From noreply at github.com  Mon Dec  1 01:19:36 2025
From: noreply at github.com (HabGab)
Date: Mon, 01 Dec 2025 00:19:36 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5d9530: dec1
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/85ec26-5d9530@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5d9530affed48819f4a48b7ac271fd1df7dbc2f1
      https://github.com/ehb54/ultrascan3/commit/5d9530affed48819f4a48b7ac271fd1df7dbc2f1
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M doc/manual/source/_static/images/manage_data.png
    M doc/manual/source/_static/images/manage_data_bhide.png
    M doc/manual/source/_static/images/manage_data_bshow.png
    M doc/manual/source/_static/images/manage_data_exp.png
    M doc/manual/source/associations.rst
    M doc/manual/source/manage_data.rst

  Log Message:
  -----------
  dec1



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From noreply at github.com  Mon Dec  1 01:34:01 2025
From: noreply at github.com (HabGab)
Date: Mon, 01 Dec 2025 00:34:01 -0800
Subject: [us-commits] [ehb54/ultrascan3] a2d247: dec 1 2
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/5d9530-513556@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a2d2472b239daf6cedc42acba15b0b6915f2057e
      https://github.com/ehb54/ultrascan3/commit/a2d2472b239daf6cedc42acba15b0b6915f2057e
  Author: Haben <gabirh at myumanitoba.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M doc/manual/source/colorgradient.rst
    A doc/manual/source/rotor.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_new.rst

  Log Message:
  -----------
  dec 1 2


  Commit: 3d09e0442360400751c497233e8f94e1d72b26a6
      https://github.com/ehb54/ultrascan3/commit/3d09e0442360400751c497233e8f94e1d72b26a6
  Author: Haben <gabirh at myumanitoba.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_select.rst
    M doc/manual/source/index.rst
    M doc/manual/source/rotor.rst
    A doc/manual/source/rotor_calibration.rst
    M doc/manual/source/solutions/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/solutions/solution_settings.rst
    A doc/manual/source/us_project.rst

  Log Message:
  -----------
  dec 1 3


  Commit: 513556f73886ba9a0f65686367cc7f02bb03fc62
      https://github.com/ehb54/ultrascan3/commit/513556f73886ba9a0f65686367cc7f02bb03fc62
  Author: Haben <gabirh at myumanitoba.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M doc/manual/source/_static/images/manage_data.png
    M doc/manual/source/_static/images/manage_data_bhide.png
    M doc/manual/source/_static/images/manage_data_bshow.png
    M doc/manual/source/_static/images/manage_data_exp.png
    M doc/manual/source/associations.rst
    M doc/manual/source/manage_data.rst

  Log Message:
  -----------
  Merge branch 'haben-Dev' of https://github.com/ehb54/ultrascan3 into haben-Dev


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From noreply at github.com  Mon Dec  1 08:19:23 2025
From: noreply at github.com (HabGab)
Date: Mon, 01 Dec 2025 07:19:23 -0800
Subject: [us-commits] [ehb54/ultrascan3] 931d9c: dec 1 4
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/513556-931d9c@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 931d9c4d9c56ebc9c76d65745eef771d14285329
      https://github.com/ehb54/ultrascan3/commit/931d9c4d9c56ebc9c76d65745eef771d14285329
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M doc/manual/source/_static/images/rotor-add.png
    M doc/manual/source/_static/images/rotor.png
    A doc/manual/source/_static/images/rotorstretch_report.png
    A doc/manual/source/_static/images/solution_edit.png
    A doc/manual/source/_static/images/solution_new.png
    A doc/manual/source/_static/images/solution_select.png
    A doc/manual/source/_static/images/solution_settings.png
    A doc/manual/source/_static/images/us_project.png
    A doc/manual/source/_static/images/us_project_add-supdata.png
    A doc/manual/source/_static/images/us_project_edit-supdata.png
    A doc/manual/source/_static/images/us_project_web.png

  Log Message:
  -----------
  dec 1 4



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From noreply at github.com  Mon Dec  1 08:33:11 2025
From: noreply at github.com (HabGab)
Date: Mon, 01 Dec 2025 07:33:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] 6a2dfb: dec 15
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/931d9c-275894@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6a2dfba26d3f055b775b90ddd0b7141e79aa49f1
      https://github.com/ehb54/ultrascan3/commit/6a2dfba26d3f055b775b90ddd0b7141e79aa49f1
  Author: Haben <gabirh at myumanitoba.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M doc/manual/source/manage_data.rst

  Log Message:
  -----------
  dec 15


  Commit: 2758949680c8ad06928ba9c216ca035a95d3be85
      https://github.com/ehb54/ultrascan3/commit/2758949680c8ad06928ba9c216ca035a95d3be85
  Author: Haben <gabirh at myumanitoba.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M doc/manual/source/_static/images/rotor-add.png
    M doc/manual/source/_static/images/rotor.png
    A doc/manual/source/_static/images/rotorstretch_report.png
    A doc/manual/source/_static/images/solution_edit.png
    A doc/manual/source/_static/images/solution_new.png
    A doc/manual/source/_static/images/solution_select.png
    A doc/manual/source/_static/images/solution_settings.png
    A doc/manual/source/_static/images/us_project.png
    A doc/manual/source/_static/images/us_project_add-supdata.png
    A doc/manual/source/_static/images/us_project_edit-supdata.png
    A doc/manual/source/_static/images/us_project_web.png

  Log Message:
  -----------
  Merge branch 'haben-Dev' of https://github.com/ehb54/ultrascan3 into haben-Dev


Compare: https://github.com/ehb54/ultrascan3/compare/931d9c4d9c56...2758949680c8

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From noreply at github.com  Mon Dec  1 11:38:49 2025
From: noreply at github.com (HabGab)
Date: Mon, 01 Dec 2025 10:38:49 -0800
Subject: [us-commits] [ehb54/ultrascan3] 3e7400: Dec 1 5
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/275894-3e7400@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3e7400a64d33139fe063c03737000de59fd0ea19
      https://github.com/ehb54/ultrascan3/commit/3e7400a64d33139fe063c03737000de59fd0ea19
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    A doc/manual/source/_static/images/report.png
    M doc/manual/source/_static/images/reporter-cmenu.png
    M doc/manual/source/_static/images/reporter.png
    A doc/manual/source/_static/images/us_project_webed.png
    A doc/manual/source/astfem_sim.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    A doc/manual/source/reporter.rst
    M doc/manual/source/rotor.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_select.rst

  Log Message:
  -----------
  Dec 1 5



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From noreply at github.com  Mon Dec  1 12:24:27 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 11:24:27 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue667/000000-815465@github.com>

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From noreply at github.com  Mon Dec  1 12:25:13 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 11:25:13 -0800
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue667/000000-f298e4@github.com>

  Branch: refs/heads/alexey-dev-for-issue667
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From noreply at github.com  Mon Dec  1 13:25:39 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 12:25:39 -0800
Subject: [us-commits] [ehb54/us3_sql] fdece3: [SQL for ]Prot_DEV -- dataDisk
 type of data to reu...
Message-ID: <ehb54/us3_sql/push/refs/heads/main/f298e4-6387cd@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3_sql
  Commit: fdece366629c8255922408c4b381a7851a008d00
      https://github.com/ehb54/us3_sql/commit/fdece366629c8255922408c4b381a7851a008d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL for ]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: d5d2aab313c1cfd788221a82090c53274047c859
      https://github.com/ehb54/us3_sql/commit/d5d2aab313c1cfd788221a82090c53274047c859
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL for -- ] Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 6387cd69192a7b10bbaf70e452ccf0a3541146a0
      https://github.com/ehb54/us3_sql/commit/6387cd69192a7b10bbaf70e452ccf0a3541146a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  Merge pull request #21 from ehb54/alexey-dev-for-issue608

Alexey dev for issue608: for ticket 608 (PR305)


Compare: https://github.com/ehb54/us3_sql/compare/f298e41935d6...6387cd69192a

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From noreply at github.com  Mon Dec  1 13:28:33 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 12:28:33 -0800
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue667/f298e4-000000@github.com>

  Branch: refs/heads/alexey-dev-for-issue667
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From noreply at github.com  Mon Dec  1 13:29:58 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 12:29:58 -0800
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue667/000000-f298e4@github.com>

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From noreply at github.com  Mon Dec  1 13:31:23 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 12:31:23 -0800
Subject: [us-commits] [ehb54/us3_sql] fdece3: [SQL for ]Prot_DEV -- dataDisk
 type of data to reu...
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue667/f298e4-e56c91@github.com>

  Branch: refs/heads/alexey-dev-for-issue667
  Home:   https://github.com/ehb54/us3_sql
  Commit: fdece366629c8255922408c4b381a7851a008d00
      https://github.com/ehb54/us3_sql/commit/fdece366629c8255922408c4b381a7851a008d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL for ]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: d5d2aab313c1cfd788221a82090c53274047c859
      https://github.com/ehb54/us3_sql/commit/d5d2aab313c1cfd788221a82090c53274047c859
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL for -- ] Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 6387cd69192a7b10bbaf70e452ccf0a3541146a0
      https://github.com/ehb54/us3_sql/commit/6387cd69192a7b10bbaf70e452ccf0a3541146a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  Merge pull request #21 from ehb54/alexey-dev-for-issue608

Alexey dev for issue608: for ticket 608 (PR305)


  Commit: e56c913418519d718af527f148fbbc9d6184ccac
      https://github.com/ehb54/us3_sql/commit/e56c913418519d718af527f148fbbc9d6184ccac
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  Merge pull request #23 from ehb54/main

Merge current main into ...


Compare: https://github.com/ehb54/us3_sql/compare/f298e41935d6...e56c91341851

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From noreply at github.com  Mon Dec  1 14:07:01 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 13:07:01 -0800
Subject: [us-commits] [ehb54/ultrascan3] 609897: PROT.DEV. dataDisk re-use
 -- filter out older comp...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue667/815465-609897@github.com>

  Branch: refs/heads/alexey-dev-issue667
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 609897d0591d9d8d0b5bf0bbb55478c8efd20337
      https://github.com/ehb54/ultrascan3/commit/609897d0591d9d8d0b5bf0bbb55478c8efd20337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing...



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From noreply at github.com  Mon Dec  1 14:30:28 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 13:30:28 -0800
Subject: [us-commits] [ehb54/ultrascan3] fe940c: [debug 1]GMP 5. ANALYSIS --
 added more processEven...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue667/609897-fe940c@github.com>

  Branch: refs/heads/alexey-dev-issue667
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fe940ce7749c9043b38aa0f91efa79a19fed6216
      https://github.com/ehb54/ultrascan3/commit/fe940ce7749c9043b38aa0f91efa79a19fed6216
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M utils/us_experiment.cpp

  Log Message:
  -----------
  [debug 1]GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...



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From noreply at github.com  Mon Dec  1 14:39:08 2025
From: noreply at github.com (ehb54)
Date: Mon, 01 Dec 2025 13:39:08 -0800
Subject: [us-commits] [ehb54/ultrascan3] b91982: Prot_DEV -- dataDisk type
 of data to reuse in Prot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-634-a/572ca3-a0665e@github.com>

  Branch: refs/heads/ehb54-issue-634-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  [1]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  [2]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    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

  Log Message:
  -----------
  [4]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h

  Log Message:
  -----------
  [55]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  [6]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [7]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [8]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [9]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [11a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [12a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [13a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  [15a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [16a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [17a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 33dfedcbd83e81f3116f6e0051eb43b762a00ce1
      https://github.com/ehb54/ultrascan3/commit/33dfedcbd83e81f3116f6e0051eb43b762a00ce1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

  Log Message:
  -----------
  Refactor `US_Plot` and related classes for modern C++ standards and improved maintainability

Replaced raw pointers with `nullptr`, leveraged modern Qt signal-slot syntax, and tightened const correctness throughout. Removed legacy Qt version checks and redundant logic for clean and readable code.


  Commit: ef64cab1de21434fe0f5d43a73d8f500c37bbfed
      https://github.com/ehb54/ultrascan3/commit/ef64cab1de21434fe0f5d43a73d8f500c37bbfed
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Fix incorrect variable usage and remove redundant `const` specifiers in `US_Plot`

Corrected variable mismatch in `connect` call for canvas color updates. Replaced redundant `const QDir` declarations with `QDir` to align with proper usage. Initialized `selSymbol` with `QwtSymbol::NoSymbol` to prevent uninitialized access.


  Commit: aa4ace94a7d0acc500543323e466222bb30c02c7
      https://github.com/ehb54/ultrascan3/commit/aa4ace94a7d0acc500543323e466222bb30c02c7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #310 from ehb54/lukas/us_plot_config

Fix us_plot config causing Curves to get symboles


  Commit: 4db2218d24fbf448f58e228e33c6634b2ddbe429
      https://github.com/ehb54/ultrascan3/commit/4db2218d24fbf448f58e228e33c6634b2ddbe429
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/codeql/docker/local.pri.gui-qt6

  Log Message:
  -----------
  issue 649, testing codeql qt6 build


  Commit: 7efd56b0064621de09905cb9d76a56f0a1c83b77
      https://github.com/ehb54/ultrascan3/commit/7efd56b0064621de09905cb9d76a56f0a1c83b77
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  issue 649, testing codeql qt6 build


  Commit: 0b5dfd84a4ed2f5328e79bef342f3fec70845310
      https://github.com/ehb54/ultrascan3/commit/0b5dfd84a4ed2f5328e79bef342f3fec70845310
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  codeql workflow remove commented section


  Commit: 522a7b53313a7a9d4d13450bbaa79b482379ab0a
      https://github.com/ehb54/ultrascan3/commit/522a7b53313a7a9d4d13450bbaa79b482379ab0a
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.gui-qt6

  Log Message:
  -----------
  Remove openglwidgets from QT configuration


  Commit: 5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
      https://github.com/ehb54/ultrascan3/commit/5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-16 (Sun, 16 Nov 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_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP [dataDisk]: 1. EXP. -- init. steps for dealing with arbitrary selection of channels in uploaded data...


  Commit: 637512db487f7224a48db9fddadac0121cd0ec6e
      https://github.com/ehb54/ultrascan3/commit/637512db487f7224a48db9fddadac0121cd0ec6e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP [dataDisk]: 1. EXP. -- [MODS to generated prtotocol check before submission] init. steps for dealing with arbitrary selection of channels in uploaded data...


  Commit: 31bffce6f2258893d277cf9e2ab6b5a2290acd70
      https://github.com/ehb54/ultrascan3/commit/31bffce6f2258893d277cf9e2ab6b5a2290acd70
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

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

  Log Message:
  -----------
  Update unit-tests.yml to include additional paths


  Commit: 17ce4b6fb272848fdced6c862bae217de71652d8
      https://github.com/ehb54/ultrascan3/commit/17ce4b6fb272848fdced6c862bae217de71652d8
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-18 (Tue, 18 Nov 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_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #316 from ehb54/alexey-dev-issue650

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP : 6.REPORTER -- ranges for CG-models...


  Commit: 6c646f633296c0b2cdf20178c282494f364c1846
      https://github.com/ehb54/ultrascan3/commit/6c646f633296c0b2cdf20178c282494f364c1846
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue608


  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: b08b1c4672f375b1df4d08eb2e61fd656c9d406d
      https://github.com/ehb54/ultrascan3/commit/b08b1c4672f375b1df4d08eb2e61fd656c9d406d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    R admin/codeql/docker/local.pri.gui-qt6
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  codeql updates to main branch


  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [2]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 0cd1156f3fead2acf306d704cca3686a6a2ec32f
      https://github.com/ehb54/ultrascan3/commit/0cd1156f3fead2acf306d704cca3686a6a2ec32f
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Merge pull request #313 from ehb54/ehb54-issue-649

issue 649, testing codeql qt6 build


  Commit: 5400614d6c78af525f22b1f858362a99edc462a1
      https://github.com/ehb54/ultrascan3/commit/5400614d6c78af525f22b1f858362a99edc462a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #319 from ehb54/main

add main stuff to alexey-dev-issue651


  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 8f345295dc5803000521a47ad53aa246df51eff7
      https://github.com/ehb54/ultrascan3/commit/8f345295dc5803000521a47ad53aa246df51eff7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #320 from ehb54/main

update to main


  Commit: 129b8d9184d5cab1189cca7b84574bf7e97dca76
      https://github.com/ehb54/ultrascan3/commit/129b8d9184d5cab1189cca7b84574bf7e97dca76
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL workflow for improved caching and builds


  Commit: 793e12c735495da5c5b6deed3355e2428e6c2a16
      https://github.com/ehb54/ultrascan3/commit/793e12c735495da5c5b6deed3355e2428e6c2a16
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Simplify build step in CodeQL analysis workflow

Removed ccache setup and git configuration from the build step.


  Commit: 0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
      https://github.com/ehb54/ultrascan3/commit/0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL analysis workflow

Refactor CodeQL analysis workflow to improve target calculation and build steps.


  Commit: 6c80777b7287a29fe978526475e6f099ca3ef827
      https://github.com/ehb54/ultrascan3/commit/6c80777b7287a29fe978526475e6f099ca3ef827
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL workflow to simplify caching and builds

Removed caching steps for ccache, utils, qwtplot3d, and gui. Added build steps for utils, qwtplot3d, and gui using qmake.


  Commit: 27c760f8c268e77d5038469cfd40243fb274f2d1
      https://github.com/ehb54/ultrascan3/commit/27c760f8c268e77d5038469cfd40243fb274f2d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update unit-tests.yml to remove path filters for push

Removed specific path filters for push events in unit-tests workflow.


  Commit: 2465409a96b820d237f9bf0c3b09b12f859060d7
      https://github.com/ehb54/ultrascan3/commit/2465409a96b820d237f9bf0c3b09b12f859060d7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update static analysis workflow trigger paths

Removed specific path triggers for push events in static analysis workflow.


  Commit: c1ac9c0b43cdde1480834d2fb742344b9649144f
      https://github.com/ehb54/ultrascan3/commit/c1ac9c0b43cdde1480834d2fb742344b9649144f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Document CMake formatter


  Commit: 391ac4d011a289eafa902e9d56eb4382491f0b66
      https://github.com/ehb54/ultrascan3/commit/391ac4d011a289eafa902e9d56eb4382491f0b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Updating nproc


  Commit: ea7559d6bcd810ed7a176871e33f0d36b49152e2
      https://github.com/ehb54/ultrascan3/commit/ea7559d6bcd810ed7a176871e33f0d36b49152e2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/unit-tests.yml
    M admin/linting/cmake/.cmake-format.yaml
    M admin/linting/cmake/README.md

  Log Message:
  -----------
  Fix minor comments


  Commit: 6e94734ca883da80e058cf4e51dee4474e9863e5
      https://github.com/ehb54/ultrascan3/commit/6e94734ca883da80e058cf4e51dee4474e9863e5
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_edit/us_edit.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_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #305 from ehb54/alexey-dev-issue608

Alexey dev issue608: Prot. Dev. for DataDisk data types


  Commit: 5ff2d239588616635adbdfaf775949a91f5d7565
      https://github.com/ehb54/ultrascan3/commit/5ff2d239588616635adbdfaf775949a91f5d7565
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update checkout action version


  Commit: 321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
      https://github.com/ehb54/ultrascan3/commit/321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  fix branches


  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 5cf42202af6d7f5544a2cf1111d44f5f1a232777
      https://github.com/ehb54/ultrascan3/commit/5cf42202af6d7f5544a2cf1111d44f5f1a232777
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL analysis workflow conditions

Removed specific file paths from pull request triggers and updated conditions for CodeQL analysis steps.


  Commit: 3f486acaa2a2e5b708f257acf949e90d1b042bbc
      https://github.com/ehb54/ultrascan3/commit/3f486acaa2a2e5b708f257acf949e90d1b042bbc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  Rename analysis job for GUI programs


  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


  Commit: 02ab6c663335530dbf4295161c2f68c1043b3874
      https://github.com/ehb54/ultrascan3/commit/02ab6c663335530dbf4295161c2f68c1043b3874
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

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


  Commit: 013afa9051723a54ff17a3431895f0e6aa65eebc
      https://github.com/ehb54/ultrascan3/commit/013afa9051723a54ff17a3431895f0e6aa65eebc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Refactor GitHub Actions workflows to enhance modularity and efficiency
- Introduce `changed-files` job to conditionally trigger workflows based on file changes.
- Add status-checking jobs for Documentation, CodeQL analysis, and Static Analysis builds.
- Improve concurrency management and file fetch depth.
- Optimize CI Docker containers and cleanup processes.
- Streamline conditional checks and matrix configurations.


  Commit: 2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
      https://github.com/ehb54/ultrascan3/commit/2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    A .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add `unit-tests-v2.yml` GitHub Actions workflow

- Introduce a new workflow for unit testing with support for configurable test filters and debug mode.
- Add a `changed-files` job to detect relevant file modifications and conditionally trigger tests.
- Implement improved concurrency management and result-checking mechanisms.
- Streamline test setup, build process, and log management for enhanced clarity and efficiency.
- Enable artifact uploads for detailed test results and logs.


  Commit: e2a9b2acaeeeac868cf1d55f459225e683e37d11
      https://github.com/ehb54/ultrascan3/commit/e2a9b2acaeeeac868cf1d55f459225e683e37d11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Normalize glob patterns in GitHub Actions workflows


  Commit: 037064b1d8968578fcb9a42ba07e275c96b38a8c
      https://github.com/ehb54/ultrascan3/commit/037064b1d8968578fcb9a42ba07e275c96b38a8c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Fix incorrect `CMAKE_MODULE_PATH` to use absolute path in `unit-tests-v2.yml` workflow


  Commit: 4c0538dff646603c4258628a076f9807a29af7c3
      https://github.com/ehb54/ultrascan3/commit/4c0538dff646603c4258628a076f9807a29af7c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Enhance `unit-tests.yml` workflow with dynamic file change detection and improved concurrency management

- Add `changed-files` job to detect relevant modifications and conditionally trigger unit tests.
- Introduce concurrency control to prevent duplicate runs.
- Expand artifacts to include additional logs for better debugging.
- Add status-checking job to validate unit testing outcomes.
- Refactor workflow for clarity and streamlined test execution.


  Commit: 12e9e1fd701da2b201e7d47b3cb642812813e4e7
      https://github.com/ehb54/ultrascan3/commit/12e9e1fd701da2b201e7d47b3cb642812813e4e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Enhance `static-analysis.yml` workflow with CPP file-specific change detection

- Add outputs and environment variables to track `.cpp` and `.h` file changes.
- Update `changed-files` step to simplify logic and rely on filtered outputs.
- Streamline file detection for first commits and pull requests.


  Commit: e94063c15730a822262820f18c468a429ac4c374
      https://github.com/ehb54/ultrascan3/commit/e94063c15730a822262820f18c468a429ac4c374
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Normalize glob pattern syntax in `unit-tests.yml` workflow


  Commit: 158b855316998f18924177b91ad5cb81e696ad53
      https://github.com/ehb54/ultrascan3/commit/158b855316998f18924177b91ad5cb81e696ad53
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Update static-analysis workflow to use latest `us3comp` container image


  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...


