From noreply at github.com  Sat Nov  1 15:23:38 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 01 Nov 2025 14:23:38 -0700
Subject: [us-commits] [ehb54/ultrascan3] 9d2f66: mod: remove qt4 code and qt
 5 checks
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/18fcc6-9d2f66@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9d2f668621b521ec83972272c72a14913582c0e2
      https://github.com/ehb54/ultrascan3/commit/9d2f668621b521ec83972272c72a14913582c0e2
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-01 (Sat, 01 Nov 2025)

  Changed paths:
    M alpha/us.cpp
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_util.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

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



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From noreply at github.com  Sat Nov  1 17:08:32 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 01 Nov 2025 16:08:32 -0700
Subject: [us-commits] [ehb54/ultrascan3] 52e0a8: fix: depreciation error
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/9d2f66-52e0a8@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 52e0a85023eb1f0cdb0de69292af086d18a1d727
      https://github.com/ehb54/ultrascan3/commit/52e0a85023eb1f0cdb0de69292af086d18a1d727
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-01 (Sat, 01 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

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



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From noreply at github.com  Sun Nov  2 03:32:51 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 02 Nov 2025 02:32:51 -0800
Subject: [us-commits] [ehb54/ultrascan3] deb377: - Add version-specific
 conditional handling for `s...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/64d841-deb377@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: deb377ae673f2e29f7a776716672ba7550739a87
      https://github.com/ehb54/ultrascan3/commit/deb377ae673f2e29f7a776716672ba7550739a87
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-02 (Sun, 02 Nov 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

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



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From noreply at github.com  Sun Nov  2 10:59:05 2025
From: noreply at github.com (ehb54)
Date: Sun, 02 Nov 2025 09:59:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] bc6d23: somo hplc global gauss
 marker colors
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev/ef4c4a-bc6d23@github.com>

  Branch: refs/heads/somo-dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bc6d238e571e663479d349b1467109c388675e21
      https://github.com/ehb54/ultrascan3/commit/bc6d238e571e663479d349b1467109c388675e21
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-02 (Sun, 02 Nov 2025)

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

  Log Message:
  -----------
  somo hplc global gauss marker colors



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From noreply at github.com  Sun Nov  2 14:47:06 2025
From: noreply at github.com (ehb54)
Date: Sun, 02 Nov 2025 13:47:06 -0800
Subject: [us-commits] [ehb54/ultrascan3] bbfe61: somo-dev
 qregexp->qregularexpression ... initial pass
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/000000-bbfe61@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bbfe61bf7a6754e06262b736ba859e14c704c6bd
      https://github.com/ehb54/ultrascan3/commit/bbfe61bf7a6754e06262b736ba859e14c704c6bd
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-02 (Sun, 02 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/src/us3i_color.cpp
    M us_somo/develop/src/us3i_gzip.cpp
    M us_somo/develop/src/us3i_plot.cpp
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_gzip.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_addresidue.cpp
    M us_somo/develop/src/us_hydrodyn_addsaxs.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_best.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_bfnb_nsa.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_config.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dammin.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_oned.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_results.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_status.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_csv_viewer.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_info.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_save.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_nth.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_dctr.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_bead_model.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_plots.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_json.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_pm.cpp
    M us_somo/develop/src/us_pm_test.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_mpi.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  somo-dev qregexp->qregularexpression ... initial pass



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From noreply at github.com  Sun Nov  2 22:26:23 2025
From: noreply at github.com (aaron-auc)
Date: Sun, 02 Nov 2025 21:26:23 -0800
Subject: [us-commits] [ehb54/ultrascan3] 7e8cbe: mod: add resizing and
 remove extra UTC in label
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/d66e17-7e8cbe@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7e8cbe171f518cc11cbdf6c45239e1232ccb5726
      https://github.com/ehb54/ultrascan3/commit/7e8cbe171f518cc11cbdf6c45239e1232ccb5726
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

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



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From noreply at github.com  Sun Nov  2 22:30:10 2025
From: noreply at github.com (aaron-auc)
Date: Sun, 02 Nov 2025 21:30:10 -0800
Subject: [us-commits] [ehb54/ultrascan3] 675780: fix: add us_win_data.h
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/7e8cbe-675780@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 675780eab109aad6807c5e89cbc50dbdbd962772
      https://github.com/ehb54/ultrascan3/commit/675780eab109aad6807c5e89cbc50dbdbd962772
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us/us.pro

