From noreply at github.com  Fri Aug  1 10:23:59 2025
From: noreply at github.com (ehb54)
Date: Fri, 01 Aug 2025 09:23:59 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2ab1a9: us-somo zeno->grpy
 correction updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/8702b2-2ab1a9@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2ab1a941849f8aee3c94ba3f7e692fbfda52ef45
      https://github.com/ehb54/ultrascan3/commit/2ab1a941849f8aee3c94ba3f7e692fbfda52ef45
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates



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From noreply at github.com  Fri Aug  1 10:48:45 2025
From: noreply at github.com (ehb54)
Date: Fri, 01 Aug 2025 09:48:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] ee6956: us-somo zeno->grpy
 correction updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/2ab1a9-ee6956@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ee69567c7ab180c096bdeb67db144ce052048ad1
      https://github.com/ehb54/ultrascan3/commit/ee69567c7ab180c096bdeb67db144ce052048ad1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates



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From noreply at github.com  Fri Aug  1 12:12:30 2025
From: noreply at github.com (ehb54)
Date: Fri, 01 Aug 2025 11:12:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] df3a3a: us-somo zeno->grpy
 correction updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/ee6956-df3a3a@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: df3a3ad7241f33bb76428e8112bbf0482d83bb04
      https://github.com/ehb54/ultrascan3/commit/df3a3ad7241f33bb76428e8112bbf0482d83bb04
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates



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From noreply at github.com  Fri Aug  1 12:55:08 2025
From: noreply at github.com (ehb54)
Date: Fri, 01 Aug 2025 11:55:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] a259b5: us-somo zeno->grpy
 correction updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/df3a3a-a259b5@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a259b56bfd6fc7a27f62bdb56ab6ead4c5fdf171
      https://github.com/ehb54/ultrascan3/commit/a259b56bfd6fc7a27f62bdb56ab6ead4c5fdf171
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates



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From noreply at github.com  Fri Aug  1 14:42:02 2025
From: noreply at github.com (ehb54)
Date: Fri, 01 Aug 2025 13:42:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9de837: us-somo zeno->grpy
 correction updates + initial re...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/a259b5-9de837@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9de837704453a79801374a02546ec1cff5061827
      https://github.com/ehb54/ultrascan3/commit/9de837704453a79801374a02546ec1cff5061827
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates + initial release prep



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From noreply at github.com  Fri Aug  1 14:44:13 2025
From: noreply at github.com (ehb54)
Date: Fri, 01 Aug 2025 13:44:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] 74311e: us-somo zeno->grpy
 correction updates + initial re...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/9de837-74311e@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 74311ec13888bf5cb371e625aa26aae0000691e2
      https://github.com/ehb54/ultrascan3/commit/74311ec13888bf5cb371e625aa26aae0000691e2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn.h

  Log Message:
  -----------
  us-somo zeno->grpy correction updates + initial release prep



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From noreply at github.com  Sat Aug  2 13:51:45 2025
From: noreply at github.com (HabGab)
Date: Sat, 02 Aug 2025 12:51:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] aa918d: markdown added
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/e7ad3b-2f8beb@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: aa918dec3338b048c1de82cbfe15e20ae6c69e55
      https://github.com/ehb54/ultrascan3/commit/aa918dec3338b048c1de82cbfe15e20ae6c69e55
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    A doc/manual/markdown/build/doctrees/environment.pickle
    A doc/manual/markdown/build/doctrees/fit_meniscus.doctree
    A doc/manual/markdown/build/doctrees/index.doctree
    A doc/manual/markdown/build/html/_downloads/81fb45f7b6931fba574ce783ce0281cc/fit_men-load.img.html
    A doc/manual/markdown/build/html/_images/fit_meniscus.png
    A doc/manual/markdown/build/html/_sources/fit_meniscus.md.txt
    A doc/manual/markdown/build/html/_sources/index.md.txt
    A doc/manual/markdown/build/html/_static/alabaster.css
    A doc/manual/markdown/build/html/_static/basic.css
    A doc/manual/markdown/build/html/_static/custom.css
    A doc/manual/markdown/build/html/_static/doctools.js
    A doc/manual/markdown/build/html/_static/documentation_options.js
    A doc/manual/markdown/build/html/_static/file.png
    A doc/manual/markdown/build/html/_static/language_data.js
    A doc/manual/markdown/build/html/_static/minus.png
    A doc/manual/markdown/build/html/_static/plus.png
    A doc/manual/markdown/build/html/_static/pygments.css
    A doc/manual/markdown/build/html/_static/searchtools.js
    A doc/manual/markdown/build/html/_static/sphinx_highlight.js
    A doc/manual/markdown/build/html/fit_meniscus.html
    A doc/manual/markdown/build/html/genindex.html
    A doc/manual/markdown/build/html/index.html
    A doc/manual/markdown/build/html/objects.inv
    A doc/manual/markdown/build/html/search.html
    A doc/manual/markdown/build/html/searchindex.js
    A doc/manual/markdown/make.bat
    A doc/manual/markdown/source/conf.py
    A doc/manual/markdown/source/fit_meniscus.md
    A doc/manual/markdown/source/index.md
    M doc/manual/sphinx/build/doctrees/environment.pickle
    A doc/manual/sphinx/build/doctrees/fit_meniscus.doctree
    M doc/manual/sphinx/build/doctrees/index.doctree
    M doc/manual/sphinx/build/doctrees/time_derivative.doctree
    M doc/manual/sphinx/build/doctrees/us_edit.doctree
    M doc/manual/sphinx/build/doctrees/us_edit_mwl.doctree
    A doc/manual/sphinx/build/html/_images/fit_men-editupd.png
    A doc/manual/sphinx/build/html/_images/fit_meniscus.png
    A doc/manual/sphinx/build/html/_images/time_derivative.png
    A doc/manual/sphinx/build/html/_images/us_edit_mwl.png
    A doc/manual/sphinx/build/html/_sources/fit_meniscus.rst.txt
    A doc/manual/sphinx/build/html/_sources/index.md.txt
    M doc/manual/sphinx/build/html/_sources/index.rst.txt
    M doc/manual/sphinx/build/html/_sources/time_derivative.rst.txt
    A doc/manual/sphinx/build/html/_sources/us_edit.md.txt
    M doc/manual/sphinx/build/html/_sources/us_edit.rst.txt
    M doc/manual/sphinx/build/html/_sources/us_edit_mwl.rst.txt
    M doc/manual/sphinx/build/html/_static/custom.css
    A doc/manual/sphinx/build/html/_static/images/Screenshot from 2025-07-31 13-12-02.png
    M doc/manual/sphinx/build/html/_static/images/fit_men-editupd.png
    M doc/manual/sphinx/build/html/_static/images/fit_meniscus.png
    M doc/manual/sphinx/build/html/_static/images/time_derivative.png
    M doc/manual/sphinx/build/html/_static/images/us_edit_mwl.png
    A doc/manual/sphinx/build/html/fit_meniscus.html
    M doc/manual/sphinx/build/html/index.html
    M doc/manual/sphinx/build/html/objects.inv
    M doc/manual/sphinx/build/html/searchindex.js
    M doc/manual/sphinx/build/html/time_derivative.html
    M doc/manual/sphinx/build/html/us_edit.html
    M doc/manual/sphinx/source/USstatic/custom.css
    A doc/manual/sphinx/source/USstatic/images/Screenshot from 2025-07-31 13-12-02.png
    M doc/manual/sphinx/source/USstatic/images/fit_men-editupd.png
    M doc/manual/sphinx/source/USstatic/images/fit_meniscus.png
    M doc/manual/sphinx/source/USstatic/images/time_derivative.png
    M doc/manual/sphinx/source/USstatic/images/us_edit_mwl.png
    M doc/manual/sphinx/source/conf.py
    A doc/manual/sphinx/source/fit_meniscus.rst
    M doc/manual/sphinx/source/index.rst
    M doc/manual/sphinx/source/time_derivative.rst
    M doc/manual/sphinx/source/us_edit.rst
    R doc/manual/sphinx/source/us_edit_mwl.rst

  Log Message:
  -----------
  markdown added


  Commit: f5745d6e2b6d5251c9495e0ce8f2cbaded00682f
      https://github.com/ehb54/ultrascan3/commit/f5745d6e2b6d5251c9495e0ce8f2cbaded00682f
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M doc/manual/markdown/build/doctrees/environment.pickle
    M doc/manual/markdown/build/doctrees/fit_meniscus.doctree
    M doc/manual/markdown/build/html/_sources/fit_meniscus.md.txt
    M doc/manual/markdown/build/html/fit_meniscus.html
    M doc/manual/markdown/build/html/index.html
    M doc/manual/markdown/build/html/objects.inv
    M doc/manual/markdown/build/html/searchindex.js
    M doc/manual/markdown/source/fit_meniscus.md

  Log Message:
  -----------
  markdown added


  Commit: 2f8beb1884a6c384767563f61a4d389f8d9d65f7
      https://github.com/ehb54/ultrascan3/commit/2f8beb1884a6c384767563f61a4d389f8d9d65f7
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M doc/manual/sphinx/build/doctrees/environment.pickle
    M doc/manual/sphinx/build/doctrees/fit_meniscus.doctree
    M doc/manual/sphinx/build/doctrees/index.doctree
    M doc/manual/sphinx/build/doctrees/time_derivative.doctree
    M doc/manual/sphinx/build/doctrees/us_edit.doctree
    M doc/manual/sphinx/build/html/_sources/advanced_config.rst.txt
    M doc/manual/sphinx/build/html/_sources/index.rst.txt
    M doc/manual/sphinx/build/html/_sources/time_derivative.rst.txt
    M doc/manual/sphinx/build/html/_sources/us_edit.rst.txt
    M doc/manual/sphinx/build/html/_static/basic.css
    M doc/manual/sphinx/build/html/_static/doctools.js
    M doc/manual/sphinx/build/html/_static/documentation_options.js
    M doc/manual/sphinx/build/html/_static/haiku.css
    M doc/manual/sphinx/build/html/_static/images/vhw_enh_groups.png
    M doc/manual/sphinx/build/html/_static/pygments.css
    M doc/manual/sphinx/build/html/_static/searchtools.js
    M doc/manual/sphinx/build/html/fit_meniscus.html
    M doc/manual/sphinx/build/html/genindex.html
    M doc/manual/sphinx/build/html/index.html
    M doc/manual/sphinx/build/html/objects.inv
    M doc/manual/sphinx/build/html/search.html
    M doc/manual/sphinx/build/html/searchindex.js
    M doc/manual/sphinx/build/html/time_derivative.html
    M doc/manual/sphinx/build/html/us_edit.html
    M doc/manual/sphinx/source/USstatic/images/vhw_enh_groups.png
    M doc/manual/sphinx/source/conf.py
    M doc/manual/sphinx/source/index.rst
    M doc/manual/sphinx/source/time_derivative.rst
    M doc/manual/sphinx/source/us_edit.rst

  Log Message:
  -----------
  sphinx


Compare: https://github.com/ehb54/ultrascan3/compare/e7ad3b9156ab...2f8beb1884a6

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From noreply at github.com  Sat Aug  2 14:34:58 2025
From: noreply at github.com (HabGab)
Date: Sat, 02 Aug 2025 13:34:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] c95888: markdown
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/2f8beb-c95888@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c958884e9725693d2282311a67a18acb98995874
      https://github.com/ehb54/ultrascan3/commit/c958884e9725693d2282311a67a18acb98995874
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-02 (Sat, 02 Aug 2025)

  Changed paths:
    M doc/manual/markdown/build/doctrees/environment.pickle
    M doc/manual/markdown/build/doctrees/index.doctree
    M doc/manual/markdown/build/html/_sources/index.md.txt
    M doc/manual/markdown/build/html/fit_meniscus.html
    M doc/manual/markdown/build/html/genindex.html
    M doc/manual/markdown/build/html/index.html
    M doc/manual/markdown/build/html/objects.inv
    M doc/manual/markdown/build/html/search.html
    M doc/manual/markdown/build/html/searchindex.js
    M doc/manual/markdown/source/index.md
    M doc/manual/sphinx/build/doctrees/environment.pickle
    M doc/manual/sphinx/build/doctrees/index.doctree
    M doc/manual/sphinx/build/doctrees/time_derivative.doctree
    M doc/manual/sphinx/build/html/_sources/index.rst.txt
    M doc/manual/sphinx/build/html/_sources/time_derivative.rst.txt
    M doc/manual/sphinx/build/html/_static/images/2dsa_main-o.png
    M doc/manual/sphinx/build/html/_static/images/second_moment.png
    M doc/manual/sphinx/build/html/_static/images/vhw_combine-combo.png
    M doc/manual/sphinx/build/html/_static/images/vhw_combine-envel.png
    M doc/manual/sphinx/build/html/_static/images/vhw_combine-selrun.png
    M doc/manual/sphinx/build/html/_static/images/vhw_combine.png
    M doc/manual/sphinx/build/html/_static/images/vhw_distribution.png
    M doc/manual/sphinx/build/html/_static/images/vhw_histogram.png
    M doc/manual/sphinx/build/html/fit_meniscus.html
    M doc/manual/sphinx/build/html/index.html
    M doc/manual/sphinx/build/html/objects.inv
    M doc/manual/sphinx/build/html/searchindex.js
    M doc/manual/sphinx/build/html/time_derivative.html
    M doc/manual/sphinx/source/USstatic/images/2dsa_main-o.png
    R doc/manual/sphinx/source/USstatic/images/Screenshot from 2025-07-31 13-12-02.png
    M doc/manual/sphinx/source/USstatic/images/second_moment.png
    M doc/manual/sphinx/source/USstatic/images/vhw_combine-combo.png
    M doc/manual/sphinx/source/USstatic/images/vhw_combine-envel.png
    M doc/manual/sphinx/source/USstatic/images/vhw_combine-selrun.png
    M doc/manual/sphinx/source/USstatic/images/vhw_combine.png
    M doc/manual/sphinx/source/USstatic/images/vhw_distribution.png
    M doc/manual/sphinx/source/USstatic/images/vhw_histogram.png
    M doc/manual/sphinx/source/conf.py
    M doc/manual/sphinx/source/index.rst
    M doc/manual/sphinx/source/time_derivative.rst

  Log Message:
  -----------
  markdown



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From noreply at github.com  Sun Aug  3 18:41:44 2025
From: noreply at github.com (aaron-auc)
Date: Sun, 03 Aug 2025 17:41:44 -0700
Subject: [us-commits] [ehb54/ultrascan3] c10302: integrated sphinx into build
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/c95888-c10302@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c10302ac27ce017dfd04619905f79264c0c96d62
      https://github.com/ehb54/ultrascan3/commit/c10302ac27ce017dfd04619905f79264c0c96d62
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-03 (Sun, 03 Aug 2025)

  Changed paths:
    M .gitignore
    R doc/manual/Makefile
    R doc/manual/html
    R doc/manual/make-docs.sh
    R doc/manual/make-html.sh
    R doc/manual/make-qdocs.sh
    R doc/manual/make-wraps.sh
    R doc/manual/markdown/build/doctrees/environment.pickle
    R doc/manual/markdown/build/doctrees/fit_meniscus.doctree
    R doc/manual/markdown/build/doctrees/index.doctree
    R doc/manual/markdown/build/html/_downloads/81fb45f7b6931fba574ce783ce0281cc/fit_men-load.img.html
    R doc/manual/markdown/build/html/_images/fit_meniscus.png
    R doc/manual/markdown/build/html/_sources/fit_meniscus.md.txt
    R doc/manual/markdown/build/html/_sources/index.md.txt
    R doc/manual/markdown/build/html/_static/alabaster.css
    R doc/manual/markdown/build/html/_static/basic.css
    R doc/manual/markdown/build/html/_static/custom.css
    R doc/manual/markdown/build/html/_static/doctools.js
    R doc/manual/markdown/build/html/_static/documentation_options.js
    R doc/manual/markdown/build/html/_static/file.png
    R doc/manual/markdown/build/html/_static/language_data.js
    R doc/manual/markdown/build/html/_static/minus.png
    R doc/manual/markdown/build/html/_static/plus.png
    R doc/manual/markdown/build/html/_static/pygments.css
    R doc/manual/markdown/build/html/_static/searchtools.js
    R doc/manual/markdown/build/html/_static/sphinx_highlight.js
    R doc/manual/markdown/build/html/fit_meniscus.html
    R doc/manual/markdown/build/html/genindex.html
    R doc/manual/markdown/build/html/index.html
    R doc/manual/markdown/build/html/objects.inv
    R doc/manual/markdown/build/html/search.html
    R doc/manual/markdown/build/html/searchindex.js
    A doc/manual/source/_static/css/custom.css
    A doc/manual/source/_static/images/2dsa_3dplot.png
    A doc/manual/source/_static/images/2dsa_advan.png
    A doc/manual/source/_static/images/2dsa_analvv.png
    A doc/manual/source/_static/images/2dsa_analys.png
    A doc/manual/source/_static/images/2dsa_main-c.png
    A doc/manual/source/_static/images/2dsa_main-o.png
    A doc/manual/source/_static/images/2dsa_resplot.png
    A doc/manual/source/_static/images/advanced_config.png
    A doc/manual/source/_static/images/analyte_details.png
    A doc/manual/source/_static/images/analytes.png
    A doc/manual/source/_static/images/associations.png
    A doc/manual/source/_static/images/astfem_sim.png
    A doc/manual/source/_static/images/buffer_edit.png
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    A doc/manual/source/_static/images/buffer_settings.png
    A doc/manual/source/_static/images/cfa_view-loadauc.png
    A doc/manual/source/_static/images/cfa_view-loadraw.png
    A doc/manual/source/_static/images/cfa_view-main.png
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    A doc/manual/source/_static/images/color-1.png
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    R doc/manual/sphinx/build/html/fit_meniscus.html
    R doc/manual/sphinx/build/html/genindex.html
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    R doc/manual/sphinx/build/html/us_edit.html
    R doc/manual/sphinx/build/html/us_edit_mwl.html
    A venv/pyvenv.cfg

  Log Message:
  -----------
  integrated sphinx into build



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From noreply at github.com  Mon Aug  4 09:29:24 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 04 Aug 2025 08:29:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] e222b9: sphinx updated README with
 Makefiles
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/c10302-e222b9@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e222b9622e0f4f07342fb5bcf4bb161cb5fd0d54
      https://github.com/ehb54/ultrascan3/commit/e222b9622e0f4f07342fb5bcf4bb161cb5fd0d54
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    A doc/manual/Makefile
    M doc/manual/README
    A doc/manual/source/Makefile

  Log Message:
  -----------
  sphinx updated README with Makefiles



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From noreply at github.com  Mon Aug  4 09:33:01 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 08:33:01 -0700
Subject: [us-commits] [ehb54/ultrascan3] 519648: somo saxs - recompute chi2
 on guinier fit
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/74311e-519648@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5196481299a31808424a7cfd017d69be78eef175
      https://github.com/ehb54/ultrascan3/commit/5196481299a31808424a7cfd017d69be78eef175
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp

  Log Message:
  -----------
  somo saxs - recompute chi2 on guinier fit



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From noreply at github.com  Mon Aug  4 09:51:19 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 08:51:19 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4d0115: somo band broadening
 emg+gmg kernel - wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/638abb-05ca1b@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4d0115033f286a213ca9175b0c0cd85c1945004b
      https://github.com/ehb54/ultrascan3/commit/4d0115033f286a213ca9175b0c0cd85c1945004b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-02 (Mon, 02 Jun 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_unicode.h
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  somo band broadening emg+gmg kernel - wip


  Commit: e5fafb0ca110755f5a29e584cbebfa44cb75b52d
      https://github.com/ehb54/ultrascan3/commit/e5fafb0ca110755f5a29e584cbebfa44cb75b52d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-03 (Tue, 03 Jun 2025)

  Changed paths:
    M us_somo/develop/include/us_band_broaden.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  somo band broadening asymmetric laplace, emg+gmg kernel - wip


  Commit: 8f846e7088e8faf36ff3f5d36fe52a9aeb6024b1
      https://github.com/ehb54/ultrascan3/commit/8f846e7088e8faf36ff3f5d36fe52a9aeb6024b1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-03 (Tue, 03 Jun 2025)

  Changed paths:
    M us_somo/develop/include/us_band_broaden.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  somo band broadening asymmetric laplace, emg+gmg kernel - swap tau sigma function order, start of variable param set - wip


  Commit: 215d00b455df4cddc6826644e930ebb826122ae9
      https://github.com/ehb54/ultrascan3/commit/215d00b455df4cddc6826644e930ebb826122ae9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-03 (Tue, 03 Jun 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  somo band broadening asymmetric laplace, emg+gmg kernel - variable param set used - wip