  Commit: 350edcd3194656d020a571d45cbe1dd872d041e2
      https://github.com/ehb54/ultrascan3/commit/350edcd3194656d020a571d45cbe1dd872d041e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #322 from ehb54/alexey-dev-issue651

Alexey dev issue651: Ind. & Combined Plots in GMP Rpeorts: CG-model-based runs (ranges), Plot Aspect Ratios, "Combined Plots" section title


  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...


  Commit: e1ce700f61527eedba262f237e41dbcc16de6de7
      https://github.com/ehb54/ultrascan3/commit/e1ce700f61527eedba262f237e41dbcc16de6de7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Update file patterns for static analysis


  Commit: aebbdda924bca0630a6b1b50f5110f340c8804aa
      https://github.com/ehb54/ultrascan3/commit/aebbdda924bca0630a6b1b50f5110f340c8804aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Update CodeQL workflow to ignore specific files

Ignore changes in us_mpi_analysis directory during file checks and update build commands.


  Commit: a4a655d619279b7bb59e01ee82fce46e875eebca
      https://github.com/ehb54/ultrascan3/commit/a4a655d619279b7bb59e01ee82fce46e875eebca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Exclude us_mpi_analysis from CodeQL analysis gui


  Commit: 14ba4d63b16861ed659ae0c204b0ee3f54589432
      https://github.com/ehb54/ultrascan3/commit/14ba4d63b16861ed659ae0c204b0ee3f54589432
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Fix syntax for exclusion in CodeQL workflow


  Commit: 770769aa570aae22f64b5b817de2320ab1b070e3
      https://github.com/ehb54/ultrascan3/commit/770769aa570aae22f64b5b817de2320ab1b070e3
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #326 from ehb54/alexey-dev-issue631

GMP 6. REPORT -- generate correct build number in the header...


  Commit: 3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
      https://github.com/ehb54/ultrascan3/commit/3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

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


  Commit: c088a80976663c552cffec04fcb0cfe084922560
      https://github.com/ehb54/ultrascan3/commit/c088a80976663c552cffec04fcb0cfe084922560
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Merge pull request #321 from ehb54/lukas/gh_actions

Lukas/gh actions


  Commit: 70cf969d22c8ecb1892bcb7a3301d101bca7aa55
      https://github.com/ehb54/ultrascan3/commit/70cf969d22c8ecb1892bcb7a3301d101bca7aa55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 815465ed2b2679fbcf4cda7c076dda6fdc89f322
      https://github.com/ehb54/ultrascan3/commit/815465ed2b2679fbcf4cda7c076dda6fdc89f322
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Merge pull request #327 from ehb54/alexey-dev-issue657

GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in FITME_AUTO & View Overlay


  Commit: a0665e28e96ec99c45bc50f07334caa76158c973
      https://github.com/ehb54/ultrascan3/commit/a0665e28e96ec99c45bc50f07334caa76158c973
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into ehb54-issue-634-a


Compare: https://github.com/ehb54/ultrascan3/compare/572ca3dc893c...a0665e28e96e

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From noreply at github.com  Mon Dec  1 14:43:45 2025
From: noreply at github.com (ehb54)
Date: Mon, 01 Dec 2025 13:43:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1d8b79: better --run handling ...
 unbuffer stdout via php ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-634-a/a0665e-1d8b79@github.com>

  Branch: refs/heads/ehb54-issue-634-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1d8b797fe1f7467a6dec44b233a5c7c2320f36e8
      https://github.com/ehb54/ultrascan3/commit/1d8b797fe1f7467a6dec44b233a5c7c2320f36e8
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M admin/us_branch/us_branch.php

  Log Message:
  -----------
  better --run handling ... unbuffer stdout via php pipe



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From noreply at github.com  Mon Dec  1 15:51:08 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 14:51:08 -0800
Subject: [us-commits] [ehb54/us3_sql] 7c4589: [SQL for -- ] PROT.DEV.
 dataDisk re-use -- filter ...
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue667/e56c91-7c4589@github.com>

  Branch: refs/heads/alexey-dev-for-issue667
  Home:   https://github.com/ehb54/us3_sql
  Commit: 7c4589095f53076255a09858c4b21c01c4120292
      https://github.com/ehb54/us3_sql/commit/7c4589095f53076255a09858c4b21c01c4120292
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL for -- ] PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing......



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From noreply at github.com  Mon Dec  1 16:23:21 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 15:23:21 -0800
Subject: [us-commits] [ehb54/us3_sql] e56c91: Merge pull request #23 from
 ehb54/main
Message-ID: <ehb54/us3_sql/push/refs/heads/main/6387cd-380476@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/us3_sql
  Commit: e56c913418519d718af527f148fbbc9d6184ccac
      https://github.com/ehb54/us3_sql/commit/e56c913418519d718af527f148fbbc9d6184ccac
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  Merge pull request #23 from ehb54/main

Merge current main into ...


  Commit: 7c4589095f53076255a09858c4b21c01c4120292
      https://github.com/ehb54/us3_sql/commit/7c4589095f53076255a09858c4b21c01c4120292
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL for -- ] PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing......


  Commit: 380476ef7883f45ce70b3d976fd17243d73814ca
      https://github.com/ehb54/us3_sql/commit/380476ef7883f45ce70b3d976fd17243d73814ca
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  Merge pull request #24 from ehb54/alexey-dev-for-issue667

Alexey dev for issue667: needed minor sql changes for ticket #667


Compare: https://github.com/ehb54/us3_sql/compare/6387cd69192a...380476ef7883

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From noreply at github.com  Mon Dec  1 16:57:07 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 01 Dec 2025 15:57:07 -0800
Subject: [us-commits] [ehb54/ultrascan3] 609897: PROT.DEV. dataDisk re-use
 -- filter out older comp...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/815465-332293@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 609897d0591d9d8d0b5bf0bbb55478c8efd20337
      https://github.com/ehb54/ultrascan3/commit/609897d0591d9d8d0b5bf0bbb55478c8efd20337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing...


  Commit: fe940ce7749c9043b38aa0f91efa79a19fed6216
      https://github.com/ehb54/ultrascan3/commit/fe940ce7749c9043b38aa0f91efa79a19fed6216
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M utils/us_experiment.cpp

  Log Message:
  -----------
  [debug 1]GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 3322930798adf89544c8645263c9a5b2b477124a
      https://github.com/ehb54/ultrascan3/commit/3322930798adf89544c8645263c9a5b2b477124a
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #330 from ehb54/alexey-dev-issue667

PROT DEV -- filter out completed dataDisk runs initiated with earlier tabular signature (not to be reprocessed)


Compare: https://github.com/ehb54/ultrascan3/compare/815465ed2b26...3322930798ad

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From noreply at github.com  Mon Dec  1 16:57:11 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 01 Dec 2025 15:57:11 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue667/fe940c-000000@github.com>

  Branch: refs/heads/alexey-dev-issue667
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Dec  1 17:04:27 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 16:04:27 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue669/000000-332293@github.com>

  Branch: refs/heads/alexey-dev-issue669
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Dec  1 18:20:51 2025
From: noreply at github.com (alexsav815)
Date: Mon, 01 Dec 2025 17:20:51 -0800
Subject: [us-commits] [ehb54/ultrascan3] af82fd: PROT.DEV.: dataDisk type --
 pass invID from the pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue669/332293-af82fd@github.com>

  Branch: refs/heads/alexey-dev-issue669
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
      https://github.com/ehb54/ultrascan3/commit/af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  PROT.DEV.: dataDisk type -- pass invID from the protocol assoc. with the datat to-be-reanalysed for download from DB: (1) during creation of a new run using data produced by different owner; (2) during re-attachment from different session/different user (which would require fresh download)...



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From noreply at github.com  Wed Dec  3 05:02:19 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 03 Dec 2025 04:02:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 609897: PROT.DEV. dataDisk re-use
 -- filter out older comp...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/06815f-c7cd4a@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 609897d0591d9d8d0b5bf0bbb55478c8efd20337
      https://github.com/ehb54/ultrascan3/commit/609897d0591d9d8d0b5bf0bbb55478c8efd20337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing...


  Commit: fe940ce7749c9043b38aa0f91efa79a19fed6216
      https://github.com/ehb54/ultrascan3/commit/fe940ce7749c9043b38aa0f91efa79a19fed6216
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M utils/us_experiment.cpp

  Log Message:
  -----------
  [debug 1]GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 3322930798adf89544c8645263c9a5b2b477124a
      https://github.com/ehb54/ultrascan3/commit/3322930798adf89544c8645263c9a5b2b477124a
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #330 from ehb54/alexey-dev-issue667

PROT DEV -- filter out completed dataDisk runs initiated with earlier tabular signature (not to be reprocessed)


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/06815f05ab2f...c7cd4ad5a59e

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From noreply at github.com  Wed Dec  3 05:05:10 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 03 Dec 2025 04:05:10 -0800
Subject: [us-commits] [ehb54/ultrascan3] af1a5c: Additional Unit Testing
 us_ana_profile, us_crc, us...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_fematch/242f9a-a1184f@github.com>

  Branch: refs/heads/lukas/us_fematch
  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: 36fbb78274624ec179e9b8eb7915d34278539ad6
      https://github.com/ehb54/ultrascan3/commit/36fbb78274624ec179e9b8eb7915d34278539ad6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-05 (Wed, 05 Mar 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  GMP | R&D : 3. IMPORT -- remove 'todo' section & reorginize GUI a bit ...


  Commit: f1a395f2789f8541cd1e9127762368a6e64c5faa
      https://github.com/ehb54/ultrascan3/commit/f1a395f2789f8541cd1e9127762368a6e64c5faa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-05 (Wed, 05 Mar 2025)

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

  Log Message:
  -----------
  GMP-ABDE : 4. EDITING -- prelim. address all points discussed ...


  Commit: 11f0b57b408e864f2f3071085f8da651d3e0747f
      https://github.com/ehb54/ultrascan3/commit/11f0b57b408e864f2f3071085f8da651d3e0747f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-06 (Thu, 06 Mar 2025)

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

  Log Message:
  -----------
  GMP-ABDE : EDITING-TO-REPORT -- skip ANALYSIS, proper finishing and switch to rpeort ...


  Commit: 97410a8ee97df46bafab7e6500fbefcee5aae2c7
      https://github.com/ehb54/ultrascan3/commit/97410a8ee97df46bafab7e6500fbefcee5aae2c7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-07 (Fri, 07 Mar 2025)

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

  Log Message:
  -----------
  GMP-ABDE, ABDE program : 4. EDITING -- when manually editing channel, treat as widget, hide/restore the rest; disbale AUTO fit in the ABDE program upon data load ...


  Commit: 3677b206ae367f13886a6cbd520cec861e631d89
      https://github.com/ehb54/ultrascan3/commit/3677b206ae367f13886a6cbd520cec861e631d89
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-10 (Mon, 10 Mar 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- progress on linear-baseline-correction approx. for each channel ...


  Commit: c052b66c83b870c3bb799e7e06bcc4c3277d22ba
      https://github.com/ehb54/ultrascan3/commit/c052b66c83b870c3bb799e7e06bcc4c3277d22ba
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-10 (Mon, 10 Mar 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- [few bugs fixed for ] progress on linear-baseline-correction approx. for each channel ...


  Commit: 0ff6374e15149181664cbb20de6d1cad9186315b
      https://github.com/ehb54/ultrascan3/commit/0ff6374e15149181664cbb20de6d1cad9186315b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-10 (Mon, 10 Mar 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- more work on porting ABDE-GMP-editing to existing framework.....


  Commit: 6b3cd7cfa20f5f8ee5092ff3dba00d2965362eaf
      https://github.com/ehb54/ultrascan3/commit/6b3cd7cfa20f5f8ee5092ff3dba00d2965362eaf
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-14 (Fri, 14 Mar 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- few bugs fixed as to compatibility of stand-alone & GMP Editing...


  Commit: f40ee9b3921c410c811c4dd28015119f77716208
      https://github.com/ehb54/ultrascan3/commit/f40ee9b3921c410c811c4dd28015119f77716208
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-16 (Sun, 16 Mar 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- progress on enabling per-triple modification of the linear baseline corrections vs. per-channel (aka apply to all); ...


  Commit: aa721800844fa90cc321728e5e88d1ef996e12d4
      https://github.com/ehb54/ultrascan3/commit/aa721800844fa90cc321728e5e88d1ef996e12d4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-17 (Mon, 17 Mar 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- [more on..] progress on enabling per-triple modification of the linear baseline corrections vs. per-channel (aka apply to all); ...


  Commit: 9e0347842ec2a652e786fd9127d87af2f05001a5
      https://github.com/ehb54/ultrascan3/commit/9e0347842ec2a652e786fd9127d87af2f05001a5
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-18 (Tue, 18 Mar 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- [gui fixes for] progress on enabling per-triple modification of the linear baseline corrections vs. per-channel (aka apply to all); ...


  Commit: 4f3dac583f4111782277ae083ee53e61de85b506
      https://github.com/ehb54/ultrascan3/commit/4f3dac583f4111782277ae083ee53e61de85b506
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-19 (Wed, 19 Mar 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- [accomodate both single- and MWL cases] progress on enabling per-triple modification of the linear baseline corrections vs. per-channel (aka apply to all); ...


  Commit: 904a95ffa39e2eda64d9678d2a9f00c26fc96d35
      https://github.com/ehb54/ultrascan3/commit/904a95ffa39e2eda64d9678d2a9f00c26fc96d35
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-19 (Wed, 19 Mar 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  GMP-ABDE: 4. EDITING -- bug fixed as to re-attaching to MWVL-to-singleMVL from Run Manager && restoring MWL gui controls ...


  Commit: aaf9d8e9266a23672860160c21a8f559501de1cc
      https://github.com/ehb54/ultrascan3/commit/aaf9d8e9266a23672860160c21a8f559501de1cc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-26 (Wed, 26 Mar 2025)

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

  Log Message:
  -----------
  GMP-ABDE: -- switch to the to-be analysis stage; proper ending of editing ...


  Commit: 68acf2c658df1cee16ca38711fd32362de481496
      https://github.com/ehb54/ultrascan3/commit/68acf2c658df1cee16ca38711fd32362de481496
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-27 (Thu, 27 Mar 2025)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  GMP-Audit-trail: -- misspelling fixed ...


  Commit: f7c02bfb100afb53049fbabc7d2f7fb26139d09c
      https://github.com/ehb54/ultrascan3/commit/f7c02bfb100afb53049fbabc7d2f7fb26139d09c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-28 (Fri, 28 Mar 2025)

  Changed paths:
    M gui/us_data_loader.cpp
    M gui/us_data_loader.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_com_project/us_com_project.pro
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_fematch/us_fematch.pro
    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_protocol_dev/us_protocol_dev.pro
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro

  Log Message:
  -----------
  GMP-ABDE: -- prep. steps for [AUTO]MWL-decomposition ...


  Commit: a909a2130600602250ff2c7d241264159790492f
      https://github.com/ehb54/ultrascan3/commit/a909a2130600602250ff2c7d241264159790492f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-28 (Fri, 28 Mar 2025)

  Changed paths:
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp

  Log Message:
  -----------
  GMP-ABDE: -- further steps for [AUTO]MWL-decomposition ...


  Commit: 5a7280eadbf62110f18d3edc6dad501f2dbc0ed4
      https://github.com/ehb54/ultrascan3/commit/5a7280eadbf62110f18d3edc6dad501f2dbc0ed4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-03-31 (Mon, 31 Mar 2025)

  Changed paths:
    M gui/us_data_loader.cpp
    M programs/us_edit/us_edit.cpp
    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_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h

  Log Message:
  -----------
  GMP-ABDE: -- (1) bug fixed in EDIT as for exclusion of all but last scan for each triple; (2) more work on porting MWL species deconv. into GMP-ABDE's ANALYSIS stage...


  Commit: 37a603409bfa0487097e0e2068dc1f6ff0084805
      https://github.com/ehb54/ultrascan3/commit/37a603409bfa0487097e0e2068dc1f6ff0084805
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-01 (Tue, 01 Apr 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 -- automated deconvolution for MWL data...


  Commit: e85004ebe04cc4e5bcac416638363b50c624dfaa
      https://github.com/ehb54/ultrascan3/commit/e85004ebe04cc4e5bcac416638363b50c624dfaa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-02 (Wed, 02 Apr 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
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- apply extinction profiles from DB (protocol) for each analyte (and buffer if specified); read and apply linear base-line corrections for each triple from edit profiles; && loop over triples & deconvolute...


  Commit: 16f83a88ccafb90a5ae28bdfbd2302738f592776
      https://github.com/ehb54/ultrascan3/commit/16f83a88ccafb90a5ae28bdfbd2302738f592776
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-03 (Thu, 03 Apr 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A CITATION.cff
    M CMakeLists.txt
    A doc/calc_model_coefficient_documentation.pdf
    A doc/calc_timestate_documentation.pdf
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_gui.h
    M gui/us_rotor_gui.cpp
    M gui/us_rotor_gui.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 programs/us_2dsa/us_2dsa.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_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_config/us_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_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_fematch/us_fematch.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_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_reporter_gmp/us_reporter_gmp.cpp
    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 utils/CMakeLists.txt
    R utils/calc_coefficient_documentation.pdf
    M utils/us_astfem_math.cpp
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_simparms.cpp

  Log Message:
  -----------
  Merge pull request #199 from ehb54/master

Merge current master to alexey-dev-ussue425


  Commit: 5e45e203a53206ff829c003d99daea34b0c249fc
      https://github.com/ehb54/ultrascan3/commit/5e45e203a53206ff829c003d99daea34b0c249fc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-03 (Thu, 03 Apr 2025)

  Changed paths:
    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_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_fematch/us_fematch.pro
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- generated SSF data after MWL-deconv. are now auto-saved into DB as a separate records...


  Commit: b0112a373e29c51f8ba74849d5b0127d9d8978ad
      https://github.com/ehb54/ultrascan3/commit/b0112a373e29c51f8ba74849d5b0127d9d8978ad
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-04 (Fri, 04 Apr 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
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/us_reporter_gmp.pro

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- port stand-alone abde normalizer to GMP framework; auto-upload deconv. data from previos mwl-spiecies-fit...


  Commit: fd5c80d8177c74905ced72a499d1ba162873b16d
      https://github.com/ehb54/ultrascan3/commit/fd5c80d8177c74905ced72a499d1ba162873b16d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-08 (Tue, 08 Apr 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_experiment.cpp

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- supress all msgs related to DB-save of SSF data in case of already saved...


  Commit: 66b456db36e56b38857266164eb4f6fe56dbce6d
      https://github.com/ehb54/ultrascan3/commit/66b456db36e56b38857266164eb4f6fe56dbce6d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-09 (Wed, 09 Apr 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:
  -----------
  GMP-ABDE: 5. ANALYSIS -- prep. for channel-by-channel processing in the normalizer program...


  Commit: d98c3484a15df726b143465f2bfbfcf71959a18a
      https://github.com/ehb54/ultrascan3/commit/d98c3484a15df726b143465f2bfbfcf71959a18a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-11 (Fri, 11 Apr 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.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
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_xpn_viewer/us_xpn_viewer.pro

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- pass ranges set in reportItems for each channels into normalizer program...


  Commit: 2eb1848d73714c7b61fe515ca0e88a8087a20486
      https://github.com/ehb54/ultrascan3/commit/2eb1848d73714c7b61fe515ca0e88a8087a20486
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-29 (Tue, 29 Apr 2025)

  Changed paths:
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    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
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    M doc/manual/mainstyle.css
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    A doc/manual/sassoc.body
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    M doc/manual/vhw_enhanced.body
    M gui/us_select_item.cpp
    M makeall.sh
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.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
    M utils/us_geturl.h

  Log Message:
  -----------
  Merge pull request #211 from ehb54/master

add current master into alxey-dev-issue425


  Commit: ee423e5ad3a0dd89e1bd4dea5cdf682d1292d0de
      https://github.com/ehb54/ultrascan3/commit/ee423e5ad3a0dd89e1bd4dea5cdf682d1292d0de
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-04-29 (Tue, 29 Apr 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- split all normalization operations by channel & save actions and normalizations accordingly...


  Commit: 64a2c9f9d597adb905f324ddb340d2e1da7852aa
      https://github.com/ehb54/ultrascan3/commit/64a2c9f9d597adb905f324ddb340d2e1da7852aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-01 (Thu, 01 May 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 1. EXP. setting -- bug fixed causing crash in rare cases when loaded investigator didn't have any solutions in the DB, and changing to investigator with the solutions in the DB did not updated solution list properly (problem existed only for ABDE type)...


  Commit: d42e72c78bde90edf16acbe07b71861d24f29994
      https://github.com/ehb54/ultrascan3/commit/d42e72c78bde90edf16acbe07b71861d24f29994
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-01 (Thu, 01 May 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-ABDE: 1. EXP. setting -- [prevent crash if there is still no solutions on the DB, inform user, close the program] bug fixed causing crash in rare cases when loaded investigator didn't have any solutions in the DB, and changing to investigator with the solutions in the DB did not updated solution list properly (problem existed only for ABDE type)...


  Commit: 5a187617baa3311542a00dc75a014971bdd522d8
      https://github.com/ehb54/ultrascan3/commit/5a187617baa3311542a00dc75a014971bdd522d8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-02 (Fri, 02 May 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- before profiles saving, compose JSON with info on each channel for normalization (and ranges intersections with integral curves in future)...


  Commit: f7f28efef6269efddcc6b39f8b6dc6971b130ec9
      https://github.com/ehb54/ultrascan3/commit/f7f28efef6269efddcc6b39f8b6dc6971b130ec9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-05 (Mon, 05 May 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-ABDE: 1. EXP. -- create 2 additional records on DB upon GMP run submission for later analysis...


  Commit: 18f4e3adbc3f1d7c659dea68f8e8499c16e27b0d
      https://github.com/ehb54/ultrascan3/commit/18f4e3adbc3f1d7c659dea68f8e8499c16e27b0d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-09 (Fri, 09 May 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS (MWL-DECONV.) -- compute percentages for APRofile ranges per channel per range, pass the info to json to be saved in DB & used in reporting; clean plots legends, colors etc.; keep track on prcessed channels and on normalization before enabling to save profiles...


  Commit: 75cc0ecc55b7bb99dbcfdb7441600f5f86bd7f9d
      https://github.com/ehb54/ultrascan3/commit/75cc0ecc55b7bb99dbcfdb7441600f5f86bd7f9d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-11 (Sun, 11 May 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- progress on accomodating both MWL-DECONV. & single-WL ABDE types in GMP analysis...


  Commit: 4174ae5ad04bc30d060301483dff29cafaddaf16
      https://github.com/ehb54/ultrascan3/commit/4174ae5ad04bc30d060301483dff29cafaddaf16
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-11 (Sun, 11 May 2025)

  Changed paths:
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    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 -- [More] progress on accomodating both MWL-DECONV. & single-WL ABDE types in GMP analysis...


