_OPT_SSL_VERIFY_SERVER_CERT` in `us_db2.cpp` for improved compatibility with specific MySQL setups.

* Document `MYSQL_OPT_SSL_VERIFY_SERVER_CERT` flag in advanced configuration manual.

* Replace deprecated `qsrand()` and `qrand()` with `QRandomGenerator` in `us_crypto.cpp` for compatibility with modern Qt API.

* Replace deprecated `mysql_optionsv()` with `mysql_options()` for SSL configuration in `us_db2.cpp` to align with modern MySQL API.

* Add support for `MYSQL_OPT_SSL_MODE` in `us_db2.cpp` to handle SSL configuration on modern MySQL versions while retaining compatibility with legacy `MYSQL_OPT_SSL_VERIFY_SERVER_CERT`.

* Replace deprecated `Qt::MidButton` with `Qt::MiddleButton` for compatibility with modern Qt API.

* Replace deprecated `QFileDialog::DirectoryOnly` with `QFileDialog::ShowDirsOnly` for compatibility with modern Qt API.

* Use `QRandomGenerator::securelySeeded()` in `us_crypto.cpp` for improved security and modern Qt API compliance.


  Commit: 1a03ab20cc40456ca64dde16388dff6b7868db64
      https://github.com/ehb54/ultrascan3/commit/1a03ab20cc40456ca64dde16388dff6b7868db64
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop....


  Commit: 8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
      https://github.com/ehb54/ultrascan3/commit/8e826acf1af8661fd6bbf08cc4d75fcdfa258d71
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-21 (Tue, 21 Oct 2025)

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

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- ind. combined plots in loop: convert units for D, MW properly to display integration ranges; add units memo in ReportItems && Global settings for combined plots guis....


  Commit: ba42be34c9a7147dfdd18b0f1487beade68f6d39
      https://github.com/ehb54/ultrascan3/commit/ba42be34c9a7147dfdd18b0f1487beade68f6d39
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_plot.cpp
    M programs/us_analysis_profile/us_analysis_profile.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_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 qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h

  Log Message:
  -----------
  qt6 migration - final touches (#293)

* Fix incorrect bitwise operator in `setFrameStyle` for message box

Corrected `||` to `|` in `setFrameStyle` to ensure proper combination of frame style flags.

* Replace `qrand`/`qsrand` usage with `QRandomGenerator` in `US_Math2` for improved random number generation and modern standards compliance.

* Replace deprecated `QWheelEvent::delta()` with `QWheelEvent::angleDelta().y()` to ensure compatibility with modern Qt versions.

* Refactor `.simplified()` usage to assign returned value explicitly across multiple files for improved readability and consistency.

* Fix missing brackets in conditional check for `pb_scan_excl` visibility

Ensure proper scoping by adding brackets to the conditional block, improving code readability and correctness.

* Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.10 and earlier.

* Enable deprecation warnings as errors and define `QT_DISABLE_DEPRECATED_UP_TO` for consistent handling of deprecated functionality across builds.

* Define `QT_DISABLE_DEPRECATED_UP_TO` to disable all deprecated functionality in Qt 6.9 and earlier.

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.

* Replace deprecated `QString::SkipEmptyParts` with `Qt::SkipEmptyParts` to ensure compatibility with modern Qt versions.


  Commit: f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
      https://github.com/ehb54/ultrascan3/commit/f0b2eeb5fd0214cdb53e4e79eadcd4088bf53345
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Enhance directory handling and noise saving logic

Added checks to prevent overwriting existing directories and prompt user for confirmation. Updated saving logic for TI and RI noises.


  Commit: 74cf8fef407532cec7439f4b6fce957a30e11b7f
      https://github.com/ehb54/ultrascan3/commit/74cf8fef407532cec7439f4b6fce957a30e11b7f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Remove disabling of save button after simulation was saved


  Commit: dc9e6549f27c2f12e35a41d74a9519fac652a318
      https://github.com/ehb54/ultrascan3/commit/dc9e6549f27c2f12e35a41d74a9519fac652a318
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Merge pull request #294 from ehb54/lukas/us_astfem_sim_saving

Enhance directory handling and noise saving logic


  Commit: 3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
      https://github.com/ehb54/ultrascan3/commit/3439e79d5dbf652dc8de9e0ea04d1f8a6ab91124
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [unit conv.]GMP Reporter -- debug stats; MW & D....


  Commit: 1eb76f7674fa95820ac254061b4539a1ba0b4dc2
      https://github.com/ehb54/ultrascan3/commit/1eb76f7674fa95820ac254061b4539a1ba0b4dc2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-22 (Wed, 22 Oct 2025)

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

  Log Message:
  -----------
  [11unit conv.]GMP Reporter -- debug stats; MW & D....


  Commit: e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
      https://github.com/ehb54/ultrascan3/commit/e519d6ca64030d2e4f71137b58b6e6f41a0c9a62
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_report_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....


  Commit: d351cf7e1466b360b85fb0cac36fe7ec8efa445f
      https://github.com/ehb54/ultrascan3/commit/d351cf7e1466b360b85fb0cac36fe7ec8efa445f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_report_gui.cpp

  Log Message:
  -----------
  [1]GMP Reporter -- units conv. for s, D20W, MW & D in both global combo- and individual plots; integr. ranges in ind. plots; specify d20W for D in units memo....