  Commit: 494ab67a48ebb0ee911a445d9159d8504f47caa6
      https://github.com/ehb54/ultrascan3/commit/494ab67a48ebb0ee911a445d9159d8504f47caa6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-03 (Tue, 03 Jun 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  somo band broadening asymmetric laplace, emg+gmg kernel - variable fitting function - wip


  Commit: ddaff9b9efbfc3e0199addc9a9a1a2e9f0c4e409
      https://github.com/ehb54/ultrascan3/commit/ddaff9b9efbfc3e0199addc9a9a1a2e9f0c4e409
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-03 (Tue, 03 Jun 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  somo band broadening asymmetric laplace, emg+gmg kernel - lm fit callback - wip


  Commit: 15334321ce669e52fae4b5c8969732813bb7a1b3
      https://github.com/ehb54/ultrascan3/commit/15334321ce669e52fae4b5c8969732813bb7a1b3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-07 (Sat, 07 Jun 2025)

  Changed paths:
    M us_somo/develop/include/us_band_broaden.h
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  band broadening - EMGhG kernel - wip


  Commit: 0e5c7f0e6cedd80919d09fdebe02994e8e6084c9
      https://github.com/ehb54/ultrascan3/commit/0e5c7f0e6cedd80919d09fdebe02994e8e6084c9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-07 (Sat, 07 Jun 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  band broadening - EMGhG kernel - wip


  Commit: c846c81b6d90fb680ca593d950ffe0e6d47f4590
      https://github.com/ehb54/ultrascan3/commit/c846c81b6d90fb680ca593d950ffe0e6d47f4590
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-07 (Sat, 07 Jun 2025)

  Changed paths:
    M us_somo/develop/include/us_band_broaden.h

  Log Message:
  -----------
  band broadening - EMGhG kernel - wip


  Commit: f410f5d8eff5288b51a29ecd9b8da3db7663afc2
      https://github.com/ehb54/ultrascan3/commit/f410f5d8eff5288b51a29ecd9b8da3db7663afc2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-08 (Sun, 08 Jun 2025)

  Changed paths:
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp

  Log Message:
  -----------
  band broadening - reporting updates - wip


  Commit: d813daaec63d4b183af5ee9007fbe7fae761ff44
      https://github.com/ehb54/ultrascan3/commit/d813daaec63d4b183af5ee9007fbe7fae761ff44
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-06-18 (Wed, 18 Jun 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp

  Log Message:
  -----------
  somo sensible warning when filename is too long for GRPY


  Commit: 8702b2a6adb9f2da81ff4a1348271dfe59558fd5
      https://github.com/ehb54/ultrascan3/commit/8702b2a6adb9f2da81ff4a1348271dfe59558fd5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-07-31 (Thu, 31 Jul 2025)

  Changed paths:
    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_unicode.h
    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_settings.cpp
    M us_somo/develop/src/us_hydrodyn_util.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction


  Commit: 2ab1a941849f8aee3c94ba3f7e692fbfda52ef45
      https://github.com/ehb54/ultrascan3/commit/2ab1a941849f8aee3c94ba3f7e692fbfda52ef45
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates


  Commit: ee69567c7ab180c096bdeb67db144ce052048ad1
      https://github.com/ehb54/ultrascan3/commit/ee69567c7ab180c096bdeb67db144ce052048ad1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates


  Commit: df3a3ad7241f33bb76428e8112bbf0482d83bb04
      https://github.com/ehb54/ultrascan3/commit/df3a3ad7241f33bb76428e8112bbf0482d83bb04
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates


  Commit: a259b56bfd6fc7a27f62bdb56ab6ead4c5fdf171
      https://github.com/ehb54/ultrascan3/commit/a259b56bfd6fc7a27f62bdb56ab6ead4c5fdf171
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates


  Commit: 9de837704453a79801374a02546ec1cff5061827
      https://github.com/ehb54/ultrascan3/commit/9de837704453a79801374a02546ec1cff5061827
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  us-somo zeno->grpy correction updates + initial release prep


  Commit: 74311ec13888bf5cb371e625aa26aae0000691e2
      https://github.com/ehb54/ultrascan3/commit/74311ec13888bf5cb371e625aa26aae0000691e2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn.h

  Log Message:
  -----------
  us-somo zeno->grpy correction updates + initial release prep


  Commit: 5196481299a31808424a7cfd017d69be78eef175
      https://github.com/ehb54/ultrascan3/commit/5196481299a31808424a7cfd017d69be78eef175
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp

  Log Message:
  -----------
  somo saxs - recompute chi2 on guinier fit


  Commit: 05ca1b1480f02b5bc7229b6ddad43065db527da0
      https://github.com/ehb54/ultrascan3/commit/05ca1b1480f02b5bc7229b6ddad43065db527da0
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_band_broaden.h
    M us_somo/develop/include/us_hydrodyn.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_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_unicode.h
    M us_somo/develop/src/us_band_broaden.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_grpy.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_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_util.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  Merge pull request #245 from ehb54/somo-dev-bb-emggmg

merge somo-dev-bb-emggmg to somo-dev


Compare: https://github.com/ehb54/ultrascan3/compare/638abb9d9798...05ca1b1480f0

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From noreply at github.com  Mon Aug  4 09:51:25 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 08:51:25 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-bb-emggmg/519648-000000@github.com>

  Branch: refs/heads/somo-dev-bb-emggmg
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Aug  4 10:46:49 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 09:46:49 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5bc207: somo saxs - recompute chi2
 on guinier fit
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/05ca1b-5bc207@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5bc207f6758ab37734b6813b5d71d3d2f5e43efb
      https://github.com/ehb54/ultrascan3/commit/5bc207f6758ab37734b6813b5d71d3d2f5e43efb
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp

  Log Message:
  -----------
  somo saxs - recompute chi2 on guinier fit



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From noreply at github.com  Mon Aug  4 14:12:53 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 13:12:53 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/000000-5bc207@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Aug  4 14:14:45 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 13:14:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] 85e259: somo remove some deprecated
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/5bc207-85e259@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 85e259f45bc145d902c03f914f24c40d2f1c07e2
      https://github.com/ehb54/ultrascan3/commit/85e259f45bc145d902c03f914f24c40d2f1c07e2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us3i_util.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_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_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_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.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_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_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_modes_bb.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_modes_bb.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_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_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
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.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_modes_bb.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_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.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_plot_util.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_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_loads.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  somo remove some deprecated



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From noreply at github.com  Mon Aug  4 15:22:50 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 14:22:50 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0fc8fc: issue 533 : convert
 QString::sprintf to asprintf i...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-533/000000-0fc8fc@github.com>

  Branch: refs/heads/ehb54-issue-533
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0fc8fc48c10614b999f6720cdcc5ffeb354dd28f
      https://github.com/ehb54/ultrascan3/commit/0fc8fc48c10614b999f6720cdcc5ffeb354dd28f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M gui/us_analyte_gui.cpp
    M gui/us_data_loader.cpp
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_run_details2.cpp
    M gui/us_tmst_plot.cpp
    M gui/us_window_message.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

  Log Message:
  -----------
  issue 533 : convert QString::sprintf to asprintf in gui & programs



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From noreply at github.com  Mon Aug  4 16:07:25 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 15:07:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] 54079b: issue 533 : convert QString
 - varname.sprintf to v...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-533/0fc8fc-54079b@github.com>

  Branch: refs/heads/ehb54-issue-533
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Mon Aug  4 17:15:36 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 16:15:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] c94fb0: somo remove final sprintf
 deprecated
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/85e259-c94fb0@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c94fb08ce72a7bf4a4ac76a67c2ab9089dc02f26
      https://github.com/ehb54/ultrascan3/commit/c94fb08ce72a7bf4a4ac76a67c2ab9089dc02f26
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us_color.cpp
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_font.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_bd_options.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_grid_atob.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_mals_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_guinier.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_pdb_tool_merge.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_hplc_modes.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_imgviewer.cpp
    M us_somo/develop/src/us_matrix.cpp
    M us_somo/develop/src/us_register.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_grid_atob_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_pat.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/src/us_util.cpp

  Log Message:
  -----------
  somo remove final sprintf deprecated



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From noreply at github.com  Mon Aug  4 18:22:36 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 17:22:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] b31eca: issue 533 : convert QString
 - the last of sprintf ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-533/54079b-b31eca@github.com>

  Branch: refs/heads/ehb54-issue-533
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Mon Aug  4 18:34:42 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 17:34:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3fd011: issue 533 : convert QString
 - the last of sprintf ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-533/b31eca-3fd011@github.com>

  Branch: refs/heads/ehb54-issue-533
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Mon Aug  4 20:28:24 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 19:28:24 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5e295c: somo remove final
 deprecated, clean up many warnings
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/c94fb0-5e295c@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5e295c4687c78ece7b88d532acb4b5556df13176
      https://github.com/ehb54/ultrascan3/commit/5e295c4687c78ece7b88d532acb4b5556df13176
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    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_tar.h
    M us_somo/develop/include/us_tnt_jama.h
    M us_somo/develop/include/us_unicode.h
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_fractal_dimension.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_fractal_dimension.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.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_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.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_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.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_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.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_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_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_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_zeno_cxx.cpp

  Log Message:
  -----------
  somo remove final deprecated, clean up many warnings



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From noreply at github.com  Mon Aug  4 20:46:08 2025
From: noreply at github.com (ehb54)
Date: Mon, 04 Aug 2025 19:46:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] 3a6a5a: somo remove more deprecated
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/5e295c-3a6a5a@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3a6a5a20f729ae35869b1429d94d1d84d7c1b00d
      https://github.com/ehb54/ultrascan3/commit/3a6a5a20f729ae35869b1429d94d1d84d7c1b00d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_util.cpp

  Log Message:
  -----------
  somo remove more deprecated



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From noreply at github.com  Tue Aug  5 13:34:15 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 05 Aug 2025 12:34:15 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4c54fb: sphinx pdf README udpate
 with Makefiles
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/e222b9-4c54fb@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4c54fbbc6ed9d4184418fd8c4bc52488b99fa5a2
      https://github.com/ehb54/ultrascan3/commit/4c54fbbc6ed9d4184418fd8c4bc52488b99fa5a2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-05 (Tue, 05 Aug 2025)

  Changed paths:
    M .gitignore
    M doc/manual/Makefile
    M doc/manual/README
    M doc/manual/source/conf.py

  Log Message:
  -----------
  sphinx pdf README udpate with Makefiles



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From noreply at github.com  Tue Aug  5 13:43:28 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 05 Aug 2025 12:43:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] 155aad: sphinx pdf index test
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/4c54fb-155aad@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 155aadc67ca38c01146c12718e672d209d7cb968
      https://github.com/ehb54/ultrascan3/commit/155aadc67ca38c01146c12718e672d209d7cb968
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-05 (Tue, 05 Aug 2025)

  Changed paths:
    M doc/manual/source/index.rst
    M doc/manual/source/us_edit.rst

  Log Message:
  -----------
  sphinx pdf index test



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From noreply at github.com  Tue Aug  5 14:06:39 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 05 Aug 2025 13:06:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6f9a71: fix typo
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/155aad-6f9a71@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6f9a71aa1d9b0c48c05d10330731b0dc052da7bc
      https://github.com/ehb54/ultrascan3/commit/6f9a71aa1d9b0c48c05d10330731b0dc052da7bc
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-05 (Tue, 05 Aug 2025)

  Changed paths:
    M doc/manual/README

  Log Message:
  -----------
  fix typo



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From noreply at github.com  Tue Aug  5 18:32:32 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 05 Aug 2025 17:32:32 -0700
Subject: [us-commits] [ehb54/ultrascan3] f684bd: change namespace
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/6f9a71-f684bd@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f684bd1b954307d2e05938381f9548958c2dda20
      https://github.com/ehb54/ultrascan3/commit/f684bd1b954307d2e05938381f9548958c2dda20
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-05 (Tue, 05 Aug 2025)

  Changed paths:
    M doc/manual/source/conf.py

  Log Message:
  -----------
  change namespace



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From noreply at github.com  Wed Aug  6 09:34:02 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 06 Aug 2025 08:34:02 -0700
Subject: [us-commits] [ehb54/ultrascan3] ed4257: update makefile to have
 clean and all
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/f684bd-ed4257@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ed42571eef45aa8fe056b8c6beed62adfa500925
      https://github.com/ehb54/ultrascan3/commit/ed42571eef45aa8fe056b8c6beed62adfa500925
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-06 (Wed, 06 Aug 2025)

  Changed paths:
    M doc/manual/Makefile
    M doc/manual/source/Makefile
    M doc/manual/source/conf.py
    M doc/manual/source/index.rst

  Log Message:
  -----------
  update makefile to have clean and all



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From noreply at github.com  Wed Aug  6 10:54:45 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 06 Aug 2025 09:54:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] 723cef: original html
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/ed4257-723cef@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 723cefc24ad612d43dd0f2ae3854264f56029d78
      https://github.com/ehb54/ultrascan3/commit/723cefc24ad612d43dd0f2ae3854264f56029d78
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-06 (Wed, 06 Aug 2025)

  Changed paths:
    A doc/manual/originalhtml/2dsa.body
    A doc/manual/originalhtml/2dsa.html
    A doc/manual/originalhtml/2dsa_3dplot.img.html
    A doc/manual/originalhtml/2dsa_advan.body
    A doc/manual/originalhtml/2dsa_advan.html
    A doc/manual/originalhtml/2dsa_analvv.body
    A doc/manual/originalhtml/2dsa_analvv.html
    A doc/manual/originalhtml/2dsa_analys.body
    A doc/manual/originalhtml/2dsa_analys.html
    A doc/manual/originalhtml/2dsa_resplot.img.html
    A doc/manual/originalhtml/advanced_config.body
    A doc/manual/originalhtml/advanced_config.html
    A doc/manual/originalhtml/analyte_details.img.html
    A doc/manual/originalhtml/analytes.body
    A doc/manual/originalhtml/analytes.html
    A doc/manual/originalhtml/associations.body
    A doc/manual/originalhtml/associations.html
    A doc/manual/originalhtml/astfem_sim.body
    A doc/manual/originalhtml/astfem_sim.html
    A doc/manual/originalhtml/buffer_edit.body
    A doc/manual/originalhtml/buffer_edit.html
    A doc/manual/originalhtml/buffer_info.img.html
    A doc/manual/originalhtml/buffer_new.body
    A doc/manual/originalhtml/buffer_new.html
    A doc/manual/originalhtml/buffer_select.body
    A doc/manual/originalhtml/buffer_select.html
    A doc/manual/originalhtml/buffer_settings.body
    A doc/manual/originalhtml/buffer_settings.html
    A doc/manual/originalhtml/cfa_view-loadauc.img.html
    A doc/manual/originalhtml/cfa_view-loadraw.img.html
    A doc/manual/originalhtml/cfa_view-statsauc.img.html
    A doc/manual/originalhtml/cfa_view-statsraw.img.html
    A doc/manual/originalhtml/cfa_viewer.body
    A doc/manual/originalhtml/cfa_viewer.html
    A doc/manual/originalhtml/colorgradient.body
    A doc/manual/originalhtml/colorgradient.html
    A doc/manual/originalhtml/combine_models.body
    A doc/manual/originalhtml/combine_models.html
    A doc/manual/originalhtml/components.body
    A doc/manual/originalhtml/components.html
    A doc/manual/originalhtml/config.body
    A doc/manual/originalhtml/config.html
    A doc/manual/originalhtml/config2.body
    A doc/manual/originalhtml/config2.html
    A doc/manual/originalhtml/convert-experiment.body
    A doc/manual/originalhtml/convert-experiment.html
    A doc/manual/originalhtml/convert-seltrip.body
    A doc/manual/originalhtml/convert-seltrip.html
    A doc/manual/originalhtml/convert.body
    A doc/manual/originalhtml/convert.html
    A doc/manual/originalhtml/data_loader.body
    A doc/manual/originalhtml/data_loader.html
    A doc/manual/originalhtml/database_config.body
    A doc/manual/originalhtml/database_config.html
    A doc/manual/originalhtml/ddist_combine-selrun.img.html
    A doc/manual/originalhtml/ddist_combine.body
    A doc/manual/originalhtml/ddist_combine.html
    A doc/manual/originalhtml/dens_match.body
    A doc/manual/originalhtml/dens_match.html
    A doc/manual/originalhtml/dens_match_mparam.body
    A doc/manual/originalhtml/dens_match_mparam.html
    A doc/manual/originalhtml/dens_match_rmvmods.body
    A doc/manual/originalhtml/dens_match_rmvmods.html
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    A doc/manual/originalhtml/experiment_general.body
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    A doc/manual/originalhtml/experiment_solutions.body
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    A doc/manual/originalhtml/export_legacy.body
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    A doc/manual/originalhtml/fe_match_adv.body
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    A doc/manual/originalhtml/images/cfa_view-statsauc.png
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    A doc/manual/originalhtml/images/combine_models-save.png
    A doc/manual/originalhtml/images/combine_models.png
    A doc/manual/originalhtml/images/components.png
    A doc/manual/originalhtml/images/config.png
    A doc/manual/originalhtml/images/config1.png
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    A doc/manual/originalhtml/images/convert-RIdata.png
    A doc/manual/originalhtml/images/convert-exclude.png
    A doc/manual/originalhtml/images/convert-experiment.png
    A doc/manual/originalhtml/images/convert-mwl.png
    A doc/manual/originalhtml/images/convert-seltrip.png
    A doc/manual/originalhtml/images/convert-subset.png
    A doc/manual/originalhtml/images/convert-tolerance.png
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    A doc/manual/originalhtml/images/densmatch_mpars_empty.png
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  Log Message:
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From noreply at github.com  Thu Aug  7 10:12:14 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 07 Aug 2025 09:12:14 -0700
Subject: [us-commits] [ehb54/ultrascan3] e37346: Clang-Format-Demonstration
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-llvm/000000-e37346@github.com>

  Branch: refs/heads/lukas/clang-format-example-llvm
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e373462185a56a03cc53d3de0bc5ead31be91283
      https://github.com/ehb54/ultrascan3/commit/e373462185a56a03cc53d3de0bc5ead31be91283
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