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



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From noreply at github.com  Mon Nov  3 12:08:32 2025
From: noreply at github.com (ehb54)
Date: Mon, 03 Nov 2025 11:08:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] 18f0d1: somo-dev qregexp 2nd round,
 wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/bbfe61-18f0d1@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 18f0d159cf42c5d35c74be39e94f013130036d4f
      https://github.com/ehb54/ultrascan3/commit/18f0d159cf42c5d35c74be39e94f013130036d4f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us3i_settings.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd_core.cpp
    M us_somo/develop/src/us_hydrodyn_beads.cpp
    M us_somo/develop/src/us_hydrodyn_beads_load.cpp
    M us_somo/develop/src/us_hydrodyn_cluster.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_dmd.cpp
    M us_somo/develop/src/us_hydrodyn_cluster_submit.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad.cpp
    M us_somo/develop/src/us_hydrodyn_dad_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc.cpp
    M us_somo/develop/src/us_hydrodyn_dad_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_dad_gui.cpp
    M us_somo/develop/src/us_hydrodyn_dad_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_dad_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_dad_options.cpp
    M us_somo/develop/src/us_hydrodyn_dad_parameters.cpp
    M us_somo/develop/src/us_hydrodyn_dad_svd.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_grpy.cpp
    M us_somo/develop/src/us_hydrodyn_hydrate.cpp
    M us_somo/develop/src/us_hydrodyn_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals.cpp
    M us_somo/develop/src/us_hydrodyn_mals_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_gui.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_options.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_svd.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_merge.cpp
    M us_somo/develop/src/us_hydrodyn_pdb_tool_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_1d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_2d.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_cormap.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_fits.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_guinier.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_baseline_best.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_conc_load.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_gui.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_makeiq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_bb.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_modes_broaden.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_movie.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_options.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_svd.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_loads.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_mw.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_screen.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_search.cpp
    M us_somo/develop/src/us_hydrodyn_script.cpp
    M us_somo/develop/src/us_hydrodyn_settings.cpp
    M us_somo/develop/src/us_hydrodyn_write.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_pdb_util.cpp
    M us_somo/develop/src/us_plot_util.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_best.cpp
    M us_somo/develop/src/us_saxs_util_dmd.cpp
    M us_somo/develop/src/us_saxs_util_extern.cpp
    M us_somo/develop/src/us_saxs_util_hydrate.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d.cpp
    M us_somo/develop/src/us_saxs_util_iqq_1d_mpi.cpp
    M us_somo/develop/src/us_saxs_util_iqq_bead_model.cpp
    M us_somo/develop/src/us_saxs_util_iqq_pdb.cpp
    M us_somo/develop/src/us_saxs_util_loads.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga.cpp
    M us_somo/develop/src/us_saxs_util_nsa_ga_mpi.cpp
    M us_somo/develop/src/us_saxs_util_pm.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp

  Log Message:
  -----------
  somo-dev qregexp 2nd round, wip



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From noreply at github.com  Mon Nov  3 13:59:36 2025
From: noreply at github.com (ehb54)
Date: Mon, 03 Nov 2025 12:59:36 -0800
Subject: [us-commits] [ehb54/ultrascan3] 020f5c: somo-dev qregexp 3rd round,
 wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/18f0d1-020f5c@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 020f5c2befce268fc59a9d7416cbd7aad90105d6
      https://github.com/ehb54/ultrascan3/commit/020f5c2befce268fc59a9d7416cbd7aad90105d6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us_csv.h
    M us_somo/develop/include/us_hydrodyn_cluster_best.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb.h
    M us_somo/develop/include/us_hydrodyn_cluster_bfnb_nsa.h
    M us_somo/develop/include/us_hydrodyn_cluster_dammin.h
    M us_somo/develop/include/us_hydrodyn_cluster_oned.h
    M us_somo/develop/include/us_hydrodyn_saxs.h
    M us_somo/develop/include/us_json.h
    M us_somo/develop/include/us_multi_column.h
    M us_somo/develop/include/us_pdb_util.h
    M us_somo/develop/include/us_saxs_cmds_t.h
    M us_somo/develop/include/us_saxs_util.h
    M us_somo/develop/include/us_vector.h
    M us_somo/develop/src/us_config.cpp
    M us_somo/develop/src/us_file_util.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_addatom.cpp
    M us_somo/develop/src/us_hydrodyn_addhybrid.cpp
    M us_somo/develop/src/us_hydrodyn_anaflex_core.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_core.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit.cpp
    M us_somo/develop/src/us_hydrodyn_dad_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_dad_util.cpp
    M us_somo/develop/src/us_hydrodyn_dmd_core.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_mals_saxs_util.cpp
    M us_somo/develop/src/us_hydrodyn_mals_util.cpp
    M us_somo/develop/src/us_hydrodyn_other.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_buffer.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_external.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_fit_global.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_hplc_util.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_iqq_sh.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_load_csv.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_pr.cpp
    M us_somo/develop/src/us_hydrodyn_supc.cpp
    M us_somo/develop/src/us_hydrodyn_zeno.cpp
    M us_somo/develop/src/us_saxs_util.cpp
    M us_somo/develop/src/us_saxs_util_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_supc_hydro.cpp
    M us_somo/develop/src/us_saxs_util_hydro_zeno_hydro.cpp
    M us_somo/develop/src/us_saxs_util_iqq.cpp
    M us_somo/develop/src/us_saxs_util_static.cpp
    M us_somo/develop/src/us_tar.cpp