  Commit: 4a68235cf595a6ec04a0deb90dd29b8aaaf6f673
      https://github.com/ehb54/ultrascan3/commit/4a68235cf595a6ec04a0deb90dd29b8aaaf6f673
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-10-23 (Thu, 23 Oct 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_report_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M utils/us_ana_profile.cpp

  Log Message:
  -----------
  Merge pull request #292 from ehb54/alexey-dev-issue604

Alexey dev issue604: Report for ind. comb. && Units for [s,D,MW] conversion and memo


  Commit: 08bd6d595eb6426644151df1b6004aa0fd8c2948
      https://github.com/ehb54/ultrascan3/commit/08bd6d595eb6426644151df1b6004aa0fd8c2948
  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
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M README.md
    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_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_dcdt/us_dcdt.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_second_moment/us_second_moment.cpp

  Log Message:
  -----------
  Lukas/master2main usglobal (#297)

* Update branch references from `master` to `main` across workflows, documentation, and build scripts. Add conditional triggers to workflows for targeted file-path changes, improving efficiency.

* Move user-level synchronization logic to `US_Win::update_user_level()` to ensure master password has only to be entered once

* Let codeql-analysis run no matter the changes

* Implement optional auto-positioning based on `US_Settings::debug_value("auto_positioning")`.

Modified multiple modules to conditionally apply global positioning logic when "auto_positioning" is enabled. Refactored `US_Widgets` to include a `global_positioning` flag and adjusted widget geometry initialization accordingly.

* Update gui/us_widgets.h
* Update programs/us_mwl_species_fit/us_mwl_species_fit.cpp


  Commit: 2569ebda100a0b333a3f529881d53c8771f9aae5
      https://github.com/ehb54/ultrascan3/commit/2569ebda100a0b333a3f529881d53c8771f9aae5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 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_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_passwd.cpp
    M gui/us_plot.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_table.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M programs/us/us.cpp
    M programs/us/us.h
    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_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.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/us_autoflow_analysis.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_config.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.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_select_lambdas.cpp
    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_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.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_eqreporter.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_integral.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
    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_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    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_rpscan.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    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_second_moment/us_second_moment.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_hydrodyn.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_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M utils/us_ana_profile.cpp
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 534-enhancement-version-upgrade

# Conflicts:
#	programs/us/us.cpp


  Commit: 102666e6eebaafe3144edfce3728a62e33ab053c
      https://github.com/ehb54/ultrascan3/commit/102666e6eebaafe3144edfce3728a62e33ab053c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    A programs/us_2dsa/CMakeLists.txt
    A programs/us_abde/CMakeLists.txt
    A programs/us_analysis_profile/CMakeLists.txt
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    A programs/us_audit_trail_gmp/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    A programs/us_colorgradient/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    A programs/us_convert/CMakeLists.txt
    A programs/us_dcdt/CMakeLists.txt
    A programs/us_ddist_combine/CMakeLists.txt
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    A programs/us_equiltime/CMakeLists.txt
    A programs/us_esigner_gmp/CMakeLists.txt
    A programs/us_export_legacy/CMakeLists.txt
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_ga_init/CMakeLists.txt
    A programs/us_globalequil/CMakeLists.txt
    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
    A programs/us_mpi_analysis/CMakeLists.txt
    A programs/us_mwl_species_sim/CMakeLists.txt
    A programs/us_mwl_spectra/CMakeLists.txt
    A programs/us_mwlr_viewer/CMakeLists.txt
    A programs/us_pcsa/CMakeLists.txt
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    A programs/us_pseudo3d_combine/CMakeLists.txt
    A programs/us_pseudo_absorbance/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    A programs/us_vhw_enhanced/CMakeLists.txt
    A programs/us_xpn_viewer/CMakeLists.txt
    M scripts/bootstrap.sh
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: simply build by adding profile config


Compare: https://github.com/ehb54/ultrascan3/compare/3a91742fcd41...102666e6eeba

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From noreply at github.com  Fri Oct 31 14:55:05 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 31 Oct 2025 13:55:05 -0700
Subject: [us-commits] [ehb54/ultrascan3] 18fcc6: mod: used if-else instead
 of series of if statements.
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/102666-18fcc6@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 18fcc684bbff2846566a57efafe210efec23cb07
      https://github.com/ehb54/ultrascan3/commit/18fcc684bbff2846566a57efafe210efec23cb07
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

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

  Log Message:
  -----------
  mod: used if-else instead of series of if statements.



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From noreply at github.com  Fri Oct 31 15:09:08 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 31 Oct 2025 14:09:08 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/000000-18fcc6@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Oct 31 15:34:51 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 31 Oct 2025 14:34:51 -0700
Subject: [us-commits] [ehb54/ultrascan3] e7a18c: - Add `is_valid_uuid`
 method to validate UUID stri...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/77d601-effe6c@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  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.


Compare: https://github.com/ehb54/ultrascan3/compare/77d60151680d...effe6ce3d4d0

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From noreply at github.com  Fri Oct 31 15:53:45 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 31 Oct 2025 14:53:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] 64d841: - Fix incorrect
 `QMessageBox` button status logic ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/effe6c-64d841@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  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`.



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From noreply at github.com  Fri Oct 31 16:33:23 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 31 Oct 2025 15:33:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5aae8e: fix: remove mac x11 lib
 dependency and references ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/18fcc6-5aae8e@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5aae8e45629593aea0b0e007a8f2166c6f60b9c4
      https://github.com/ehb54/ultrascan3/commit/5aae8e45629593aea0b0e007a8f2166c6f60b9c4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  fix: remove mac x11 lib dependency and references to us_window_message



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From noreply at github.com  Fri Oct 31 19:06:10 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 31 Oct 2025 18:06:10 -0700
Subject: [us-commits] [ehb54/ultrascan3] d66e17: fix: antialiasing
 deprecation in qpainter
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/5aae8e-d66e17@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d66e17404eb6616c8b39235715683f81791c61b3
      https://github.com/ehb54/ultrascan3/commit/d66e17404eb6616c8b39235715683f81791c61b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: antialiasing deprecation in qpainter



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