  Changed paths:
    M admin/release/ubuntu/mathops.h
    M admin/shm_ipc/main.cpp
    M admin/shm_open/main.cpp
    M admin/shmutil/main.cpp
    M alpha/us.cpp
    M gui/us_abstractrotor_gui.cpp
    M gui/us_abstractrotor_gui.h
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_associations_gui.cpp
    M gui/us_associations_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_choice.cpp
    M gui/us_choice.h
    M gui/us_colorgradIO.cpp
    M gui/us_colorgradIO.h
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_combined_plots_parms_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M gui/us_edit_spectrum.cpp
    M gui/us_edit_spectrum.h
    M gui/us_editor.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_editor_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinctfitter_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_failed_gmp_run_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    M gui/us_gui_util.h
    M gui/us_help.cpp
    M gui/us_help.h
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_investigator.cpp
    M gui/us_investigator.h
    M gui/us_license.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M gui/us_loadable_noise.cpp
    M gui/us_loadable_noise.h
    M gui/us_mac_utils.c
    M gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_minimize.h
    M gui/us_model_editor.cpp
    M 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_mwl_data.cpp
    M gui/us_mwl_data.h
    M gui/us_new_spectrum.cpp
    M gui/us_new_spectrum.h
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_pixmaps.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_project_gui.cpp
    M gui/us_project_gui.h
    M gui/us_properties.cpp
    M gui/us_properties.h
    M gui/us_report_general_gui.cpp
    M gui/us_report_general_gui.h
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_resids_bitmap.cpp
    M gui/us_resids_bitmap.h
    M gui/us_rotor_gui.cpp
    M gui/us_rotor_gui.h
    M gui/us_run_details2.cpp
    M gui/us_run_details2.h
    M gui/us_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_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.cpp
    M gui/us_select_runs.h
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_table.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_tmst_plot.h
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M gui/us_widgets_dialog.h
    M gui/us_win_utils.c
    M gui/us_win_utils.h
    M gui/us_window_message.cpp
    M gui/us_window_message.h
    M gui/us_x11_utils.c
    M gui/us_x11_utils.h
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us_win_data.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_2dsa.h
    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_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.cpp
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_resplot_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_2dsa/us_show_norm.h
    M programs/us_2dsa/us_worker_2d.cpp
    M programs/us_2dsa/us_worker_2d.h
    M programs/us_2dsa/us_worker_calcnorm.cpp
    M programs/us_2dsa/us_worker_calcnorm.h
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_abde_main.h
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_main.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_analyte/us_analyte_main.cpp
    M programs/us_assign_reviewers_gmp/us_assign_reviewers_gmp_main.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_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp_main.cpp
    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_main.cpp
    M programs/us_buffer/us_buffer_main.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_buoyancy/us_buoyancy_main.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    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/us_com_project_main.cpp
    M programs/us_com_project_academic/us_com_project_academic_main.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_combine_models/us_combine_models.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.cpp
    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_database.h
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_newxpnhost_db.h
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_convert/us_convert_main.cpp
    M programs/us_convert/us_convertio.cpp
    M programs/us_convert/us_convertio.h
    M programs/us_convert/us_experiment.cpp
    M programs/us_convert/us_experiment.h
    M programs/us_convert/us_experiment_gui.cpp
    M programs/us_convert/us_experiment_gui.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_get_run.h
    M programs/us_convert/us_intensity.cpp
    M programs/us_convert/us_intensity.h
    M programs/us_convert/us_select_triples.cpp
    M programs/us_convert/us_select_triples.h
    M programs/us_convert/us_selectbox.cpp
    M programs/us_convert/us_selectbox.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_ddist_combine_main.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_ddist_combine/us_select_rundd.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_density_match.h
    M programs/us_density_match/us_model_params.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.cpp
    M programs/us_density_match/us_remove_models.h
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_constraints_edit.h
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_dmga_init/us_dmga_init.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_main.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.cpp
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_get_edit.cpp
    M programs/us_edit/us_get_edit.h
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_edit/us_ri_noise.h
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_edit/us_select_lambdas.h
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_equiltime/us_equiltime.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_esigner_gmp/us_esigner_gmp_main.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_experiment_main.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_export_legacy/us_export.h
    M programs/us_extinction/us_extinction_main.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.h
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_dmga_mc_stats.h
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_fematch_main.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fematch/us_resplot_fem.h
    M programs/us_fematch/us_thread_worker.cpp
    M programs/us_fematch/us_thread_worker.h
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqhistogram.h
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmath.h
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_eqreporter.h
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_fit_worker.h
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_globalequil/us_globeq_data.h
    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_adpars.h
    M programs/us_globalequil/us_model_select.cpp
    M programs/us_globalequil/us_model_select.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_helpdaemon/us_helpdaemon.h
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_investigator/us_investigator_main.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_license/us_license.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_model.h
    M programs/us_manage_data/us_data_process.cpp
    M programs/us_manage_data/us_data_process.h
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_data_tree.h
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_manage_data/us_manage_data.h
    M programs/us_manage_data/us_sync_exper.cpp
    M programs/us_manage_data/us_sync_exper.h
    M programs/us_model_gui/main.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_modelmetrics/us_modelmetrics.h
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/2dsa_worker.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/pcsa_worker.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_analysis.h
    M programs/us_mpi_analysis/us_mpi_parse.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_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_fit/us_mwl_species_fit_main.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwl_run.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_pcsa/us_plot_control_pc.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_resplot_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_pcsa/us_worker_pc.cpp
    M programs/us_pcsa/us_worker_pc.h
    M programs/us_predict1/us_predict1_main.cpp
    M programs/us_predict2/us_predict2.cpp
    M programs/us_predict2/us_predict2.h
    M programs/us_predict2/us_predict2_main.cpp
    M programs/us_project/us_project_main.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_protocol_dev/us_protocol_dev_main.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine_main.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pabs_common.cpp
    M programs/us_pseudo_absorbance/us_pabs_common.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.h
    M programs/us_pseudo_absorbance/us_refScan_dataIO.cpp
    M programs/us_pseudo_absorbance/us_refScan_dataIO.h
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_experiment_gui_ra.h
    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_get_dbrun_ra.h
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_intensity_ra.h
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_mwlramp.h
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp.h
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_ramp/us_selectbox_ra.cpp
    M programs/us_ramp/us_selectbox_ra.h
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_rasmol_control/us_rasmol_control.h
    M programs/us_reassign_reviewers_gmp/us_reassign_reviewers_gmp_main.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter/us_sync_db.h
    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_main.cpp
    M programs/us_rotor/us_rotor_main.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_get_dbexp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_sassoc/us_sassoc_main.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_solution/us_solution_main.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_tmst_viewer/us_tmst_viewer.cpp
    M programs/us_tmst_viewer/us_tmst_viewer.h
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_select_runid.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhw_combine.h
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.h
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M programs/us_xpn_viewer/us_xpn_viewer_main.cpp
    M qwtplot3d/3rdparty/gl2ps/gl2ps.c
    M qwtplot3d/3rdparty/gl2ps/gl2ps.h
    M qwtplot3d/examples/autoswitch/autoswitch.cpp
    M qwtplot3d/examples/autoswitch/autoswitch.h
    M qwtplot3d/examples/axes/src/axes.h
    M qwtplot3d/examples/axes/src/axesmainwindow.cpp
    M qwtplot3d/examples/axes/src/axesmainwindow.h
    M qwtplot3d/examples/axes/src/main.cpp
    M qwtplot3d/examples/enrichments/src/enrichmentmainwindow.cpp
    M qwtplot3d/examples/enrichments/src/enrichmentmainwindow.h
    M qwtplot3d/examples/enrichments/src/enrichments.cpp
    M qwtplot3d/examples/enrichments/src/enrichments.h
    M qwtplot3d/examples/enrichments/src/main.cpp
    M qwtplot3d/examples/mesh2/src/colormapreader.cpp
    M qwtplot3d/examples/mesh2/src/colormapreader.h
    M qwtplot3d/examples/mesh2/src/designerworkaround.cpp
    M qwtplot3d/examples/mesh2/src/designerworkaround.h
    M qwtplot3d/examples/mesh2/src/femreader.h
    M qwtplot3d/examples/mesh2/src/functions.h
    M qwtplot3d/examples/mesh2/src/lightingdlg.cpp
    M qwtplot3d/examples/mesh2/src/lightingdlg.h
    M qwtplot3d/examples/mesh2/src/lightingdlgbaseimpl.cpp
    M qwtplot3d/examples/mesh2/src/lightingdlgbaseimpl.h
    M qwtplot3d/examples/mesh2/src/main.cpp
    M qwtplot3d/examples/mesh2/src/mesh.cpp
    M qwtplot3d/examples/mesh2/src/mesh2mainwindow.cpp
    M qwtplot3d/examples/mesh2/src/mesh2mainwindow.h
    M qwtplot3d/examples/simpleplot/simpleplot.cpp
    M qwtplot3d/include/qwt3d_autoptr.h
    M qwtplot3d/include/qwt3d_autoscaler.h
    M qwtplot3d/include/qwt3d_axis.h
    M qwtplot3d/include/qwt3d_color.h
    M qwtplot3d/include/qwt3d_colorlegend.h
    M qwtplot3d/include/qwt3d_coordsys.h
    M qwtplot3d/include/qwt3d_drawable.h
    M qwtplot3d/include/qwt3d_enrichment.h
    M qwtplot3d/include/qwt3d_enrichment_std.h
    M qwtplot3d/include/qwt3d_function.h
    M qwtplot3d/include/qwt3d_global.h
    M qwtplot3d/include/qwt3d_graphplot.h
    M qwtplot3d/include/qwt3d_gridmapping.h
    M qwtplot3d/include/qwt3d_helper.h
    M qwtplot3d/include/qwt3d_io.h
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_io_reader.h
    M qwtplot3d/include/qwt3d_label.h
    M qwtplot3d/include/qwt3d_mapping.h
    M qwtplot3d/include/qwt3d_multiplot.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_parametricsurface.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_portability.h
    M qwtplot3d/include/qwt3d_scale.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/include/qwt3d_types.h
    M qwtplot3d/include/qwt3d_volumeplot.h
    M qwtplot3d/src/qwt3d_autoscaler.cpp
    M qwtplot3d/src/qwt3d_axis.cpp
    M qwtplot3d/src/qwt3d_color.cpp
    M qwtplot3d/src/qwt3d_colorlegend.cpp
    M qwtplot3d/src/qwt3d_coordsys.cpp
    M qwtplot3d/src/qwt3d_dataviews.cpp
    M qwtplot3d/src/qwt3d_drawable.cpp
    M qwtplot3d/src/qwt3d_enrichment_std.cpp
    M qwtplot3d/src/qwt3d_function.cpp
    M qwtplot3d/src/qwt3d_gridmapping.cpp
    M qwtplot3d/src/qwt3d_gridplot.cpp
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_io_reader.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_meshplot.cpp
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_parametricsurface.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_scale.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    M qwtplot3d/src/qwt3d_types.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M test/modelbuilder/us_modelbuilder.h
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_datafiles.h
    M test/utils/test_us_simparams.cpp
    M test/utils/test_us_simparams.h
    M test/utils/test_us_util.cpp
    M test/utils/test_us_util.h
    M test/utils/test_us_utils_main.cpp
    M us_somo/attic/docs/calc.c
    M us_somo/develop/3dplot/D_calc.cpp
    M us_somo/develop/3dplot/colormapreader.cpp
    M us_somo/develop/3dplot/colormapreader.h
    M us_somo/develop/3dplot/femreader.h
    M us_somo/develop/3dplot/functions.h
    M us_somo/develop/3dplot/lightingdlg.cpp
    M us_somo/develop/3dplot/lightingdlg.h
    M us_somo/develop/3dplot/lightingdlgbase.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/3dplot/mesh.cpp
    M us_somo/develop/3dplot/mesh2mainwindow.cpp
    M us_somo/develop/3dplot/mesh2mainwindow.h
    M us_somo/develop/3dplot/mesh2mainwindowbase.cpp
    M us_somo/develop/3dplot/mesh2mainwindowbase.h
    M us_somo/develop/include/Eigen/src/Cholesky/LDLT.h
    M us_somo/develop/include/Eigen/src/Cholesky/LLT.h
    M us_somo/develop/include/Eigen/src/Cholesky/LLT_LAPACKE.h
    M us_somo/develop/include/Eigen/src/CholmodSupport/CholmodSupport.h
    M us_somo/develop/include/Eigen/src/Core/ArithmeticSequence.h
    M us_somo/develop/include/Eigen/src/Core/Array.h
    M us_somo/develop/include/Eigen/src/Core/ArrayBase.h
    M us_somo/develop/include/Eigen/src/Core/ArrayWrapper.h
    M us_somo/develop/include/Eigen/src/Core/Assign.h
    M us_somo/develop/include/Eigen/src/Core/AssignEvaluator.h
    M us_somo/develop/include/Eigen/src/Core/Assign_MKL.h
    M us_somo/develop/include/Eigen/src/Core/BandMatrix.h
    M us_somo/develop/include/Eigen/src/Core/Block.h
    M us_somo/develop/include/Eigen/src/Core/BooleanRedux.h
    M us_somo/develop/include/Eigen/src/Core/CommaInitializer.h
    M us_somo/develop/include/Eigen/src/Core/ConditionEstimator.h
    M us_somo/develop/include/Eigen/src/Core/CoreEvaluators.h
    M us_somo/develop/include/Eigen/src/Core/CoreIterators.h
    M us_somo/develop/include/Eigen/src/Core/CwiseBinaryOp.h
    M us_somo/develop/include/Eigen/src/Core/CwiseNullaryOp.h
    M us_somo/develop/include/Eigen/src/Core/CwiseTernaryOp.h
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    M us_somo/develop/include/Eigen/src/Core/CwiseUnaryView.h
    M us_somo/develop/include/Eigen/src/Core/DenseBase.h
    M us_somo/develop/include/Eigen/src/Core/DenseCoeffsBase.h
    M us_somo/develop/include/Eigen/src/Core/DenseStorage.h
    M us_somo/develop/include/Eigen/src/Core/Diagonal.h
    M us_somo/develop/include/Eigen/src/Core/DiagonalMatrix.h
    M us_somo/develop/include/Eigen/src/Core/DiagonalProduct.h
    M us_somo/develop/include/Eigen/src/Core/Dot.h
    M us_somo/develop/include/Eigen/src/Core/EigenBase.h
    M us_somo/develop/include/Eigen/src/Core/ForceAlignedAccess.h
    M us_somo/develop/include/Eigen/src/Core/Fuzzy.h
    M us_somo/develop/include/Eigen/src/Core/GeneralProduct.h
    M us_somo/develop/include/Eigen/src/Core/GenericPacketMath.h
    M us_somo/develop/include/Eigen/src/Core/GlobalFunctions.h
    M us_somo/develop/include/Eigen/src/Core/IO.h
    M us_somo/develop/include/Eigen/src/Core/IndexedView.h
    M us_somo/develop/include/Eigen/src/Core/Inverse.h
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    M us_somo/develop/include/Eigen/src/Core/PlainObjectBase.h
    M us_somo/develop/include/Eigen/src/Core/Product.h
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    M us_somo/develop/include/us_hydrodyn_overlap.h
    M us_somo/develop/include/us_hydrodyn_overlap_reduction.h
    M us_somo/develop/include/us_hydrodyn_pat.h
    M us_somo/develop/include/us_hydrodyn_pat_hydro.h
    M us_somo/develop/include/us_hydrodyn_pdb_parsing.h
    M us_somo/develop/include/us_hydrodyn_pdb_tool.h
    M us_somo/develop/include/us_hydrodyn_pdb_tool_merge.h
    M us_somo/develop/include/us_hydrodyn_pdb_tool_renum.h
    M us_somo/develop/include/us_hydrodyn_pdb_tool_selres.h
    M us_somo/develop/include/us_hydrodyn_pdb_tool_sort.h
    M us_somo/develop/include/us_hydrodyn_pdb_visualization.h
    M us_somo/develop/include/us_hydrodyn_pdbdefs.h
    M us_somo/develop/include/us_hydrodyn_results.h
    M us_somo/develop/include/us_hydrodyn_sas_options_bead_model.h
    M us_somo/develop/include/us_hydrodyn_sas_options_curve.h
    M us_somo/develop/include/us_hydrodyn_sas_options_experimental.h
    M us_somo/develop/include/us_hydrodyn_sas_options_guinier.h
    M us_somo/develop/include/us_hydrodyn_sas_options_hydration.h
    M us_somo/develop/include/us_hydrodyn_sas_options_misc.h
    M us_somo/develop/include/us_hydrodyn_sas_options_sans.h
    M us_somo/develop/include/us_hydrodyn_sas_options_saxs.h
    M us_somo/develop/include/us_hydrodyn_sas_options_xsr.h
    M us_somo/develop/include/us_hydrodyn_save.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_1d.h
    M us_somo/develop/include/us_hydrodyn_saxs_2d.h
    M us_somo/develop/include/us_hydrodyn_saxs_buffer.h
    M us_somo/develop/include/us_hydrodyn_saxs_buffer_conc.h
    M us_somo/develop/include/us_hydrodyn_saxs_buffer_conc_load.h
    M us_somo/develop/include/us_hydrodyn_saxs_buffer_nth.h
    M us_somo/develop/include/us_hydrodyn_saxs_conc.h
    M us_somo/develop/include/us_hydrodyn_saxs_cormap.h
    M us_somo/develop/include/us_hydrodyn_saxs_guinier_frames.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_baseline_best.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_bl.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_ciq.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_conc.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_conc_csv_frames.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_conc_load.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_dctr.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit_global.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_gauss_mode.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_movie.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_nth.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_options.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_p3d.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_parameters.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_scale_trend.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_simulate.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_svd.h
    M us_somo/develop/include/us_hydrodyn_saxs_ift.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_load_csv.h
    M us_somo/develop/include/us_hydrodyn_saxs_iqq_residuals.h
    M us_somo/develop/include/us_hydrodyn_saxs_load_csv.h
    M us_somo/develop/include/us_hydrodyn_saxs_mw.h
    M us_somo/develop/include/us_hydrodyn_saxs_options.h
    M us_somo/develop/include/us_hydrodyn_saxs_residuals.h
    M us_somo/develop/include/us_hydrodyn_saxs_screen.h
    M us_somo/develop/include/us_hydrodyn_saxs_search.h
    M us_somo/develop/include/us_hydrodyn_supc.h
    M us_somo/develop/include/us_hydrodyn_supc_hydro.h
    M us_somo/develop/include/us_hydrodyn_vdw_overlap.h
    M us_somo/develop/include/us_hydrodyn_xsr.h
    M us_somo/develop/include/us_hydrodyn_zeno.h
    M us_somo/develop/include/us_hydrodyn_zeno_hydro.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_license.h
    M us_somo/develop/include/us_limsconv.h
    M us_somo/develop/include/us_lm.h
    M us_somo/develop/include/us_lud.h
    M us_somo/develop/include/us_math.h
    M us_somo/develop/include/us_matrix.h
    M us_somo/develop/include/us_mqt.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.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_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_constraints.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_defines.h
    M utils/us_dmga_constr.cpp
    M utils/us_dmga_constr.h
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_extern.h
    M utils/us_extinctutils.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_http_post.cpp
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_lm.h
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_project.h
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_report_gmp.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_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.cpp
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_solve_sim.h
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h

  Log Message:
  -----------
  Clang-Format-Demonstration



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From noreply at github.com  Thu Aug  7 10:13:08 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 07 Aug 2025 09:13:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] 57684f: Merge pull request #244
 from ehb54/lukas/us_astfem...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-llvm/e37346-3494ff@github.com>

  Branch: refs/heads/lukas/clang-format-example-llvm
  Home:   https://github.com/ehb54/ultrascan3
  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: 3494ffe744db0592d4bb22a6f23a83e5004c923d
      https://github.com/ehb54/ultrascan3/commit/3494ffe744db0592d4bb22a6f23a83e5004c923d
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

  Changed paths:

  Log Message:
  -----------
  Merge pull request #247 from ehb54/master

Merge pull request #244 from ehb54/lukas/us_astfem_sim_baseline_offset


Compare: https://github.com/ehb54/ultrascan3/compare/e373462185a5...3494ffe744db

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From noreply at github.com  Thu Aug  7 10:25:16 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 07 Aug 2025 09:25:16 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-microsoft/000000-57684f@github.com>

  Branch: refs/heads/lukas/clang-format-example-microsoft
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Aug  7 10:26:58 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 07 Aug 2025 09:26:58 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-gnu/000000-57684f@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  Thu Aug  7 10:27:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 07 Aug 2025 09:27:59 -0700
Subject: [us-commits] [ehb54/ultrascan3] 139586: Clang-Format-Demonstration
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-google/000000-139586@github.com>

  Branch: refs/heads/lukas/clang-format-example-google
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1395869797bc76c0393419b9c91fc15b3523c462
      https://github.com/ehb54/ultrascan3/commit/1395869797bc76c0393419b9c91fc15b3523c462
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