  Commit: fe10072d2d56c1c83e145faaefbf17146a92413c
      https://github.com/ehb54/ultrascan3/commit/fe10072d2d56c1c83e145faaefbf17146a92413c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-12 (Mon, 12 May 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  GMP-ABDE: 1. EXP. -- hierarchical checks before run submission enforcing number of conditions for solutions, extinct. profiles, ranges - both for SWL and MWL-DECONV. experiments...


  Commit: 0228986fa9a4a3653d802eaed73eed6e29e113d2
      https://github.com/ehb54/ultrascan3/commit/0228986fa9a4a3653d802eaed73eed6e29e113d2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-13 (Tue, 13 May 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- [More, more] progress on accomodating both MWL-DECONV. & single-WL ABDE types in GMP analysis...


  Commit: 1a9fce71cc056ef952dae2fa67512802aa7e73d1
      https://github.com/ehb54/ultrascan3/commit/1a9fce71cc056ef952dae2fa67512802aa7e73d1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-13 (Tue, 13 May 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- implement (1) switch from  MWL-DECONV. || single-WL ABDE types in GMP analysis to REPORT; (2) switch from ABDE-analysis to Run Manager, both when just want to return, or when ABDE profiles already saved form different session...


  Commit: bd8f08dc9de642c5dfdf5c3592d0d5b6192245f2
      https://github.com/ehb54/ultrascan3/commit/bd8f08dc9de642c5dfdf5c3592d0d5b6192245f2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-14 (Wed, 14 May 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- pass & store in DB additional info required for ABDE plots restoration in REPORT...


  Commit: 8a6e905de9cba1b09ca1c9205ea1e52462e9a266
      https://github.com/ehb54/ultrascan3/commit/8a6e905de9cba1b09ca1c9205ea1e52462e9a266
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-14 (Wed, 14 May 2025)

  Changed paths:
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- major prep. steps for reconstructing ABDE profile plots & ranges-percentages in the subsequesnt REPORT stage...


  Commit: a91bab7f8a743643cd2135af67bb247dd6dfe833
      https://github.com/ehb54/ultrascan3/commit/a91bab7f8a743643cd2135af67bb247dd6dfe833
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-15 (Thu, 15 May 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- ALL steps for reconstructing ABDE profile plots & ranges-percentages in the subsequesnt REPORT stage...


  Commit: c5e1f54ccc1dd1e99d7c360d26d3cfb2c3973443
      https://github.com/ehb54/ultrascan3/commit/c5e1f54ccc1dd1e99d7c360d26d3cfb2c3973443
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-16 (Fri, 16 May 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    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 -- [ADD passing RMSD of the spectral deconv. for each channel into ABDE norm & later REPORT] ALL steps for reconstructing ABDE profile plots & ranges-percentages in the subsequesnt REPORT stage...


  Commit: 84405506d08408364790332c02105f79d00f5df1
      https://github.com/ehb54/ultrascan3/commit/84405506d08408364790332c02105f79d00f5df1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-16 (Fri, 16 May 2025)

  Changed paths:
    M gui/us_gui_util.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- progress on ABDE GMP reporting...


  Commit: 78f1a182dfa7f71b5cc44c8ace4cd9fa215c6405
      https://github.com/ehb54/ultrascan3/commit/78f1a182dfa7f71b5cc44c8ace4cd9fa215c6405
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-19 (Mon, 19 May 2025)

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

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- [MORE ] progress on ABDE GMP reporting...


  Commit: 0a2beabcae1b687c5687c4b2450fd1af74dfc220
      https://github.com/ehb54/ultrascan3/commit/0a2beabcae1b687c5687c4b2450fd1af74dfc220
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-19 (Mon, 19 May 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_report_gmp.cpp

  Log Message:
  -----------
  Merge pull request #220 from ehb54/master

Merge latest master into alexey-dev-issue425 (ABDE dev.)


  Commit: ba9596172bb5ac437f7715f3df79e08a1e249dbb
      https://github.com/ehb54/ultrascan3/commit/ba9596172bb5ac437f7715f3df79e08a1e249dbb
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-19 (Mon, 19 May 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- [MORE 11] progress on ABDE GMP reporting...


  Commit: 183b6de5faf3ba6ce984692955573dbabb2fb8e4
      https://github.com/ehb54/ultrascan3/commit/183b6de5faf3ba6ce984692955573dbabb2fb8e4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-19 (Mon, 19 May 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- [MORE 22] progress on ABDE GMP reporting...


  Commit: 57366bd055ebc2cbe566db6512a5cb05df5921e2
      https://github.com/ehb54/ultrascan3/commit/57366bd055ebc2cbe566db6512a5cb05df5921e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-20 (Tue, 20 May 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP-ABDE: 6. REPORT -- in every chanels report, indicate if it's MWL-Deconv. or not...


  Commit: a6539c9236ab2859156a08cf63545c460a93a3c1
      https://github.com/ehb54/ultrascan3/commit/a6539c9236ab2859156a08cf63545c460a93a3c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-27 (Tue, 27 May 2025)

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

  Log Message:
  -----------
  GMP REPORTER: stand_alone -- adapt and modify stand-alone program to generate custom reports for ABDE experiments...


  Commit: 26b0b429314fbc2915a25a1c3e54c86adfbfa497
      https://github.com/ehb54/ultrascan3/commit/26b0b429314fbc2915a25a1c3e54c86adfbfa497
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-28 (Wed, 28 May 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp

  Log Message:
  -----------
  GMP-ABDE: 5. ANALYSIS -- bug fixed: do not try to read (unexisting) RMSDs for single-wvl type of exp....


  Commit: 2434b5657469571d06a4087ec9ce699ab1170a0a
      https://github.com/ehb54/ultrascan3/commit/2434b5657469571d06a4087ec9ce699ab1170a0a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-28 (Wed, 28 May 2025)

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

  Log Message:
  -----------
  GMP REPORTER: stand_alone -- work on modified per-channel section; (simpler) 2-level tree, reflect protocols parms. for [auto]- & user-selected items for [custom]-report...


  Commit: cf6bc031cac6df21321a972bd936ec2a28cd6be6
      https://github.com/ehb54/ultrascan3/commit/cf6bc031cac6df21321a972bd936ec2a28cd6be6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-29 (Thu, 29 May 2025)

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

  Log Message:
  -----------
  GMP REPORTER: stand_alone && GMP -- USer-interactions: 5. ANALYSIS - different processing for velocity and ABDE types; make sure all timestamps in UTC to be consistent with the rest of report parts...


  Commit: 4407f9e2833642dd3c71488b515b5960db37ba8e
      https://github.com/ehb54/ultrascan3/commit/4407f9e2833642dd3c71488b515b5960db37ba8e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-30 (Fri, 30 May 2025)

  Changed paths:
    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_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [Same for Audit Trail Program -- ] GMP REPORTER: stand_alone && GMP -- USer-interactions: 5. ANALYSIS - different processing for velocity and ABDE types; make sure all timestamps in UTC to be consistent with the rest of report parts...


  Commit: fdf13a360a448b311b961c794c8bc49115d6eb0c
      https://github.com/ehb54/ultrascan3/commit/fdf13a360a448b311b961c794c8bc49115d6eb0c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-30 (Fri, 30 May 2025)

  Changed paths:
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp

  Log Message:
  -----------
  [BUG fixed  -- GUI generation for Analysis part of audit ][Same for Audit Trail Program -- ] GMP REPORTER: stand_alone && GMP -- USer-interactions: 5. ANALYSIS - different processing for velocity and ABDE types; make sure all timestamps in UTC to be consistent with the rest of report parts...


  Commit: 8b106375d8b90fc30ae4722410cdb0a8b8d44f36
      https://github.com/ehb54/ultrascan3/commit/8b106375d8b90fc30ae4722410cdb0a8b8d44f36
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-30 (Fri, 30 May 2025)

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

  Log Message:
  -----------
  GMP REPORTER: stand_alone && GMP -- add UTC timestamps for analysis & aditing to each channel's info...


  Commit: a5fafaea78544856e935ea197d76bd9a23ec2004
      https://github.com/ehb54/ultrascan3/commit/a5fafaea78544856e935ea197d76bd9a23ec2004
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-30 (Fri, 30 May 2025)

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

  Log Message:
  -----------
  GMP REPORTER: stand_alone && GMP -- add info on analyte(s) and buffer (if selected) used in MWL-deconv. to each channel's analysis sections...


  Commit: 61bf76cfc06ef318b0751e2b1b55e2d568d0d99f
      https://github.com/ehb54/ultrascan3/commit/61bf76cfc06ef318b0751e2b1b55e2d568d0d99f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-01 (Sun, 01 Jun 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP REPORTER: GMP -- [bug fixed --] building per-channel tree in background is still required to re-use stand-alone program in ABDE-reporting GMP stage...


  Commit: a855b7702e1f3b865c7f926cd18c111bb863102d
      https://github.com/ehb54/ultrascan3/commit/a855b7702e1f3b865c7f926cd18c111bb863102d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-01 (Sun, 01 Jun 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP REPORTER: GMP -- [bug fixed --] properly close/delete ABDE-normalizer widget before reattaching (esp. with different types of analsyis), and to prevent memory leak...


  Commit: 740e6773a1733535a6ffbef1e8f336f0cc569dbc
      https://github.com/ehb54/ultrascan3/commit/740e6773a1733535a6ffbef1e8f336f0cc569dbc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-01 (Sun, 01 Jun 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP REPORTER: GMP -- restore deletion of the primary autoflow record after report generation (was suppressed for tests)...


  Commit: 875b77a5bc8555b51afa86826f004882b5c5bd3c
      https://github.com/ehb54/ultrascan3/commit/875b77a5bc8555b51afa86826f004882b5c5bd3c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-02 (Mon, 02 Jun 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP REPORTER: GMP & stans-alone -- revised AProfile sections for each channel; ref. & used refs.  channels info ...


  Commit: 2704fd06df2d50c8eb569579d4cecebe4cbef948
      https://github.com/ehb54/ultrascan3/commit/2704fd06df2d50c8eb569579d4cecebe4cbef948
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-02 (Mon, 02 Jun 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  GMP REPORTER: GMP & stans-alone -- pass info for meniscus positions manualy seletced from etit-to-analysis-to-report ...


  Commit: bb17e697fa40e2e1b1d9cb8f30302a496ca6d107
      https://github.com/ehb54/ultrascan3/commit/bb17e697fa40e2e1b1d9cb8f30302a496ca6d107
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-03 (Tue, 03 Jun 2025)

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

  Log Message:
  -----------
  GMP REPORTER: GMP & stans-alone -- prep.steps for getting distributions info from abde-norm. & generating per-channel .csv files with hyperlinks in report...


  Commit: 991d00bc2c7e70807593a0fbb7d7aab905d6c108
      https://github.com/ehb54/ultrascan3/commit/991d00bc2c7e70807593a0fbb7d7aab905d6c108
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-04 (Wed, 04 Jun 2025)

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

  Log Message:
  -----------
  ABDE-GMP 5.ANALYSIS && 6. REPORT: add hyperlinks to .csv formatted files for ABDE profiles (r-pos, dna, prot, integr.-dna, integr-protein) for each channel; add option to show/hide ranges passed from AProfile in abde-plots; lots of bugs fixed as to proper abde plots generation...


  Commit: c0ee5b659e94c0d5673e0a77bf318d22ca82637a
      https://github.com/ehb54/ultrascan3/commit/c0ee5b659e94c0d5673e0a77bf318d22ca82637a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-04 (Wed, 04 Jun 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  ABDE-GMP 5.ANALYSIS && 6. REPORT: bug fixed for different extracting menisc. info & .csv file generation for SWL- and MWL- cases...


  Commit: eab6517df1299fd0bb557c89ec6a7612074e88a3
      https://github.com/ehb54/ultrascan3/commit/eab6517df1299fd0bb557c89ec6a7612074e88a3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-04 (Wed, 04 Jun 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp

  Log Message:
  -----------
  ABDE-GMP 5.ANALYSIS && 6. REPORT: use rotating list of symbols to plot aprofile's ranges in ABDE sitributions for each channel...


  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: fe9db1b044aa3072202b9d53cbee4f36706626f7
      https://github.com/ehb54/ultrascan3/commit/fe9db1b044aa3072202b9d53cbee4f36706626f7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-09 (Mon, 09 Jun 2025)

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

  Log Message:
  -----------
  GMP && R&D: reduce timeout for checking connecitions & allow for datDisk only if all machines are inaccessible...


  Commit: e7ce0a2755510be41ed631543dc4b56f1343e95f
      https://github.com/ehb54/ultrascan3/commit/e7ce0a2755510be41ed631543dc4b56f1343e95f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-10 (Tue, 10 Jun 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  ABDE-GMP 5.ANALYSIS && 6. REPORT: latest updates for analysis and report...


  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: 12dd6370e011685566749afe283898a6bfa25c9c
      https://github.com/ehb54/ultrascan3/commit/12dd6370e011685566749afe283898a6bfa25c9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-16 (Mon, 16 Jun 2025)

  Changed paths:
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  ABDE-GMP 5.ANALYSIS && 6. REPORT: diff. colors for ANBDE plots && corresponding legends...


  Commit: 8cc9d653aaf77bff14cfee7252d2e72dc5f6dca3
      https://github.com/ehb54/ultrascan3/commit/8cc9d653aaf77bff14cfee7252d2e72dc5f6dca3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-16 (Mon, 16 Jun 2025)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  GMP && R&D: do not show  'allow for datDisk only' message for R&D \ if all machines are inaccessible...


  Commit: 68cc1e1ca4886fffdeaa328d98582c236ff3fec6
      https://github.com/ehb54/ultrascan3/commit/68cc1e1ca4886fffdeaa328d98582c236ff3fec6
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-16 (Mon, 16 Jun 2025)

  Changed paths:
    M programs/us_com_project/us_com_project_gui.cpp

  Log Message:
  -----------
  GMP && R&D: the R&D program still needs to exit if all machines are inaccessible...


  Commit: cd907ffab32ed140285aae198653c9646fdeeab2
      https://github.com/ehb54/ultrascan3/commit/cd907ffab32ed140285aae198653c9646fdeeab2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-06-19 (Thu, 19 Jun 2025)

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

  Log Message:
  -----------
  Merge pull request #228 from ehb54/alexey-dev-issue482

GMP && R&D: reduce timeout for checking connecitions & allow for datDafromDisk only


  Commit: a12c2af02d5e024c4b0146b0053e2f6e89a6938f
      https://github.com/ehb54/ultrascan3/commit/a12c2af02d5e024c4b0146b0053e2f6e89a6938f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-20 (Fri, 20 Jun 2025)

  Changed paths:
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_predict1.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M utils/us_hydrosim.cpp
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_model.cpp
    M utils/us_model.h

  Log Message:
  -----------
  Merge pull request #230 from ehb54/master

Add all master commits to alexey-dev-issue425


  Commit: 0244ffea2b66f290eba21f8350a4b528601b5df8
      https://github.com/ehb54/ultrascan3/commit/0244ffea2b66f290eba21f8350a4b528601b5df8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-22 (Sun, 22 Jun 2025)

  Changed paths:
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  GMP && R&D - ABDE-GMP test: few bugs fixed...


  Commit: 9f5deea4c10e1c3c8abb9ec595158179385c8cd3
      https://github.com/ehb54/ultrascan3/commit/9f5deea4c10e1c3c8abb9ec595158179385c8cd3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-22 (Sun, 22 Jun 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP && R&D - ABDE-GMP test: [1]few bugs fixed...


  Commit: 413c8b44dc84893c703c037cdb4b18e3da7deb21
      https://github.com/ehb54/ultrascan3/commit/413c8b44dc84893c703c037cdb4b18e3da7deb21
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-06-26 (Thu, 26 Jun 2025)

  Changed paths:
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M gui/us_gui_util.cpp
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    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_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_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_convert/us_experiment.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/us_fematch.pro
    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_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_protocol_dev/us_protocol_dev.pro
    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_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h

  Log Message:
  -----------
  Merge pull request #231 from ehb54/alexey-dev-issue425

alexey-dev-issue425 into master: ABDE-GMP-framework


  Commit: 7f41403c11d16207f41e52d19ed79721596f0cfc
      https://github.com/ehb54/ultrascan3/commit/7f41403c11d16207f41e52d19ed79721596f0cfc
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-06-26 (Thu, 26 Jun 2025)

  Changed paths:
    M gui/us_tmst_plot.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp

  Log Message:
  -----------
  GMP REPORT, custom REPORT -- reduce dependency of all graphs in the report (run detals, vel. fit, RMSD, pseudo3D, combined ddist., ABDE profiles etc.) on the user-font-settings in us_config:Fonts:: tests showed this resulted in strange appearence of graphs for font sizes deviating significanlty from 10pt;  ...


  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
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_09.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_10.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_11.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_12.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_13.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_14.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_15.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_16.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_17.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_18.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_19.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_20.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_21.png
    A doc/manual/images/gmp/data_acquisition/experiment/gmp_data_acquisition_experiment_22.png
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    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: 7955b04759144d529f2d4084665bde0f957e17dd
      https://github.com/ehb54/ultrascan3/commit/7955b04759144d529f2d4084665bde0f957e17dd
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-01 (Tue, 01 Jul 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP: 5.ANALYSIS->FITMEN_AUTO  -- when bad meniscus values determined, do not block triple processing from other sessions by an informative dialog until accepting it & scheduling subsequent jobs for deletion ...


  Commit: 4c91ff52630c5f78841b7cd8ccfa25837d4219ef
      https://github.com/ehb54/ultrascan3/commit/4c91ff52630c5f78841b7cd8ccfa25837d4219ef
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-01 (Tue, 01 Jul 2025)

  Changed paths:
    M programs/us_fit_meniscus/us_fit_meniscus.cpp

  Log Message:
  -----------
  debug...


  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: 210578c4bfa228134d63d733246cb4b435926dde
      https://github.com/ehb54/ultrascan3/commit/210578c4bfa228134d63d733246cb4b435926dde
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-02 (Wed, 02 Jul 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP: 5.ANALYSIS->FITMEN_AUTO  -- capture a case when fitmen_auto resulted in 'NaN' value for meniscus pos.: inform, schedule jobs for this triple (and other triples in a channel if MWL) for deletion; proceed with other triples ...


  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: 068eaac9fa06edc4cfd20f62c61b374d889b3a9c
      https://github.com/ehb54/ultrascan3/commit/068eaac9fa06edc4cfd20f62c61b374d889b3a9c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-07 (Mon, 07 Jul 2025)

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

  Log Message:
  -----------
  GMP: 4. EDIT, manual edit  -- pass meniscus & data range values even when edited in the respective fields ...


  Commit: 472c38b2ebbd72614ebd517dc0a352c96c1ae4e8
      https://github.com/ehb54/ultrascan3/commit/472c38b2ebbd72614ebd517dc0a352c96c1ae4e8
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-07 (Mon, 07 Jul 2025)

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

  Log Message:
  -----------
  [SUPress unit test] GMP: 4. EDIT, manual edit  -- pass meniscus & data range values even when edited in the respective fields ...


  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: 979963e4605cc85409eeacc155721dc1e5b79f28
      https://github.com/ehb54/ultrascan3/commit/979963e4605cc85409eeacc155721dc1e5b79f28
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-07-10 (Thu, 10 Jul 2025)

  Changed paths:
    M gui/us_tmst_plot.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.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

  Log Message:
  -----------
  Merge pull request #235 from ehb54/alexey-dev-issues508-512

Alexey dev issues508 512: adresses tickets 508 through 513


  Commit: 3d92fb038d0a0f0245392b9a40837d4a3dfe0657
      https://github.com/ehb54/ultrascan3/commit/3d92fb038d0a0f0245392b9a40837d4a3dfe0657
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-07-10 (Thu, 10 Jul 2025)

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

  Log Message:
  -----------
  Merge pull request #236 from ehb54/alexey-dev-issue518_and_520

Ticket 520: manual edit: pass meniscus & data_Range values to downstream analysis


  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: 859978434d116db61ecdbe5e618d3a84f7c6459f
      https://github.com/ehb54/ultrascan3/commit/859978434d116db61ecdbe5e618d3a84f7c6459f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [FIX]: Ensure the initialization of all UI elements to prevent crashes


  Commit: 1e85b92c4b5f8109a9dfa91ebfc923e0c47a2f86
      https://github.com/ehb54/ultrascan3/commit/1e85b92c4b5f8109a9dfa91ebfc923e0c47a2f86
  Author: SophiaBird95 <135044923+SophiaBird95 at users.noreply.github.com>
  Date:   2025-07-23 (Wed, 23 Jul 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  Merge pull request #241 from ehb54/lukas/us_edit_range_crash

[FIX]: Ensure the initialization of all UI elements to prevent crashes


  Commit: 7d9480f193d0c9d60197993aa28f94b9415f8be1
      https://github.com/ehb54/ultrascan3/commit/7d9480f193d0c9d60197993aa28f94b9415f8be1
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-07-27 (Sun, 27 Jul 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:
  -----------
  adds the ability to include a constant baseline offset for simulated ASTFEM data (negative/positive offset in conc. values)


  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: ce6b9d4d1c215c81821202ffa9c5ee2e75121bd8
      https://github.com/ehb54/ultrascan3/commit/ce6b9d4d1c215c81821202ffa9c5ee2e75121bd8
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-07-30 (Wed, 30 Jul 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 #242 from demeler/demeler-simparams

adds the ability to include a constant baseline offset for simulated ?


  Commit: c78356ceca1122bd033b1a94a73b9ce7aa072596
      https://github.com/ehb54/ultrascan3/commit/c78356ceca1122bd033b1a94a73b9ce7aa072596
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-07-30 (Wed, 30 Jul 2025)

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

  Log Message:
  -----------
  Update y-axis scaling logic for improved band-forming and baseline handling

Refined y-axis scaling to properly account for band-forming logic and added support for baseline offset adjustments. Adjusted axis auto-scaling for co-sedimenting solutes.


  Commit: 57684f67ee3645cf2fc63000c3faa5cca4ad7df1
      https://github.com/ehb54/ultrascan3/commit/57684f67ee3645cf2fc63000c3faa5cca4ad7df1
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-07-30 (Wed, 30 Jul 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 #244 from ehb54/lukas/us_astfem_sim_baseline_offset

Simulate constant baseline offset in us_astfem_sim


  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: 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: 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
    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
    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:
  -----------
  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:
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    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
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    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
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    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_dammin_opts.cpp
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    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
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    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
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    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
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    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: 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: 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: 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: 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: 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)

  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
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    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
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    M us_somo/develop/src/us_hydrodyn_other.cpp
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    M us_somo/develop/src/us_hydrodyn_saxs_hplc_plots.cpp
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    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
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    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
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    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
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    M us_somo/develop/src/us_saxs_util_best.cpp
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    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


  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: 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


  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


  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


  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


  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


  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: 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


  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


  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


  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: 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


  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


  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


  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


  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


  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


  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.