  Log Message:
  -----------
  somo-dev qregexp 3rd round, wip



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From noreply at github.com  Mon Nov  3 15:49:14 2025
From: noreply at github.com (alexsav815)
Date: Mon, 03 Nov 2025 14:49:14 -0800
Subject: [us-commits] [ehb54/ultrascan3] b91982: Prot_DEV -- dataDisk type
 of data to reuse in Prot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/08bd6d-b91982@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

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



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From noreply at github.com  Mon Nov  3 16:21:46 2025
From: noreply at github.com (alexsav815)
Date: Mon, 03 Nov 2025 15:21:46 -0800
Subject: [us-commits] [ehb54/ultrascan3] 04ac91: [1]Prot_DEV -- dataDisk
 type of data to reuse in P...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/b91982-04ac91@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

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



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From noreply at github.com  Mon Nov  3 17:04:52 2025
From: noreply at github.com (alexsav815)
Date: Mon, 03 Nov 2025 16:04:52 -0800
Subject: [us-commits] [ehb54/ultrascan3] a107de: [2]Prot_DEV -- dataDisk
 type of data to reuse in P...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/04ac91-a107de@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

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

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



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From noreply at github.com  Mon Nov  3 19:01:15 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 03 Nov 2025 18:01:15 -0800
Subject: [us-commits] [ehb54/ultrascan3] 320d50: fix: splash screen resizing
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/675780-320d50@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 320d50900efb79fdee663f85ef36825cc55e3c3d
      https://github.com/ehb54/ultrascan3/commit/320d50900efb79fdee663f85ef36825cc55e3c3d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h

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



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From noreply at github.com  Mon Nov  3 19:06:30 2025
From: noreply at github.com (alexsav815)
Date: Mon, 03 Nov 2025 18:06:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 773455: [3]Prot_DEV -- dataDisk
 type of data to reuse in P...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/a107de-773455@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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



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From noreply at github.com  Mon Nov  3 22:27:24 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 03 Nov 2025 21:27:24 -0800
Subject: [us-commits] [ehb54/ultrascan3] e2b735: fix: revert icons
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/320d50-e2b735@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e2b73576bf779849331ede9bc596170ef3add7d8
      https://github.com/ehb54/ultrascan3/commit/e2b73576bf779849331ede9bc596170ef3add7d8
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png

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



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From noreply at github.com  Mon Nov  3 23:50:59 2025
From: noreply at github.com (aaron-auc)
Date: Mon, 03 Nov 2025 22:50:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] 53c47a: mod: build defaults to 90%
 cores and vcpkg in home...
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/e2b735-53c47a@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 53c47afaad0a6c5e254d3d2ff216638d871f21a4
      https://github.com/ehb54/ultrascan3/commit/53c47afaad0a6c5e254d3d2ff216638d871f21a4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M scripts/build.sh

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



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From noreply at github.com  Tue Nov  4 09:54:42 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 08:54:42 -0800
Subject: [us-commits] [ehb54/ultrascan3] 93bc9e: somo-dev qt6 updates ... wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/020f5c-93bc9e@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 93bc9ee5954afd87816723fc5f54ba6709581ea9
      https://github.com/ehb54/ultrascan3/commit/93bc9ee5954afd87816723fc5f54ba6709581ea9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us3i_gui_util.h
    M us_somo/develop/include/us_extern.h
    M us_somo/develop/include/us_hydrodyn_cluster.h
    M us_somo/develop/include/us_version.h
    M us_somo/develop/src/qwt/scrollbar.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us3i_gui_util.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_hydrodyn_saxs_legend.cpp

  Log Message:
  -----------
  somo-dev qt6 updates ... wip



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From noreply at github.com  Tue Nov  4 09:56:34 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 08:56:34 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5dc48c: somo-dev qt6 updates ... wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/93bc9e-5dc48c@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5dc48cadfac3d739a020e4a75a1b436c58e9b81e
      https://github.com/ehb54/ultrascan3/commit/5dc48cadfac3d739a020e4a75a1b436c58e9b81e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  somo-dev qt6 updates ... wip



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From noreply at github.com  Tue Nov  4 10:08:52 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 09:08:52 -0800
Subject: [us-commits] [ehb54/ultrascan3] bbf98e: somo-dev qt6 updates ... wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/5dc48c-bbf98e@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bbf98e2edd61b0d2e408a79506885ef0efd8fad3
      https://github.com/ehb54/ultrascan3/commit/bbf98e2edd61b0d2e408a79506885ef0efd8fad3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  somo-dev qt6 updates ... wip



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From noreply at github.com  Tue Nov  4 10:21:19 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 09:21:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4206bd: somo-dev qt6 ... wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/bbf98e-4206bd@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4206bdc2c975463444ade4c318197b0d59f46925
      https://github.com/ehb54/ultrascan3/commit/4206bdc2c975463444ade4c318197b0d59f46925
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  somo-dev qt6 ... wip