  Changed paths:
    M admin/release/ubuntu/mathops.h
    M admin/shm_ipc/main.cpp
    M admin/shm_open/main.cpp
    M admin/shmutil/main.cpp
    M alpha/us.cpp
    M gui/us_abstractrotor_gui.cpp
    M gui/us_abstractrotor_gui.h
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_associations_gui.cpp
    M gui/us_associations_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_choice.cpp
    M gui/us_choice.h
    M gui/us_colorgradIO.cpp
    M gui/us_colorgradIO.h
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_combined_plots_parms_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M gui/us_edit_spectrum.cpp
    M gui/us_edit_spectrum.h
    M gui/us_editor.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_editor_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinctfitter_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_failed_gmp_run_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    M gui/us_gui_util.h
    M gui/us_help.cpp
    M gui/us_help.h
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_investigator.cpp
    M gui/us_investigator.h
    M gui/us_license.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M gui/us_loadable_noise.cpp
    M gui/us_loadable_noise.h
    M gui/us_mac_utils.c
    M gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_minimize.h
    M gui/us_model_editor.cpp
    M 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_mwl_data.cpp
    M gui/us_mwl_data.h
    M gui/us_new_spectrum.cpp
    M gui/us_new_spectrum.h
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_pixmaps.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_project_gui.cpp
    M gui/us_project_gui.h
    M gui/us_properties.cpp
    M gui/us_properties.h
    M gui/us_report_general_gui.cpp
    M gui/us_report_general_gui.h
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_resids_bitmap.cpp
    M gui/us_resids_bitmap.h
    M gui/us_rotor_gui.cpp
    M gui/us_rotor_gui.h
    M gui/us_run_details2.cpp
    M gui/us_run_details2.h
    M gui/us_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_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.cpp
    M gui/us_select_runs.h
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_table.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_tmst_plot.h
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M gui/us_widgets_dialog.h
    M gui/us_win_utils.c
    M gui/us_win_utils.h
    M gui/us_window_message.cpp
    M gui/us_window_message.h
    M gui/us_x11_utils.c
    M gui/us_x11_utils.h
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us_win_data.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_2dsa.h
    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_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.cpp
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_resplot_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_2dsa/us_show_norm.h
    M programs/us_2dsa/us_worker_2d.cpp
    M programs/us_2dsa/us_worker_2d.h
    M programs/us_2dsa/us_worker_calcnorm.cpp
    M programs/us_2dsa/us_worker_calcnorm.h
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_abde_main.h
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_main.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_analyte/us_analyte_main.cpp
    M programs/us_assign_reviewers_gmp/us_assign_reviewers_gmp_main.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_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp_main.cpp
    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_main.cpp
    M programs/us_buffer/us_buffer_main.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_buoyancy/us_buoyancy_main.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    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/us_com_project_main.cpp
    M programs/us_com_project_academic/us_com_project_academic_main.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_combine_models/us_combine_models.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.cpp
    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_database.h
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_newxpnhost_db.h
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_convert/us_convert_main.cpp
    M programs/us_convert/us_convertio.cpp
    M programs/us_convert/us_convertio.h
    M programs/us_convert/us_experiment.cpp
    M programs/us_convert/us_experiment.h
    M programs/us_convert/us_experiment_gui.cpp
    M programs/us_convert/us_experiment_gui.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_get_run.h
    M programs/us_convert/us_intensity.cpp
    M programs/us_convert/us_intensity.h
    M programs/us_convert/us_select_triples.cpp
    M programs/us_convert/us_select_triples.h
    M programs/us_convert/us_selectbox.cpp
    M programs/us_convert/us_selectbox.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_ddist_combine_main.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_ddist_combine/us_select_rundd.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_density_match.h
    M programs/us_density_match/us_model_params.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.cpp
    M programs/us_density_match/us_remove_models.h
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_constraints_edit.h
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_dmga_init/us_dmga_init.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_main.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.cpp
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_get_edit.cpp
    M programs/us_edit/us_get_edit.h
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_edit/us_ri_noise.h
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_edit/us_select_lambdas.h
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_equiltime/us_equiltime.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_esigner_gmp/us_esigner_gmp_main.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_experiment_main.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_export_legacy/us_export.h
    M programs/us_extinction/us_extinction_main.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.h
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_dmga_mc_stats.h
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_fematch_main.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fematch/us_resplot_fem.h
    M programs/us_fematch/us_thread_worker.cpp
    M programs/us_fematch/us_thread_worker.h
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqhistogram.h
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmath.h
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_eqreporter.h
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_fit_worker.h
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_globalequil/us_globeq_data.h
    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_adpars.h
    M programs/us_globalequil/us_model_select.cpp
    M programs/us_globalequil/us_model_select.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_helpdaemon/us_helpdaemon.h
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_investigator/us_investigator_main.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_license/us_license.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_model.h
    M programs/us_manage_data/us_data_process.cpp
    M programs/us_manage_data/us_data_process.h
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_data_tree.h
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_manage_data/us_manage_data.h
    M programs/us_manage_data/us_sync_exper.cpp
    M programs/us_manage_data/us_sync_exper.h
    M programs/us_model_gui/main.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_modelmetrics/us_modelmetrics.h
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/2dsa_worker.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/pcsa_worker.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_analysis.h
    M programs/us_mpi_analysis/us_mpi_parse.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_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_fit/us_mwl_species_fit_main.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwl_run.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_pcsa/us_plot_control_pc.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_resplot_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_pcsa/us_worker_pc.cpp
    M programs/us_pcsa/us_worker_pc.h
    M programs/us_predict1/us_predict1_main.cpp
    M programs/us_predict2/us_predict2.cpp
    M programs/us_predict2/us_predict2.h
    M programs/us_predict2/us_predict2_main.cpp
    M programs/us_project/us_project_main.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_protocol_dev/us_protocol_dev_main.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine_main.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pabs_common.cpp
    M programs/us_pseudo_absorbance/us_pabs_common.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.h
    M programs/us_pseudo_absorbance/us_refScan_dataIO.cpp
    M programs/us_pseudo_absorbance/us_refScan_dataIO.h
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_experiment_gui_ra.h
    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_get_dbrun_ra.h
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_intensity_ra.h
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_mwlramp.h
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp.h
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_ramp/us_selectbox_ra.cpp
    M programs/us_ramp/us_selectbox_ra.h
    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_rasmol_control/us_rasmol_control.h
    M programs/us_reassign_reviewers_gmp/us_reassign_reviewers_gmp_main.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter/us_reporter.h
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter/us_sync_db.h
    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_main.cpp
    M programs/us_rotor/us_rotor_main.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_rotor_calibration/us_get_dbexp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_sassoc/us_sassoc_main.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_solution/us_solution_main.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_tmst_viewer/us_tmst_viewer.cpp
    M programs/us_tmst_viewer/us_tmst_viewer.h
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_select_runid.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhw_combine.h
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.h
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.h
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M programs/us_xpn_viewer/us_xpn_viewer_main.cpp
    M qwtplot3d/3rdparty/gl2ps/gl2ps.c
    M qwtplot3d/3rdparty/gl2ps/gl2ps.h
    M qwtplot3d/examples/autoswitch/autoswitch.cpp
    M qwtplot3d/examples/autoswitch/autoswitch.h
    M qwtplot3d/examples/axes/src/axes.h
    M qwtplot3d/examples/axes/src/axesmainwindow.cpp
    M qwtplot3d/examples/axes/src/axesmainwindow.h
    M qwtplot3d/examples/axes/src/main.cpp
    M qwtplot3d/examples/enrichments/src/enrichmentmainwindow.cpp
    M qwtplot3d/examples/enrichments/src/enrichmentmainwindow.h
    M qwtplot3d/examples/enrichments/src/enrichments.cpp
    M qwtplot3d/examples/enrichments/src/enrichments.h
    M qwtplot3d/examples/enrichments/src/main.cpp
    M qwtplot3d/examples/mesh2/src/colormapreader.cpp
    M qwtplot3d/examples/mesh2/src/colormapreader.h
    M qwtplot3d/examples/mesh2/src/designerworkaround.cpp
    M qwtplot3d/examples/mesh2/src/designerworkaround.h
    M qwtplot3d/examples/mesh2/src/femreader.h
    M qwtplot3d/examples/mesh2/src/functions.h
    M qwtplot3d/examples/mesh2/src/lightingdlg.cpp
    M qwtplot3d/examples/mesh2/src/lightingdlg.h
    M qwtplot3d/examples/mesh2/src/lightingdlgbaseimpl.cpp
    M qwtplot3d/examples/mesh2/src/lightingdlgbaseimpl.h
    M qwtplot3d/examples/mesh2/src/main.cpp
    M qwtplot3d/examples/mesh2/src/mesh.cpp
    M qwtplot3d/examples/mesh2/src/mesh2mainwindow.cpp
    M qwtplot3d/examples/mesh2/src/mesh2mainwindow.h
    M qwtplot3d/examples/simpleplot/simpleplot.cpp
    M qwtplot3d/include/qwt3d_autoptr.h
    M qwtplot3d/include/qwt3d_autoscaler.h
    M qwtplot3d/include/qwt3d_axis.h
    M qwtplot3d/include/qwt3d_color.h
    M qwtplot3d/include/qwt3d_colorlegend.h
    M qwtplot3d/include/qwt3d_coordsys.h
    M qwtplot3d/include/qwt3d_drawable.h
    M qwtplot3d/include/qwt3d_enrichment.h
    M qwtplot3d/include/qwt3d_enrichment_std.h
    M qwtplot3d/include/qwt3d_function.h
    M qwtplot3d/include/qwt3d_global.h
    M qwtplot3d/include/qwt3d_graphplot.h
    M qwtplot3d/include/qwt3d_gridmapping.h
    M qwtplot3d/include/qwt3d_helper.h
    M qwtplot3d/include/qwt3d_io.h
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_io_reader.h
    M qwtplot3d/include/qwt3d_label.h
    M qwtplot3d/include/qwt3d_mapping.h
    M qwtplot3d/include/qwt3d_multiplot.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_parametricsurface.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_portability.h
    M qwtplot3d/include/qwt3d_scale.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/include/qwt3d_types.h
    M qwtplot3d/include/qwt3d_volumeplot.h
    M qwtplot3d/src/qwt3d_autoscaler.cpp
    M qwtplot3d/src/qwt3d_axis.cpp
    M qwtplot3d/src/qwt3d_color.cpp
    M qwtplot3d/src/qwt3d_colorlegend.cpp
    M qwtplot3d/src/qwt3d_coordsys.cpp
    M qwtplot3d/src/qwt3d_dataviews.cpp
    M qwtplot3d/src/qwt3d_drawable.cpp
    M qwtplot3d/src/qwt3d_enrichment_std.cpp
    M qwtplot3d/src/qwt3d_function.cpp
    M qwtplot3d/src/qwt3d_gridmapping.cpp
    M qwtplot3d/src/qwt3d_gridplot.cpp
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_io_reader.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_meshplot.cpp
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_parametricsurface.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_scale.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    M qwtplot3d/src/qwt3d_types.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M test/modelbuilder/us_modelbuilder.h
    M test/utils/test_us_datafiles.cpp
    M test/utils/test_us_datafiles.h
    M test/utils/test_us_simparams.cpp
    M test/utils/test_us_simparams.h
    M test/utils/test_us_util.cpp
    M test/utils/test_us_util.h
    M test/utils/test_us_utils_main.cpp
    M us_somo/attic/docs/calc.c
    M us_somo/develop/3dplot/D_calc.cpp
    M us_somo/develop/3dplot/colormapreader.cpp
    M us_somo/develop/3dplot/colormapreader.h
    M us_somo/develop/3dplot/femreader.h
    M us_somo/develop/3dplot/functions.h
    M us_somo/develop/3dplot/lightingdlg.cpp
    M us_somo/develop/3dplot/lightingdlg.h
    M us_somo/develop/3dplot/lightingdlgbase.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/3dplot/mesh.cpp
    M us_somo/develop/3dplot/mesh2mainwindow.cpp
    M us_somo/develop/3dplot/mesh2mainwindow.h
    M us_somo/develop/3dplot/mesh2mainwindowbase.cpp
    M us_somo/develop/3dplot/mesh2mainwindowbase.h
    M us_somo/develop/include/Eigen/src/Cholesky/LDLT.h
    M us_somo/develop/include/Eigen/src/Cholesky/LLT.h
    M us_somo/develop/include/Eigen/src/Cholesky/LLT_LAPACKE.h
    M us_somo/develop/include/Eigen/src/CholmodSupport/CholmodSupport.h
    M us_somo/develop/include/Eigen/src/Core/ArithmeticSequence.h
    M us_somo/develop/include/Eigen/src/Core/Array.h
    M us_somo/develop/include/Eigen/src/Core/ArrayBase.h
    M us_somo/develop/include/Eigen/src/Core/ArrayWrapper.h
    M us_somo/develop/include/Eigen/src/Core/Assign.h
    M us_somo/develop/include/Eigen/src/Core/AssignEvaluator.h
    M us_somo/develop/include/Eigen/src/Core/Assign_MKL.h
    M us_somo/develop/include/Eigen/src/Core/BandMatrix.h
    M us_somo/develop/include/Eigen/src/Core/Block.h
    M us_somo/develop/include/Eigen/src/Core/BooleanRedux.h
    M us_somo/develop/include/Eigen/src/Core/CommaInitializer.h
    M us_somo/develop/include/Eigen/src/Core/ConditionEstimator.h
    M us_somo/develop/include/Eigen/src/Core/CoreEvaluators.h
    M us_somo/develop/include/Eigen/src/Core/CoreIterators.h
    M us_somo/develop/include/Eigen/src/Core/CwiseBinaryOp.h
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    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_project.h
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_report_gmp.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_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.cpp
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_solve_sim.h
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h

  Log Message:
  -----------
  Clang-Format-Demonstration



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From noreply at github.com  Thu Aug  7 10:37:21 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 07 Aug 2025 09:37:21 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5a3a57: Clang-Format-Demonstration
 GNU
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/clang-format-example-gnu/57684f-5a3a57@github.com>

  Branch: refs/heads/lukas/clang-format-example-gnu
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5a3a5743d26ef864b8e4d82e791ffd2bc68a747c
      https://github.com/ehb54/ultrascan3/commit/5a3a5743d26ef864b8e4d82e791ffd2bc68a747c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

  Changed paths:
    M admin/release/ubuntu/mathops.h
    M admin/shm_ipc/main.cpp
    M admin/shm_open/main.cpp
    M admin/shmutil/main.cpp
    M alpha/us.cpp
    M gui/us_abstractrotor_gui.cpp
    M gui/us_abstractrotor_gui.h
    M gui/us_analysis_base2.cpp
    M gui/us_analysis_base2.h
    M gui/us_analyte_gui.cpp
    M gui/us_analyte_gui.h
    M gui/us_associations_gui.cpp
    M gui/us_associations_gui.h
    M gui/us_buffer_gui.cpp
    M gui/us_buffer_gui.h
    M gui/us_choice.cpp
    M gui/us_choice.h
    M gui/us_colorgradIO.cpp
    M gui/us_colorgradIO.h
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_combined_plots_parms_gui.h
    M gui/us_csv_loader.cpp
    M gui/us_csv_loader.h
    M gui/us_data_loader.cpp
    M gui/us_data_loader.h
    M gui/us_edit_spectrum.cpp
    M gui/us_edit_spectrum.h
    M gui/us_editor.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_editor_gui.h
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinctfitter_gui.h
    M gui/us_extinction_gui.cpp
    M gui/us_extinction_gui.h
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_failed_gmp_run_gui.h
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    M gui/us_gui_util.h
    M gui/us_help.cpp
    M gui/us_help.h
    M gui/us_images.cpp
    M gui/us_images.h
    M gui/us_investigator.cpp
    M gui/us_investigator.h
    M gui/us_license.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_load_auc.h
    M gui/us_loadable_noise.cpp
    M gui/us_loadable_noise.h
    M gui/us_mac_utils.c
    M gui/us_mac_utils.h
    M gui/us_minimize.cpp
    M gui/us_minimize.h
    M gui/us_model_editor.cpp
    M 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_mwl_data.cpp
    M gui/us_mwl_data.h
    M gui/us_new_spectrum.cpp
    M gui/us_new_spectrum.h
    M gui/us_noise_loader.cpp
    M gui/us_noise_loader.h
    M gui/us_passwd.cpp
    M gui/us_passwd.h
    M gui/us_pixmaps.h
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_project_gui.cpp
    M gui/us_project_gui.h
    M gui/us_properties.cpp
    M gui/us_properties.h
    M gui/us_report_general_gui.cpp
    M gui/us_report_general_gui.h
    M gui/us_report_gui.cpp
    M gui/us_report_gui.h
    M gui/us_resids_bitmap.cpp
    M gui/us_resids_bitmap.h
    M gui/us_rotor_gui.cpp
    M gui/us_rotor_gui.h
    M gui/us_run_details2.cpp
    M gui/us_run_details2.h
    M gui/us_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_edits.h
    M gui/us_select_item.cpp
    M gui/us_select_item.h
    M gui/us_select_runs.cpp
    M gui/us_select_runs.h
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M gui/us_solution_gui.cpp
    M gui/us_solution_gui.h
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_table.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_tmst_plot.h
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M gui/us_widgets_dialog.h
    M gui/us_win_utils.c
    M gui/us_win_utils.h
    M gui/us_window_message.cpp
    M gui/us_window_message.h
    M gui/us_x11_utils.c
    M gui/us_x11_utils.h
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us/us_win_data.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_2dsa.h
    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_adv_analysis_2d.h
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.h
    M programs/us_2dsa/us_plot_control_2d.cpp
    M programs/us_2dsa/us_plot_control_2d.h
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_resplot_2d.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_2dsa/us_show_norm.h
    M programs/us_2dsa/us_worker_2d.cpp
    M programs/us_2dsa/us_worker_2d.h
    M programs/us_2dsa/us_worker_calcnorm.cpp
    M programs/us_2dsa/us_worker_calcnorm.h
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_abde_main.h
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_analysis_profile/us_anapro_main.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_analyte/us_analyte_main.cpp
    M programs/us_assign_reviewers_gmp/us_assign_reviewers_gmp_main.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_audit_trail_gmp/us_audit_trail_gmp.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp_main.cpp
    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_main.cpp
    M programs/us_buffer/us_buffer_main.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_buoyancy/us_buoyancy_main.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_colorgradient/us_colorgradient.h
    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/us_com_project_main.cpp
    M programs/us_com_project_academic/us_com_project_academic_main.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_combine_models/us_combine_models.h
    M programs/us_config/us_admin.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.cpp
    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_database.h
    M programs/us_config/us_font.cpp
    M programs/us_config/us_font.h
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_newxpnhost_db.h
    M programs/us_config/us_xpnhost.cpp
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_convert/us_convert_main.cpp
    M programs/us_convert/us_convertio.cpp
    M programs/us_convert/us_convertio.h
    M programs/us_convert/us_experiment.cpp
    M programs/us_convert/us_experiment.h
    M programs/us_convert/us_experiment_gui.cpp
    M programs/us_convert/us_experiment_gui.h
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_get_run.h
    M programs/us_convert/us_intensity.cpp
    M programs/us_convert/us_intensity.h
    M programs/us_convert/us_select_triples.cpp
    M programs/us_convert/us_select_triples.h
    M programs/us_convert/us_selectbox.cpp
    M programs/us_convert/us_selectbox.h
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_dcdt/us_dcdt.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_ddist_combine/us_ddist_combine_main.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_ddist_combine/us_select_rundd.h
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_density_match.h
    M programs/us_density_match/us_model_params.cpp
    M programs/us_density_match/us_model_params.h
    M programs/us_density_match/us_remove_models.cpp
    M programs/us_density_match/us_remove_models.h
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_dmga_init/us_constraints_edit.h
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_dmga_init/us_dmga_init.h
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_main.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_edit/us_exclude_profile.cpp
    M programs/us_edit/us_exclude_profile.h
    M programs/us_edit/us_get_edit.cpp
    M programs/us_edit/us_get_edit.h
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_edit/us_ri_noise.h
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_edit/us_select_lambdas.h
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_equiltime/us_equiltime.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.h
    M programs/us_esigner_gmp/us_esigner_gmp_main.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_experiment_main.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_export_legacy/us_export.h
    M programs/us_extinction/us_extinction_main.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.h
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_adv_dmgamc.h
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_advanced_fem.h
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_dmga_mc_stats.h
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_fematch.h
    M programs/us_fematch/us_fematch_main.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fematch/us_resplot_fem.h
    M programs/us_fematch/us_thread_worker.cpp
    M programs/us_fematch/us_thread_worker.h
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_fit_meniscus/us_fit_meniscus_main.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqfit_control.h
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqhistogram.h
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmath.h
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqmodel_control.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_eqreporter.h
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_fit_worker.h
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_globalequil/us_globeq_data.h
    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_adpars.h
    M programs/us_globalequil/us_model_select.cpp
    M programs/us_globalequil/us_model_select.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_grid_editor/us_grid_editor.h
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_helpdaemon/us_helpdaemon.h
    M programs/us_integral/us_delete_models.cpp
    M programs/us_integral/us_delete_models.h
    M programs/us_integral/us_integral.cpp
    M programs/us_integral/us_integral.h
    M programs/us_investigator/us_investigator_main.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_license/us_license.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_model.h
    M programs/us_manage_data/us_data_process.cpp
    M programs/us_manage_data/us_data_process.h
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_data_tree.h
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_manage_data/us_manage_data.h
    M programs/us_manage_data/us_sync_exper.cpp
    M programs/us_manage_data/us_sync_exper.h
    M programs/us_model_gui/main.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_modelmetrics/us_modelmetrics.h
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/2dsa_worker.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/pcsa_worker.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_analysis.h
    M programs/us_mpi_analysis/us_mpi_parse.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_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_species_fit/us_mwl_species_fit_main.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.h
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwl_run.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.h
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_adv_analysis_pc.h
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.h
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mlplot.h
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_mrecs_loader.h
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa.h
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_pcsa/us_plot_control_pc.cpp
    M programs/us_pcsa/us_plot_control_pc.h
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_resplot_pc.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_pcsa/us_worker_pc.cpp
    M programs/us_pcsa/us_worker_pc.h
    M programs/us_predict1/us_predict1_main.cpp
    M programs/us_predict2/us_predict2.cpp
    M programs/us_predict2/us_predict2.h
    M programs/us_predict2/us_predict2_main.cpp
    M programs/us_project/us_project_main.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_protocol_dev/us_protocol_dev_main.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.h
    M programs/us_pseudo3d_combine/us_pseudo3d_combine_main.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.h
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.h
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pabs_common.cpp
    M programs/us_pseudo_absorbance/us_pabs_common.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.h
    M programs/us_pseudo_absorbance/us_refScan_dataIO.cpp
    M programs/us_pseudo_absorbance/us_refScan_dataIO.h
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_query_rmsd/us_query_rmsd.h
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_experiment_gui_ra.h
    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_get_dbrun_ra.h
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_intensity_ra.h
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_mwlramp.h
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp.h
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    M programs/us_ramp/us_ramp_gui.h
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_ramp/us_select_triples_ra.h
    M programs/us_ramp/us_selectbox_ra.cpp
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    M programs/us_rasmol_control/us_rasmol_control.cpp
    M programs/us_rasmol_control/us_rasmol_control.h
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    M programs/us_reporter/us_reporter.h
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    M programs/us_reporter_gmp/us_reporter_gmp_main.cpp
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    M programs/us_rotor_calibration/us_get_dbexp.cpp
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    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_sassoc/us_sassoc_main.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_second_moment/us_second_moment.h
    M programs/us_solution/us_solution_main.cpp
    M programs/us_spectrum/us_spectrum.cpp
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    M programs/us_tmst_viewer/us_tmst_viewer.cpp
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    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
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    M programs/us_vhw_enhanced/us_distrib_plot.cpp
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    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
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    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.h
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.h
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    M qwtplot3d/3rdparty/gl2ps/gl2ps.c
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    M qwtplot3d/examples/autoswitch/autoswitch.cpp
    M qwtplot3d/examples/autoswitch/autoswitch.h
    M qwtplot3d/examples/axes/src/axes.h
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    M qwtplot3d/examples/mesh2/src/functions.h
    M qwtplot3d/examples/mesh2/src/lightingdlg.cpp
    M qwtplot3d/examples/mesh2/src/lightingdlg.h
    M qwtplot3d/examples/mesh2/src/lightingdlgbaseimpl.cpp
    M qwtplot3d/examples/mesh2/src/lightingdlgbaseimpl.h
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    M qwtplot3d/examples/simpleplot/simpleplot.cpp
    M qwtplot3d/include/qwt3d_autoptr.h
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    M qwtplot3d/include/qwt3d_drawable.h
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    M qwtplot3d/include/qwt3d_plot.h
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    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/include/qwt3d_types.h
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    M qwtplot3d/src/qwt3d_dataviews.cpp
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    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_meshplot.cpp
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_parametricsurface.cpp
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    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
    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_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_p3d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_scale_trend.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_simulate.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_stack.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_ift.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_residuals.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_options.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_residuals.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_util.cpp
    M us_somo/develop/src/us_hydrodyn_vdw_overlap.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_xsr.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_license.cpp
    M us_somo/develop/src/us_lm.cpp
    M us_somo/develop/src/us_lud.cpp
    M us_somo/develop/src/us_math.cpp
    M us_somo/develop/src/us_matrix.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_plot_zoom.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_best.cpp
    M us_somo/develop/src/us_pm_best_cylinder.cpp
    M us_somo/develop/src/us_pm_best_ellipsoid.cpp
    M us_somo/develop/src/us_pm_best_sphere.cpp
    M us_somo/develop/src/us_pm_best_spheroid.cpp
    M us_somo/develop/src/us_pm_best_torus.cpp
    M us_somo/develop/src/us_pm_best_torus_segment.cpp
    M us_somo/develop/src/us_pm_fitness.cpp
    M us_somo/develop/src/us_pm_ga.cpp
    M us_somo/develop/src/us_pm_objects.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_register.cpp
    M us_somo/develop/src/us_saxs_gp.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_a2sb.cpp
    M us_somo/develop/src/us_saxs_util_asab1.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_c2check.cpp
    M us_somo/develop/src/us_saxs_util_crysol.cpp
    M us_somo/develop/src/us_saxs_util_cuda.cpp
    M us_somo/develop/src/us_saxs_util_dammin.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_gui_only.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_asab1_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_ift.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.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_nsa_gsm.cpp
    M us_somo/develop/src/us_saxs_util_nsa_sga.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_pm_mpi.cpp
    M us_somo/develop/src/us_saxs_util_sgp.cpp
    M us_somo/develop/src/us_saxs_util_sgp_phys.cpp
    M us_somo/develop/src/us_saxs_util_ssbond.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_sh.cpp
    M us_somo/develop/src/us_surfracer.cpp
    M us_somo/develop/src/us_svd.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/src/us_thread.cpp
    M us_somo/develop/src/us_timer.cpp
    M us_somo/develop/src/us_util.cpp
    M us_somo/develop/src/us_vector.cpp
    M us_somo/develop/src/us_vvv.cpp
    M us_somo/develop/src/us_write_config.cpp
    M us_somo/develop/src/us_zeno_cxx.cpp
    M us_somo/develop/src/us_zeno_cxx_nf.cpp
    M us_somo/develop/us3_config/main.cpp
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_admin/main.cpp
    M us_somo/develop/us_cluster_server_t/main.cpp
    M us_somo/develop/us_cluster_server_t/us_cluster_server_config.h
    M us_somo/develop/us_cluster_server_t/us_cluster_server_global.h
    M us_somo/develop/us_cluster_server_t/us_cluster_server_sockets.h
    M us_somo/develop/us_saxs_cmds_mpi/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi_cuda/main.cpp
    M us_somo/develop/us_saxs_cmds_mpi_cuda/us_cuda.h
    M us_somo/develop/us_saxs_cmds_mpi_cuda/us_semaphore.cpp
    M us_somo/develop/us_saxs_cmds_mpi_cuda/us_semaphore.h
    M us_somo/develop/us_saxs_cmds_t/main.cpp
    M us_somo/develop/us_saxs_cmds_t/us_cuda.h
    M us_somo/extra/genapp/templates/cluster.cpp
    M us_somo/extra/genapp/templates/cluster.h
    M us_somo/extra/genapp/templates/dialog.cpp
    M us_somo/extra/genapp/templates/dialog.h
    M us_somo/extra/genapp/templates/frame.cpp
    M us_somo/extra/genapp/templates/frame.h
    M us_somo/extra/genapp/templates/saxs_util.cpp
    M us_somo/extra/genapp/templates/standard.cpp
    M us_somo/extra/genapp/templates/standard.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_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.cpp
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_constraints.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_defines.h
    M utils/us_dmga_constr.cpp
    M utils/us_dmga_constr.h
    M utils/us_eprofile.cpp
    M utils/us_eprofile.h
    M utils/us_extern.h
    M utils/us_extinctutils.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.cpp
    M utils/us_hardware.h
    M utils/us_http_post.cpp
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_lm.h
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_project.h
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_report_gmp.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_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.cpp
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_solve_sim.h
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.cpp
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h