  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


  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


  Commit: 9d2f668621b521ec83972272c72a14913582c0e2
      https://github.com/ehb54/ultrascan3/commit/9d2f668621b521ec83972272c72a14913582c0e2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-01 (Sat, 01 Nov 2025)

  Changed paths:
    M alpha/us.cpp
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_util.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.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_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_equiltime/us_equiltime.cpp
    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
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.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_globalequil.cpp
    M programs/us_modelmetrics/us_modelmetrics.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_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.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_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

  Log Message:
  -----------
  mod: remove qt4 code and qt 5 checks


  Commit: 52e0a85023eb1f0cdb0de69292af086d18a1d727
      https://github.com/ehb54/ultrascan3/commit/52e0a85023eb1f0cdb0de69292af086d18a1d727
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-01 (Sat, 01 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: depreciation error


  Commit: 7e8cbe171f518cc11cbdf6c45239e1232ccb5726
      https://github.com/ehb54/ultrascan3/commit/7e8cbe171f518cc11cbdf6c45239e1232ccb5726
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M admin/cmake/GenerateVersion.cmake
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    R scripts/bootstrap.sh
    A scripts/build.sh

  Log Message:
  -----------
  mod: add resizing and remove extra UTC in label


  Commit: 675780eab109aad6807c5e89cbc50dbdbd962772
      https://github.com/ehb54/ultrascan3/commit/675780eab109aad6807c5e89cbc50dbdbd962772
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us/us.pro

  Log Message:
  -----------
  fix: add us_win_data.h


  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  [1]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  [2]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 320d50900efb79fdee663f85ef36825cc55e3c3d
      https://github.com/ehb54/ultrascan3/commit/320d50900efb79fdee663f85ef36825cc55e3c3d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    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
    M gui/images/us3-splash.png
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h

  Log Message:
  -----------
  fix: splash screen resizing


  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: e2b73576bf779849331ede9bc596170ef3add7d8
      https://github.com/ehb54/ultrascan3/commit/e2b73576bf779849331ede9bc596170ef3add7d8
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    R etc/README
    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
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    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 etc/us3-splash.png

  Log Message:
  -----------
  fix: revert icons


  Commit: 53c47afaad0a6c5e254d3d2ff216638d871f21a4
      https://github.com/ehb54/ultrascan3/commit/53c47afaad0a6c5e254d3d2ff216638d871f21a4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: build defaults to 90% cores and vcpkg in home directory


  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    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

  Log Message:
  -----------
  [4]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h

  Log Message:
  -----------
  [55]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 33d884f14decc31d36934b0a03e70bbed41854c9
      https://github.com/ehb54/ultrascan3/commit/33d884f14decc31d36934b0a03e70bbed41854c9
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  mod: set a single time and reuse


  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  [6]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 95598eae4d07bf9dc43bf02d6e58967bba5d282e
      https://github.com/ehb54/ultrascan3/commit/95598eae4d07bf9dc43bf02d6e58967bba5d282e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: additional contributors link


  Commit: 08cb87c1bc238f8c201c7774797bb3d3de8bcf85
      https://github.com/ehb54/ultrascan3/commit/08cb87c1bc238f8c201c7774797bb3d3de8bcf85
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    R etc/README
    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
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    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 etc/us3-splash.png
    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
    M gui/images/us3-splash.png
    M gui/libus_gui.pro
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    R scripts/bootstrap.sh
    A scripts/build.sh

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/534-enhancement-version-upgrade' into 597-request-qt-6-migration-remove-qt-4-code

# Conflicts:
#	programs/us/us.cpp


  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [7]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: baf9c94ac111af67948654073232919352e65f28
      https://github.com/ehb54/ultrascan3/commit/baf9c94ac111af67948654073232919352e65f28
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

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


  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [8]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [9]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [11a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [12a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 6e58c37381bd4ac5dea4ae822375df0d0cbc7b9a
      https://github.com/ehb54/ultrascan3/commit/6e58c37381bd4ac5dea4ae822375df0d0cbc7b9a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  fix: add one newline


  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [13a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 13f85df6ceb512735407e0c337d01f57429991dc
      https://github.com/ehb54/ultrascan3/commit/13f85df6ceb512735407e0c337d01f57429991dc
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/Us3QrcCheck.cmake
    M admin/cmake/Us3Resources.cmake
    M admin/cmake/UsDefinesParser.cmake
    M admin/cmake/platform-config.cmake
    M doc/manual/CMakeLists.txt
    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_query_rmsd/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  fix: add one newline


  Commit: 208da0fac807bb4eab07d69d438597dfb03b8a52
      https://github.com/ehb54/ultrascan3/commit/208da0fac807bb4eab07d69d438597dfb03b8a52
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #301 from ehb54/597-request-qt-6-migration-remove-qt-4-code

597 request qt 6 migration remove qt 4 code


  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  [15a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [16a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [17a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 33dfedcbd83e81f3116f6e0051eb43b762a00ce1
      https://github.com/ehb54/ultrascan3/commit/33dfedcbd83e81f3116f6e0051eb43b762a00ce1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

  Log Message:
  -----------
  Refactor `US_Plot` and related classes for modern C++ standards and improved maintainability

Replaced raw pointers with `nullptr`, leveraged modern Qt signal-slot syntax, and tightened const correctness throughout. Removed legacy Qt version checks and redundant logic for clean and readable code.


  Commit: ef64cab1de21434fe0f5d43a73d8f500c37bbfed
      https://github.com/ehb54/ultrascan3/commit/ef64cab1de21434fe0f5d43a73d8f500c37bbfed
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Fix incorrect variable usage and remove redundant `const` specifiers in `US_Plot`

Corrected variable mismatch in `connect` call for canvas color updates. Replaced redundant `const QDir` declarations with `QDir` to align with proper usage. Initialized `selSymbol` with `QwtSymbol::NoSymbol` to prevent uninitialized access.


  Commit: aa4ace94a7d0acc500543323e466222bb30c02c7
      https://github.com/ehb54/ultrascan3/commit/aa4ace94a7d0acc500543323e466222bb30c02c7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #310 from ehb54/lukas/us_plot_config

Fix us_plot config causing Curves to get symboles


  Commit: 4db2218d24fbf448f58e228e33c6634b2ddbe429
      https://github.com/ehb54/ultrascan3/commit/4db2218d24fbf448f58e228e33c6634b2ddbe429
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/codeql/docker/local.pri.gui-qt6

  Log Message:
  -----------
  issue 649, testing codeql qt6 build


  Commit: 7efd56b0064621de09905cb9d76a56f0a1c83b77
      https://github.com/ehb54/ultrascan3/commit/7efd56b0064621de09905cb9d76a56f0a1c83b77
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  issue 649, testing codeql qt6 build


  Commit: 0b5dfd84a4ed2f5328e79bef342f3fec70845310
      https://github.com/ehb54/ultrascan3/commit/0b5dfd84a4ed2f5328e79bef342f3fec70845310
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  codeql workflow remove commented section


  Commit: 522a7b53313a7a9d4d13450bbaa79b482379ab0a
      https://github.com/ehb54/ultrascan3/commit/522a7b53313a7a9d4d13450bbaa79b482379ab0a
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.gui-qt6

  Log Message:
  -----------
  Remove openglwidgets from QT configuration


  Commit: 5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
      https://github.com/ehb54/ultrascan3/commit/5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-16 (Sun, 16 Nov 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_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP [dataDisk]: 1. EXP. -- init. steps for dealing with arbitrary selection of channels in uploaded data...


  Commit: 637512db487f7224a48db9fddadac0121cd0ec6e
      https://github.com/ehb54/ultrascan3/commit/637512db487f7224a48db9fddadac0121cd0ec6e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP [dataDisk]: 1. EXP. -- [MODS to generated prtotocol check before submission] init. steps for dealing with arbitrary selection of channels in uploaded data...


  Commit: 31bffce6f2258893d277cf9e2ab6b5a2290acd70
      https://github.com/ehb54/ultrascan3/commit/31bffce6f2258893d277cf9e2ab6b5a2290acd70
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

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

  Log Message:
  -----------
  Update unit-tests.yml to include additional paths


  Commit: 17ce4b6fb272848fdced6c862bae217de71652d8
      https://github.com/ehb54/ultrascan3/commit/17ce4b6fb272848fdced6c862bae217de71652d8
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-18 (Tue, 18 Nov 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_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #316 from ehb54/alexey-dev-issue650

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP : 6.REPORTER -- ranges for CG-models...


  Commit: 6c646f633296c0b2cdf20178c282494f364c1846
      https://github.com/ehb54/ultrascan3/commit/6c646f633296c0b2cdf20178c282494f364c1846
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue608


  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: b08b1c4672f375b1df4d08eb2e61fd656c9d406d
      https://github.com/ehb54/ultrascan3/commit/b08b1c4672f375b1df4d08eb2e61fd656c9d406d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    R admin/codeql/docker/local.pri.gui-qt6
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  codeql updates to main branch


  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [2]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 0cd1156f3fead2acf306d704cca3686a6a2ec32f
      https://github.com/ehb54/ultrascan3/commit/0cd1156f3fead2acf306d704cca3686a6a2ec32f
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Merge pull request #313 from ehb54/ehb54-issue-649

issue 649, testing codeql qt6 build


  Commit: 5400614d6c78af525f22b1f858362a99edc462a1
      https://github.com/ehb54/ultrascan3/commit/5400614d6c78af525f22b1f858362a99edc462a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #319 from ehb54/main

add main stuff to alexey-dev-issue651


  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 8f345295dc5803000521a47ad53aa246df51eff7
      https://github.com/ehb54/ultrascan3/commit/8f345295dc5803000521a47ad53aa246df51eff7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #320 from ehb54/main

update to main


  Commit: 129b8d9184d5cab1189cca7b84574bf7e97dca76
      https://github.com/ehb54/ultrascan3/commit/129b8d9184d5cab1189cca7b84574bf7e97dca76
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL workflow for improved caching and builds


  Commit: 793e12c735495da5c5b6deed3355e2428e6c2a16
      https://github.com/ehb54/ultrascan3/commit/793e12c735495da5c5b6deed3355e2428e6c2a16
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Simplify build step in CodeQL analysis workflow

Removed ccache setup and git configuration from the build step.


  Commit: 0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
      https://github.com/ehb54/ultrascan3/commit/0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL analysis workflow

Refactor CodeQL analysis workflow to improve target calculation and build steps.


  Commit: 6c80777b7287a29fe978526475e6f099ca3ef827
      https://github.com/ehb54/ultrascan3/commit/6c80777b7287a29fe978526475e6f099ca3ef827
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL workflow to simplify caching and builds

Removed caching steps for ccache, utils, qwtplot3d, and gui. Added build steps for utils, qwtplot3d, and gui using qmake.


  Commit: 27c760f8c268e77d5038469cfd40243fb274f2d1
      https://github.com/ehb54/ultrascan3/commit/27c760f8c268e77d5038469cfd40243fb274f2d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update unit-tests.yml to remove path filters for push

Removed specific path filters for push events in unit-tests workflow.


  Commit: 2465409a96b820d237f9bf0c3b09b12f859060d7
      https://github.com/ehb54/ultrascan3/commit/2465409a96b820d237f9bf0c3b09b12f859060d7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update static analysis workflow trigger paths

Removed specific path triggers for push events in static analysis workflow.


  Commit: c1ac9c0b43cdde1480834d2fb742344b9649144f
      https://github.com/ehb54/ultrascan3/commit/c1ac9c0b43cdde1480834d2fb742344b9649144f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Document CMake formatter


  Commit: 391ac4d011a289eafa902e9d56eb4382491f0b66
      https://github.com/ehb54/ultrascan3/commit/391ac4d011a289eafa902e9d56eb4382491f0b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Updating nproc


  Commit: ea7559d6bcd810ed7a176871e33f0d36b49152e2
      https://github.com/ehb54/ultrascan3/commit/ea7559d6bcd810ed7a176871e33f0d36b49152e2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/unit-tests.yml
    M admin/linting/cmake/.cmake-format.yaml
    M admin/linting/cmake/README.md

  Log Message:
  -----------
  Fix minor comments


  Commit: 6e94734ca883da80e058cf4e51dee4474e9863e5
      https://github.com/ehb54/ultrascan3/commit/6e94734ca883da80e058cf4e51dee4474e9863e5
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_edit/us_edit.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_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #305 from ehb54/alexey-dev-issue608

Alexey dev issue608: Prot. Dev. for DataDisk data types


  Commit: 5ff2d239588616635adbdfaf775949a91f5d7565
      https://github.com/ehb54/ultrascan3/commit/5ff2d239588616635adbdfaf775949a91f5d7565
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update checkout action version


  Commit: 321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
      https://github.com/ehb54/ultrascan3/commit/321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  fix branches


  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 5cf42202af6d7f5544a2cf1111d44f5f1a232777
      https://github.com/ehb54/ultrascan3/commit/5cf42202af6d7f5544a2cf1111d44f5f1a232777
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL analysis workflow conditions

Removed specific file paths from pull request triggers and updated conditions for CodeQL analysis steps.


  Commit: 3f486acaa2a2e5b708f257acf949e90d1b042bbc
      https://github.com/ehb54/ultrascan3/commit/3f486acaa2a2e5b708f257acf949e90d1b042bbc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  Rename analysis job for GUI programs


  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


  Commit: 02ab6c663335530dbf4295161c2f68c1043b3874
      https://github.com/ehb54/ultrascan3/commit/02ab6c663335530dbf4295161c2f68c1043b3874
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

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


  Commit: 013afa9051723a54ff17a3431895f0e6aa65eebc
      https://github.com/ehb54/ultrascan3/commit/013afa9051723a54ff17a3431895f0e6aa65eebc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Refactor GitHub Actions workflows to enhance modularity and efficiency
- Introduce `changed-files` job to conditionally trigger workflows based on file changes.
- Add status-checking jobs for Documentation, CodeQL analysis, and Static Analysis builds.
- Improve concurrency management and file fetch depth.
- Optimize CI Docker containers and cleanup processes.
- Streamline conditional checks and matrix configurations.


  Commit: 2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
      https://github.com/ehb54/ultrascan3/commit/2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    A .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add `unit-tests-v2.yml` GitHub Actions workflow

- Introduce a new workflow for unit testing with support for configurable test filters and debug mode.
- Add a `changed-files` job to detect relevant file modifications and conditionally trigger tests.
- Implement improved concurrency management and result-checking mechanisms.
- Streamline test setup, build process, and log management for enhanced clarity and efficiency.
- Enable artifact uploads for detailed test results and logs.


  Commit: e2a9b2acaeeeac868cf1d55f459225e683e37d11
      https://github.com/ehb54/ultrascan3/commit/e2a9b2acaeeeac868cf1d55f459225e683e37d11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Normalize glob patterns in GitHub Actions workflows


  Commit: 037064b1d8968578fcb9a42ba07e275c96b38a8c
      https://github.com/ehb54/ultrascan3/commit/037064b1d8968578fcb9a42ba07e275c96b38a8c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Fix incorrect `CMAKE_MODULE_PATH` to use absolute path in `unit-tests-v2.yml` workflow


  Commit: 4c0538dff646603c4258628a076f9807a29af7c3
      https://github.com/ehb54/ultrascan3/commit/4c0538dff646603c4258628a076f9807a29af7c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Enhance `unit-tests.yml` workflow with dynamic file change detection and improved concurrency management

- Add `changed-files` job to detect relevant modifications and conditionally trigger unit tests.
- Introduce concurrency control to prevent duplicate runs.
- Expand artifacts to include additional logs for better debugging.
- Add status-checking job to validate unit testing outcomes.
- Refactor workflow for clarity and streamlined test execution.


  Commit: 12e9e1fd701da2b201e7d47b3cb642812813e4e7
      https://github.com/ehb54/ultrascan3/commit/12e9e1fd701da2b201e7d47b3cb642812813e4e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Enhance `static-analysis.yml` workflow with CPP file-specific change detection

- Add outputs and environment variables to track `.cpp` and `.h` file changes.
- Update `changed-files` step to simplify logic and rely on filtered outputs.
- Streamline file detection for first commits and pull requests.


  Commit: e94063c15730a822262820f18c468a429ac4c374
      https://github.com/ehb54/ultrascan3/commit/e94063c15730a822262820f18c468a429ac4c374
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Normalize glob pattern syntax in `unit-tests.yml` workflow


  Commit: 158b855316998f18924177b91ad5cb81e696ad53
      https://github.com/ehb54/ultrascan3/commit/158b855316998f18924177b91ad5cb81e696ad53
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Update static-analysis workflow to use latest `us3comp` container image


  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...


  Commit: 350edcd3194656d020a571d45cbe1dd872d041e2
      https://github.com/ehb54/ultrascan3/commit/350edcd3194656d020a571d45cbe1dd872d041e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #322 from ehb54/alexey-dev-issue651

Alexey dev issue651: Ind. & Combined Plots in GMP Rpeorts: CG-model-based runs (ranges), Plot Aspect Ratios, "Combined Plots" section title


  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...


  Commit: e1ce700f61527eedba262f237e41dbcc16de6de7
      https://github.com/ehb54/ultrascan3/commit/e1ce700f61527eedba262f237e41dbcc16de6de7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Update file patterns for static analysis


  Commit: aebbdda924bca0630a6b1b50f5110f340c8804aa
      https://github.com/ehb54/ultrascan3/commit/aebbdda924bca0630a6b1b50f5110f340c8804aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Update CodeQL workflow to ignore specific files

Ignore changes in us_mpi_analysis directory during file checks and update build commands.


  Commit: a4a655d619279b7bb59e01ee82fce46e875eebca
      https://github.com/ehb54/ultrascan3/commit/a4a655d619279b7bb59e01ee82fce46e875eebca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Exclude us_mpi_analysis from CodeQL analysis gui


  Commit: 14ba4d63b16861ed659ae0c204b0ee3f54589432
      https://github.com/ehb54/ultrascan3/commit/14ba4d63b16861ed659ae0c204b0ee3f54589432
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Fix syntax for exclusion in CodeQL workflow


  Commit: 770769aa570aae22f64b5b817de2320ab1b070e3
      https://github.com/ehb54/ultrascan3/commit/770769aa570aae22f64b5b817de2320ab1b070e3
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #326 from ehb54/alexey-dev-issue631

GMP 6. REPORT -- generate correct build number in the header...


  Commit: 3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
      https://github.com/ehb54/ultrascan3/commit/3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

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


  Commit: c088a80976663c552cffec04fcb0cfe084922560
      https://github.com/ehb54/ultrascan3/commit/c088a80976663c552cffec04fcb0cfe084922560
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Merge pull request #321 from ehb54/lukas/gh_actions

Lukas/gh actions


  Commit: 70cf969d22c8ecb1892bcb7a3301d101bca7aa55
      https://github.com/ehb54/ultrascan3/commit/70cf969d22c8ecb1892bcb7a3301d101bca7aa55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 815465ed2b2679fbcf4cda7c076dda6fdc89f322
      https://github.com/ehb54/ultrascan3/commit/815465ed2b2679fbcf4cda7c076dda6fdc89f322
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Merge pull request #327 from ehb54/alexey-dev-issue657

GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in FITME_AUTO & View Overlay


  Commit: 609897d0591d9d8d0b5bf0bbb55478c8efd20337
      https://github.com/ehb54/ultrascan3/commit/609897d0591d9d8d0b5bf0bbb55478c8efd20337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing...


  Commit: fe940ce7749c9043b38aa0f91efa79a19fed6216
      https://github.com/ehb54/ultrascan3/commit/fe940ce7749c9043b38aa0f91efa79a19fed6216
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M utils/us_experiment.cpp

  Log Message:
  -----------
  [debug 1]GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 3322930798adf89544c8645263c9a5b2b477124a
      https://github.com/ehb54/ultrascan3/commit/3322930798adf89544c8645263c9a5b2b477124a
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #330 from ehb54/alexey-dev-issue667

PROT DEV -- filter out completed dataDisk runs initiated with earlier tabular signature (not to be reprocessed)


  Commit: a1184f12e7a9378bcfcd00e8f716984ab23d3d30
      https://github.com/ehb54/ultrascan3/commit/a1184f12e7a9378bcfcd00e8f716984ab23d3d30
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-03 (Wed, 03 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    A .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    A .github/workflows/unit-tests.yml
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    M README.md
    A admin/cmake/FindQwt.cmake
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    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
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    R doc/manual/README
    A doc/manual/README.md
    M doc/manual/advanced_config.body
    A gui/CMakeLists.txt
    M gui/libus_gui.pro
    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
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M gui/us_edit_spectrum.cpp
    M gui/us_editor_gui.cpp
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M gui/us_loadable_noise.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    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_new_spectrum.cpp
    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_plot.h
    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_general_gui.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
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    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
    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
    A programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_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
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    A programs/us_analysis_profile/CMakeLists.txt
    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
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.h
    A programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_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.pro
    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_com_project_academic/us_com_project_academic.pro
    A programs/us_combine_models/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    A programs/us_config/CMakeLists.txt
    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
    A programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_select_rundd.cpp
    A programs/us_density_match/CMakeLists.txt
    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
    A programs/us_dmga_init/CMakeLists.txt
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    A programs/us_edit/CMakeLists.txt
    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
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    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.pro
    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_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    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_fematch.pro
    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
    A programs/us_ga_init/CMakeLists.txt
    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
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_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
    A programs/us_grid_editor/CMakeLists.txt
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    A programs/us_helpdaemon/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp
    A programs/us_integral/CMakeLists.txt
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_integral.cpp
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    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
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    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_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_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
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    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
    A programs/us_pcsa/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_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_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    A programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    A programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    A programs/us_ramp/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
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter/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_reporter_gmp/us_reporter_gmp.pro
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    A qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    A scripts/build.sh
    A test-docker.sh
    M test/CMakeLists.txt
    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/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_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
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    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_defines.h
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h
    M utils/us_gzip.cpp
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    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
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

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


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From noreply at github.com  Wed Dec  3 08:20:29 2025
From: noreply at github.com (Borries Demeler)
Date: Wed, 03 Dec 2025 07:20:29 -0800
Subject: [us-commits] [ehb54/ultrascan3] af82fd: PROT.DEV.: dataDisk type --
 pass invID from the pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/332293-7d8562@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
      https://github.com/ehb54/ultrascan3/commit/af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  PROT.DEV.: dataDisk type -- pass invID from the protocol assoc. with the datat to-be-reanalysed for download from DB: (1) during creation of a new run using data produced by different owner; (2) during re-attachment from different session/different user (which would require fresh download)...


  Commit: 7d85624ca8988e36c4f8b7c31b1d647b049c5e20
      https://github.com/ehb54/ultrascan3/commit/7d85624ca8988e36c4f8b7c31b1d647b049c5e20
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-03 (Wed, 03 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #331 from ehb54/alexey-dev-issue669

PROT.DEV.: dataDisk type -- pass correct invID  (data owner)


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From noreply at github.com  Thu Dec  4 09:32:32 2025
From: noreply at github.com (ehb54)
Date: Thu, 04 Dec 2025 08:32:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] af82fd: PROT.DEV.: dataDisk type --
 pass invID from the pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/c7cd4a-3e70e0@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
      https://github.com/ehb54/ultrascan3/commit/af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  PROT.DEV.: dataDisk type -- pass invID from the protocol assoc. with the datat to-be-reanalysed for download from DB: (1) during creation of a new run using data produced by different owner; (2) during re-attachment from different session/different user (which would require fresh download)...