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From noreply at github.com  Tue Nov  4 10:24:46 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 09:24:46 -0800
Subject: [us-commits] [ehb54/ultrascan3] 94578d: somo-dev qt6 updates ... wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/4206bd-94578d@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 94578df67d4f74c00d23685dcc6b9f1f72577ead
      https://github.com/ehb54/ultrascan3/commit/94578df67d4f74c00d23685dcc6b9f1f72577ead
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/us3_hydrodyn/main.cpp
    M us_somo/develop/us_saxs_cmds_t/main.cpp

  Log Message:
  -----------
  somo-dev qt6 updates ... wip



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From noreply at github.com  Tue Nov  4 10:45:32 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 09:45:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5e343b: somo-dev qt6 updates remove
 qwt_compat.h
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/94578d-5e343b@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5e343bf7c66094e6a764f781da0fe3c49121f062
      https://github.com/ehb54/ultrascan3/commit/5e343bf7c66094e6a764f781da0fe3c49121f062
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us_somo/develop/include/us3i_plot.h

  Log Message:
  -----------
  somo-dev qt6 updates remove qwt_compat.h



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From noreply at github.com  Tue Nov  4 11:15:58 2025
From: noreply at github.com (alexsav815)
Date: Tue, 04 Nov 2025 10:15:58 -0800
Subject: [us-commits] [ehb54/us3_sql]
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue608/000000-f298e4@github.com>

  Branch: refs/heads/alexey-dev-for-issue608
  Home:   https://github.com/ehb54/us3_sql

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From noreply at github.com  Tue Nov  4 11:30:05 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 10:30:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] 030dbb: somo-dev qt6 wip
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/5e343b-030dbb@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 030dbb8ec9ad65f1f035530663651b27dde1310d
      https://github.com/ehb54/ultrascan3/commit/030dbb8ec9ad65f1f035530663651b27dde1310d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  somo-dev qt6 wip



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From noreply at github.com  Tue Nov  4 12:36:56 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 11:36:56 -0800
Subject: [us-commits] [ehb54/ultrascan3] be2ee4: somo-dev load denss mm fit
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/030dbb-be2ee4@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: be2ee4eb9eabecdcf3f8996ea99d9b442d701750
      https://github.com/ehb54/ultrascan3/commit/be2ee4eb9eabecdcf3f8996ea99d9b442d701750
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  somo-dev load denss mm fit



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From noreply at github.com  Tue Nov  4 12:40:33 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 11:40:33 -0800
Subject: [us-commits] [ehb54/ultrascan3] 3573f2: Stop tracking us_revision.h
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/be2ee4-3573f2@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3573f26e2adf3994546595e13d2b90141a683cc8
      https://github.com/ehb54/ultrascan3/commit/3573f26e2adf3994546595e13d2b90141a683cc8
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    R us_somo/develop/include/us_revision.h

  Log Message:
  -----------
  Stop tracking us_revision.h



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From noreply at github.com  Tue Nov  4 13:04:56 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 12:04:56 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4e1bd9: somo-dev band broaden
 size_t offset -> ptrdiff_t
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/3573f2-4e1bd9@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4e1bd960713104673a6e3c787346ee5664d265bf
      https://github.com/ehb54/ultrascan3/commit/4e1bd960713104673a6e3c787346ee5664d265bf
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  somo-dev band broaden size_t offset -> ptrdiff_t



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From noreply at github.com  Tue Nov  4 13:10:40 2025
From: noreply at github.com (alexsav815)
Date: Tue, 04 Nov 2025 12:10:40 -0800
Subject: [us-commits] [ehb54/ultrascan3] 7fc942: [4]Prot_DEV -- Prep. steps
 for dealing with dataDi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/773455-7fc942@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

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



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From noreply at github.com  Tue Nov  4 13:31:31 2025
From: noreply at github.com (ehb54)
Date: Tue, 04 Nov 2025 12:31:31 -0800
Subject: [us-commits] [ehb54/ultrascan3] 418e00: somo-dev minor text update
Message-ID: <ehb54/ultrascan3/push/refs/heads/somo-dev-qt6-regexp/4e1bd9-418e00@github.com>

  Branch: refs/heads/somo-dev-qt6-regexp
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 418e00417996f4cd2fa2605e4e1f88100256ecea
      https://github.com/ehb54/ultrascan3/commit/418e00417996f4cd2fa2605e4e1f88100256ecea
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

  Log Message:
  -----------
  somo-dev minor text update



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From noreply at github.com  Tue Nov  4 13:42:40 2025
From: noreply at github.com (alexsav815)
Date: Tue, 04 Nov 2025 12:42:40 -0800
Subject: [us-commits] [ehb54/ultrascan3] cff3d6: [55]Prot_DEV -- Prep. steps
 for dealing with dataD...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/7fc942-cff3d6@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