  Log Message:
  -----------
  Clang-Format-Demonstration GNU



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From noreply at github.com  Fri Aug  8 09:52:32 2025
From: noreply at github.com (alexsav815)
Date: Fri, 08 Aug 2025 08:52:32 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7d9480: adds the ability to include
 a constant baseline of...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue529/b04c6a-43b419@github.com>

  Branch: refs/heads/alexey-dev-issue529
  Home:   https://github.com/ehb54/ultrascan3
  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: 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: 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


Compare: https://github.com/ehb54/ultrascan3/compare/b04c6a0e3ca8...43b41962e22e

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From noreply at github.com  Mon Aug 11 09:36:48 2025
From: noreply at github.com (ehb54)
Date: Mon, 11 Aug 2025 08:36:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] 57b65a: somo zeno warn message only
 if correction selected...
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/3a6a5a-57b65a@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 57b65afc46bc91f5c6878354642b22c65ba66f43
      https://github.com/ehb54/ultrascan3/commit/57b65afc46bc91f5c6878354642b22c65ba66f43
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  somo zeno warn message only if correction selected, allow quit, text update



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From noreply at github.com  Mon Aug 11 16:00:47 2025
From: noreply at github.com (ehb54)
Date: Mon, 11 Aug 2025 15:00:47 -0700
Subject: [us-commits] [ehb54/us3_sql] d5ecd5: [SQL for GMP-ABDE -- ]
 GMP-ABDE: 1. EXP. -- create...
Message-ID: <ehb54/us3_sql/push/refs/heads/master/5b7620-26a635@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/us3_sql
  Commit: d5ecd5e97c85d85728c1f244e906c1a0dafa933d
      https://github.com/ehb54/us3_sql/commit/d5ecd5e97c85d85728c1f244e906c1a0dafa933d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-05 (Mon, 05 May 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

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


  Commit: 94ab9f117b92105b216b1f3fb7115ae31d739977
      https://github.com/ehb54/us3_sql/commit/94ab9f117b92105b216b1f3fb7115ae31d739977
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-11 (Sun, 11 May 2025)

  Changed paths:
    M us3_autoflow_procs.sql

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


  Commit: 0225739955b083dff1d7d8590414de68d248f298
      https://github.com/ehb54/us3_sql/commit/0225739955b083dff1d7d8590414de68d248f298
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-13 (Tue, 13 May 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

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


  Commit: 2017e699286f66daec6b0c100c44a831df7e395b
      https://github.com/ehb54/us3_sql/commit/2017e699286f66daec6b0c100c44a831df7e395b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-14 (Wed, 14 May 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

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


  Commit: 8139df042a72d0b5a2005e14b11e634e135b5ce2
      https://github.com/ehb54/us3_sql/commit/8139df042a72d0b5a2005e14b11e634e135b5ce2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-05-29 (Thu, 29 May 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL for -- ] 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: 26a635a296b37ca73ada4bf98500b47654fc331c
      https://github.com/ehb54/us3_sql/commit/26a635a296b37ca73ada4bf98500b47654fc331c
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  Merge pull request #17 from ehb54/alexey-dev-issue425

Alexey dev issue425:SQL for ABDE GMP framework


Compare: https://github.com/ehb54/us3_sql/compare/5b762070f13c...26a635a296b3

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From noreply at github.com  Mon Aug 11 16:37:22 2025
From: noreply at github.com (HabGab)
Date: Mon, 11 Aug 2025 15:37:22 -0700
Subject: [us-commits] [ehb54/ultrascan3] 08758d: sphinx :D
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/723cef-ac44c7@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 08758dc386186cdbdb46bf7d4049541985ee1175
      https://github.com/ehb54/ultrascan3/commit/08758dc386186cdbdb46bf7d4049541985ee1175
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-06 (Wed, 06 Aug 2025)

  Changed paths:
    A doc/manual/markdown/build/doctrees/vhw_combine.doctree
    A doc/manual/markdown/build/html/_downloads/09267fbfb48386bb84fa7e72e075e944/fit_meniscus.png
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    A doc/manual/markdown/source/vhw_combine.md
    A doc/manual/sphinx/build/doctrees/advanced_config.doctree
    M doc/manual/sphinx/build/doctrees/environment.pickle
    M doc/manual/sphinx/build/doctrees/index.doctree
    A doc/manual/sphinx/build/doctrees/pseudo3d_combine.doctree
    A doc/manual/sphinx/build/doctrees/second_moment.doctree
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    A doc/manual/sphinx/build/html/_images/vhw_histogram.png
    M doc/manual/sphinx/build/html/_sources/index.rst.txt
    A doc/manual/sphinx/build/html/_sources/pseudo3d_combine.rst.txt
    A doc/manual/sphinx/build/html/_sources/second_moment.rst.txt
    A doc/manual/sphinx/build/html/_sources/vhw_combine.rst.txt
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    A doc/manual/sphinx/build/html/_sources/vhw_enhanced.rst.txt
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    A doc/manual/sphinx/build/html/_static/images/gmp/vhw_distribution.png
    M doc/manual/sphinx/build/html/_static/images/load_model_distrib.png
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    M doc/manual/sphinx/build/html/index.html
    M doc/manual/sphinx/build/html/objects.inv
    A doc/manual/sphinx/build/html/pseudo3d_combine.html
    M doc/manual/sphinx/build/html/searchindex.js
    A doc/manual/sphinx/build/html/second_moment.html
    A doc/manual/sphinx/build/html/vhw_combine.html
    A doc/manual/sphinx/build/html/vhw_distrib_plot.html
    A doc/manual/sphinx/build/html/vhw_enhanced.html
    A doc/manual/sphinx/build/html/vwh_combine.html
    M doc/manual/sphinx/source/USstatic/images/ddist_combine.png
    M doc/manual/sphinx/source/USstatic/images/load_model_distrib.png
    M doc/manual/sphinx/source/USstatic/images/pseudo3d_comb_rmv.png
    M doc/manual/sphinx/source/USstatic/images/pseudo3d_combine.png
    M doc/manual/sphinx/source/USstatic/images/select_runs.png
    A doc/manual/sphinx/source/USstatic/images/vhw_enh_groups_res.png
    A doc/manual/sphinx/source/advanced_config.rst
    M doc/manual/sphinx/source/index.rst
    A doc/manual/sphinx/source/pseudo3d_combine.rst
    A doc/manual/sphinx/source/second_moment.rst
    A doc/manual/sphinx/source/temp.txt
    A doc/manual/sphinx/source/vhw_combine.rst
    A doc/manual/sphinx/source/vhw_distrib_plot.rst
    A doc/manual/sphinx/source/vhw_enhanced.rst

  Log Message:
  -----------
  sphinx :D


  Commit: cf353857e4f310e3c8be082a2ddc01bb8cde4fee
      https://github.com/ehb54/ultrascan3/commit/cf353857e4f310e3c8be082a2ddc01bb8cde4fee
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-06 (Wed, 06 Aug 2025)

  Changed paths:
    M .gitignore
    A doc/manual/#Makefile#
    M doc/manual/README
    R doc/manual/html
    R doc/manual/markdown/build/doctrees/environment.pickle
    R doc/manual/markdown/build/doctrees/fit_meniscus.doctree
    R doc/manual/markdown/build/doctrees/index.doctree
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    R doc/manual/markdown/build/html/_images/fit_meniscus.png
    R doc/manual/markdown/build/html/_sources/fit_meniscus.md.txt
    R doc/manual/markdown/build/html/_sources/index.md.txt
    R doc/manual/markdown/build/html/_static/alabaster.css
    R doc/manual/markdown/build/html/_static/basic.css
    R doc/manual/markdown/build/html/_static/custom.css
    R doc/manual/markdown/build/html/_static/doctools.js
    R doc/manual/markdown/build/html/_static/documentation_options.js
    R doc/manual/markdown/build/html/_static/file.png
    R doc/manual/markdown/build/html/_static/language_data.js
    R doc/manual/markdown/build/html/_static/minus.png
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    R doc/manual/markdown/build/html/_static/pygments.css
    R doc/manual/markdown/build/html/_static/searchtools.js
    R doc/manual/markdown/build/html/_static/sphinx_highlight.js
    R doc/manual/markdown/build/html/fit_meniscus.html
    R doc/manual/markdown/build/html/genindex.html
    R doc/manual/markdown/build/html/index.html
    R doc/manual/markdown/build/html/objects.inv
    R doc/manual/markdown/build/html/search.html
    R doc/manual/markdown/build/html/searchindex.js
    A doc/manual/source/Makefile
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  Commit: 95b579e37b79cd6f2be9488e4cf52d198ce75707
      https://github.com/ehb54/ultrascan3/commit/95b579e37b79cd6f2be9488e4cf52d198ce75707
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-06 (Wed, 06 Aug 2025)

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  Log Message:
  -----------
  sphinx
:wq

merge branch 'haben-Dev' of github.com:ehb54/ultrascan3 into haben-Dev


  Commit: 3c5d03acc34b86b7e83f143e4d8b4335706fbddd
      https://github.com/ehb54/ultrascan3/commit/3c5d03acc34b86b7e83f143e4d8b4335706fbddd
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

  Changed paths:
    M doc/manual/sphinx/build/doctrees/environment.pickle
    M doc/manual/sphinx/build/doctrees/index.doctree
    M doc/manual/sphinx/build/doctrees/pseudo3d_combine.doctree
    M doc/manual/sphinx/build/doctrees/second_moment.doctree
    M doc/manual/sphinx/build/doctrees/vhw_enhanced.doctree
    M doc/manual/sphinx/build/html/index.html
    M doc/manual/sphinx/build/html/objects.inv
    M doc/manual/sphinx/build/html/searchindex.js
    M doc/manual/sphinx/source/USstatic/custom.css
    M doc/manual/sphinx/source/USstatic/images/2dsa_advan.png
    M doc/manual/sphinx/source/USstatic/images/2dsa_analys.png
    M doc/manual/sphinx/source/USstatic/images/2dsa_main-c.png
    M doc/manual/sphinx/source/USstatic/images/2dsa_main-o.png
    M doc/manual/sphinx/source/USstatic/images/color-1.png
    M doc/manual/sphinx/source/USstatic/images/color-2.png
    M doc/manual/sphinx/source/USstatic/images/combine_models-idedit.png
    M doc/manual/sphinx/source/USstatic/images/combine_models-save.png
    M doc/manual/sphinx/source/USstatic/images/combine_models.png
    M doc/manual/sphinx/source/USstatic/images/data_loader-edits.png
    M doc/manual/sphinx/source/USstatic/images/database.png
    M doc/manual/sphinx/source/USstatic/images/ddist_combine-selrun.png
    M doc/manual/sphinx/source/USstatic/images/fe_match_3dplot.png
    M doc/manual/sphinx/source/USstatic/images/fe_match_adv.png
    M doc/manual/sphinx/source/USstatic/images/fe_match_sim5.png
    M doc/manual/sphinx/source/USstatic/images/ga_initialize.png
    M doc/manual/sphinx/source/USstatic/images/master-pw.png
    M doc/manual/sphinx/source/USstatic/images/optima_config_edit.png
    M doc/manual/sphinx/source/USstatic/images/optima_config_new.png
    M doc/manual/sphinx/source/USstatic/images/optima_host_config.png
    M doc/manual/sphinx/source/USstatic/images/us_investigator-2.png
    M doc/manual/sphinx/source/USstatic/images/us_investigator.png
    M doc/manual/sphinx/source/USstatic/images/usfont-2.png
    R doc/manual/sphinx/source/advanced_config.rst
    M doc/manual/sphinx/source/conf.py
    M doc/manual/sphinx/source/fit_meniscus.rst
    M doc/manual/sphinx/source/index.rst
    R doc/manual/sphinx/source/pseudo3d_combine.rst
    M doc/manual/sphinx/source/second_moment.rst
    M doc/manual/sphinx/source/temp.txt
    M doc/manual/sphinx/source/time_derivative.rst
    M doc/manual/sphinx/source/us_edit.rst
    M doc/manual/sphinx/source/vhw_distrib_plot.rst
    M doc/manual/sphinx/source/vhw_enhanced.rst

  Log Message:
  -----------
  sphinx with Video


  Commit: ac44c78183aac1dfb347c236b58d7603cea9f01e
      https://github.com/ehb54/ultrascan3/commit/ac44c78183aac1dfb347c236b58d7603cea9f01e
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

  Changed paths:
    M doc/manual/sphinx/build/doctrees/environment.pickle
    M doc/manual/sphinx/build/doctrees/index.doctree
    M doc/manual/sphinx/build/html/index.html
    M doc/manual/sphinx/build/html/objects.inv
    M doc/manual/sphinx/build/html/searchindex.js
    M doc/manual/sphinx/source/USstatic/images/us_modelmetrics-0.png
    M doc/manual/sphinx/source/conf.py
    M doc/manual/sphinx/source/index.rst

  Log Message:
  -----------
  sphinx + video


Compare: https://github.com/ehb54/ultrascan3/compare/723cefc24ad6...ac44c78183aa

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From noreply at github.com  Mon Aug 11 17:54:44 2025
From: noreply at github.com (HabGab)
Date: Mon, 11 Aug 2025 16:54:44 -0700
Subject: [us-commits] [ehb54/ultrascan3] 758f5b: sphinx +video
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/ac44c7-758f5b@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 758f5b8a00af385844fd46b8e52cb59d533f4f67
      https://github.com/ehb54/ultrascan3/commit/758f5b8a00af385844fd46b8e52cb59d533f4f67
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