  Commit: 7d85624ca8988e36c4f8b7c31b1d647b049c5e20
      https://github.com/ehb54/ultrascan3/commit/7d85624ca8988e36c4f8b7c31b1d647b049c5e20
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-03 (Wed, 03 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #331 from ehb54/alexey-dev-issue669

PROT.DEV.: dataDisk type -- pass correct invID  (data owner)


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/c7cd4ad5a59e...3e70e06b8a38

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From noreply at github.com  Thu Dec  4 22:30:01 2025
From: noreply at github.com (HabGab)
Date: Thu, 04 Dec 2025 21:30:01 -0800
Subject: [us-commits] [ehb54/ultrascan3] 835560: Dec 2
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/3e7400-835560@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 83556069a5e45c7dbc5d79fc3d4d76c7048ee872
      https://github.com/ehb54/ultrascan3/commit/83556069a5e45c7dbc5d79fc3d4d76c7048ee872
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-02 (Tue, 02 Dec 2025)

  Changed paths:
    M doc/manual/source/_static/images/astfem_sim.png
    A doc/manual/source/_static/images/custom_grid.png
    M doc/manual/source/_static/images/model_editor.png
    M doc/manual/source/_static/images/rotor-save-calibration.png
    M doc/manual/source/_static/images/simparams.png
    M doc/manual/source/astfem_sim.rst
    A doc/manual/source/beckman_openauc.rst
    A doc/manual/source/buoyancy_editor.rst
    R doc/manual/source/custom_grid.rst
    A doc/manual/source/grid_editor.rst
    M doc/manual/source/index.rst
    M doc/manual/source/manage_data.rst
    A doc/manual/source/mwl_species_fit.rst
    A doc/manual/source/mwl_species_sim.rst
    A doc/manual/source/mwl_spectra.rst
    A doc/manual/source/mwlr_viewer.rst
    A doc/manual/source/predict2.rst
    M doc/manual/source/reporter.rst
    M doc/manual/source/rotor.rst
    A doc/manual/source/sassoc.rst
    A doc/manual/source/simparams.rst
    A doc/manual/source/us_buoyancy.rst
    A doc/manual/source/us_equiltime.rst
    A doc/manual/source/us_fds_filemanager.rst

  Log Message:
  -----------
  Dec 2



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From noreply at github.com  Sat Dec  6 19:23:50 2025
From: noreply at github.com (HabGab)
Date: Sat, 06 Dec 2025 18:23:50 -0800
Subject: [us-commits] [ehb54/ultrascan3] b46379: Dec 6
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/835560-b46379@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b463793afc9147a4bb2e039f930cf223187b1c8f
      https://github.com/ehb54/ultrascan3/commit/b463793afc9147a4bb2e039f930cf223187b1c8f
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-06 (Sat, 06 Dec 2025)

  Changed paths:
    A doc/manual/source/_static/images/sassoc.png
    R doc/manual/source/_static/images/sassoc/sassoc_01.png
    R doc/manual/source/_static/images/sassoc/sassoc_02.png
    M doc/manual/source/beckman_openauc.rst
    M doc/manual/source/buoyancy_editor.rst
    M doc/manual/source/index.rst
    M doc/manual/source/mwl_species_fit.rst
    M doc/manual/source/mwl_species_sim.rst
    M doc/manual/source/mwl_spectra.rst
    M doc/manual/source/mwlr_viewer.rst
    M doc/manual/source/predict2.rst
    M doc/manual/source/sassoc.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_equiltime.rst
    M doc/manual/source/us_fds_filemanager.rst

  Log Message:
  -----------
  Dec 6



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From noreply at github.com  Sat Dec  6 21:10:56 2025
From: noreply at github.com (HabGab)
Date: Sat, 06 Dec 2025 20:10:56 -0800
Subject: [us-commits] [ehb54/ultrascan3] 250d06: dec 6 2
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/b46379-250d06@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 250d06a86e2ced22896e00b79c7ba3078449febc
      https://github.com/ehb54/ultrascan3/commit/250d06a86e2ced22896e00b79c7ba3078449febc
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-06 (Sat, 06 Dec 2025)

  Changed paths:
    A doc/manual/source/_static/images/predict2.png
    M doc/manual/source/buoyancy_editor.rst
    A doc/manual/source/dmga_init.rst
    A doc/manual/source/experiment/cells.rst
    A doc/manual/source/experiment/general.rst
    A doc/manual/source/experiment/import.rst
    A doc/manual/source/experiment/liveupdata.rst
    A doc/manual/source/experiment/photomult.rst
    A doc/manual/source/experiment/rotor.rst
    A doc/manual/source/experiment/speeds.rst
    A doc/manual/source/experiment/submit.rst
    M doc/manual/source/grid_editor.rst
    M doc/manual/source/index.rst
    M doc/manual/source/mwl_species_fit.rst
    M doc/manual/source/mwl_species_sim.rst
    M doc/manual/source/mwl_spectra.rst
    M doc/manual/source/mwlr_viewer.rst
    M doc/manual/source/predict2.rst
    A doc/manual/source/ramp_data.rst
    A doc/manual/source/register.rst
    A doc/manual/source/tmst_viewer.rst
    M doc/manual/source/us_buoyancy.rst
    M doc/manual/source/us_equiltime.rst
    A doc/manual/source/us_extinction.rst
    M doc/manual/source/us_fds_filemanager.rst
    A doc/manual/source/us_spectrum.rst

  Log Message:
  -----------
  dec 6 2



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From noreply at github.com  Sat Dec  6 21:20:07 2025
From: noreply at github.com (HabGab)
Date: Sat, 06 Dec 2025 20:20:07 -0800
Subject: [us-commits] [ehb54/ultrascan3] 0f7487: dec 6 3
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/250d06-43186b@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0f7487d99c0d60fc64b4ba08eb9eb6fd7db5730f
      https://github.com/ehb54/ultrascan3/commit/0f7487d99c0d60fc64b4ba08eb9eb6fd7db5730f
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-06 (Sat, 06 Dec 2025)

  Changed paths:
    M doc/manual/source/experiment/index.rst
    R doc/manual/source/experiment/liveupdata.rst
    A doc/manual/source/experiment/liveupdate.rst

  Log Message:
  -----------
  dec 6 3


  Commit: 43186bb2a63cc9087732063bcc4e82f5f7e32699
      https://github.com/ehb54/ultrascan3/commit/43186bb2a63cc9087732063bcc4e82f5f7e32699
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-06 (Sat, 06 Dec 2025)

  Changed paths:
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  dec 6 4


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From noreply at github.com  Mon Dec  8 23:47:46 2025
From: noreply at github.com (HabGab)
Date: Mon, 08 Dec 2025 22:47:46 -0800
Subject: [us-commits] [ehb54/ultrascan3] b9980d: dec 8
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/43186b-b9980d@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b9980db4934fff2af3abc09b8cf6af6d820d5abc
      https://github.com/ehb54/ultrascan3/commit/b9980db4934fff2af3abc09b8cf6af6d820d5abc
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    A doc/manual/source/dmga_init_constr.rst
    M doc/manual/source/index.rst

  Log Message:
  -----------
  dec 8



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From noreply at github.com  Tue Dec  9 14:29:52 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 09 Dec 2025 13:29:52 -0800
Subject: [us-commits] [ehb54/ultrascan3] c6506c: calculate the confidence
 intervals based on accumu...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/7d8562-fac3bd@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c6506c7244d4b5a0983f0b4b904c963afb1424ff
      https://github.com/ehb54/ultrascan3/commit/c6506c7244d4b5a0983f0b4b904c963afb1424ff
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  calculate the confidence intervals based on accumulated concentration over sorted values


  Commit: aff3811250880ef52f2b3e6568f97d43ae958654
      https://github.com/ehb54/ultrascan3/commit/aff3811250880ef52f2b3e6568f97d43ae958654
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  us_solutedata.cpp: Constructs the idxs vector with an initial size, replace stable_sort with sort std function


  Commit: fac3bd3f8d097359906b91580ee196ef7eff219c
      https://github.com/ehb54/ultrascan3/commit/fac3bd3f8d097359906b91580ee196ef7eff219c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge pull request #332 from samo38/issue_672

issue 672: confidence interval problem


Compare: https://github.com/ehb54/ultrascan3/compare/7d85624ca898...fac3bd3f8d09

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From noreply at github.com  Tue Dec  9 14:48:22 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 09 Dec 2025 13:48:22 -0800
Subject: [us-commits] [ehb54/ultrascan3] c6506c: calculate the confidence
 intervals based on accumu...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/3e70e0-eacada@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c6506c7244d4b5a0983f0b4b904c963afb1424ff
      https://github.com/ehb54/ultrascan3/commit/c6506c7244d4b5a0983f0b4b904c963afb1424ff
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  calculate the confidence intervals based on accumulated concentration over sorted values


  Commit: aff3811250880ef52f2b3e6568f97d43ae958654
      https://github.com/ehb54/ultrascan3/commit/aff3811250880ef52f2b3e6568f97d43ae958654
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  us_solutedata.cpp: Constructs the idxs vector with an initial size, replace stable_sort with sort std function


  Commit: fac3bd3f8d097359906b91580ee196ef7eff219c
      https://github.com/ehb54/ultrascan3/commit/fac3bd3f8d097359906b91580ee196ef7eff219c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge pull request #332 from samo38/issue_672

issue 672: confidence interval problem


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

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

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


Compare: https://github.com/ehb54/ultrascan3/compare/3e70e06b8a38...eacada70d7c4

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From noreply at github.com  Tue Dec  9 19:09:36 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 09 Dec 2025 18:09:36 -0800
Subject: [us-commits] [ehb54/ultrascan3] 12a48a: Additional Unit Testing
 us_ana_profile, us_crc, us...
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/b9980d-993565@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 12a48a8f79892aa2f3d9e597d2c3643565aaa10d
      https://github.com/ehb54/ultrascan3/commit/12a48a8f79892aa2f3d9e597d2c3643565aaa10d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  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: eb35e450adfafa8e58b295afb08bb31df0f5c49a
      https://github.com/ehb54/ultrascan3/commit/eb35e450adfafa8e58b295afb08bb31df0f5c49a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  Changed paths:
    M CMakeLists.txt
    M doc/manual/source/ramp_data.rst
    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: 9935654325ea8d494d69842a20e2de4e98243004
      https://github.com/ehb54/ultrascan3/commit/9935654325ea8d494d69842a20e2de4e98243004
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  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


Compare: https://github.com/ehb54/ultrascan3/compare/b9980db4934f...9935654325ea

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From noreply at github.com  Wed Dec 10 12:18:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 10 Dec 2025 11:18:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] c90cc6: Enhance CMake configuration
 for Qt5 and Qt6 suppor...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/eacada-c90cc6@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c90cc6690c06b1be85cf82126319a190c30d6505
      https://github.com/ehb54/ultrascan3/commit/c90cc6690c06b1be85cf82126319a190c30d6505
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-10 (Wed, 10 Dec 2025)

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

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



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From noreply at github.com  Wed Dec 10 13:34:22 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 10 Dec 2025 12:34:22 -0800
Subject: [us-commits] [ehb54/ultrascan3] 609897: PROT.DEV. dataDisk re-use
 -- filter out older comp...
Message-ID: <ehb54/ultrascan3/push/refs/heads/notices-fix/75dc17-9e26d2@github.com>

  Branch: refs/heads/notices-fix
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 609897d0591d9d8d0b5bf0bbb55478c8efd20337
      https://github.com/ehb54/ultrascan3/commit/609897d0591d9d8d0b5bf0bbb55478c8efd20337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing...


  Commit: fe940ce7749c9043b38aa0f91efa79a19fed6216
      https://github.com/ehb54/ultrascan3/commit/fe940ce7749c9043b38aa0f91efa79a19fed6216
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M utils/us_experiment.cpp

  Log Message:
  -----------
  [debug 1]GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 3322930798adf89544c8645263c9a5b2b477124a
      https://github.com/ehb54/ultrascan3/commit/3322930798adf89544c8645263c9a5b2b477124a
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #330 from ehb54/alexey-dev-issue667

PROT DEV -- filter out completed dataDisk runs initiated with earlier tabular signature (not to be reprocessed)


  Commit: af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
      https://github.com/ehb54/ultrascan3/commit/af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  PROT.DEV.: dataDisk type -- pass invID from the protocol assoc. with the datat to-be-reanalysed for download from DB: (1) during creation of a new run using data produced by different owner; (2) during re-attachment from different session/different user (which would require fresh download)...


  Commit: 7d85624ca8988e36c4f8b7c31b1d647b049c5e20
      https://github.com/ehb54/ultrascan3/commit/7d85624ca8988e36c4f8b7c31b1d647b049c5e20
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-03 (Wed, 03 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #331 from ehb54/alexey-dev-issue669

PROT.DEV.: dataDisk type -- pass correct invID  (data owner)


  Commit: c6506c7244d4b5a0983f0b4b904c963afb1424ff
      https://github.com/ehb54/ultrascan3/commit/c6506c7244d4b5a0983f0b4b904c963afb1424ff
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  calculate the confidence intervals based on accumulated concentration over sorted values


  Commit: aff3811250880ef52f2b3e6568f97d43ae958654
      https://github.com/ehb54/ultrascan3/commit/aff3811250880ef52f2b3e6568f97d43ae958654
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  us_solutedata.cpp: Constructs the idxs vector with an initial size, replace stable_sort with sort std function


  Commit: fac3bd3f8d097359906b91580ee196ef7eff219c
      https://github.com/ehb54/ultrascan3/commit/fac3bd3f8d097359906b91580ee196ef7eff219c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge pull request #332 from samo38/issue_672

issue 672: confidence interval problem


  Commit: 9e26d202aea3d0b07a3777f0f7955724c84e55b8
      https://github.com/ehb54/ultrascan3/commit/9e26d202aea3d0b07a3777f0f7955724c84e55b8
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-10 (Wed, 10 Dec 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


Compare: https://github.com/ehb54/ultrascan3/compare/75dc17665cd2...9e26d202aea3

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From noreply at github.com  Thu Dec 11 09:18:45 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 11 Dec 2025 08:18:45 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/3f56d2-000000@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Dec 11 09:20:51 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 11 Dec 2025 08:20:51 -0800
Subject: [us-commits] [ehb54/ultrascan3] ea0b94: 8. AProfile: Report -- a
 sublte bug fixed for corr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_xpn_viewer_timestate/37fd8b-2bbf47@github.com>

  Branch: refs/heads/lukas/us_xpn_viewer_timestate
  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: 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: 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: 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: 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: 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: 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


  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


  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


  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


  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


  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: 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


  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


  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


  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: 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


  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


  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


  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


  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


  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


  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.


  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


  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


  Commit: 9d2f668621b521ec83972272c72a14913582c0e2
      https://github.com/ehb54/ultrascan3/commit/9d2f668621b521ec83972272c72a14913582c0e2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-01 (Sat, 01 Nov 2025)

  Changed paths:
    M alpha/us.cpp
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_util.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.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_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_equiltime/us_equiltime.cpp
    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
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.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_globalequil.cpp
    M programs/us_modelmetrics/us_modelmetrics.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_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.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_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

  Log Message:
  -----------
  mod: remove qt4 code and qt 5 checks


  Commit: 52e0a85023eb1f0cdb0de69292af086d18a1d727
      https://github.com/ehb54/ultrascan3/commit/52e0a85023eb1f0cdb0de69292af086d18a1d727
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-01 (Sat, 01 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: depreciation error


  Commit: 7e8cbe171f518cc11cbdf6c45239e1232ccb5726
      https://github.com/ehb54/ultrascan3/commit/7e8cbe171f518cc11cbdf6c45239e1232ccb5726
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M admin/cmake/GenerateVersion.cmake
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    R scripts/bootstrap.sh
    A scripts/build.sh

  Log Message:
  -----------
  mod: add resizing and remove extra UTC in label


  Commit: 675780eab109aad6807c5e89cbc50dbdbd962772
      https://github.com/ehb54/ultrascan3/commit/675780eab109aad6807c5e89cbc50dbdbd962772
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us/us.pro

  Log Message:
  -----------
  fix: add us_win_data.h


  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  [1]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

  Log Message:
  -----------
  [2]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 320d50900efb79fdee663f85ef36825cc55e3c3d
      https://github.com/ehb54/ultrascan3/commit/320d50900efb79fdee663f85ef36825cc55e3c3d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    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
    M gui/images/us3-splash.png
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h

  Log Message:
  -----------
  fix: splash screen resizing


  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: e2b73576bf779849331ede9bc596170ef3add7d8
      https://github.com/ehb54/ultrascan3/commit/e2b73576bf779849331ede9bc596170ef3add7d8
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    R etc/README
    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
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    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 etc/us3-splash.png

  Log Message:
  -----------
  fix: revert icons


  Commit: 53c47afaad0a6c5e254d3d2ff216638d871f21a4
      https://github.com/ehb54/ultrascan3/commit/53c47afaad0a6c5e254d3d2ff216638d871f21a4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M scripts/build.sh

  Log Message:
  -----------
  mod: build defaults to 90% cores and vcpkg in home directory


  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    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

  Log Message:
  -----------
  [4]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h

  Log Message:
  -----------
  [55]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 33d884f14decc31d36934b0a03e70bbed41854c9
      https://github.com/ehb54/ultrascan3/commit/33d884f14decc31d36934b0a03e70bbed41854c9
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  mod: set a single time and reuse


  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  [6]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 95598eae4d07bf9dc43bf02d6e58967bba5d282e
      https://github.com/ehb54/ultrascan3/commit/95598eae4d07bf9dc43bf02d6e58967bba5d282e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: additional contributors link


  Commit: 08cb87c1bc238f8c201c7774797bb3d3de8bcf85
      https://github.com/ehb54/ultrascan3/commit/08cb87c1bc238f8c201c7774797bb3d3de8bcf85
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    R etc/README
    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
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    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 etc/us3-splash.png
    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
    M gui/images/us3-splash.png
    M gui/libus_gui.pro
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    R scripts/bootstrap.sh
    A scripts/build.sh

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/534-enhancement-version-upgrade' into 597-request-qt-6-migration-remove-qt-4-code

# Conflicts:
#	programs/us/us.cpp


  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [7]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: baf9c94ac111af67948654073232919352e65f28
      https://github.com/ehb54/ultrascan3/commit/baf9c94ac111af67948654073232919352e65f28
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

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


  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [8]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [9]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [11a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [12a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 6e58c37381bd4ac5dea4ae822375df0d0cbc7b9a
      https://github.com/ehb54/ultrascan3/commit/6e58c37381bd4ac5dea4ae822375df0d0cbc7b9a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M .gitignore

  Log Message:
  -----------
  fix: add one newline


  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [13a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 13f85df6ceb512735407e0c337d01f57429991dc
      https://github.com/ehb54/ultrascan3/commit/13f85df6ceb512735407e0c337d01f57429991dc
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/Us3QrcCheck.cmake
    M admin/cmake/Us3Resources.cmake
    M admin/cmake/UsDefinesParser.cmake
    M admin/cmake/platform-config.cmake
    M doc/manual/CMakeLists.txt
    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_query_rmsd/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  fix: add one newline


  Commit: 208da0fac807bb4eab07d69d438597dfb03b8a52
      https://github.com/ehb54/ultrascan3/commit/208da0fac807bb4eab07d69d438597dfb03b8a52
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #301 from ehb54/597-request-qt-6-migration-remove-qt-4-code

597 request qt 6 migration remove qt 4 code


  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  [15a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [16a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [17a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 33dfedcbd83e81f3116f6e0051eb43b762a00ce1
      https://github.com/ehb54/ultrascan3/commit/33dfedcbd83e81f3116f6e0051eb43b762a00ce1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

  Log Message:
  -----------
  Refactor `US_Plot` and related classes for modern C++ standards and improved maintainability

Replaced raw pointers with `nullptr`, leveraged modern Qt signal-slot syntax, and tightened const correctness throughout. Removed legacy Qt version checks and redundant logic for clean and readable code.


  Commit: ef64cab1de21434fe0f5d43a73d8f500c37bbfed
      https://github.com/ehb54/ultrascan3/commit/ef64cab1de21434fe0f5d43a73d8f500c37bbfed
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp

  Log Message:
  -----------
  Fix incorrect variable usage and remove redundant `const` specifiers in `US_Plot`

Corrected variable mismatch in `connect` call for canvas color updates. Replaced redundant `const QDir` declarations with `QDir` to align with proper usage. Initialized `selSymbol` with `QwtSymbol::NoSymbol` to prevent uninitialized access.


  Commit: aa4ace94a7d0acc500543323e466222bb30c02c7
      https://github.com/ehb54/ultrascan3/commit/aa4ace94a7d0acc500543323e466222bb30c02c7
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #310 from ehb54/lukas/us_plot_config

Fix us_plot config causing Curves to get symboles


  Commit: 4db2218d24fbf448f58e228e33c6634b2ddbe429
      https://github.com/ehb54/ultrascan3/commit/4db2218d24fbf448f58e228e33c6634b2ddbe429
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/codeql/docker/local.pri.gui-qt6

  Log Message:
  -----------
  issue 649, testing codeql qt6 build


  Commit: 7efd56b0064621de09905cb9d76a56f0a1c83b77
      https://github.com/ehb54/ultrascan3/commit/7efd56b0064621de09905cb9d76a56f0a1c83b77
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  issue 649, testing codeql qt6 build


  Commit: 0b5dfd84a4ed2f5328e79bef342f3fec70845310
      https://github.com/ehb54/ultrascan3/commit/0b5dfd84a4ed2f5328e79bef342f3fec70845310
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  codeql workflow remove commented section


  Commit: 522a7b53313a7a9d4d13450bbaa79b482379ab0a
      https://github.com/ehb54/ultrascan3/commit/522a7b53313a7a9d4d13450bbaa79b482379ab0a
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.gui-qt6

  Log Message:
  -----------
  Remove openglwidgets from QT configuration


  Commit: 5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
      https://github.com/ehb54/ultrascan3/commit/5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-16 (Sun, 16 Nov 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_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  GMP [dataDisk]: 1. EXP. -- init. steps for dealing with arbitrary selection of channels in uploaded data...


  Commit: 637512db487f7224a48db9fddadac0121cd0ec6e
      https://github.com/ehb54/ultrascan3/commit/637512db487f7224a48db9fddadac0121cd0ec6e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  GMP [dataDisk]: 1. EXP. -- [MODS to generated prtotocol check before submission] init. steps for dealing with arbitrary selection of channels in uploaded data...


  Commit: 31bffce6f2258893d277cf9e2ab6b5a2290acd70
      https://github.com/ehb54/ultrascan3/commit/31bffce6f2258893d277cf9e2ab6b5a2290acd70
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

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

  Log Message:
  -----------
  Update unit-tests.yml to include additional paths


  Commit: 17ce4b6fb272848fdced6c862bae217de71652d8
      https://github.com/ehb54/ultrascan3/commit/17ce4b6fb272848fdced6c862bae217de71652d8
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-18 (Tue, 18 Nov 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_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #316 from ehb54/alexey-dev-issue650

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP : 6.REPORTER -- ranges for CG-models...