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



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From noreply at github.com  Tue Nov  4 13:48:55 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 04 Nov 2025 12:48:55 -0800
Subject: [us-commits] [ehb54/ultrascan3] 33d884: mod: set a single time and
 reuse
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/53c47a-33d884@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 33d884f14decc31d36934b0a03e70bbed41854c9
      https://github.com/ehb54/ultrascan3/commit/33d884f14decc31d36934b0a03e70bbed41854c9
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

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



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From noreply at github.com  Tue Nov  4 14:22:59 2025
From: noreply at github.com (alexsav815)
Date: Tue, 04 Nov 2025 13:22:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] c280a6: [6]Prot_DEV -- Prep. steps
 for dealing with dataDi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/cff3d6-c280a6@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

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

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



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From noreply at github.com  Tue Nov  4 15:03:22 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 04 Nov 2025 14:03:22 -0800
Subject: [us-commits] [ehb54/ultrascan3] 95598e: mod: additional
 contributors link
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/33d884-95598e@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 95598eae4d07bf9dc43bf02d6e58967bba5d282e
      https://github.com/ehb54/ultrascan3/commit/95598eae4d07bf9dc43bf02d6e58967bba5d282e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us/us.cpp

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



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From noreply at github.com  Tue Nov  4 15:42:19 2025
From: noreply at github.com (alexsav815)
Date: Tue, 04 Nov 2025 14:42:19 -0800
Subject: [us-commits] [ehb54/us3_sql] fdece3: [SQL for ]Prot_DEV -- dataDisk
 type of data to reu...
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue608/f298e4-fdece3@github.com>

  Branch: refs/heads/alexey-dev-for-issue608
  Home:   https://github.com/ehb54/us3_sql
  Commit: fdece366629c8255922408c4b381a7851a008d00
      https://github.com/ehb54/us3_sql/commit/fdece366629c8255922408c4b381a7851a008d00
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M us3_autoflow_procs.sql

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



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From noreply at github.com  Tue Nov  4 15:43:11 2025
From: noreply at github.com (alexsav815)
Date: Tue, 04 Nov 2025 14:43:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1e35e7: [7]Prot_DEV -- Prep. steps
 for dealing with dataDi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/c280a6-1e35e7@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

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



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From noreply at github.com  Tue Nov  4 15:44:43 2025
From: noreply at github.com (aaron-auc)
Date: Tue, 04 Nov 2025 14:44:43 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5aae8e: fix: remove mac x11 lib
 dependency and references ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/52e0a8-baf9c9@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5aae8e45629593aea0b0e007a8f2166c6f60b9c4
      https://github.com/ehb54/ultrascan3/commit/5aae8e45629593aea0b0e007a8f2166c6f60b9c4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  fix: remove mac x11 lib dependency and references to us_window_message


  Commit: d66e17404eb6616c8b39235715683f81791c61b3
      https://github.com/ehb54/ultrascan3/commit/d66e17404eb6616c8b39235715683f81791c61b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: antialiasing deprecation in qpainter


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

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

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


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

  Changed paths:
    M programs/us/us.pro

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h

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


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

  Changed paths:
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png

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


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

  Changed paths:
    M scripts/build.sh

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M gui/libus_gui.pro
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    R scripts/bootstrap.sh
    A scripts/build.sh

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

# Conflicts:
#	programs/us/us.cpp


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

  Changed paths:
    M programs/us/us.cpp

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


Compare: https://github.com/ehb54/ultrascan3/compare/52e0a85023eb...baf9c94ac111

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From noreply at github.com  Tue Nov  4 19:55:32 2025
From: noreply at github.com (alexsav815)
Date: Tue, 04 Nov 2025 18:55:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] 86e9df: [8]Prot_DEV -- Prep. steps
 for dealing with dataDi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/1e35e7-86e9df@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

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



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From noreply at github.com  Wed Nov  5 15:48:30 2025
From: noreply at github.com (alexsav815)
Date: Wed, 05 Nov 2025 14:48:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 47aced: [9]Prot_DEV -- Prep. steps
 for dealing with dataDi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/86e9df-47aced@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

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



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From noreply at github.com  Wed Nov  5 16:19:45 2025
From: noreply at github.com (alexsav815)
Date: Wed, 05 Nov 2025 15:19:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] bf902b: [10]Prot_DEV -- [run names
 for sunsequent PDs] Pre...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/47aced-bf902b@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

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



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From noreply at github.com  Wed Nov  5 16:23:08 2025
From: noreply at github.com (alexsav815)
Date: Wed, 05 Nov 2025 15:23:08 -0800
Subject: [us-commits] [ehb54/ultrascan3] d24d57: [10a]Prot_DEV -- [run names
 for sunsequent PDs] Pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/bf902b-d24d57@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