  Changed paths:
    A doc/manual/source/#Makefile#

  Log Message:
  -----------
  sphinx +video



To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications

From noreply at github.com  Mon Aug 11 18:29:27 2025
From: noreply at github.com (HabGab)
Date: Mon, 11 Aug 2025 17:29:27 -0700
Subject: [us-commits] [ehb54/ultrascan3] 5187ea: sphinx +video
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/758f5b-5187ea@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5187ea4b07f70b3050bfc8df418641b9e63032d6
      https://github.com/ehb54/ultrascan3/commit/5187ea4b07f70b3050bfc8df418641b9e63032d6
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

  Changed paths:
    A doc/manual/source/2dsa.rst
    A doc/manual/source/2dsa_simulated.rst
    A doc/manual/source/3d_plot.rst
    M doc/manual/source/_static/css/custom.css
    A doc/manual/source/_static/custom.css
    M doc/manual/source/_static/images/2dsa_advan.png
    M doc/manual/source/_static/images/2dsa_analys.png
    M doc/manual/source/_static/images/2dsa_main-c.png
    M doc/manual/source/_static/images/2dsa_main-o.png
    M doc/manual/source/_static/images/color-1.png
    M doc/manual/source/_static/images/color-2.png
    M doc/manual/source/_static/images/combine_models-idedit.png
    M doc/manual/source/_static/images/combine_models-save.png
    M doc/manual/source/_static/images/combine_models.png
    A doc/manual/source/_static/images/config_plot.png
    M doc/manual/source/_static/images/data_loader-edits.png
    M doc/manual/source/_static/images/database.png
    M doc/manual/source/_static/images/ddist_combine-selrun.png
    M doc/manual/source/_static/images/ddist_combine.png
    A doc/manual/source/_static/images/fe_load_data.png
    A doc/manual/source/_static/images/fe_load_model_distrib.png
    M doc/manual/source/_static/images/fe_match_3dplot.png
    M doc/manual/source/_static/images/fe_match_adv.png
    A doc/manual/source/_static/images/fe_match_all.png
    A doc/manual/source/_static/images/fe_match_allct.png
    M doc/manual/source/_static/images/fe_match_sim5.png
    A doc/manual/source/_static/images/ga_initialize-o.png
    A doc/manual/source/_static/images/ga_initialize-p.png
    M doc/manual/source/_static/images/ga_initialize.png
    A doc/manual/source/_static/images/ga_report-1.png
    A doc/manual/source/_static/images/ga_report-2.png
    A doc/manual/source/_static/images/ga_report-3.png
    A doc/manual/source/_static/images/idist_comb_selPre.png
    A doc/manual/source/_static/images/idist_comb_seldis.png
    A doc/manual/source/_static/images/idist_combine.png
    M doc/manual/source/_static/images/master-pw.png
    M doc/manual/source/_static/images/optima_config_edit.png
    M doc/manual/source/_static/images/optima_config_new.png
    M doc/manual/source/_static/images/optima_host_config.png
    A doc/manual/source/_static/images/plot_controls.png
    A doc/manual/source/_static/images/print.png
    A doc/manual/source/_static/images/process_crash.png
    A doc/manual/source/_static/images/process_crash2.png
    A doc/manual/source/_static/images/rmsd_query-c.png
    A doc/manual/source/_static/images/rmsd_query-o.png
    A doc/manual/source/_static/images/run_details.png
    M doc/manual/source/_static/images/us_investigator-2.png
    M doc/manual/source/_static/images/us_investigator.png
    M doc/manual/source/_static/images/us_modelmetrics-0.png
    A doc/manual/source/_static/images/us_modmet_report.png
    M doc/manual/source/_static/images/usfont-2.png
    A doc/manual/source/_static/images/vhw_enh_groups_res.png
    A doc/manual/source/combine_models.rst
    A doc/manual/source/common_dialogs.rst
    M doc/manual/source/conf.py
    A doc/manual/source/config.rst
    A doc/manual/source/custom_grid.rst
    A doc/manual/source/ddist_combine.rst
    A doc/manual/source/fe_match.rst
    A doc/manual/source/fe_match_simulate.rst
    M doc/manual/source/fit_meniscus.rst
    A doc/manual/source/ga_initialize.rst
    A doc/manual/source/idist_combine.rst
    A doc/manual/source/import.rst
    M doc/manual/source/index.rst
    A doc/manual/source/pseudo3d.rst
    M doc/manual/source/pseudo3d_combine.rst.txt
    A doc/manual/source/rmsd_query.rst
    A doc/manual/source/run_details.rst
    A doc/manual/source/second_moment.rst
    M doc/manual/source/second_moment.rst.txt
    A doc/manual/source/start_page.rst
    A doc/manual/source/temp.txt
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_edit.rst
    A doc/manual/source/us_investigator.rst
    A doc/manual/source/us_modelmetrics.rst
    A doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_combine.rst.txt
    A doc/manual/source/vhw_distrib_plot.rst
    M doc/manual/source/vhw_distrib_plot.rst.txt
    A doc/manual/source/vhw_enhanced.rst
    M doc/manual/source/vhw_enhanced.rst.txt
    M doc/manual/source/vwh_combine.rst.txt
    M doc/manual/sphinx/build/doctrees/environment.pickle
    M doc/manual/sphinx/build/doctrees/index.doctree
    M doc/manual/sphinx/build/html/index.html
    M doc/manual/sphinx/build/html/objects.inv
    M doc/manual/sphinx/build/html/searchindex.js
    M doc/manual/sphinx/source/index.rst

  Log Message:
  -----------
  sphinx +video



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From noreply at github.com  Tue Aug 12 10:24:26 2025
From: noreply at github.com (ehb54)
Date: Tue, 12 Aug 2025 09:24:26 -0700
Subject: [us-commits] [ehb54/ultrascan3] ff02f8: somo - clear warnings as
 appropriate for release
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/57b65a-7d2d99@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ff02f8a99be56bdd46a08e6fd339b01dec616e39
      https://github.com/ehb54/ultrascan3/commit/ff02f8a99be56bdd46a08e6fd339b01dec616e39
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_revision.h
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_ffd.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_beads.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_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_powerfit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_scale.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_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp

  Log Message:
  -----------
  somo - clear warnings as appropriate for release


  Commit: 7d2d99ddf4f52d64985b0b5dcafafb43278aac09
      https://github.com/ehb54/ultrascan3/commit/7d2d99ddf4f52d64985b0b5dcafafb43278aac09
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  somo zeno - move grpy message before file write check


Compare: https://github.com/ehb54/ultrascan3/compare/57b65afc46bc...7d2d99ddf4f5

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From noreply at github.com  Tue Aug 12 15:16:51 2025
From: noreply at github.com (SophiaBird95)
Date: Tue, 12 Aug 2025 14:16:51 -0700
Subject: [us-commits] [ehb54/ultrascan3] b04c6a: GMP | R&D -- MWL exp.:
 remove lambda-start/end but...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/57684f-6c42a3@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  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: 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: 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


Compare: https://github.com/ehb54/ultrascan3/compare/57684f67ee36...6c42a3106a9f

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From noreply at github.com  Tue Aug 12 15:57:27 2025
From: noreply at github.com (alexsav815)
Date: Tue, 12 Aug 2025 14:57:27 -0700
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-issue536/000000-26a635@github.com>

  Branch: refs/heads/alexey-dev-issue536
  Home:   https://github.com/ehb54/us3_sql

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From noreply at github.com  Tue Aug 12 15:59:18 2025
From: noreply at github.com (alexsav815)
Date: Tue, 12 Aug 2025 14:59:18 -0700
Subject: [us-commits] [ehb54/us3_sql] 2bf4c1: [SQL update for ] -- small fix
 for one of the stor...
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-issue536/26a635-2bf4c1@github.com>

  Branch: refs/heads/alexey-dev-issue536
  Home:   https://github.com/ehb54/us3_sql
  Commit: 2bf4c177f916b50b316c65a2fa24bde7f66434ca
      https://github.com/ehb54/us3_sql/commit/2bf4c177f916b50b316c65a2fa24bde7f66434ca
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL update for ] -- small fix for one of the stored procs called during run sum=bmissio.....



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From noreply at github.com  Tue Aug 12 20:54:51 2025
From: noreply at github.com (ehb54)
Date: Tue, 12 Aug 2025 19:54:51 -0700
Subject: [us-commits] [ehb54/us3_sql] 2bf4c1: [SQL update for ] -- small fix
 for one of the stor...
Message-ID: <ehb54/us3_sql/push/refs/heads/master/26a635-9375d5@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/us3_sql
  Commit: 2bf4c177f916b50b316c65a2fa24bde7f66434ca
      https://github.com/ehb54/us3_sql/commit/2bf4c177f916b50b316c65a2fa24bde7f66434ca
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  [SQL update for ] -- small fix for one of the stored procs called during run sum=bmissio.....


  Commit: 9375d5d070933b3493b5e3685a40bb51ecfa959c
      https://github.com/ehb54/us3_sql/commit/9375d5d070933b3493b5e3685a40bb51ecfa959c
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M us3_autoflow_procs.sql

  Log Message:
  -----------
  Merge pull request #18 from ehb54/alexey-dev-issue536

[SQL update for ] -- small fix for one of the stored procs called dur?


Compare: https://github.com/ehb54/us3_sql/compare/26a635a296b3...9375d5d07093

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From noreply at github.com  Wed Aug 13 12:09:58 2025
From: noreply at github.com (HabGab)
Date: Wed, 13 Aug 2025 11:09:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] ff35d6: source
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/5187ea-b739a2@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ff35d64d4de3a5cef62929fb1ea8b829060a2a0c
      https://github.com/ehb54/ultrascan3/commit/ff35d64d4de3a5cef62929fb1ea8b829060a2a0c
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M doc/manual/source/#Makefile#
    M doc/manual/source/2dsa.rst
    M doc/manual/source/2dsa_simulated.rst
    M doc/manual/source/3d_plot.rst
    M doc/manual/source/Makefile
    M doc/manual/source/_static/images/buffer_edit.png
    A doc/manual/source/_static/images/buffer_edit_setting.png
    A doc/manual/source/_static/images/buffer_edit_spectrum.png
    M doc/manual/source/_static/images/buffer_info.png
    A doc/manual/source/_static/images/buffer_manage_spectrum.png
    M doc/manual/source/_static/images/buffer_new.png
    M doc/manual/source/_static/images/buffer_select.png
    M doc/manual/source/_static/images/buffer_settings.png
    A doc/manual/source/_static/images/spectrum_extinction.png
    A doc/manual/source/_static/images/upload_fit_spectrum.png
    R doc/manual/source/advanced_config.html
    A doc/manual/source/analyte.rst
    A doc/manual/source/buffer.rst
    M doc/manual/source/combine_models.rst
    M doc/manual/source/conf.py
    A doc/manual/source/conf.py-orig.081225
    M doc/manual/source/config.rst
    A doc/manual/source/dens_match.rst
    M doc/manual/source/fe_match.rst
    M doc/manual/source/fe_match_simulate.rst
    M doc/manual/source/ga_initialize.rst
    A doc/manual/source/gmp.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst
    M doc/manual/source/pseudo3d.rst
    R doc/manual/source/pseudo3d_combine.html
    R doc/manual/source/pseudo3d_combine.rst.txt
    R doc/manual/source/second_moment.html
    M doc/manual/source/second_moment.rst
    R doc/manual/source/second_moment.rst.txt
    M doc/manual/source/start_page.rst
    M doc/manual/source/time_derivative.rst
    M doc/manual/source/us_edit.rst
    M doc/manual/source/us_investigator.rst
    R doc/manual/source/vhw_combine.html
    R doc/manual/source/vhw_combine.rst.txt
    R doc/manual/source/vhw_distrib_plot.html
    R doc/manual/source/vhw_distrib_plot.rst.txt
    R doc/manual/source/vhw_enhanced.html
    M doc/manual/source/vhw_enhanced.rst
    R doc/manual/source/vhw_enhanced.rst.txt
    R doc/manual/source/vwh_combine.html
    R doc/manual/source/vwh_combine.rst.txt

  Log Message:
  -----------
  source


  Commit: b739a2c6bf1d14efd83c88d27873a3a582bf6e76
      https://github.com/ehb54/ultrascan3/commit/b739a2c6bf1d14efd83c88d27873a3a582bf6e76
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M doc/manual/source/pseudo3d.rst
    M doc/manual/sphinx/source/USstatic/images/buffer_edit.png
    M doc/manual/sphinx/source/USstatic/images/buffer_info.png
    M doc/manual/sphinx/source/USstatic/images/buffer_select.png
    M doc/manual/sphinx/source/USstatic/images/densmatch_main.png

  Log Message:
  -----------
  source


Compare: https://github.com/ehb54/ultrascan3/compare/5187ea4b07f7...b739a2c6bf1d

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From noreply at github.com  Wed Aug 13 16:40:17 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 15:40:17 -0700
Subject: [us-commits] [ehb54/ultrascan3] ffef3b: somo doc updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/7d2d99-ffef3b@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ffef3bf8caf88b5d9d5a277dadcc446cce68a571
      https://github.com/ehb54/ultrascan3/commit/ffef3bf8caf88b5d9d5a277dadcc446cce68a571
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    A us_somo/somo/doc/manual/somo/Somo_BeadModel_functions_August2025.png
    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_hydro_zeno.html

  Log Message:
  -----------
  somo doc updates



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From noreply at github.com  Wed Aug 13 16:43:22 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 15:43:22 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6/ffef3b-000000@github.com>

  Branch: refs/heads/somo-dev-qt6
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Aug 13 16:43:18 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 15:43:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] 85e259: somo remove some deprecated
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/5bc207-e3fcfc@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 85e259f45bc145d902c03f914f24c40d2f1c07e2
      https://github.com/ehb54/ultrascan3/commit/85e259f45bc145d902c03f914f24c40d2f1c07e2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us3i_util.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_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_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_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.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_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_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_modes_bb.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_modes_bb.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_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_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
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.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_modes_bb.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_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.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_plot_util.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_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_loads.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  somo remove some deprecated


  Commit: c94fb08ce72a7bf4a4ac76a67c2ab9089dc02f26
      https://github.com/ehb54/ultrascan3/commit/c94fb08ce72a7bf4a4ac76a67c2ab9089dc02f26
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us_color.cpp
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_font.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_bd_options.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_grid_atob.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_mals_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_guinier.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_pdb_tool_merge.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_hplc_modes.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_imgviewer.cpp
    M us_somo/develop/src/us_matrix.cpp
    M us_somo/develop/src/us_register.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_grid_atob_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_pat.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/src/us_util.cpp

  Log Message:
  -----------
  somo remove final sprintf deprecated


  Commit: 5e295c4687c78ece7b88d532acb4b5556df13176
      https://github.com/ehb54/ultrascan3/commit/5e295c4687c78ece7b88d532acb4b5556df13176
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    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_tar.h
    M us_somo/develop/include/us_tnt_jama.h
    M us_somo/develop/include/us_unicode.h
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_fractal_dimension.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_fractal_dimension.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.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_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.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_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.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_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.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_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_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_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_zeno_cxx.cpp

  Log Message:
  -----------
  somo remove final deprecated, clean up many warnings


  Commit: 3a6a5a20f729ae35869b1429d94d1d84d7c1b00d
      https://github.com/ehb54/ultrascan3/commit/3a6a5a20f729ae35869b1429d94d1d84d7c1b00d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-04 (Mon, 04 Aug 2025)

  Changed paths:
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_util.cpp

  Log Message:
  -----------
  somo remove more deprecated


  Commit: 57b65afc46bc91f5c6878354642b22c65ba66f43
      https://github.com/ehb54/ultrascan3/commit/57b65afc46bc91f5c6878354642b22c65ba66f43
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  somo zeno warn message only if correction selected, allow quit, text update


  Commit: ff02f8a99be56bdd46a08e6fd339b01dec616e39
      https://github.com/ehb54/ultrascan3/commit/ff02f8a99be56bdd46a08e6fd339b01dec616e39
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_revision.h
    M us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_ffd.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_beads.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_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_powerfit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_scale.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_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp

  Log Message:
  -----------
  somo - clear warnings as appropriate for release


  Commit: 7d2d99ddf4f52d64985b0b5dcafafb43278aac09
      https://github.com/ehb54/ultrascan3/commit/7d2d99ddf4f52d64985b0b5dcafafb43278aac09
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_zeno.cpp

  Log Message:
  -----------
  somo zeno - move grpy message before file write check


  Commit: ffef3bf8caf88b5d9d5a277dadcc446cce68a571
      https://github.com/ehb54/ultrascan3/commit/ffef3bf8caf88b5d9d5a277dadcc446cce68a571
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    A us_somo/somo/doc/manual/somo/Somo_BeadModel_functions_August2025.png
    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_hydro_zeno.html

  Log Message:
  -----------
  somo doc updates


  Commit: e3fcfc4a383a54844007d6da440dc25fa5d3726e
      https://github.com/ehb54/ultrascan3/commit/e3fcfc4a383a54844007d6da440dc25fa5d3726e
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    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_revision.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/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_util.cpp
    M 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_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_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_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_advanced.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_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_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_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
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.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_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
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.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_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_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_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_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
    A us_somo/somo/doc/manual/somo/Somo_BeadModel_functions_August2025.png
    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_hydro_zeno.html

  Log Message:
  -----------
  Merge pull request #252 from ehb54/somo-dev-qt6

merge somo-dev-qt6 to somo-dev


Compare: https://github.com/ehb54/ultrascan3/compare/5bc207f6758a...e3fcfc4a383a

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From noreply at github.com  Wed Aug 13 17:00:36 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 16:00:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] c72de8: doc email fix
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/e3fcfc-c72de8@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c72de8c9af87237bd9e902c0af888aeb3b13d6e6
      https://github.com/ehb54/ultrascan3/commit/c72de8c9af87237bd9e902c0af888aeb3b13d6e6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M us_somo/somo/doc/manual/somo/IntegralBaselineTheory.html
    M us_somo/somo/doc/manual/somo/baseline_best.html
    M us_somo/somo/doc/manual/somo/copyright.html
    M us_somo/somo/doc/manual/somo/cormap.html
    M us_somo/somo/doc/manual/somo/dad_parameters.html
    M us_somo/somo/doc/manual/somo/fractal_dimension_options.html
    M us_somo/somo/doc/manual/somo/mals_options.html
    M us_somo/somo/doc/manual/somo/mals_parameters.html
    M us_somo/somo/doc/manual/somo/mals_saxs_options.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_Gaussian_theory.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_ciq.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_conc_csv_frames.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_dctr.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_nth.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_options.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_p3d.html
    M us_somo/somo/doc/manual/somo/saxs_hplc_parameters.html
    M us_somo/somo/doc/manual/somo/saxs_ift.html
    M us_somo/somo/doc/manual/somo/somo.html
    M us_somo/somo/doc/manual/somo/somo_BEST_Analysis.html
    M us_somo/somo/doc/manual/somo/somo_BEST_setup.html
    M us_somo/somo/doc/manual/somo/somo_Dammin_Dammif_bead_model_properties.html
    M us_somo/somo/doc/manual/somo/somo_SAXS_search.html
    M us_somo/somo/doc/manual/somo/somo_add_saxs.html
    M us_somo/somo/doc/manual/somo/somo_addatom.html
    M us_somo/somo/doc/manual/somo/somo_addhybridization.html
    M us_somo/somo/doc/manual/somo/somo_advanced_config.html
    M us_somo/somo/doc/manual/somo/somo_anaflex_options.html
    M us_somo/somo/doc/manual/somo/somo_asa.html
    M us_somo/somo/doc/manual/somo/somo_batch.html
    M us_somo/somo/doc/manual/somo/somo_bd_options.html
    M us_somo/somo/doc/manual/somo/somo_bead_model_format.html
    M us_somo/somo/doc/manual/somo/somo_bead_output.html
    M us_somo/somo/doc/manual/somo/somo_cluster.html
    M us_somo/somo/doc/manual/somo/somo_cluster_advanced_options.html
    M us_somo/somo/doc/manual/somo/somo_cluster_config.html
    M us_somo/somo/doc/manual/somo/somo_cluster_dmd.html
    M us_somo/somo/doc/manual/somo/somo_cluster_results.html
    M us_somo/somo/doc/manual/somo/somo_cluster_status.html
    M us_somo/somo/doc/manual/somo/somo_cluster_submit.html
    M us_somo/somo/doc/manual/somo/somo_comparative.html
    M us_somo/somo/doc/manual/somo/somo_dammin_opts.html
    M us_somo/somo/doc/manual/somo/somo_dmd_options.html
    M us_somo/somo/doc/manual/somo/somo_file.html
    M us_somo/somo/doc/manual/somo/somo_grid.html
    M us_somo/somo/doc/manual/somo/somo_grid_overlap.html
    M us_somo/somo/doc/manual/somo/somo_hydro.html
    M us_somo/somo/doc/manual/somo/somo_hydro_expert_mode.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html_old
    M us_somo/somo/doc/manual/somo/somo_mals.html
    M us_somo/somo/doc/manual/somo/somo_mals_saxs.html
    M us_somo/somo/doc/manual/somo/somo_misc.html
    M us_somo/somo/doc/manual/somo/somo_overlap.html
    M us_somo/somo/doc/manual/somo/somo_pdb_editor.html
    M us_somo/somo/doc/manual/somo/somo_pdb_editor_merge.html
    M us_somo/somo/doc/manual/somo/somo_pdb_parsing.html
    M us_somo/somo/doc/manual/somo/somo_pdb_parsing_expert_mode.html
    M us_somo/somo/doc/manual/somo/somo_pdb_visualization.html
    M us_somo/somo/doc/manual/somo/somo_residue.html
    M us_somo/somo/doc/manual/somo/somo_results.html
    M us_somo/somo/doc/manual/somo/somo_save.html
    M us_somo/somo/doc/manual/somo/somo_saxs.html
    M us_somo/somo/doc/manual/somo/somo_saxs_buffer.html
    M us_somo/somo/doc/manual/somo/somo_saxs_conc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_baseline_corr.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_fit.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_linear_baselines.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_movie.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_skewedGauss.html
    M us_somo/somo/doc/manual/somo/somo_saxs_hplc_svd.html
    M us_somo/somo/doc/manual/somo/somo_saxs_iqq_residuals.html
    M us_somo/somo/doc/manual/somo/somo_saxs_load_csv.html
    M us_somo/somo/doc/manual/somo/somo_saxs_mw.html
    M us_somo/somo/doc/manual/somo/somo_saxs_options.html
    M us_somo/somo/doc/manual/somo/somo_saxs_residuals.html
    M us_somo/somo/doc/manual/somo/somo_show_hydro.html
    M us_somo/somo/doc/manual/somo/somo_uv_vis.html
    M us_somo/somo/doc/manual/somo/somo_vdw_overlap.html
    M us_somo/somo/doc/manual/somo/underconstruction.html
    M us_somo/somo/doc/manual/somo/uv_vis_options.html