  Commit: 6c646f633296c0b2cdf20178c282494f364c1846
      https://github.com/ehb54/ultrascan3/commit/6c646f633296c0b2cdf20178c282494f364c1846
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue608


  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: b08b1c4672f375b1df4d08eb2e61fd656c9d406d
      https://github.com/ehb54/ultrascan3/commit/b08b1c4672f375b1df4d08eb2e61fd656c9d406d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    R admin/codeql/docker/local.pri.gui-qt6
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  codeql updates to main branch


  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [2]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 0cd1156f3fead2acf306d704cca3686a6a2ec32f
      https://github.com/ehb54/ultrascan3/commit/0cd1156f3fead2acf306d704cca3686a6a2ec32f
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Merge pull request #313 from ehb54/ehb54-issue-649

issue 649, testing codeql qt6 build


  Commit: 5400614d6c78af525f22b1f858362a99edc462a1
      https://github.com/ehb54/ultrascan3/commit/5400614d6c78af525f22b1f858362a99edc462a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #319 from ehb54/main

add main stuff to alexey-dev-issue651


  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 8f345295dc5803000521a47ad53aa246df51eff7
      https://github.com/ehb54/ultrascan3/commit/8f345295dc5803000521a47ad53aa246df51eff7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Merge pull request #320 from ehb54/main

update to main


  Commit: 129b8d9184d5cab1189cca7b84574bf7e97dca76
      https://github.com/ehb54/ultrascan3/commit/129b8d9184d5cab1189cca7b84574bf7e97dca76
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL workflow for improved caching and builds


  Commit: 793e12c735495da5c5b6deed3355e2428e6c2a16
      https://github.com/ehb54/ultrascan3/commit/793e12c735495da5c5b6deed3355e2428e6c2a16
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Simplify build step in CodeQL analysis workflow

Removed ccache setup and git configuration from the build step.


  Commit: 0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
      https://github.com/ehb54/ultrascan3/commit/0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL analysis workflow

Refactor CodeQL analysis workflow to improve target calculation and build steps.


  Commit: 6c80777b7287a29fe978526475e6f099ca3ef827
      https://github.com/ehb54/ultrascan3/commit/6c80777b7287a29fe978526475e6f099ca3ef827
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL workflow to simplify caching and builds

Removed caching steps for ccache, utils, qwtplot3d, and gui. Added build steps for utils, qwtplot3d, and gui using qmake.


  Commit: 27c760f8c268e77d5038469cfd40243fb274f2d1
      https://github.com/ehb54/ultrascan3/commit/27c760f8c268e77d5038469cfd40243fb274f2d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update unit-tests.yml to remove path filters for push

Removed specific path filters for push events in unit-tests workflow.


  Commit: 2465409a96b820d237f9bf0c3b09b12f859060d7
      https://github.com/ehb54/ultrascan3/commit/2465409a96b820d237f9bf0c3b09b12f859060d7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update static analysis workflow trigger paths

Removed specific path triggers for push events in static analysis workflow.


  Commit: c1ac9c0b43cdde1480834d2fb742344b9649144f
      https://github.com/ehb54/ultrascan3/commit/c1ac9c0b43cdde1480834d2fb742344b9649144f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Document CMake formatter


  Commit: 391ac4d011a289eafa902e9d56eb4382491f0b66
      https://github.com/ehb54/ultrascan3/commit/391ac4d011a289eafa902e9d56eb4382491f0b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Updating nproc


  Commit: ea7559d6bcd810ed7a176871e33f0d36b49152e2
      https://github.com/ehb54/ultrascan3/commit/ea7559d6bcd810ed7a176871e33f0d36b49152e2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/unit-tests.yml
    M admin/linting/cmake/.cmake-format.yaml
    M admin/linting/cmake/README.md

  Log Message:
  -----------
  Fix minor comments


  Commit: 6e94734ca883da80e058cf4e51dee4474e9863e5
      https://github.com/ehb54/ultrascan3/commit/6e94734ca883da80e058cf4e51dee4474e9863e5
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_edit/us_edit.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_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #305 from ehb54/alexey-dev-issue608

Alexey dev issue608: Prot. Dev. for DataDisk data types


  Commit: 5ff2d239588616635adbdfaf775949a91f5d7565
      https://github.com/ehb54/ultrascan3/commit/5ff2d239588616635adbdfaf775949a91f5d7565
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  Update checkout action version


  Commit: 321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
      https://github.com/ehb54/ultrascan3/commit/321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  fix branches


  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 5cf42202af6d7f5544a2cf1111d44f5f1a232777
      https://github.com/ehb54/ultrascan3/commit/5cf42202af6d7f5544a2cf1111d44f5f1a232777
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  Refactor CodeQL analysis workflow conditions

Removed specific file paths from pull request triggers and updated conditions for CodeQL analysis steps.


  Commit: 3f486acaa2a2e5b708f257acf949e90d1b042bbc
      https://github.com/ehb54/ultrascan3/commit/3f486acaa2a2e5b708f257acf949e90d1b042bbc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

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

  Log Message:
  -----------
  Rename analysis job for GUI programs


  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


  Commit: 02ab6c663335530dbf4295161c2f68c1043b3874
      https://github.com/ehb54/ultrascan3/commit/02ab6c663335530dbf4295161c2f68c1043b3874
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

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


  Commit: 013afa9051723a54ff17a3431895f0e6aa65eebc
      https://github.com/ehb54/ultrascan3/commit/013afa9051723a54ff17a3431895f0e6aa65eebc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Refactor GitHub Actions workflows to enhance modularity and efficiency
- Introduce `changed-files` job to conditionally trigger workflows based on file changes.
- Add status-checking jobs for Documentation, CodeQL analysis, and Static Analysis builds.
- Improve concurrency management and file fetch depth.
- Optimize CI Docker containers and cleanup processes.
- Streamline conditional checks and matrix configurations.


  Commit: 2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
      https://github.com/ehb54/ultrascan3/commit/2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    A .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add `unit-tests-v2.yml` GitHub Actions workflow

- Introduce a new workflow for unit testing with support for configurable test filters and debug mode.
- Add a `changed-files` job to detect relevant file modifications and conditionally trigger tests.
- Implement improved concurrency management and result-checking mechanisms.
- Streamline test setup, build process, and log management for enhanced clarity and efficiency.
- Enable artifact uploads for detailed test results and logs.


  Commit: e2a9b2acaeeeac868cf1d55f459225e683e37d11
      https://github.com/ehb54/ultrascan3/commit/e2a9b2acaeeeac868cf1d55f459225e683e37d11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Normalize glob patterns in GitHub Actions workflows


  Commit: 037064b1d8968578fcb9a42ba07e275c96b38a8c
      https://github.com/ehb54/ultrascan3/commit/037064b1d8968578fcb9a42ba07e275c96b38a8c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Fix incorrect `CMAKE_MODULE_PATH` to use absolute path in `unit-tests-v2.yml` workflow


  Commit: 4c0538dff646603c4258628a076f9807a29af7c3
      https://github.com/ehb54/ultrascan3/commit/4c0538dff646603c4258628a076f9807a29af7c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Enhance `unit-tests.yml` workflow with dynamic file change detection and improved concurrency management

- Add `changed-files` job to detect relevant modifications and conditionally trigger unit tests.
- Introduce concurrency control to prevent duplicate runs.
- Expand artifacts to include additional logs for better debugging.
- Add status-checking job to validate unit testing outcomes.
- Refactor workflow for clarity and streamlined test execution.


  Commit: 12e9e1fd701da2b201e7d47b3cb642812813e4e7
      https://github.com/ehb54/ultrascan3/commit/12e9e1fd701da2b201e7d47b3cb642812813e4e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Enhance `static-analysis.yml` workflow with CPP file-specific change detection

- Add outputs and environment variables to track `.cpp` and `.h` file changes.
- Update `changed-files` step to simplify logic and rely on filtered outputs.
- Streamline file detection for first commits and pull requests.


  Commit: e94063c15730a822262820f18c468a429ac4c374
      https://github.com/ehb54/ultrascan3/commit/e94063c15730a822262820f18c468a429ac4c374
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Normalize glob pattern syntax in `unit-tests.yml` workflow


  Commit: 158b855316998f18924177b91ad5cb81e696ad53
      https://github.com/ehb54/ultrascan3/commit/158b855316998f18924177b91ad5cb81e696ad53
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

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

  Log Message:
  -----------
  Update static-analysis workflow to use latest `us3comp` container image


  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...


  Commit: 350edcd3194656d020a571d45cbe1dd872d041e2
      https://github.com/ehb54/ultrascan3/commit/350edcd3194656d020a571d45cbe1dd872d041e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #322 from ehb54/alexey-dev-issue651

Alexey dev issue651: Ind. & Combined Plots in GMP Rpeorts: CG-model-based runs (ranges), Plot Aspect Ratios, "Combined Plots" section title


  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...


  Commit: e1ce700f61527eedba262f237e41dbcc16de6de7
      https://github.com/ehb54/ultrascan3/commit/e1ce700f61527eedba262f237e41dbcc16de6de7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Update file patterns for static analysis


  Commit: aebbdda924bca0630a6b1b50f5110f340c8804aa
      https://github.com/ehb54/ultrascan3/commit/aebbdda924bca0630a6b1b50f5110f340c8804aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Update CodeQL workflow to ignore specific files

Ignore changes in us_mpi_analysis directory during file checks and update build commands.


  Commit: a4a655d619279b7bb59e01ee82fce46e875eebca
      https://github.com/ehb54/ultrascan3/commit/a4a655d619279b7bb59e01ee82fce46e875eebca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Exclude us_mpi_analysis from CodeQL analysis gui


  Commit: 14ba4d63b16861ed659ae0c204b0ee3f54589432
      https://github.com/ehb54/ultrascan3/commit/14ba4d63b16861ed659ae0c204b0ee3f54589432
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

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

  Log Message:
  -----------
  Fix syntax for exclusion in CodeQL workflow


  Commit: 770769aa570aae22f64b5b817de2320ab1b070e3
      https://github.com/ehb54/ultrascan3/commit/770769aa570aae22f64b5b817de2320ab1b070e3
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #326 from ehb54/alexey-dev-issue631

GMP 6. REPORT -- generate correct build number in the header...


  Commit: 3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
      https://github.com/ehb54/ultrascan3/commit/3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

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


  Commit: c088a80976663c552cffec04fcb0cfe084922560
      https://github.com/ehb54/ultrascan3/commit/c088a80976663c552cffec04fcb0cfe084922560
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Merge pull request #321 from ehb54/lukas/gh_actions

Lukas/gh actions


  Commit: 70cf969d22c8ecb1892bcb7a3301d101bca7aa55
      https://github.com/ehb54/ultrascan3/commit/70cf969d22c8ecb1892bcb7a3301d101bca7aa55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 815465ed2b2679fbcf4cda7c076dda6fdc89f322
      https://github.com/ehb54/ultrascan3/commit/815465ed2b2679fbcf4cda7c076dda6fdc89f322
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Merge pull request #327 from ehb54/alexey-dev-issue657

GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in FITME_AUTO & View Overlay


  Commit: 609897d0591d9d8d0b5bf0bbb55478c8efd20337
      https://github.com/ehb54/ultrascan3/commit/609897d0591d9d8d0b5bf0bbb55478c8efd20337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT.DEV. dataDisk re-use -- filter out older completed dataDisk GMP runs for re-processing...


  Commit: fe940ce7749c9043b38aa0f91efa79a19fed6216
      https://github.com/ehb54/ultrascan3/commit/fe940ce7749c9043b38aa0f91efa79a19fed6216
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

  Changed paths:
    M utils/us_experiment.cpp

  Log Message:
  -----------
  [debug 1]GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 3322930798adf89544c8645263c9a5b2b477124a
      https://github.com/ehb54/ultrascan3/commit/3322930798adf89544c8645263c9a5b2b477124a
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #330 from ehb54/alexey-dev-issue667

PROT DEV -- filter out completed dataDisk runs initiated with earlier tabular signature (not to be reprocessed)


  Commit: af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
      https://github.com/ehb54/ultrascan3/commit/af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  PROT.DEV.: dataDisk type -- pass invID from the protocol assoc. with the datat to-be-reanalysed for download from DB: (1) during creation of a new run using data produced by different owner; (2) during re-attachment from different session/different user (which would require fresh download)...


  Commit: 7d85624ca8988e36c4f8b7c31b1d647b049c5e20
      https://github.com/ehb54/ultrascan3/commit/7d85624ca8988e36c4f8b7c31b1d647b049c5e20
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-03 (Wed, 03 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #331 from ehb54/alexey-dev-issue669

PROT.DEV.: dataDisk type -- pass correct invID  (data owner)


  Commit: c6506c7244d4b5a0983f0b4b904c963afb1424ff
      https://github.com/ehb54/ultrascan3/commit/c6506c7244d4b5a0983f0b4b904c963afb1424ff
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  calculate the confidence intervals based on accumulated concentration over sorted values


  Commit: aff3811250880ef52f2b3e6568f97d43ae958654
      https://github.com/ehb54/ultrascan3/commit/aff3811250880ef52f2b3e6568f97d43ae958654
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  us_solutedata.cpp: Constructs the idxs vector with an initial size, replace stable_sort with sort std function


  Commit: fac3bd3f8d097359906b91580ee196ef7eff219c
      https://github.com/ehb54/ultrascan3/commit/fac3bd3f8d097359906b91580ee196ef7eff219c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge pull request #332 from samo38/issue_672

issue 672: confidence interval problem


  Commit: 2bbf479b2120feddeaee7fadcfbbb78e53d79378
      https://github.com/ehb54/ultrascan3/commit/2bbf479b2120feddeaee7fadcfbbb78e53d79378
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-11 (Thu, 11 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    M README.md
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    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 admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    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
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    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_general_gui.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_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_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
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_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
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    A programs/us_combine_models/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    A programs/us_config/CMakeLists.txt
    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_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    A programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_select_rundd.cpp
    A programs/us_density_match/CMakeLists.txt
    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
    A programs/us_dmga_init/CMakeLists.txt
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_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
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_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
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp
    A programs/us_integral/CMakeLists.txt
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_integral.cpp
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    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
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    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/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
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    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
    A programs/us_pcsa/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_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    A programs/us_ramp/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_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/modelbuilder/us_modelbuilder.cpp
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    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/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_buffer.cpp
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h
    M utils/us_gzip.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    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_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

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


Compare: https://github.com/ehb54/ultrascan3/compare/37fd8b74401f...2bbf479b2120

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From noreply at github.com  Thu Dec 11 09:33:14 2025
From: noreply at github.com (ehb54)
Date: Thu, 11 Dec 2025 08:33:14 -0800
Subject: [us-commits] [ehb54/ultrascan3] af82fd: PROT.DEV.: dataDisk type --
 pass invID from the pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_fematch/a1184f-19bed8@github.com>

  Branch: refs/heads/lukas/us_fematch
  Home:   https://github.com/ehb54/ultrascan3
  Commit: af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
      https://github.com/ehb54/ultrascan3/commit/af82fdc5c2ed2e8bf13ae52c9996e28545c1a9fa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-12-01 (Mon, 01 Dec 2025)

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

  Log Message:
  -----------
  PROT.DEV.: dataDisk type -- pass invID from the protocol assoc. with the datat to-be-reanalysed for download from DB: (1) during creation of a new run using data produced by different owner; (2) during re-attachment from different session/different user (which would require fresh download)...


  Commit: 7d85624ca8988e36c4f8b7c31b1d647b049c5e20
      https://github.com/ehb54/ultrascan3/commit/7d85624ca8988e36c4f8b7c31b1d647b049c5e20
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-03 (Wed, 03 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #331 from ehb54/alexey-dev-issue669

PROT.DEV.: dataDisk type -- pass correct invID  (data owner)


  Commit: c6506c7244d4b5a0983f0b4b904c963afb1424ff
      https://github.com/ehb54/ultrascan3/commit/c6506c7244d4b5a0983f0b4b904c963afb1424ff
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  calculate the confidence intervals based on accumulated concentration over sorted values


  Commit: aff3811250880ef52f2b3e6568f97d43ae958654
      https://github.com/ehb54/ultrascan3/commit/aff3811250880ef52f2b3e6568f97d43ae958654
  Author: Saeed <github.com/samo38>
  Date:   2025-12-08 (Mon, 08 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  us_solutedata.cpp: Constructs the idxs vector with an initial size, replace stable_sort with sort std function


  Commit: fac3bd3f8d097359906b91580ee196ef7eff219c
      https://github.com/ehb54/ultrascan3/commit/fac3bd3f8d097359906b91580ee196ef7eff219c
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-09 (Tue, 09 Dec 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge pull request #332 from samo38/issue_672

issue 672: confidence interval problem


  Commit: 19bed82f07bbfc423940773a303b2f9f80b8fb63
      https://github.com/ehb54/ultrascan3/commit/19bed82f07bbfc423940773a303b2f9f80b8fb63
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-11 (Thu, 11 Dec 2025)

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/a1184f12e7a9...19bed82f07bb

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From noreply at github.com  Fri Dec 12 05:57:54 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 04:57:54 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-building/4a0bd4-000000@github.com>

  Branch: refs/heads/lukas/cmake-building
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Dec 12 05:58:00 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 04:58:00 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-llvm/3494ff-000000@github.com>

  Branch: refs/heads/lukas/clang-format-example-llvm
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Dec 12 05:58:04 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 04:58:04 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-gnu/5a3a57-000000@github.com>

  Branch: refs/heads/lukas/clang-format-example-gnu
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Dec 12 05:58:02 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 04:58:02 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-google/139586-000000@github.com>

  Branch: refs/heads/lukas/clang-format-example-google
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Dec 12 09:54:35 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 08:54:35 -0800
Subject: [us-commits] [ehb54/ultrascan3] 560d73: Add overlay ports for
 `qwtplot3d` with support for...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/c90cc6-748528@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 560d7338f7f1ce606716df47c6d22e66427dc74b
      https://github.com/ehb54/ultrascan3/commit/560d7338f7f1ce606716df47c6d22e66427dc74b
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

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

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


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

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

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


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

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

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


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

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

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


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

  Changed paths:
    M CMakeLists.txt

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


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

  Changed paths:
    M CMakePresets.json
    M vcpkg.json

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/c90cc6690c06...7485285209c8

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From noreply at github.com  Fri Dec 12 10:20:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 09:20:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] 05fcfe: Add new `base-qt5-qwt616`
 preset and refactor Qt5 ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/748528-05fcfe@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 05fcfe57f6acbc11cc86599a4c6cd79df932904e
      https://github.com/ehb54/ultrascan3/commit/05fcfe57f6acbc11cc86599a4c6cd79df932904e
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

  Changed paths:
    M CMakePresets.json

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



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From noreply at github.com  Fri Dec 12 10:21:53 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 09:21:53 -0800
Subject: [us-commits] [ehb54/ultrascan3] b6d77d: Simplify `vcpkg.json`
 dependencies for `qwt-6-3-0-...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/05fcfe-b6d77d@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b6d77d788c73d678ed8809aef7927dde929b92a3
      https://github.com/ehb54/ultrascan3/commit/b6d77d788c73d678ed8809aef7927dde929b92a3
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

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

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



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From noreply at github.com  Fri Dec 12 15:29:41 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 12 Dec 2025 14:29:41 -0800
Subject: [us-commits] [ehb54/ultrascan3] 279b0a: Update `qwt-6-3-0-qt5`
 overlay port: add Qt5 confi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/b6d77d-f09d40@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 279b0ac8ed33b11b36efd374afe030708a44c890
      https://github.com/ehb54/ultrascan3/commit/279b0ac8ed33b11b36efd374afe030708a44c890
  Author: Doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-12 (Fri, 12 Dec 2025)

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

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


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

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

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


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

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

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


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

  Changed paths:
    M CMakePresets.json
    M vcpkg.json

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


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

  Changed paths:
    M programs/us_fit_meniscus/CMakeLists.txt

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


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

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

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


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

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

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


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

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

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


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

  Changed paths:
    M gui/CMakeLists.txt

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


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

  Changed paths:
    M programs/CMakeLists.txt

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


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/b6d77d788c73...f09d400fba03

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From noreply at github.com  Sun Dec 14 04:36:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 14 Dec 2025 03:36:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] 148505: - Optimize scan processing
 logic in `us_xpn_data.cpp`
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_xpn_viewer_timestate/2bbf47-148505@github.com>

  Branch: refs/heads/lukas/us_xpn_viewer_timestate
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 148505e424408bdef6ae5fb53c753b8508191b5c
      https://github.com/ehb54/ultrascan3/commit/148505e424408bdef6ae5fb53c753b8508191b5c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-14 (Sun, 14 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  - Optimize scan processing logic in `us_xpn_data.cpp`
  - Use `QVector::reserve` to preallocate scan storage based on total scan count.
  - Refactor scan sorting to include `omega2t` as a tiebreaker for time.
  - Safeguard against empty scan arrays when accessing the last element.
- Fix typo in comments ("incase" ? "in case").