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



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From noreply at github.com  Wed Nov  5 16:42:17 2025
From: noreply at github.com (alexsav815)
Date: Wed, 05 Nov 2025 15:42:17 -0800
Subject: [us-commits] [ehb54/ultrascan3] 21d578: [11a]Prot_DEV -- [run names
 for sunsequent PDs] Pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/d24d57-21d578@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

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



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From noreply at github.com  Wed Nov  5 17:34:19 2025
From: noreply at github.com (alexsav815)
Date: Wed, 05 Nov 2025 16:34:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1b35ec: [12a]Prot_DEV -- [run names
 for sunsequent PDs] Pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/21d578-1b35ec@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

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

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



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From noreply at github.com  Wed Nov  5 17:52:46 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 05 Nov 2025 16:52:46 -0800
Subject: [us-commits] [ehb54/ultrascan3] 6e58c3: fix: add one newline
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/baf9c9-6e58c3@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6e58c37381bd4ac5dea4ae822375df0d0cbc7b9a
      https://github.com/ehb54/ultrascan3/commit/6e58c37381bd4ac5dea4ae822375df0d0cbc7b9a
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M .gitignore

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



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From noreply at github.com  Wed Nov  5 18:07:08 2025
From: noreply at github.com (alexsav815)
Date: Wed, 05 Nov 2025 17:07:08 -0800
Subject: [us-commits] [ehb54/ultrascan3] 07982e: [13a]Prot_DEV -- [run names
 for sunsequent PDs] Pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/1b35ec-07982e@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

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



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From noreply at github.com  Wed Nov  5 19:15:13 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 05 Nov 2025 18:15:13 -0800
Subject: [us-commits] [ehb54/ultrascan3] 13f85d: fix: add one newline
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/6e58c3-13f85d@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 13f85df6ceb512735407e0c337d01f57429991dc
      https://github.com/ehb54/ultrascan3/commit/13f85df6ceb512735407e0c337d01f57429991dc
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/Us3QrcCheck.cmake
    M admin/cmake/Us3Resources.cmake
    M admin/cmake/UsDefinesParser.cmake
    M admin/cmake/platform-config.cmake
    M doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt

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



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From noreply at github.com  Wed Nov  5 19:41:49 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 05 Nov 2025 18:41:49 -0800
Subject: [us-commits] [ehb54/ultrascan3] cefb4f: add: cmake build update
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/08bd6d-208da0@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cefb4f09592f41675136902739310639b3013aca
      https://github.com/ehb54/ultrascan3/commit/cefb4f09592f41675136902739310639b3013aca
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    M gui/CMakeLists.txt
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_fit_meniscus/CMakeLists.txt
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/bootstrap.sh
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt
    M utils/us_defines.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  add: cmake build update


  Commit: aaeaad6c02761cee619ff74a0115ebbed284238d
      https://github.com/ehb54/ultrascan3/commit/aaeaad6c02761cee619ff74a0115ebbed284238d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    A .gitmodules

  Log Message:
  -----------
  add: vcpkg submodule


  Commit: 752239a4b3601d73dc40a986b5616f860208f51e
      https://github.com/ehb54/ultrascan3/commit/752239a4b3601d73dc40a986b5616f860208f51e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_choice.cpp
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot3d.cpp
    M gui/us_predict1.cpp
    M gui/us_project_gui.cpp
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M gui/us_widgets_dialog.h
    M programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_adv_analysis_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_plot_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.cpp
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_experiment_gui.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_convert/us_select_triples.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.cpp
    M programs/us_density_match/us_remove_models.cpp
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_exclude_profile.cpp
    M programs/us_edit/us_get_edit.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.h
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_long_messagebox.h
    M programs/us_globalequil/us_model_adpars.cpp
    M programs/us_globalequil/us_model_select.cpp
    M programs/us_integral/us_delete_models.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/dmga_worker.cpp
    M programs/us_mpi_analysis/ga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp
    M utils/us_buffer.cpp
    M utils/us_gzip.cpp
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into 534-enhancement-version-upgrade

# Conflicts:
#	gui/us_window_message.cpp
#	programs/us_rasmol_control/us_rasmol_control.cpp


  Commit: aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
      https://github.com/ehb54/ultrascan3/commit/aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-19 (Sun, 19 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    M etc/us3-splash.png
    M gui/CMakeLists.txt
    M gui/images/us3-splash.png
    M programs/CMakeLists.txt
    M programs/us/us.cpp
    M utils/us_defines.h

  Log Message:
  -----------
  add: version to splash screen


  Commit: 7f79da6635b8554a946f428c516d36f3cc0025cf
      https://github.com/ehb54/ultrascan3/commit/7f79da6635b8554a946f428c516d36f3cc0025cf
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A doc/manual/CMakeLists.txt
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h

  Log Message:
  -----------
  mod: color palette


  Commit: d396732b1811c44b0e9b297acf9dbb04b42f5b9e
      https://github.com/ehb54/ultrascan3/commit/d396732b1811c44b0e9b297acf9dbb04b42f5b9e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/UsDefinesParser.cmake
    M utils/us_defines.h