  Log Message:
  -----------
  doc email fix



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From noreply at github.com  Wed Aug 13 17:04:14 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 16:04:14 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/000000-6c42a3@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Aug 13 17:04:40 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 16:04:40 -0700
Subject: [us-commits] [ehb54/ultrascan3] d3d86f: somo doc updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/6c42a3-d3d86f@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Wed Aug 13 17:13:03 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 16:13:03 -0700
Subject: [us-commits] [ehb54/ultrascan3] a2305a: somo updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/d3d86f-a2305a@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Wed Aug 13 19:16:13 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 18:16:13 -0700
Subject: [us-commits] [ehb54/ultrascan3] 535c65: widen zeno hydro window
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/a2305a-535c65@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Wed Aug 13 19:18:00 2025
From: noreply at github.com (ehb54)
Date: Wed, 13 Aug 2025 18:18:00 -0700
Subject: [us-commits] [ehb54/ultrascan3] 0786d0: widen zeno hydro window
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/c72de8-0786d0@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0786d084039346a3fb7c468d9a09f040ae4411cf
      https://github.com/ehb54/ultrascan3/commit/0786d084039346a3fb7c468d9a09f040ae4411cf
  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



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From noreply at github.com  Thu Aug 14 13:24:46 2025
From: noreply at github.com (ehb54)
Date: Thu, 14 Aug 2025 12:24:46 -0700
Subject: [us-commits] [ehb54/ultrascan3] 067234: review updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/535c65-067234@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Thu Aug 14 13:31:28 2025
From: noreply at github.com (ehb54)
Date: Thu, 14 Aug 2025 12:31:28 -0700
Subject: [us-commits] [ehb54/ultrascan3] 010cbe: review updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/067234-010cbe@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Thu Aug 14 13:34:45 2025
From: noreply at github.com (ehb54)
Date: Thu, 14 Aug 2025 12:34:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7c8812: review updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/010cbe-7c8812@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Thu Aug 14 13:36:59 2025
From: noreply at github.com (ehb54)
Date: Thu, 14 Aug 2025 12:36:59 -0700
Subject: [us-commits] [ehb54/ultrascan3] f76772: review updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/7c8812-f76772@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Thu Aug 14 13:44:39 2025
From: noreply at github.com (ehb54)
Date: Thu, 14 Aug 2025 12:44:39 -0700
Subject: [us-commits] [ehb54/ultrascan3] bdd026: review updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/f76772-bdd026@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Thu Aug 14 13:56:40 2025
From: noreply at github.com (ehb54)
Date: Thu, 14 Aug 2025 12:56:40 -0700
Subject: [us-commits] [ehb54/ultrascan3] 46e6d4: review updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/bdd026-46e6d4@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Thu Aug 14 14:13:36 2025
From: noreply at github.com (ehb54)
Date: Thu, 14 Aug 2025 13:13:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] f7f4c3: review updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-pre-auc2025/46e6d4-f7f4c3@github.com>

  Branch: refs/heads/somo-pre-auc2025
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Thu Aug 14 15:17:04 2025
From: noreply at github.com (Borries Demeler)
Date: Thu, 14 Aug 2025 14:17:04 -0700
Subject: [us-commits] [ehb54/ultrascan3] 95345c: add widgets and methods to
 switch between the cons...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/6c42a3-15b11a@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 95345c95c9d0a94b098e06a51f808abb44eca73c
      https://github.com/ehb54/ultrascan3/commit/95345c95c9d0a94b098e06a51f808abb44eca73c
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

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

  Log Message:
  -----------
  add widgets and methods to switch between the constant and varying z-values


  Commit: f1bc04efe3561e38ed1e9efb0ea052d095e0bdc9
      https://github.com/ehb54/ultrascan3/commit/f1bc04efe3561e38ed1e9efb0ea052d095e0bdc9
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-05 (Tue, 05 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: a new widget US_Grid_ZFunction added to set a function for varying z-values


  Commit: 9fefa61cdfe86961bddcc680ce15393cc20a58a4
      https://github.com/ehb54/ultrascan3/commit/9fefa61cdfe86961bddcc680ce15393cc20a58a4
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor.cpp: large update in GUI in the z-value function setter


  Commit: 16bf97037e8256a037e5ebe4007eafefbb000e2c
      https://github.com/ehb54/ultrascan3/commit/16bf97037e8256a037e5ebe4007eafefbb000e2c
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: fixed the issue with labeling and min/max of the dependent variables


  Commit: 24be34a5c69ff149a560999f823643c7b0792349
      https://github.com/ehb54/ultrascan3/commit/24be34a5c69ff149a560999f823643c7b0792349
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: finishe curve fitting and data plotting


  Commit: 9400854e36aec49322a546bb77d2b71df01a6ab3
      https://github.com/ehb54/ultrascan3/commit/9400854e36aec49322a546bb77d2b71df01a6ab3
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  s_grid_editor: correct plot min/max. rename min and max labels of the z-axis


  Commit: 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: 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: 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


Compare: https://github.com/ehb54/ultrascan3/compare/6c42a3106a9f...15b11afbf5ab

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From noreply at github.com  Fri Aug 15 07:03:22 2025
From: noreply at github.com (ehb54)
Date: Fri, 15 Aug 2025 06:03:22 -0700
Subject: [us-commits] [ehb54/ultrascan3] d3d86f: somo doc updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/15b11a-c488e3@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  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
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    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
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    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: 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
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    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
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    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
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    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_powerfit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_movie.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_plots.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
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    M us_somo/develop/src/us_hydrodyn_dammin_opts.cpp
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    M us_somo/develop/src/us_hydrodyn_load.cpp
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    M us_somo/develop/src/us_hydrodyn_results.cpp
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    A us_somo/develop/src/us_hydrodyn_saxs_buffer_fit.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_buffer_gui.cpp
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    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
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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_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


Compare: https://github.com/ehb54/ultrascan3/compare/15b11afbf5ab...c488e3526460

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From noreply at github.com  Fri Aug 15 07:42:48 2025
From: noreply at github.com (ehb54)
Date: Fri, 15 Aug 2025 06:42:48 -0700
Subject: [us-commits] [ehb54/ultrascan3] f57e5f: Delete
 us_somo/develop/include/us_revision.h
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-538-1/000000-f57e5f@github.com>

  Branch: refs/heads/ehb54-issue-538-1
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Fri Aug 15 07:47:49 2025
From: noreply at github.com (ehb54)
Date: Fri, 15 Aug 2025 06:47:49 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4ab58a: somo dev updates to match
 pre auc2025
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/0786d0-4ab58a@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4ab58a31423974894a5169837ff91b47f730384c
      https://github.com/ehb54/ultrascan3/commit/4ab58a31423974894a5169837ff91b47f730384c
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-15 (Fri, 15 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    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:
  -----------
  somo dev updates to match pre auc2025



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From noreply at github.com  Fri Aug 15 09:45:18 2025
From: noreply at github.com (ehb54)
Date: Fri, 15 Aug 2025 08:45:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] f57e5f: Delete
 us_somo/develop/include/us_revision.h
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/c488e3-b3e7a2@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  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


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From noreply at github.com  Fri Aug 15 09:45:22 2025
From: noreply at github.com (ehb54)
Date: Fri, 15 Aug 2025 08:45:22 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-538-1/f57e5f-000000@github.com>

  Branch: refs/heads/ehb54-issue-538-1
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From noreply at github.com  Sat Aug 16 18:33:33 2025
From: noreply at github.com (ehb54)
Date: Sat, 16 Aug 2025 17:33:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] e6f85d: missing manual page
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-538-2/000000-e6f85d@github.com>

  Branch: refs/heads/ehb54-issue-538-2
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Sat Aug 16 20:47:27 2025
From: noreply at github.com (ehb54)
Date: Sat, 16 Aug 2025 19:47:27 -0700
Subject: [us-commits] [ehb54/ultrascan3] 566d9a: somo-dev fix for windows
 symbols
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/4ab58a-566d9a@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 566d9a6677b6d2182f5d4b4b150c7425f53bc1bf
      https://github.com/ehb54/ultrascan3/commit/566d9a6677b6d2182f5d4b4b150c7425f53bc1bf
  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-dev fix for windows symbols



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From noreply at github.com  Sat Aug 16 20:50:18 2025
From: noreply at github.com (ehb54)
Date: Sat, 16 Aug 2025 19:50:18 -0700
Subject: [us-commits] [ehb54/ultrascan3] 2c7eb2: somo - fix for windows
 unicode
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-538-2/e6f85d-2c7eb2@github.com>

  Branch: refs/heads/ehb54-issue-538-2
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Sat Aug 16 21:19:25 2025
From: noreply at github.com (ehb54)
Date: Sat, 16 Aug 2025 20:19:25 -0700
Subject: [us-commits] [ehb54/ultrascan3] b6169a: additional comment line
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-538-2/2c7eb2-b6169a@github.com>

  Branch: refs/heads/ehb54-issue-538-2
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Sat Aug 16 21:20:17 2025
From: noreply at github.com (ehb54)
Date: Sat, 16 Aug 2025 20:20:17 -0700
Subject: [us-commits] [ehb54/ultrascan3] 43ea17: add comment line
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/566d9a-43ea17@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 43ea1704d3366478242cb53cdc63d5655d5feded
      https://github.com/ehb54/ultrascan3/commit/43ea1704d3366478242cb53cdc63d5655d5feded
  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:
  -----------
  add comment line



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From noreply at github.com  Sun Aug 17 10:11:58 2025
From: noreply at github.com (ehb54)
Date: Sun, 17 Aug 2025 09:11:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] e6f85d: missing manual page
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/b3e7a2-b43e6b@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  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


Compare: https://github.com/ehb54/ultrascan3/compare/b3e7a2ce827a...b43e6bb7fdc3

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From noreply at github.com  Tue Aug 19 07:44:42 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 19 Aug 2025 06:44:42 -0700
Subject: [us-commits] [ehb54/ultrascan3] d1d54f: FIX: Adjust the calculation
 of the standard deviat...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_ga_init_stddev/000000-d1d54f@github.com>

  Branch: refs/heads/lukas/us_ga_init_stddev
  Home:   https://github.com/ehb54/ultrascan3
  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



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From noreply at github.com  Tue Aug 19 19:57:10 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 19 Aug 2025 18:57:10 -0700
Subject: [us-commits] [ehb54/ultrascan3] d1d54f: FIX: Adjust the calculation
 of the standard deviat...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/b43e6b-42cef0@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  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


Compare: https://github.com/ehb54/ultrascan3/compare/b43e6bb7fdc3...42cef0425363

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From noreply at github.com  Tue Aug 19 19:57:13 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 19 Aug 2025 18:57:13 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_ga_init_stddev/d1d54f-000000@github.com>

  Branch: refs/heads/lukas/us_ga_init_stddev
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From noreply at github.com  Tue Aug 26 10:37:54 2025
From: noreply at github.com (HabGab)
Date: Tue, 26 Aug 2025 09:37:54 -0700
Subject: [us-commits] [ehb54/ultrascan3] 30106b: latest
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/b739a2-30106b@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 30106bec47b79dce2c858fffdfcb0ec0daa5af6e
      https://github.com/ehb54/ultrascan3/commit/30106bec47b79dce2c858fffdfcb0ec0daa5af6e
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-08-26 (Tue, 26 Aug 2025)

  Changed paths:
    M doc/manual/source/conf.py
    A haben at LAPTOP-GEMRVMH3/2dsa.html
    A haben at LAPTOP-GEMRVMH3/2dsa_simulated.html
    A haben at LAPTOP-GEMRVMH3/3d_plot.html
    A haben at LAPTOP-GEMRVMH3/_images/2dsa_advan.png
    A haben at LAPTOP-GEMRVMH3/_images/2dsa_analys.png
    A haben at LAPTOP-GEMRVMH3/_images/2dsa_main-c.png
    A haben at LAPTOP-GEMRVMH3/_images/2dsa_main-o.png
    A haben at LAPTOP-GEMRVMH3/_images/advanced_config.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_edit.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_edit_setting.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_edit_spectrum.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_info.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_manage_spectrum.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_new.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_select.png
    A haben at LAPTOP-GEMRVMH3/_images/buffer_settings.png
    A haben at LAPTOP-GEMRVMH3/_images/color-1.png
    A haben at LAPTOP-GEMRVMH3/_images/color-2.png
    A haben at LAPTOP-GEMRVMH3/_images/combine_models-idedit.png
    A haben at LAPTOP-GEMRVMH3/_images/combine_models-save.png
    A haben at LAPTOP-GEMRVMH3/_images/combine_models.png
    A haben at LAPTOP-GEMRVMH3/_images/config.png
    A haben at LAPTOP-GEMRVMH3/_images/config_plot.png
    A haben at LAPTOP-GEMRVMH3/_images/data_loader-edits.png
    A haben at LAPTOP-GEMRVMH3/_images/database.png
    A haben at LAPTOP-GEMRVMH3/_images/ddist_combine-selrun.png
    A haben at LAPTOP-GEMRVMH3/_images/ddist_combine.png
    A haben at LAPTOP-GEMRVMH3/_images/densmatch_main.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_load_data.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_load_model_distrib.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_match.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_match_3dplot.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_match_adv.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_match_allct.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_match_sim1.png
    A haben at LAPTOP-GEMRVMH3/_images/fe_match_sim5.png
    A haben at LAPTOP-GEMRVMH3/_images/fit_men-editupd.png
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    A haben at LAPTOP-GEMRVMH3/_sources/fit_meniscus.rst.txt
    A haben at LAPTOP-GEMRVMH3/_sources/ga_initialize.rst.txt
    A haben at LAPTOP-GEMRVMH3/_sources/gmp.rst.txt
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    A haben at LAPTOP-GEMRVMH3/_static/images/manage_data_cmenu-1.png
    A haben at LAPTOP-GEMRVMH3/_static/images/manage_data_cmenu-2.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/model_editor.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/mwlr_view_pltctrl.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/pcsa_mlines-sigm1.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/plot_controls.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/predict2-1.png
    A haben at LAPTOP-GEMRVMH3/_static/images/print.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/pseudo3d_comb_rmv.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/register.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/reporter-details.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/reporter-saveprof.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/reporter-viewitem.png
    A haben at LAPTOP-GEMRVMH3/_static/images/reporter.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/rotor-add.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/rotorstretch-1.png
    A haben at LAPTOP-GEMRVMH3/_static/images/rotorstretch-2.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/rotorstretch-4.png
    A haben at LAPTOP-GEMRVMH3/_static/images/rotorstretch-5.png
    A haben at LAPTOP-GEMRVMH3/_static/images/rotorstretch-6.png
    A haben at LAPTOP-GEMRVMH3/_static/images/rotorstretch-7.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/sassoc/sassoc_01.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/second_moment.png
    A haben at LAPTOP-GEMRVMH3/_static/images/select_edits.png
    A haben at LAPTOP-GEMRVMH3/_static/images/select_runs.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/us_convert/us_convert_03.png
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    A haben at LAPTOP-GEMRVMH3/_static/images/us_convert/us_convert_14.png
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    A html/custom_grid.html
    A html/ddist_combine.html
    A html/dens_match.html
    A html/fe_match.html
    A html/fe_match_simulate.html
    A html/fit_meniscus.html
    A html/ga_initialize.html
    A html/genindex.html
    A html/gmp.html
    A html/idist_combine.html
    A html/import.html
    A html/index.html
    A html/objects.inv
    A html/pseudo3d.html
    A html/rmsd_query.html
    A html/run_details.html
    A html/search.html
    A html/searchindex.js
    A html/second_moment.html
    A html/start_page.html
    A html/time_derivative.html
    A html/us_edit.html
    A html/us_investigator.html
    A html/us_modelmetrics.html
    A html/vhw_combine.html
    A html/vhw_distrib_plot.html
    A html/vhw_enhanced.html

  Log Message:
  -----------
  latest



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From noreply at github.com  Tue Aug 26 13:38:30 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 26 Aug 2025 12:38:30 -0700
Subject: [us-commits] [ehb54/ultrascan3] 235214: makefile update
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/30106b-235214@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 235214f1b9604af8888760d0164abd6363524560
      https://github.com/ehb54/ultrascan3/commit/235214f1b9604af8888760d0164abd6363524560
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-08-26 (Tue, 26 Aug 2025)

  Changed paths:
    R doc/manual/#Makefile#
    M doc/manual/Makefile
    R doc/manual/source/#Makefile#
    M doc/manual/source/Makefile
    M doc/manual/source/conf.py
    M doc/manual/source/requirements.txt

  Log Message:
  -----------
  makefile update



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From noreply at github.com  Wed Aug 27 09:15:57 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 08:15:57 -0700
Subject: [us-commits] [ehb54/ultrascan3] 76e2cf: working set of util unit
 tests
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/0ce7f8-76e2cf@github.com>

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



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From noreply at github.com  Wed Aug 27 09:32:06 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 08:32:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] 7f4140: GMP REPORT,
 custom REPORT -- reduce dependency of ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/76e2cf-3a4240@github.com>

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


Compare: https://github.com/ehb54/ultrascan3/compare/76e2cf6ae4e7...3a4240895ec2

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From noreply at github.com  Wed Aug 27 09:34:23 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 08:34:23 -0700
Subject: [us-commits] [ehb54/ultrascan3] b04c6a: GMP | R&D -- MWL exp.:
 remove lambda-start/end but...
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/3a4240-eb5398@github.com>

  Branch: refs/heads/aaron-dev-test-utils
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b04c6a0e3ca869fe82ecb0c371d7429d546a479c
      https://github.com/ehb54/ultrascan3/commit/b04c6a0e3ca869fe82ecb0c371d7429d546a479c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-07-29 (Tue, 29 Jul 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  GMP | R&D -- MWL exp.: remove lambda-start/end buttons as spurious user interactions.....