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From noreply at github.com  Mon Dec 15 09:17:21 2025
From: noreply at github.com (ehb54)
Date: Mon, 15 Dec 2025 08:17:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] bbfe61: somo-dev
 qregexp->qregularexpression ... initial pass
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/bc6d23-4fed2b@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bbfe61bf7a6754e06262b736ba859e14c704c6bd
      https://github.com/ehb54/ultrascan3/commit/bbfe61bf7a6754e06262b736ba859e14c704c6bd
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-02 (Sun, 02 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.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_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.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_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.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_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  somo-dev qregexp->qregularexpression ... initial pass


  Commit: 18f0d159cf42c5d35c74be39e94f013130036d4f
      https://github.com/ehb54/ultrascan3/commit/18f0d159cf42c5d35c74be39e94f013130036d4f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us3i_settings.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_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.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_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.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_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  somo-dev qregexp 2nd round, wip


  Commit: 020f5c2befce268fc59a9d7416cbd7aad90105d6
      https://github.com/ehb54/ultrascan3/commit/020f5c2befce268fc59a9d7416cbd7aad90105d6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_file_util.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_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    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_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp

  Log Message:
  -----------
  somo-dev qregexp 3rd round, wip


  Commit: 93bc9ee5954afd87816723fc5f54ba6709581ea9
      https://github.com/ehb54/ultrascan3/commit/93bc9ee5954afd87816723fc5f54ba6709581ea9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us_extern.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_version.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp

  Log Message:
  -----------
  somo-dev qt6 updates ... wip


  Commit: 5dc48cadfac3d739a020e4a75a1b436c58e9b81e
      https://github.com/ehb54/ultrascan3/commit/5dc48cadfac3d739a020e4a75a1b436c58e9b81e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us_extern.h

  Log Message:
  -----------
  somo-dev qt6 updates ... wip


  Commit: bbf98e2edd61b0d2e408a79506885ef0efd8fad3
      https://github.com/ehb54/ultrascan3/commit/bbf98e2edd61b0d2e408a79506885ef0efd8fad3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_other.cpp

  Log Message:
  -----------
  somo-dev qt6 updates ... wip


  Commit: 4206bdc2c975463444ade4c318197b0d59f46925
      https://github.com/ehb54/ultrascan3/commit/4206bdc2c975463444ade4c318197b0d59f46925
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_other.cpp

  Log Message:
  -----------
  somo-dev qt6 ... wip


  Commit: 94578df67d4f74c00d23685dcc6b9f1f72577ead
      https://github.com/ehb54/ultrascan3/commit/94578df67d4f74c00d23685dcc6b9f1f72577ead
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  somo-dev qt6 updates ... wip


  Commit: 5e343bf7c66094e6a764f781da0fe3c49121f062
      https://github.com/ehb54/ultrascan3/commit/5e343bf7c66094e6a764f781da0fe3c49121f062
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us3i_plot.h

  Log Message:
  -----------
  somo-dev qt6 updates remove qwt_compat.h


  Commit: 030dbb8ec9ad65f1f035530663651b27dde1310d
      https://github.com/ehb54/ultrascan3/commit/030dbb8ec9ad65f1f035530663651b27dde1310d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_mqt.cpp

  Log Message:
  -----------
  somo-dev qt6 wip


  Commit: be2ee4eb9eabecdcf3f8996ea99d9b442d701750
      https://github.com/ehb54/ultrascan3/commit/be2ee4eb9eabecdcf3f8996ea99d9b442d701750
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp

  Log Message:
  -----------
  somo-dev load denss mm fit


  Commit: 3573f26e2adf3994546595e13d2b90141a683cc8
      https://github.com/ehb54/ultrascan3/commit/3573f26e2adf3994546595e13d2b90141a683cc8
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    R us_somo/develop/include/us_revision.h

  Log Message:
  -----------
  Stop tracking us_revision.h


  Commit: 4e1bd960713104673a6e3c787346ee5664d265bf
      https://github.com/ehb54/ultrascan3/commit/4e1bd960713104673a6e3c787346ee5664d265bf
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_band_broaden.cpp

  Log Message:
  -----------
  somo-dev band broaden size_t offset -> ptrdiff_t


  Commit: 418e00417996f4cd2fa2605e4e1f88100256ecea
      https://github.com/ehb54/ultrascan3/commit/418e00417996f4cd2fa2605e4e1f88100256ecea
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp

  Log Message:
  -----------
  somo-dev minor text update


  Commit: 4fed2b558a9a7c4f441fd05636cd35e2d8409077
      https://github.com/ehb54/ultrascan3/commit/4fed2b558a9a7c4f441fd05636cd35e2d8409077
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    R us_somo/develop/include/us_revision.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_version.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  Merge pull request #303 from ehb54/somo-dev-qt6-regexp

Somo dev qt6 regexp


Compare: https://github.com/ehb54/ultrascan3/compare/bc6d238e571e...4fed2b558a9a

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From noreply at github.com  Mon Dec 15 09:17:28 2025
From: noreply at github.com (ehb54)
Date: Mon, 15 Dec 2025 08:17:28 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/418e00-000000@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Dec 15 09:35:42 2025
From: noreply at github.com (ehb54)
Date: Mon, 15 Dec 2025 08:35:42 -0800
Subject: [us-commits] [ehb54/ultrascan3] 37703a: somo qt6 branch - initial
 commit from somo-dev
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/000000-37703a@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
      https://github.com/ehb54/ultrascan3/commit/37703a8dfbfa2d698e212c71fa75af7e0fa4cd82
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us3i_plot.h
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/include/us_zeno_cxx.h
    M us_somo/develop/include/us_zeno_cxx_nf.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_mqt.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi/us_saxs_cmds_mpi.pro
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev



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From noreply at github.com  Mon Dec 15 09:53:40 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 15 Dec 2025 08:53:40 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_xpn_viewer_timestate/148505-000000@github.com>

  Branch: refs/heads/lukas/us_xpn_viewer_timestate
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Dec 15 09:53:34 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 15 Dec 2025 08:53:34 -0800
Subject: [us-commits] [ehb54/ultrascan3] bb0aa9: Refactor scan handling in
 `us_xpn_data.cpp` for im...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/fac3bd-5fa8a7@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
      https://github.com/ehb54/ultrascan3/commit/bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-28 (Sun, 28 Sep 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Refactor scan handling in `us_xpn_data.cpp` for improved sorting and speed step calculation

Replaced direct usage of `scanData` with a centralized `scans` vector for consistent access and sorting by time. Updated speed step computation and related logic to utilize the sorted vector, enhancing clarity and maintainability.


  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


  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.


  Commit: 2bbf479b2120feddeaee7fadcfbbb78e53d79378
      https://github.com/ehb54/ultrascan3/commit/2bbf479b2120feddeaee7fadcfbbb78e53d79378
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-11 (Thu, 11 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    M README.md
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    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 admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    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
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    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_general_gui.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_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_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
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_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
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    A programs/us_combine_models/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    A programs/us_config/CMakeLists.txt
    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_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    A programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_select_rundd.cpp
    A programs/us_density_match/CMakeLists.txt
    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
    A programs/us_dmga_init/CMakeLists.txt
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_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
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_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
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp
    A programs/us_integral/CMakeLists.txt
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_integral.cpp
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    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
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    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/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
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    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
    A programs/us_pcsa/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_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    A programs/us_ramp/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_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/modelbuilder/us_modelbuilder.cpp
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    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/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_buffer.cpp
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h
    M utils/us_gzip.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    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_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

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


  Commit: 148505e424408bdef6ae5fb53c753b8508191b5c
      https://github.com/ehb54/ultrascan3/commit/148505e424408bdef6ae5fb53c753b8508191b5c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-14 (Sun, 14 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  - Optimize scan processing logic in `us_xpn_data.cpp`
  - Use `QVector::reserve` to preallocate scan storage based on total scan count.
  - Refactor scan sorting to include `omega2t` as a tiebreaker for time.
  - Safeguard against empty scan arrays when accessing the last element.
- Fix typo in comments ("incase" ? "in case").


  Commit: 5fa8a71f76528dc06f16fa456f07507966e64751
      https://github.com/ehb54/ultrascan3/commit/5fa8a71f76528dc06f16fa456f07507966e64751
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #334 from ehb54/lukas/us_xpn_viewer_timestate

Increase precision/coverage for us_xpn_viewer generated timestates


Compare: https://github.com/ehb54/ultrascan3/compare/fac3bd3f8d09...5fa8a71f7652

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From noreply at github.com  Mon Dec 15 10:02:36 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 15 Dec 2025 09:02:36 -0800
Subject: [us-commits] [ehb54/ultrascan3] bb0aa9: Refactor scan handling in
 `us_xpn_data.cpp` for im...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/f09d40-d3e888@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
      https://github.com/ehb54/ultrascan3/commit/bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-28 (Sun, 28 Sep 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Refactor scan handling in `us_xpn_data.cpp` for improved sorting and speed step calculation

Replaced direct usage of `scanData` with a centralized `scans` vector for consistent access and sorting by time. Updated speed step computation and related logic to utilize the sorted vector, enhancing clarity and maintainability.


  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


  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.


  Commit: 2bbf479b2120feddeaee7fadcfbbb78e53d79378
      https://github.com/ehb54/ultrascan3/commit/2bbf479b2120feddeaee7fadcfbbb78e53d79378
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-11 (Thu, 11 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    M README.md
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    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 admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    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
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    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_general_gui.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_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_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
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_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
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    A programs/us_combine_models/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    A programs/us_config/CMakeLists.txt
    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_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    A programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_select_rundd.cpp
    A programs/us_density_match/CMakeLists.txt
    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
    A programs/us_dmga_init/CMakeLists.txt
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_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
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_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
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp
    A programs/us_integral/CMakeLists.txt
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_integral.cpp
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    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
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    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/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
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    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
    A programs/us_pcsa/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_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    A programs/us_ramp/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_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/modelbuilder/us_modelbuilder.cpp
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    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/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_buffer.cpp
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h
    M utils/us_gzip.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    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_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

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


  Commit: 148505e424408bdef6ae5fb53c753b8508191b5c
      https://github.com/ehb54/ultrascan3/commit/148505e424408bdef6ae5fb53c753b8508191b5c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-14 (Sun, 14 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  - Optimize scan processing logic in `us_xpn_data.cpp`
  - Use `QVector::reserve` to preallocate scan storage based on total scan count.
  - Refactor scan sorting to include `omega2t` as a tiebreaker for time.
  - Safeguard against empty scan arrays when accessing the last element.
- Fix typo in comments ("incase" ? "in case").


  Commit: 5fa8a71f76528dc06f16fa456f07507966e64751
      https://github.com/ehb54/ultrascan3/commit/5fa8a71f76528dc06f16fa456f07507966e64751
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #334 from ehb54/lukas/us_xpn_viewer_timestate

Increase precision/coverage for us_xpn_viewer generated timestates


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

  Changed paths:
    M utils/us_xpn_data.cpp

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


Compare: https://github.com/ehb54/ultrascan3/compare/f09d400fba03...d3e888e267c9

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From noreply at github.com  Tue Dec 16 05:00:46 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 16 Dec 2025 04:00:46 -0800
Subject: [us-commits] [ehb54/ultrascan3] df86df: Refactor
 `us_program_common` CMake linkage for Ult...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/d3e888-d9f790@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: df86df9039cb75f8b70c9f3cb92badd78dd35e1b
      https://github.com/ehb54/ultrascan3/commit/df86df9039cb75f8b70c9f3cb92badd78dd35e1b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M programs/CMakeLists.txt

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


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

  Changed paths:
    M gui/CMakeLists.txt

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


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

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

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


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

  Changed paths:
    M utils/us_extern.h

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


Compare: https://github.com/ehb54/ultrascan3/compare/d3e888e267c9...d9f790e9a362

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From noreply at github.com  Tue Dec 16 08:14:52 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 07:14:52 -0800
Subject: [us-commits] [ehb54/ultrascan3] 9cc80a: codeql debug info
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/37703a-9cc80a@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9cc80a805f0c89d30fd663cffa4e544bdccfddd6
      https://github.com/ehb54/ultrascan3/commit/9cc80a805f0c89d30fd663cffa4e544bdccfddd6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

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

  Log Message:
  -----------
  codeql debug info



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From noreply at github.com  Tue Dec 16 08:33:12 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 07:33:12 -0800
Subject: [us-commits] [ehb54/ultrascan3] 8f49d1: remove us_color from
 libus_somo
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/9cc80a-8f49d1@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8f49d1cadd471936ba76ad95fe0001436a3685a7
      https://github.com/ehb54/ultrascan3/commit/8f49d1cadd471936ba76ad95fe0001436a3685a7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M us_somo/develop/libus_somo.pro

  Log Message:
  -----------
  remove us_color from libus_somo



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From noreply at github.com  Tue Dec 16 08:42:08 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 07:42:08 -0800
Subject: [us-commits] [ehb54/ultrascan3] 426acc: remove us_color from
 libus_somo
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/4fed2b-426acc@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 426acc14b3ad93e08c77a22d612362ef15dce992
      https://github.com/ehb54/ultrascan3/commit/426acc14b3ad93e08c77a22d612362ef15dce992
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M us_somo/develop/libus_somo.pro

  Log Message:
  -----------
  remove us_color from libus_somo



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From noreply at github.com  Tue Dec 16 09:38:34 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 08:38:34 -0800
Subject: [us-commits] [ehb54/ultrascan3] 642330: additional debugs,
 temp relax deprecations
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/8f49d1-642330@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 642330d0e7562d863f6471b57e528cdf5aec013c
      https://github.com/ehb54/ultrascan3/commit/642330d0e7562d863f6471b57e528cdf5aec013c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  additional debugs, temp relax deprecations



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From noreply at github.com  Tue Dec 16 09:45:26 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 08:45:26 -0800
Subject: [us-commits] [ehb54/ultrascan3] fcd5db: additional debugs,
 temp relax deprecations
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/642330-fcd5db@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
      https://github.com/ehb54/ultrascan3/commit/fcd5db1f23ea8d24dfda6dcb66c321e1e670bef4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

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

  Log Message:
  -----------
  additional debugs, temp relax deprecations



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From noreply at github.com  Tue Dec 16 10:22:20 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 09:22:20 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1a808d: additional debugs,
 temp relax deprecations
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/fcd5db-1a808d@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1a808d5061ef553acf0aa97a83c04af9d82970bc
      https://github.com/ehb54/ultrascan3/commit/1a808d5061ef553acf0aa97a83c04af9d82970bc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

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

  Log Message:
  -----------
  additional debugs, temp relax deprecations



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From noreply at github.com  Tue Dec 16 11:32:12 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 10:32:12 -0800
Subject: [us-commits] [ehb54/ultrascan3] 24783d: restore deprecations
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/1a808d-24783d@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 24783d42d61d7132dd5622e8027c9f6f59de5608
      https://github.com/ehb54/ultrascan3/commit/24783d42d61d7132dd5622e8027c9f6f59de5608
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  restore deprecations



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From noreply at github.com  Tue Dec 16 11:32:54 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 10:32:54 -0800
Subject: [us-commits] [ehb54/ultrascan3] bb0aa9: Refactor scan handling in
 `us_xpn_data.cpp` for im...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/24783d-c37b59@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
      https://github.com/ehb54/ultrascan3/commit/bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-28 (Sun, 28 Sep 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Refactor scan handling in `us_xpn_data.cpp` for improved sorting and speed step calculation

Replaced direct usage of `scanData` with a centralized `scans` vector for consistent access and sorting by time. Updated speed step computation and related logic to utilize the sorted vector, enhancing clarity and maintainability.


  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


  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.


  Commit: 2bbf479b2120feddeaee7fadcfbbb78e53d79378
      https://github.com/ehb54/ultrascan3/commit/2bbf479b2120feddeaee7fadcfbbb78e53d79378
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-11 (Thu, 11 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    M README.md
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    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 admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    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
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    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_general_gui.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_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_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
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_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
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    A programs/us_combine_models/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    A programs/us_config/CMakeLists.txt
    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_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    A programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_select_rundd.cpp
    A programs/us_density_match/CMakeLists.txt
    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
    A programs/us_dmga_init/CMakeLists.txt
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_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
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_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
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp
    A programs/us_integral/CMakeLists.txt
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_integral.cpp
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    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
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    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/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
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    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
    A programs/us_pcsa/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_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    A programs/us_ramp/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_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/modelbuilder/us_modelbuilder.cpp
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    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/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_buffer.cpp
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h
    M utils/us_gzip.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    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_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

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


  Commit: 148505e424408bdef6ae5fb53c753b8508191b5c
      https://github.com/ehb54/ultrascan3/commit/148505e424408bdef6ae5fb53c753b8508191b5c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-14 (Sun, 14 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  - Optimize scan processing logic in `us_xpn_data.cpp`
  - Use `QVector::reserve` to preallocate scan storage based on total scan count.
  - Refactor scan sorting to include `omega2t` as a tiebreaker for time.
  - Safeguard against empty scan arrays when accessing the last element.
- Fix typo in comments ("incase" ? "in case").


  Commit: 5fa8a71f76528dc06f16fa456f07507966e64751
      https://github.com/ehb54/ultrascan3/commit/5fa8a71f76528dc06f16fa456f07507966e64751
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #334 from ehb54/lukas/us_xpn_viewer_timestate

Increase precision/coverage for us_xpn_viewer generated timestates


  Commit: c37b59afbb01c067585c5da09c200e295282decc
      https://github.com/ehb54/ultrascan3/commit/c37b59afbb01c067585c5da09c200e295282decc
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


Compare: https://github.com/ehb54/ultrascan3/compare/24783d42d61d...c37b59afbb01

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From noreply at github.com  Tue Dec 16 11:47:47 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 10:47:47 -0800
Subject: [us-commits] [ehb54/ultrascan3] 59ba4b: codeql fix
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/c37b59-cfd594@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 59ba4be5192bd4024037ed7173a13061a59c41ce
      https://github.com/ehb54/ultrascan3/commit/59ba4be5192bd4024037ed7173a13061a59c41ce
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

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

  Log Message:
  -----------
  codeql fix


  Commit: cfd59439653a91b6cdcfd88d8a348ccb934a6cba
      https://github.com/ehb54/ultrascan3/commit/cfd59439653a91b6cdcfd88d8a348ccb934a6cba
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  somo qt6 branch - initial commit from somo-dev


Compare: https://github.com/ehb54/ultrascan3/compare/c37b59afbb01...cfd59439653a

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From noreply at github.com  Tue Dec 16 12:15:39 2025
From: noreply at github.com (ehb54)
Date: Tue, 16 Dec 2025 11:15:39 -0800
Subject: [us-commits] [ehb54/ultrascan3] 46434a: relax somo error for test
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/cfd594-46434a@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 46434a20d02da7dd7cb8edb14455747838aae8e4
      https://github.com/ehb54/ultrascan3/commit/46434a20d02da7dd7cb8edb14455747838aae8e4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-16 (Tue, 16 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  relax somo error for test



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From noreply at github.com  Wed Dec 17 09:51:31 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 08:51:31 -0800
Subject: [us-commits] [ehb54/ultrascan3] 25e92e: fix: version check for
 notices restricted to major...
Message-ID: <ehb54/ultrascan3/push/refs/heads/notices-fix/9e26d2-70e83b@github.com>

  Branch: refs/heads/notices-fix
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
      https://github.com/ehb54/ultrascan3/commit/25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  fix: version check for notices restricted to major.minor


  Commit: 70e83bb9142d7fb78b9a37fc95e1ad669986270e
      https://github.com/ehb54/ultrascan3/commit/70e83bb9142d7fb78b9a37fc95e1ad669986270e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/9e26d202aea3...70e83bb9142d

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From noreply at github.com  Wed Dec 17 09:55:21 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 08:55:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] bb0aa9: Refactor scan handling in
 `us_xpn_data.cpp` for im...
Message-ID: <ehb54/ultrascan3/push/refs/heads/notices-fix/70e83b-c3955b@github.com>

  Branch: refs/heads/notices-fix
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
      https://github.com/ehb54/ultrascan3/commit/bb0aa9e39a0dbe5f7e27e10da64bf65846b81337
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-09-28 (Sun, 28 Sep 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Refactor scan handling in `us_xpn_data.cpp` for improved sorting and speed step calculation

Replaced direct usage of `scanData` with a centralized `scans` vector for consistent access and sorting by time. Updated speed step computation and related logic to utilize the sorted vector, enhancing clarity and maintainability.


  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


  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.


  Commit: 2bbf479b2120feddeaee7fadcfbbb78e53d79378
      https://github.com/ehb54/ultrascan3/commit/2bbf479b2120feddeaee7fadcfbbb78e53d79378
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-11 (Thu, 11 Dec 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    M README.md
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    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 admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M doc/manual/advanced_config.body
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    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
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    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_general_gui.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_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_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
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_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
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    A programs/us_combine_models/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    A programs/us_config/CMakeLists.txt
    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_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    A programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_select_rundd.cpp
    A programs/us_density_match/CMakeLists.txt
    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
    A programs/us_dmga_init/CMakeLists.txt
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_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
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.pro
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_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
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    M programs/us_helpdaemon/us_helpdaemon.cpp
    A programs/us_integral/CMakeLists.txt
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_integral.cpp
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    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
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    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/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
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    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
    A programs/us_pcsa/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_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.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_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    A programs/us_ramp/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_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/modelbuilder/us_modelbuilder.cpp
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    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/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_buffer.cpp
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_defines.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h
    M utils/us_gzip.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    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_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

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


  Commit: 148505e424408bdef6ae5fb53c753b8508191b5c
      https://github.com/ehb54/ultrascan3/commit/148505e424408bdef6ae5fb53c753b8508191b5c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-14 (Sun, 14 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  - Optimize scan processing logic in `us_xpn_data.cpp`
  - Use `QVector::reserve` to preallocate scan storage based on total scan count.
  - Refactor scan sorting to include `omega2t` as a tiebreaker for time.
  - Safeguard against empty scan arrays when accessing the last element.
- Fix typo in comments ("incase" ? "in case").


  Commit: 5fa8a71f76528dc06f16fa456f07507966e64751
      https://github.com/ehb54/ultrascan3/commit/5fa8a71f76528dc06f16fa456f07507966e64751
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-12-15 (Mon, 15 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #334 from ehb54/lukas/us_xpn_viewer_timestate

Increase precision/coverage for us_xpn_viewer generated timestates


  Commit: c3955b4314255b88df4e2a3348f620b8439c6ac6
      https://github.com/ehb54/ultrascan3/commit/c3955b4314255b88df4e2a3348f620b8439c6ac6
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


Compare: https://github.com/ehb54/ultrascan3/compare/70e83bb9142d...c3955b431425

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From noreply at github.com  Wed Dec 17 10:29:26 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 09:29:26 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/000000-5fa8a7@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Dec 17 10:49:29 2025
From: noreply at github.com (ehb54)
Date: Wed, 17 Dec 2025 09:49:29 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4bafd3: Update compiler flags and
 defines in local.pri.somo
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/46434a-4bafd3@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4bafd3f55ff93229f51bcd4cd0ece35195af707c
      https://github.com/ehb54/ultrascan3/commit/4bafd3f55ff93229f51bcd4cd0ece35195af707c
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Update compiler flags and defines in local.pri.somo



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From noreply at github.com  Wed Dec 17 11:42:30 2025
From: noreply at github.com (ehb54)
Date: Wed, 17 Dec 2025 10:42:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 0dfac5: somo fix for datetime in
 dirhist
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/426acc-0dfac5@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0dfac5414e8867092d438dd11cbce1b1bab59e9c
      https://github.com/ehb54/ultrascan3/commit/0dfac5414e8867092d438dd11cbce1b1bab59e9c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo fix for datetime in dirhist



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From noreply at github.com  Wed Dec 17 11:58:00 2025
From: noreply at github.com (ehb54)
Date: Wed, 17 Dec 2025 10:58:00 -0800
Subject: [us-commits] [ehb54/ultrascan3] a7e3fd: somo datetime dirhist fix
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/4bafd3-a7e3fd@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a7e3fd4276bf018f3e37d73c4e11598037b8d409
      https://github.com/ehb54/ultrascan3/commit/a7e3fd4276bf018f3e37d73c4e11598037b8d409
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo datetime dirhist fix



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From noreply at github.com  Wed Dec 17 12:06:13 2025
From: noreply at github.com (ehb54)
Date: Wed, 17 Dec 2025 11:06:13 -0800
Subject: [us-commits] [ehb54/ultrascan3] 34d353: Clean up deprecated warning
 flags in local.pri.somo
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/a7e3fd-34d353@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
      https://github.com/ehb54/ultrascan3/commit/34d3536c8fd88c19ef2ecf8c3a1d440cfc915abf
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M admin/codeql/docker/local.pri.somo

  Log Message:
  -----------
  Clean up deprecated warning flags in local.pri.somo

Removed deprecated warning definitions for Qt.