  Log Message:
  -----------
  mod: get version description for build from us_defines


  Commit: 0c3758833374f0f823c94711990117ec205ab239
      https://github.com/ehb54/ultrascan3/commit/0c3758833374f0f823c94711990117ec205ab239
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: remove OS from splash screen


  Commit: 11bbb002a0e60f0eae185c97adcae193b1ad6b40
      https://github.com/ehb54/ultrascan3/commit/11bbb002a0e60f0eae185c97adcae193b1ad6b40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/images/us3-splash.png
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: better font handling improved image


  Commit: 4375dec9c287500081a412353bd6a8d4b0dbd015
      https://github.com/ehb54/ultrascan3/commit/4375dec9c287500081a412353bd6a8d4b0dbd015
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png

  Log Message:
  -----------
  mod: update icons


  Commit: 515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
      https://github.com/ehb54/ultrascan3/commit/515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    A etc/us3-icon-128x128.xpm
    A etc/us3-icon-32x32.ico

  Log Message:
  -----------
  add: icons for all extensions


  Commit: 1f221d2f71c97c26c68d54f94c404ec7a1455bc3
      https://github.com/ehb54/ultrascan3/commit/1f221d2f71c97c26c68d54f94c404ec7a1455bc3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: remove qt4 code


  Commit: 2db3a5f9997a9b2eb153a6af2832c0b693d5e640
      https://github.com/ehb54/ultrascan3/commit/2db3a5f9997a9b2eb153a6af2832c0b693d5e640
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: format code


  Commit: 3a91742fcd41c424cda2dfa8b85cd80aadc2255b
      https://github.com/ehb54/ultrascan3/commit/3a91742fcd41c424cda2dfa8b85cd80aadc2255b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    A etc/README

  Log Message:
  -----------
  add: image readme for image conversion


  Commit: 2569ebda100a0b333a3f529881d53c8771f9aae5
      https://github.com/ehb54/ultrascan3/commit/2569ebda100a0b333a3f529881d53c8771f9aae5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M CMakeLists.txt
    M README.md
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    M admin/release/ubuntu_qt6/Dockerfile
    M doc/manual/advanced_config.body
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_passwd.cpp
    M gui/us_plot.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_table.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa_process.cpp
    M programs/us_2dsa/us_2dsa_process.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_config.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/dmga_worker.cpp
    M programs/us_mpi_analysis/ga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/parallel_masters.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/pmasters_compjob.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M utils/us_ana_profile.cpp
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 534-enhancement-version-upgrade

# Conflicts:
#	programs/us/us.cpp


  Commit: 102666e6eebaafe3144edfce3728a62e33ab053c
      https://github.com/ehb54/ultrascan3/commit/102666e6eebaafe3144edfce3728a62e33ab053c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    A programs/us_2dsa/CMakeLists.txt
    A programs/us_abde/CMakeLists.txt
    A programs/us_analysis_profile/CMakeLists.txt
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    A programs/us_audit_trail_gmp/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    A programs/us_colorgradient/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    A programs/us_convert/CMakeLists.txt
    A programs/us_dcdt/CMakeLists.txt
    A programs/us_ddist_combine/CMakeLists.txt
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    A programs/us_equiltime/CMakeLists.txt
    A programs/us_esigner_gmp/CMakeLists.txt
    A programs/us_export_legacy/CMakeLists.txt
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_ga_init/CMakeLists.txt
    A programs/us_globalequil/CMakeLists.txt
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    A programs/us_mpi_analysis/CMakeLists.txt
    A programs/us_mwl_species_sim/CMakeLists.txt
    A programs/us_mwl_spectra/CMakeLists.txt
    A programs/us_mwlr_viewer/CMakeLists.txt
    A programs/us_pcsa/CMakeLists.txt
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    A programs/us_pseudo3d_combine/CMakeLists.txt
    A programs/us_pseudo_absorbance/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    A programs/us_vhw_enhanced/CMakeLists.txt
    A programs/us_xpn_viewer/CMakeLists.txt
    M scripts/bootstrap.sh
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: simply build by adding profile config


  Commit: 18fcc684bbff2846566a57efafe210efec23cb07
      https://github.com/ehb54/ultrascan3/commit/18fcc684bbff2846566a57efafe210efec23cb07
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

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

  Log Message:
  -----------
  mod: used if-else instead of series of if statements.