  Commit: 95345c95c9d0a94b098e06a51f808abb44eca73c
      https://github.com/ehb54/ultrascan3/commit/95345c95c9d0a94b098e06a51f808abb44eca73c
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-01 (Fri, 01 Aug 2025)

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

  Log Message:
  -----------
  add widgets and methods to switch between the constant and varying z-values


  Commit: f1bc04efe3561e38ed1e9efb0ea052d095e0bdc9
      https://github.com/ehb54/ultrascan3/commit/f1bc04efe3561e38ed1e9efb0ea052d095e0bdc9
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-05 (Tue, 05 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: a new widget US_Grid_ZFunction added to set a function for varying z-values


  Commit: 9fefa61cdfe86961bddcc680ce15393cc20a58a4
      https://github.com/ehb54/ultrascan3/commit/9fefa61cdfe86961bddcc680ce15393cc20a58a4
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor.cpp: large update in GUI in the z-value function setter


  Commit: 16bf97037e8256a037e5ebe4007eafefbb000e2c
      https://github.com/ehb54/ultrascan3/commit/16bf97037e8256a037e5ebe4007eafefbb000e2c
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: fixed the issue with labeling and min/max of the dependent variables


  Commit: 24be34a5c69ff149a560999f823643c7b0792349
      https://github.com/ehb54/ultrascan3/commit/24be34a5c69ff149a560999f823643c7b0792349
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: finishe curve fitting and data plotting


  Commit: 9400854e36aec49322a546bb77d2b71df01a6ab3
      https://github.com/ehb54/ultrascan3/commit/9400854e36aec49322a546bb77d2b71df01a6ab3
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-07 (Thu, 07 Aug 2025)

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

  Log Message:
  -----------
  s_grid_editor: correct plot min/max. rename min and max labels of the z-axis


  Commit: 43b41962e22e4af8e1616b048ce38b8c3714aafa
      https://github.com/ehb54/ultrascan3/commit/43b41962e22e4af8e1616b048ce38b8c3714aafa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-08-08 (Fri, 08 Aug 2025)

  Changed paths:
    M gui/us_sim_params_gui.cpp
    M gui/us_sim_params_gui.h
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h

  Log Message:
  -----------
  Merge pull request #250 from ehb54/master

Bring the branch into up-to-date state with the master


  Commit: d4427c298c0021926269eced3660ad13ddb57da1
      https://github.com/ehb54/ultrascan3/commit/d4427c298c0021926269eced3660ad13ddb57da1
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-08 (Fri, 08 Aug 2025)

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

  Log Message:
  -----------
  completed US_Grid_ZFunction and add functions to parse z expression


  Commit: b28b060a27873c104daa81b246b10d28c06719a7
      https://github.com/ehb54/ultrascan3/commit/b28b060a27873c104daa81b246b10d28c06719a7
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-11 (Mon, 11 Aug 2025)

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

  Log Message:
  -----------
  renamed some of slots. set z-value function is merged to the main program.


  Commit: 9502025efbe734d0d076441a4ce57152c1cb5be1
      https://github.com/ehb54/ultrascan3/commit/9502025efbe734d0d076441a4ce57152c1cb5be1
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

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

  Log Message:
  -----------
  update some variable name and pick a new sorting approach


  Commit: 82dba023d20a191fd66a944d637a5c2ad2b16a87
      https://github.com/ehb54/ultrascan3/commit/82dba023d20a191fd66a944d637a5c2ad2b16a87
  Author: Saeed <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

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

  Log Message:
  -----------
  completed import/export the model file


  Commit: 6c42a3106a9fc648137eb52b102fd9906fd2e1dc
      https://github.com/ehb54/ultrascan3/commit/6c42a3106a9fc648137eb52b102fd9906fd2e1dc
  Author: SophiaBird95 <135044923+SophiaBird95 at users.noreply.github.com>
  Date:   2025-08-12 (Tue, 12 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Merge pull request #243 from ehb54/alexey-dev-issue529

GMP | R&D -- MWL exp.: remove lambda-start/end buttons as spurious user intractions


  Commit: a467c94674c461b9cdf1bf4861ff3b0d826153c4
      https://github.com/ehb54/ultrascan3/commit/a467c94674c461b9cdf1bf4861ff3b0d826153c4
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

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

  Log Message:
  -----------
  parse parameters that already set up in the set-function widget


  Commit: f11e93fa0fdafa964feeb508673735618375692c
      https://github.com/ehb54/ultrascan3/commit/f11e93fa0fdafa964feeb508673735618375692c
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

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

  Log Message:
  -----------
  us_grid_editor: put comments in the header file.


  Commit: 1d528556d364d7b6609e4bd1bdd42e511a7de5a7
      https://github.com/ehb54/ultrascan3/commit/1d528556d364d7b6609e4bd1bdd42e511a7de5a7
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'upstream/master' into issue_532


  Commit: d3d86f69dd9b0447a7a21aa29b0b9fccab83f8fa
      https://github.com/ehb54/ultrascan3/commit/d3d86f69dd9b0447a7a21aa29b0b9fccab83f8fa
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M us_somo/somo/doc/manual/somo/somo-Zeno_optionsNew.png
    M us_somo/somo/doc/manual/somo/somo-main0new.png
    M us_somo/somo/doc/manual/somo/somo-main4.png
    M us_somo/somo/doc/manual/somo/somo.html
    M us_somo/somo/doc/manual/somo/somo_cluster_config.html
    M us_somo/somo/doc/manual/somo/somo_hydro_zeno.html

  Log Message:
  -----------
  somo doc updates


  Commit: a2305a2a45f9bc2b4172267de5ac724cd8ffc3d7
      https://github.com/ehb54/ultrascan3/commit/a2305a2a45f9bc2b4172267de5ac724cd8ffc3d7
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    A us_somo/develop/include/us_band_broaden.h
    M us_somo/develop/include/us_hydrodyn.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_dad.h
    M us_somo/develop/include/us_hydrodyn_hydro.h
    M us_somo/develop/include/us_hydrodyn_hydro_zeno.h
    M us_somo/develop/include/us_hydrodyn_mals.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_buffer.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_ciq.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_movie.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_matrix.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pfortran.h
    A us_somo/develop/include/us_revision.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_tar.h
    M us_somo/develop/include/us_tnt_jama.h
    M us_somo/develop/include/us_unicode.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_util.cpp
    A us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_color.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_ffd.cpp
    M us_somo/develop/src/us_font.cpp
    M us_somo/develop/src/us_fractal_dimension.cpp
    M us_somo/develop/src/us_help.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_load_results_opts.cpp
    M us_somo/develop/src/us_hydrodyn_bd_options.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_advanced.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_powerfit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_movie.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_plots.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dammin_opts.cpp
    M us_somo/develop/src/us_hydrodyn_fractal_dimension.cpp
    M us_somo/develop/src/us_hydrodyn_grid_atob.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate_align.cpp
    M us_somo/develop/src/us_hydrodyn_hydro.cpp
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_mals_movie.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_plots.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gg.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_scale.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_movie.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_misc.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pat.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_results.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_buffer_fit.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_buffer_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_ciq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gg.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    A us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_wheel.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_residuals.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_util.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_imgviewer.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_matrix.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_plot_zoom.cpp
    M us_somo/develop/src/us_pm_fitness.cpp
    M us_somo/develop/src/us_register.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_guinier.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydrate_align.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_grid_atob_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_pat_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_pat.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp
    M us_somo/develop/src/us_util.cpp
    M us_somo/develop/src/us_zeno_cxx.cpp

  Log Message:
  -----------
  somo updates


  Commit: 535c6595f0301d0e1fd51fde59f6be1526723374
      https://github.com/ehb54/ultrascan3/commit/535c6595f0301d0e1fd51fde59f6be1526723374
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-13 (Wed, 13 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_hydro_zeno.cpp

  Log Message:
  -----------
  widen zeno hydro window


  Commit: 067234bbefc26d45806d7b7158a217a02a231acc
      https://github.com/ehb54/ultrascan3/commit/067234bbefc26d45806d7b7158a217a02a231acc
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h

  Log Message:
  -----------
  review updates


  Commit: 010cbe3ff2174263913aa0739e19022fba47b4e5
      https://github.com/ehb54/ultrascan3/commit/010cbe3ff2174263913aa0739e19022fba47b4e5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_config.cpp

  Log Message:
  -----------
  review updates


  Commit: 7c8812172d1813b891f93df82d27f1cb5a9e5540
      https://github.com/ehb54/ultrascan3/commit/7c8812172d1813b891f93df82d27f1cb5a9e5540
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_config.cpp

  Log Message:
  -----------
  review updates


  Commit: f767720f6aacfc70d69615a82f364cb9e31e4d06
      https://github.com/ehb54/ultrascan3/commit/f767720f6aacfc70d69615a82f364cb9e31e4d06
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_config.cpp

  Log Message:
  -----------
  review updates


  Commit: bdd0264a5a222af75694013a39418b3df8caaf62
      https://github.com/ehb54/ultrascan3/commit/bdd0264a5a222af75694013a39418b3df8caaf62
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp

  Log Message:
  -----------
  review updates


  Commit: 46e6d45623e94e8ee5f4caee294f0d4f725cf040
      https://github.com/ehb54/ultrascan3/commit/46e6d45623e94e8ee5f4caee294f0d4f725cf040
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp

  Log Message:
  -----------
  review updates


  Commit: f7f4c399680fe23d645fa3995b1d2666f48a0d05
      https://github.com/ehb54/ultrascan3/commit/f7f4c399680fe23d645fa3995b1d2666f48a0d05
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_util.cpp

  Log Message:
  -----------
  review updates


  Commit: 15b11afbf5ab46b92562c790b64ab027ad3a4a81
      https://github.com/ehb54/ultrascan3/commit/15b11afbf5ab46b92562c790b64ab027ad3a4a81
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-08-14 (Thu, 14 Aug 2025)

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

  Log Message:
  -----------
  Merge pull request #251 from samo38/issue_532

Ticket 532: Custom Grid Enhancement


  Commit: c488e35264600c64881f4e2b9a64eda47383e724
      https://github.com/ehb54/ultrascan3/commit/c488e35264600c64881f4e2b9a64eda47383e724
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-15 (Fri, 15 Aug 2025)

  Changed paths:
    A us_somo/develop/include/us_band_broaden.h
    M us_somo/develop/include/us_hydrodyn.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_dad.h
    M us_somo/develop/include/us_hydrodyn_hydro.h
    M us_somo/develop/include/us_hydrodyn_hydro_zeno.h
    M us_somo/develop/include/us_hydrodyn_mals.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_hydrodyn_saxs_buffer.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_ciq.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_fit.h
    M us_somo/develop/include/us_hydrodyn_saxs_hplc_movie.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_matrix.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pfortran.h
    A us_somo/develop/include/us_revision.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_tar.h
    M us_somo/develop/include/us_tnt_jama.h
    M us_somo/develop/include/us_unicode.h
    M us_somo/develop/libus_somo.pro
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_util.cpp
    A us_somo/develop/src/us_band_broaden.cpp
    M us_somo/develop/src/us_color.cpp
    M us_somo/develop/src/us_config_gui.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_ffd.cpp
    M us_somo/develop/src/us_font.cpp
    M us_somo/develop/src/us_fractal_dimension.cpp
    M us_somo/develop/src/us_help.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_bd_load_results_opts.cpp
    M us_somo/develop/src/us_hydrodyn_bd_options.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_advanced.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gg.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_powerfit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_movie.cpp
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  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:
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  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:
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  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:
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  somo - fix for windows unicode


  Commit: b6169ad5a2b7f4daab15c47ac7732818cc7c68f2
      https://github.com/ehb54/ultrascan3/commit/b6169ad5a2b7f4daab15c47ac7732818cc7c68f2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-08-16 (Sat, 16 Aug 2025)

  Changed paths:
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  additional comment line


  Commit: b43e6bb7fdc3a74faaf03cdc5edf23c76875b783
      https://github.com/ehb54/ultrascan3/commit/b43e6bb7fdc3a74faaf03cdc5edf23c76875b783
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-08-17 (Sun, 17 Aug 2025)

  Changed paths:
    M us_somo/develop/include/us3_defines.h
    M us_somo/develop/src/us_saxs_util_static.cpp
    A us_somo/somo/doc/manual/somo/somo_ZENO_correction_warning.png

  Log Message:
  -----------
  Merge pull request #255 from ehb54/ehb54-issue-538-2

missing manual page, special character issue on windows


  Commit: d1d54f83278fbf935b3d77dd5369947ee304a9f8
      https://github.com/ehb54/ultrascan3/commit/d1d54f83278fbf935b3d77dd5369947ee304a9f8
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-08-19 (Tue, 19 Aug 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
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  FIX: Adjust the calculation of the standard deviation for the weights


  Commit: 42cef0425363b1b72f8c2a1d0d9346f1f00773b0
      https://github.com/ehb54/ultrascan3/commit/42cef0425363b1b72f8c2a1d0d9346f1f00773b0
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-08-19 (Tue, 19 Aug 2025)

  Changed paths:
    M programs/us_ga_init/us_solutedata.cpp

  Log Message:
  -----------
  Merge pull request #256 from ehb54/lukas/us_ga_init_stddev

FIX: Adjust the calculation of the standard deviation for the weights


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

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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
    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


Compare: https://github.com/ehb54/ultrascan3/compare/3a4240895ec2...eb5398d28312

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From noreply at github.com  Wed Aug 27 15:47:11 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 14:47:11 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6c17ff: set to lowercase ius_db2.h
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/eb5398-6c17ff@github.com>

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



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From noreply at github.com  Wed Aug 27 16:54:33 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 15:54:33 -0700
Subject: [us-commits] [ehb54/ultrascan3] 483c6d: add cmake hint file
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/6c17ff-483c6d@github.com>

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



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From noreply at github.com  Wed Aug 27 17:19:08 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 16:19:08 -0700
Subject: [us-commits] [ehb54/ultrascan3] 76997c: iusdb changes
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/483c6d-76997c@github.com>

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



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From noreply at github.com  Wed Aug 27 18:07:06 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 17:07:06 -0700
Subject: [us-commits] [ehb54/ultrascan3] 295b4c: iusdb add qstring
 constuctor, turn off static anal...
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/76997c-295b4c@github.com>

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



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From noreply at github.com  Wed Aug 27 18:33:36 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 27 Aug 2025 17:33:36 -0700
Subject: [us-commits] [ehb54/ultrascan3] 4ba0f8: error in gui build related
 to iusdb2
Message-ID: <ehb54/ultrascan3/push/refs/heads/aaron-dev-test-utils/295b4c-4ba0f8@github.com>

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



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From noreply at github.com  Thu Aug 28 08:39:24 2025
From: noreply at github.com (alexsav815)
Date: Thu, 28 Aug 2025 07:39:24 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue544/000000-42cef0@github.com>

  Branch: refs/heads/alexey-dev-issue544
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Aug 28 11:53:50 2025
From: noreply at github.com (alexsav815)
Date: Thu, 28 Aug 2025 10:53:50 -0700
Subject: [us-commits] [ehb54/ultrascan3] 44bab6: GMP | R&D: 2. LIVE_UPDATE
 -- potential fixes for d...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue544/42cef0-44bab6@github.com>

  Branch: refs/heads/alexey-dev-issue544
  Home:   https://github.com/ehb54/ultrascan3
  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...



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From noreply at github.com  Thu Aug 28 14:39:53 2025
From: noreply at github.com (alexsav815)
Date: Thu, 28 Aug 2025 13:39:53 -0700
Subject: [us-commits] [ehb54/ultrascan3] 54c576: [1]GMP | R&D: 2.
 LIVE_UPDATE -- potential fixes fo...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue544/44bab6-54c576@github.com>

  Branch: refs/heads/alexey-dev-issue544
  Home:   https://github.com/ehb54/ultrascan3
  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...



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From noreply at github.com  Thu Aug 28 14:43:52 2025
From: noreply at github.com (alexsav815)
Date: Thu, 28 Aug 2025 13:43:52 -0700
Subject: [us-commits] [ehb54/ultrascan3] 6eb23e: [2]GMP | R&D: 2.
 LIVE_UPDATE -- potential fixes fo...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue544/54c576-6eb23e@github.com>

  Branch: refs/heads/alexey-dev-issue544
  Home:   https://github.com/ehb54/ultrascan3
  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...



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From noreply at github.com  Thu Aug 28 19:25:37 2025
From: noreply at github.com (alexsav815)
Date: Thu, 28 Aug 2025 18:25:37 -0700
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue545/000000-42cef0@github.com>

  Branch: refs/heads/alexey-dev-issue545
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Aug 28 19:34:35 2025
From: noreply at github.com (alexsav815)
Date: Thu, 28 Aug 2025 18:34:35 -0700
Subject: [us-commits] [ehb54/ultrascan3] b8424a: GMP | R&D: Run MANAGER --
 fix for the wrong event ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue545/42cef0-b8424a@github.com>

  Branch: refs/heads/alexey-dev-issue545
  Home:   https://github.com/ehb54/ultrascan3
  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...



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From noreply at github.com  Fri Aug 29 02:04:41 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 29 Aug 2025 01:04:41 -0700
Subject: [us-commits] [ehb54/ultrascan3] b8424a: GMP | R&D: Run MANAGER --
 fix for the wrong event ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/42cef0-a60894@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  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?


Compare: https://github.com/ehb54/ultrascan3/compare/42cef0425363...a6089455c047

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From noreply at github.com  Fri Aug 29 02:06:58 2025
From: noreply at github.com (Borries Demeler)
Date: Fri, 29 Aug 2025 01:06:58 -0700
Subject: [us-commits] [ehb54/ultrascan3] 44bab6: GMP | R&D: 2. LIVE_UPDATE
 -- potential fixes for d...
Message-ID: <ehb54/ultrascan3/push/refs/heads/master/a60894-55c201@github.com>

  Branch: refs/heads/master
  Home:   https://github.com/ehb54/ultrascan3
  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: 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


Compare: https://github.com/ehb54/ultrascan3/compare/a6089455c047...55c201891699

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From noreply at github.com  Fri Aug 29 10:42:27 2025
From: noreply at github.com (HabGab)
Date: Fri, 29 Aug 2025 09:42:27 -0700
Subject: [us-commits] [ehb54/ultrascan3] f0c0f0: Aug 28
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/235214-f62622@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f0c0f0be2222f595334e55b2f81158d48f2889d7
      https://github.com/ehb54/ultrascan3/commit/f0c0f0be2222f595334e55b2f81158d48f2889d7
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-08-28 (Thu, 28 Aug 2025)

  Changed paths:
    M doc/manual/source/2dsa.rst
    A doc/manual/source/2dsa_simulate.rst
    R doc/manual/source/2dsa_simulated.rst
    M doc/manual/source/3d_plot.rst
    A doc/manual/source/_static/images/D20W_bar.png
    A doc/manual/source/_static/images/MW-bar.png
    A doc/manual/source/_static/images/RINplot.png
    A doc/manual/source/_static/images/TINplot.png
    A doc/manual/source/_static/images/add_RIN-TIN.png
    A doc/manual/source/_static/images/add_RIN.png
    A doc/manual/source/_static/images/add_TIN.png
    A doc/manual/source/_static/images/bitmap.png
    A doc/manual/source/_static/images/fe_match_simulated.png
    A doc/manual/source/_static/images/fe_match_viewer.png
    A doc/manual/source/_static/images/fe_sim-1.png
    A doc/manual/source/_static/images/fe_sim-2.png
    A doc/manual/source/_static/images/residualplot.png
    A doc/manual/source/_static/images/residuals.png
    A doc/manual/source/_static/images/s20W_bar.png
    A doc/manual/source/_static/images/simulatedReport.png
    M doc/manual/source/config.rst
    M doc/manual/source/fe_match.rst
    M doc/manual/source/fe_match_simulate.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/gmp.rst
    M doc/manual/source/index.rst
    M doc/manual/source/rmsd_query.rst

  Log Message:
  -----------
  Aug 28


  Commit: f62622bceb6f96d08b4ad09ac4cc87ff38881b18
      https://github.com/ehb54/ultrascan3/commit/f62622bceb6f96d08b4ad09ac4cc87ff38881b18
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-08-29 (Fri, 29 Aug 2025)

  Changed paths:
    M doc/manual/source/3d_plot.rst
    M doc/manual/source/index.rst
    A doc/manual/source/pcsa.rst

  Log Message:
  -----------
  Aug 29


Compare: https://github.com/ehb54/ultrascan3/compare/235214f1b960...f62622bceb6f

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From noreply at github.com  Fri Aug 29 17:26:45 2025
From: noreply at github.com (HabGab)
Date: Fri, 29 Aug 2025 16:26:45 -0700
Subject: [us-commits] [ehb54/ultrascan3] 484daa: aug 29th
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/f62622-484daa@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 484daa7587119e0292864b52d365aa7a7b4240d2
      https://github.com/ehb54/ultrascan3/commit/484daa7587119e0292864b52d365aa7a7b4240d2
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-08-29 (Fri, 29 Aug 2025)

  Changed paths:
    M doc/manual/source/2dsa_simulate.rst
    A doc/manual/source/_static/images/fit_men_bot.png
    A doc/manual/source/_static/images/hori_cs.png
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  aug 29th



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