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From noreply at github.com  Wed Dec 17 13:25:10 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 12:25:10 -0800
Subject: [us-commits] [ehb54/ultrascan3] 75dc17: fix: version check for
 notices
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/5fa8a7-e02a51@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 75dc17665cd257146092a569f966700373e3c0b3
      https://github.com/ehb54/ultrascan3/commit/75dc17665cd257146092a569f966700373e3c0b3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-28 (Fri, 28 Nov 2025)

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

  Log Message:
  -----------
  fix: version check for notices


  Commit: 9e26d202aea3d0b07a3777f0f7955724c84e55b8
      https://github.com/ehb54/ultrascan3/commit/9e26d202aea3d0b07a3777f0f7955724c84e55b8
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-10 (Wed, 10 Dec 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: 25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
      https://github.com/ehb54/ultrascan3/commit/25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  fix: version check for notices restricted to major.minor


  Commit: 70e83bb9142d7fb78b9a37fc95e1ad669986270e
      https://github.com/ehb54/ultrascan3/commit/70e83bb9142d7fb78b9a37fc95e1ad669986270e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

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


  Commit: c3955b4314255b88df4e2a3348f620b8439c6ac6
      https://github.com/ehb54/ultrascan3/commit/c3955b4314255b88df4e2a3348f620b8439c6ac6
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: e02a512dec8150c5aa1691cdbca496bc8fa36e80
      https://github.com/ehb54/ultrascan3/commit/e02a512dec8150c5aa1691cdbca496bc8fa36e80
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #329 from ehb54/notices-fix

fix: version check for notices


Compare: https://github.com/ehb54/ultrascan3/compare/5fa8a71f7652...e02a512dec81

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From noreply at github.com  Wed Dec 17 13:26:11 2025
From: noreply at github.com (ehb54)
Date: Wed, 17 Dec 2025 12:26:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] 75dc17: fix: version check for
 notices
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-qt6/34d353-87377f@github.com>

  Branch: refs/heads/somo-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 75dc17665cd257146092a569f966700373e3c0b3
      https://github.com/ehb54/ultrascan3/commit/75dc17665cd257146092a569f966700373e3c0b3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-28 (Fri, 28 Nov 2025)

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

  Log Message:
  -----------
  fix: version check for notices


  Commit: 9e26d202aea3d0b07a3777f0f7955724c84e55b8
      https://github.com/ehb54/ultrascan3/commit/9e26d202aea3d0b07a3777f0f7955724c84e55b8
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-10 (Wed, 10 Dec 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: 25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
      https://github.com/ehb54/ultrascan3/commit/25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  fix: version check for notices restricted to major.minor


  Commit: 70e83bb9142d7fb78b9a37fc95e1ad669986270e
      https://github.com/ehb54/ultrascan3/commit/70e83bb9142d7fb78b9a37fc95e1ad669986270e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

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


  Commit: c3955b4314255b88df4e2a3348f620b8439c6ac6
      https://github.com/ehb54/ultrascan3/commit/c3955b4314255b88df4e2a3348f620b8439c6ac6
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: e02a512dec8150c5aa1691cdbca496bc8fa36e80
      https://github.com/ehb54/ultrascan3/commit/e02a512dec8150c5aa1691cdbca496bc8fa36e80
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #329 from ehb54/notices-fix

fix: version check for notices


  Commit: 87377fece32656c6472a465a06493b17084169fe
      https://github.com/ehb54/ultrascan3/commit/87377fece32656c6472a465a06493b17084169fe
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into somo-qt6


Compare: https://github.com/ehb54/ultrascan3/compare/34d3536c8fd8...87377fece326

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From noreply at github.com  Wed Dec 17 16:35:57 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 15:35:57 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1d6b2a: mod: revision script to use
 git commit date and time
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/5fa8a7-1d6b2a@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1d6b2a17ebace2b32b7a84a8656e3f43c9efa8b4
      https://github.com/ehb54/ultrascan3/commit/1d6b2a17ebace2b32b7a84a8656e3f43c9efa8b4
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M programs/us/revision.sh

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



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From noreply at github.com  Wed Dec 17 16:36:22 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 15:36:22 -0800
Subject: [us-commits] [ehb54/ultrascan3] 75dc17: fix: version check for
 notices
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/1d6b2a-df7167@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 75dc17665cd257146092a569f966700373e3c0b3
      https://github.com/ehb54/ultrascan3/commit/75dc17665cd257146092a569f966700373e3c0b3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-28 (Fri, 28 Nov 2025)

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

  Log Message:
  -----------
  fix: version check for notices


  Commit: 9e26d202aea3d0b07a3777f0f7955724c84e55b8
      https://github.com/ehb54/ultrascan3/commit/9e26d202aea3d0b07a3777f0f7955724c84e55b8
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-10 (Wed, 10 Dec 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: 25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
      https://github.com/ehb54/ultrascan3/commit/25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  fix: version check for notices restricted to major.minor


  Commit: 70e83bb9142d7fb78b9a37fc95e1ad669986270e
      https://github.com/ehb54/ultrascan3/commit/70e83bb9142d7fb78b9a37fc95e1ad669986270e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

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


  Commit: c3955b4314255b88df4e2a3348f620b8439c6ac6
      https://github.com/ehb54/ultrascan3/commit/c3955b4314255b88df4e2a3348f620b8439c6ac6
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: e02a512dec8150c5aa1691cdbca496bc8fa36e80
      https://github.com/ehb54/ultrascan3/commit/e02a512dec8150c5aa1691cdbca496bc8fa36e80
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #329 from ehb54/notices-fix

fix: version check for notices


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/1d6b2a17ebac...df7167edd6a9

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From noreply at github.com  Wed Dec 17 20:04:01 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 19:04:01 -0800
Subject: [us-commits] [ehb54/ultrascan3] 463a20: mod: cmake update to use
 git commit date and time
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/df7167-463a20@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 463a20612262393b49dd4ca80148e0c0fcbeb108
      https://github.com/ehb54/ultrascan3/commit/463a20612262393b49dd4ca80148e0c0fcbeb108
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

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



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From noreply at github.com  Wed Dec 17 20:10:47 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 17 Dec 2025 19:10:47 -0800
Subject: [us-commits] [ehb54/ultrascan3] 89f3f3: fix: filename reverted
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/463a20-89f3f3@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 89f3f3c6557b041b72007f43decf13f661ceae2e
      https://github.com/ehb54/ultrascan3/commit/89f3f3c6557b041b72007f43decf13f661ceae2e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

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



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From noreply at github.com  Thu Dec 18 09:11:20 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 18 Dec 2025 08:11:20 -0800
Subject: [us-commits] [ehb54/ultrascan3] 75dc17: fix: version check for
 notices
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/d9f790-fa2314@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 75dc17665cd257146092a569f966700373e3c0b3
      https://github.com/ehb54/ultrascan3/commit/75dc17665cd257146092a569f966700373e3c0b3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-28 (Fri, 28 Nov 2025)

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

  Log Message:
  -----------
  fix: version check for notices


  Commit: 9e26d202aea3d0b07a3777f0f7955724c84e55b8
      https://github.com/ehb54/ultrascan3/commit/9e26d202aea3d0b07a3777f0f7955724c84e55b8
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-10 (Wed, 10 Dec 2025)

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

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: 25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
      https://github.com/ehb54/ultrascan3/commit/25e92ef951c10aebddb0ef9dc4f91528ee6fcfa8
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  fix: version check for notices restricted to major.minor


  Commit: 70e83bb9142d7fb78b9a37fc95e1ad669986270e
      https://github.com/ehb54/ultrascan3/commit/70e83bb9142d7fb78b9a37fc95e1ad669986270e
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

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


  Commit: c3955b4314255b88df4e2a3348f620b8439c6ac6
      https://github.com/ehb54/ultrascan3/commit/c3955b4314255b88df4e2a3348f620b8439c6ac6
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge branch 'main' into notices-fix


  Commit: e02a512dec8150c5aa1691cdbca496bc8fa36e80
      https://github.com/ehb54/ultrascan3/commit/e02a512dec8150c5aa1691cdbca496bc8fa36e80
  Author: aaron-auc <95181880+aaron-auc at users.noreply.github.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

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

  Log Message:
  -----------
  Merge pull request #329 from ehb54/notices-fix

fix: version check for notices


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/d9f790e9a362...fa23140e88f2

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From noreply at github.com  Thu Dec 18 11:18:59 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 18 Dec 2025 10:18:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] 6d0e03: fix: only show delta on
 tracked file changes
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/89f3f3-6d0e03@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6d0e037362d1d3eee6b34d6c87fecb03ed56bc35
      https://github.com/ehb54/ultrascan3/commit/6d0e037362d1d3eee6b34d6c87fecb03ed56bc35
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

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

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



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From noreply at github.com  Thu Dec 18 13:08:24 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 18 Dec 2025 12:08:24 -0800
Subject: [us-commits] [ehb54/ultrascan3] 8cd250: fix: check tracked file
 changes
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/6d0e03-8cd250@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8cd2500e840339baf525a08fb150964ec3355fc0
      https://github.com/ehb54/ultrascan3/commit/8cd2500e840339baf525a08fb150964ec3355fc0
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

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

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



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From noreply at github.com  Thu Dec 18 13:25:21 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 18 Dec 2025 12:25:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] 107cb2: fix: remove build term from
 splash
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/8cd250-107cb2@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 107cb20eb507bf616842dd36d780663f6d20549a
      https://github.com/ehb54/ultrascan3/commit/107cb20eb507bf616842dd36d780663f6d20549a
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

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



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From noreply at github.com  Thu Dec 18 13:34:32 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 18 Dec 2025 12:34:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] 040225: fix: time was not in utc
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/107cb2-040225@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 040225ce1b554cde2af83441f8507e05ef14962b
      https://github.com/ehb54/ultrascan3/commit/040225ce1b554cde2af83441f8507e05ef14962b
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

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

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



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From noreply at github.com  Thu Dec 18 17:07:47 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 18 Dec 2025 16:07:47 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/666-bug-icons-dont-fill-space-on-new-macos/000000-e02a51@github.com>

  Branch: refs/heads/666-bug-icons-dont-fill-space-on-new-macos
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Dec 18 19:29:32 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 18 Dec 2025 18:29:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] ef6f3b: mod: icons remove border
Message-ID: <ehb54/ultrascan3/push/refs/heads/666-bug-icons-dont-fill-space-on-new-macos/e02a51-ef6f3b@github.com>

  Branch: refs/heads/666-bug-icons-dont-fill-space-on-new-macos
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ef6f3bd3f96408decfe78facbf37acadc5834997
      https://github.com/ehb54/ultrascan3/commit/ef6f3bd3f96408decfe78facbf37acadc5834997
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

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

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



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From noreply at github.com  Thu Dec 18 19:50:54 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 18 Dec 2025 18:50:54 -0800
Subject: [us-commits] [ehb54/ultrascan3] b18cfd: mod: update about info
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/040225-b18cfd@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b18cfde249b29b29b8733d537141a5ff3524407f
      https://github.com/ehb54/ultrascan3/commit/b18cfde249b29b29b8733d537141a5ff3524407f
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-18 (Thu, 18 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

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



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From noreply at github.com  Fri Dec 19 06:46:20 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 19 Dec 2025 05:46:20 -0800
Subject: [us-commits] [ehb54/ultrascan3] df5ad6: - Replace `images.qrc` with
 dynamically generated ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/fa2314-df5ad6@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: df5ad6ee3ef0ca36aa3672b571d5cccea0856c20
      https://github.com/ehb54/ultrascan3/commit/df5ad6ee3ef0ca36aa3672b571d5cccea0856c20
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

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

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



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From noreply at github.com  Fri Dec 19 06:52:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 19 Dec 2025 05:52:59 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/legacy_data_import/000000-e02a51@github.com>

  Branch: refs/heads/lukas/legacy_data_import
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Dec 19 07:29:27 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 19 Dec 2025 06:29:27 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5b2c72: Change runType assignment
 from values to keys
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/legacy_data_import/e02a51-5b2c72@github.com>

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

  Changed paths:
    M gui/us_convert_gui.cpp

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



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From noreply at github.com  Fri Dec 19 07:31:04 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 19 Dec 2025 06:31:04 -0800
Subject: [us-commits] [ehb54/ultrascan3] 002ebf: Change runtype assignment
 from values to keys
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/legacy_data_import/5b2c72-002ebf@github.com>

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

  Changed paths:
    M programs/us_legacy_converter/us_legacy_converter.cpp

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



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From noreply at github.com  Fri Dec 19 10:30:23 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 19 Dec 2025 09:30:23 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5b2c72: Change runType assignment
 from values to keys
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/e02a51-4fed5b@github.com>

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

  Changed paths:
    M gui/us_convert_gui.cpp

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


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

  Changed paths:
    M programs/us_legacy_converter/us_legacy_converter.cpp

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


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

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

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

Fix import from legacy data


Compare: https://github.com/ehb54/ultrascan3/compare/e02a512dec81...4fed5b3095bf

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From noreply at github.com  Fri Dec 19 10:30:26 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 19 Dec 2025 09:30:26 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/legacy_data_import/002ebf-000000@github.com>

  Branch: refs/heads/lukas/legacy_data_import
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Dec 19 10:44:30 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 19 Dec 2025 09:44:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5b2c72: Change runType assignment
 from values to keys
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/df5ad6-d12fce@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5b2c72b8ee1af841045b5f6f313d4a390fa6e786
      https://github.com/ehb54/ultrascan3/commit/5b2c72b8ee1af841045b5f6f313d4a390fa6e786
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.cpp

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


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

  Changed paths:
    M programs/us_legacy_converter/us_legacy_converter.cpp

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


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

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

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

Fix import from legacy data


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/df5ad6ee3ef0...d12fcee27d2f

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From noreply at github.com  Sat Dec 20 14:43:24 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 20 Dec 2025 13:43:24 -0800
Subject: [us-commits] [ehb54/ultrascan3] 7c33cc: add: additional authors
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/b18cfd-7c33cc@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7c33cc761e271a6cb89b3002c67bfd0ac5f406c9
      https://github.com/ehb54/ultrascan3/commit/7c33cc761e271a6cb89b3002c67bfd0ac5f406c9
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-20 (Sat, 20 Dec 2025)

  Changed paths:
    M programs/us/us.cpp

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



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From noreply at github.com  Sat Dec 20 15:13:33 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 20 Dec 2025 14:13:33 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5b2c72: Change runType assignment
 from values to keys
Message-ID: <ehb54/ultrascan3/push/refs/heads/670-bug-us_revisionh-dependency-issue/7c33cc-81762a@github.com>

  Branch: refs/heads/670-bug-us_revisionh-dependency-issue
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5b2c72b8ee1af841045b5f6f313d4a390fa6e786
      https://github.com/ehb54/ultrascan3/commit/5b2c72b8ee1af841045b5f6f313d4a390fa6e786
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-19 (Fri, 19 Dec 2025)

  Changed paths:
    M gui/us_convert_gui.cpp

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


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

  Changed paths:
    M programs/us_legacy_converter/us_legacy_converter.cpp

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


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

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

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

Fix import from legacy data


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/7c33cc761e27...81762adc9c91

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From noreply at github.com  Mon Dec 22 10:26:12 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 22 Dec 2025 09:26:12 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1d6b2a: mod: revision script to use
 git commit date and time
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/4fed5b-4f98a6@github.com>

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

  Changed paths:
    M programs/us/revision.sh

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

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

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

git commit date and time


Compare: https://github.com/ehb54/ultrascan3/compare/4fed5b3095bf...4f98a669ba7f

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From noreply at github.com  Mon Dec 22 15:53:51 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 22 Dec 2025 14:53:51 -0800
Subject: [us-commits] [ehb54/us3lims_dbinst] e03df8: Implement job selection
 features with persistent s...
Message-ID: <ehb54/us3lims_dbinst/push/refs/heads/queue_viewer_update/000000-e03df8@github.com>

  Branch: refs/heads/queue_viewer_update
  Home:   https://github.com/ehb54/us3lims_dbinst
  Commit: e03df8e2bbc3934c8e48c2fceded14dab08f72cb
      https://github.com/ehb54/us3lims_dbinst/commit/e03df8e2bbc3934c8e48c2fceded14dab08f72cb
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-22 (Mon, 22 Dec 2025)

  Changed paths:
    M css/queue_viewer.css
    M js/queue_viewer.js
    M queue_content.php
    M queue_viewer.php

  Log Message:
  -----------
  Implement job selection features with persistent state and bulk actions

- Added JavaScript utilities to support selection toggling at granular levels (job, run, analysis type, status).
- Introduced session-based persistence for job selections via `sessionStorage`.
- Enhanced queue content with a summary table and controls for selection and bulk deletion.
- Updated PHP backend to handle authorized job deletions with new helper functions.
- Adjusted CSS for improved styling and layout of the selection UI.



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From noreply at github.com  Mon Dec 22 16:29:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 22 Dec 2025 15:29:59 -0800
Subject: [us-commits] [ehb54/us3lims_dbinst] 3a3da7: Improve validation,
 HTML escaping, and resource cl...
Message-ID: <ehb54/us3lims_dbinst/push/refs/heads/queue_viewer_update/e03df8-3a3da7@github.com>

  Branch: refs/heads/queue_viewer_update
  Home:   https://github.com/ehb54/us3lims_dbinst
  Commit: 3a3da767a02243522c73d06775fdff8d3dc1c470
      https://github.com/ehb54/us3lims_dbinst/commit/3a3da767a02243522c73d06775fdff8d3dc1c470
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-23 (Tue, 23 Dec 2025)

  Changed paths:
    M js/queue_viewer.js
    M queue_content.php
    M queue_viewer.php

  Log Message:
  -----------
  Improve validation, HTML escaping, and resource cleanup in queue management

- Added checks for undefined `gfacID` in `queue_viewer.php` to prevent errors on missing POST data.
- Escaped HTML special characters in `queue_content.php` to prevent injection vulnerabilities.
- Ensured proper cleanup of database resources with added `mysqli_close()` calls.
- Refactored JavaScript form creation in `queue_viewer.js` for better readability and consistency.



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From noreply at github.com  Tue Dec 23 02:32:56 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 23 Dec 2025 01:32:56 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1d6b2a: mod: revision script to use
 git commit date and time
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/d12fce-bf5c79@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1d6b2a17ebace2b32b7a84a8656e3f43c9efa8b4
      https://github.com/ehb54/ultrascan3/commit/1d6b2a17ebace2b32b7a84a8656e3f43c9efa8b4
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-12-17 (Wed, 17 Dec 2025)

  Changed paths:
    M programs/us/revision.sh

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

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

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

git commit date and time


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/d12fcee27d2f...bf5c7965f6f3

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From noreply at github.com  Mon Dec 29 02:07:16 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 01:07:16 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/000000-4f98a6@github.com>

  Branch: refs/heads/lukas/db_connection
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Dec 29 03:46:54 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 02:46:54 -0800
Subject: [us-commits] [ehb54/ultrascan3] aede93: Refactor SSL configuration
 in `us_db2.cpp`:
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/4f98a6-f719fc@github.com>

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

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

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

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


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

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

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

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


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

  Changed paths:
    M CMakeLists.txt

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


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

  Changed paths:
    M programs/CMakeLists.txt

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


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

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

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

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


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

  Changed paths:
    M gui/CMakeLists.txt

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


Compare: https://github.com/ehb54/ultrascan3/compare/4f98a669ba7f...f719fc16c1a0

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From noreply at github.com  Mon Dec 29 04:09:36 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 03:09:36 -0800
Subject: [us-commits] [ehb54/ultrascan3] 33e95b: Set minimum TLS version for
 database connection
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/f719fc-33e95b@github.com>

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

  Changed paths:
    M utils/us_db2.cpp

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

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



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From noreply at github.com  Mon Dec 29 04:23:00 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 03:23:00 -0800
Subject: [us-commits] [ehb54/ultrascan3] b2c3bf: Cleanup
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/33e95b-b2c3bf@github.com>

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

  Changed paths:
    M utils/us_db2.cpp

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



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From noreply at github.com  Mon Dec 29 04:30:56 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 03:30:56 -0800
Subject: [us-commits] [ehb54/ultrascan3] 67c9dc: Fix parameter name from
 'error' to 'err'
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/b2c3bf-67c9dc@github.com>

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

  Changed paths:
    M utils/ius_db2.h

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



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From noreply at github.com  Mon Dec 29 04:48:45 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 03:48:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] 56eb2d: Add noise reuse option in
 2D analysis and update d...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_2dsa_noise_reuse/000000-56eb2d@github.com>

  Branch: refs/heads/lukas/us_2dsa_noise_reuse
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 56eb2dc2ac1fbc68361d95e211e3b4ca6caa2a08
      https://github.com/ehb54/ultrascan3/commit/56eb2dc2ac1fbc68361d95e211e3b4ca6caa2a08
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-12-29 (Mon, 29 Dec 2025)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa.h
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.h

  Log Message:
  -----------
  Add noise reuse option in 2D analysis and update data handling logic

- Introduce `reuse_ti_noise` and `reuse_ri_noise` flags for 2D analysis.
- Add user prompts to reuse time-invariant and radially invariant noises.
- Implement logic to apply and combine previously used noise corrections.
- Update `us_2dsa` and `us_analysis_control_2d` to manage noise reuse across datasets.
- Extend noise-related accessors in `us_2dsa.h` and `us_2dsa.cpp` for consistency.



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From noreply at github.com  Mon Dec 29 05:20:26 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 04:20:26 -0800
Subject: [us-commits] [ehb54/ultrascan3] e7e29e: Prevent accessing the
 second channel in a one chan...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/67c9dc-4f95fa@github.com>

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

  Changed paths:
    M test/utils/test_us_simparms.cpp

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

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


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

  Changed paths:
    M test/utils/test_us_ana_profile.cpp

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


Compare: https://github.com/ehb54/ultrascan3/compare/67c9dc8ad7b8...4f95fa8faa84

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From noreply at github.com  Mon Dec 29 08:45:07 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 29 Dec 2025 07:45:07 -0800
Subject: [us-commits] [ehb54/ultrascan3] c8038b: Update `us_utils` to
 enforce symbol visibility and...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/4f95fa-abc1f5@github.com>

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

  Changed paths:
    M utils/CMakeLists.txt

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

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

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


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

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

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

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

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


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

  Changed paths:
    M gui/CMakeLists.txt

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

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


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

  Changed paths:
    M CMakeLists.txt

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/4f95fa8faa84...abc1f5a67e0e

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From noreply at github.com  Tue Dec 30 11:28:19 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 30 Dec 2025 10:28:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1e5681: Add VCPKG_TARGET_TRIPLET
 for Linux dynamic build
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/abc1f5-1e5681@github.com>

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

  Changed paths:
    M CMakePresets.json

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



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From noreply at github.com  Wed Dec 31 08:36:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 31 Dec 2025 07:36:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] a6e209: Refine TLS cipher suite
 definition for enhanced se...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/db_connection/1e5681-a6e209@github.com>

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

  Changed paths:
    M utils/us_db2.cpp

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

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



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