  Commit: 5aae8e45629593aea0b0e007a8f2166c6f60b9c4
      https://github.com/ehb54/ultrascan3/commit/5aae8e45629593aea0b0e007a8f2166c6f60b9c4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  fix: remove mac x11 lib dependency and references to us_window_message


  Commit: d66e17404eb6616c8b39235715683f81791c61b3
      https://github.com/ehb54/ultrascan3/commit/d66e17404eb6616c8b39235715683f81791c61b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: antialiasing deprecation in qpainter


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

  Changed paths:
    M alpha/us.cpp
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_util.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

  Changed paths:
    M programs/us/us.pro

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h

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


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

  Changed paths:
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png

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


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

  Changed paths:
    M scripts/build.sh

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M gui/libus_gui.pro
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    R scripts/bootstrap.sh
    A scripts/build.sh

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

# Conflicts:
#	programs/us/us.cpp


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M .gitignore

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


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

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/Us3QrcCheck.cmake
    M admin/cmake/Us3Resources.cmake
    M admin/cmake/UsDefinesParser.cmake
    M admin/cmake/platform-config.cmake
    M doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt

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


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

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

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

597 request qt 6 migration remove qt 4 code


Compare: https://github.com/ehb54/ultrascan3/compare/08bd6d595eb6...208da0fac807

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From noreply at github.com  Wed Nov  5 19:42:00 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 05 Nov 2025 18:42:00 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/13f85d-000000@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Nov  5 20:08:49 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 05 Nov 2025 19:08:49 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/95598e-000000@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Nov  6 07:28:10 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 06 Nov 2025 06:28:10 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/000000-95598e@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Nov  6 07:28:58 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 06 Nov 2025 06:28:58 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/000000-13f85d@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Nov  6 11:32:28 2025
From: noreply at github.com (ehb54)
Date: Thu, 06 Nov 2025 10:32:28 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/000000-208da0@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Nov  6 11:44:08 2025
From: noreply at github.com (ehb54)
Date: Thu, 06 Nov 2025 10:44:08 -0800
Subject: [us-commits] [ehb54/ultrascan3] a05991: testing dockerfiles
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/208da0-a05991@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a05991e06fa9bde2c458757462d5c06d637ca0ae
      https://github.com/ehb54/ultrascan3/commit/a05991e06fa9bde2c458757462d5c06d637ca0ae
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    A admin/release/testing/redhat8_qt6_src/Dockerfile
    A admin/release/testing/redhat8_qt6_src/local.pri.gui
    A admin/release/testing/redhat8_qt6_src/local.pri.somo
    A admin/release/testing/redhat_qt5_qwt630/Dockerfile
    A admin/release/testing/redhat_qt5_qwt630/local.pri.gui
    A admin/release/testing/redhat_qt5_qwt630/local.pri.somo
    A admin/release/testing/redhat_qt6_src/Dockerfile
    A admin/release/testing/redhat_qt6_src/local.pri.gui
    A admin/release/testing/redhat_qt6_src/local.pri.somo

  Log Message:
  -----------
  testing dockerfiles



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From noreply at github.com  Thu Nov  6 11:45:05 2025
From: noreply at github.com (ehb54)
Date: Thu, 06 Nov 2025 10:45:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] 3489f2: Update Dockerfile
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/a05991-3489f2@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3489f250bb3ee95c545e144ffbaf0b2124c65968
      https://github.com/ehb54/ultrascan3/commit/3489f250bb3ee95c545e144ffbaf0b2124c65968
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat8_qt6_src/Dockerfile

  Log Message:
  -----------
  Update Dockerfile



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From noreply at github.com  Thu Nov  6 17:10:28 2025
From: noreply at github.com (HabGab)
Date: Thu, 06 Nov 2025 16:10:28 -0800
Subject: [us-commits] [ehb54/ultrascan3] 00f578: Nov6
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/729897-00f578@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 00f5784667400718ea9d93deb1fdcc6274166782
      https://github.com/ehb54/ultrascan3/commit/00f5784667400718ea9d93deb1fdcc6274166782
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    A doc/manual/source/_static/images/pcsa_all.png
    A doc/manual/source/_static/images/pcsa_bitmap.png
    A doc/manual/source/_static/images/pcsa_mline_sigm.png
    A doc/manual/source/_static/images/pcsa_mline_str.png
    A doc/manual/source/_static/images/pcsa_mline_unsim.png
    A doc/manual/source/_static/images/pcsa_report.png
    A doc/manual/source/_static/images/pcsa_res_viewer.png
    A doc/manual/source/_static/images/pcsa_rpscan.png
    A doc/manual/source/_static/images/pcsa_rpscan_sim.png
    M doc/manual/source/_static/images/us_project1.png
    M doc/manual/source/common_dialogs.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/index.rst
    M doc/manual/source/pcsa/index.rst
    M doc/manual/source/pcsa/pcsa.rst
    A doc/manual/source/pcsa/pcsa_adv.rst
    M doc/manual/source/pcsa/pcsa_analys.rst
    A doc/manual/source/pcsa/pcsa_mlines.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    A doc/manual/source/pcsa/pcsa_rpscan.rst
    M doc/manual/source/projects/index.rst
    M doc/manual/source/solutions/index.rst
    A doc/manual/source/xpn_viewer.rst

  Log Message:
  -----------
  Nov6



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From noreply at github.com  Thu Nov  6 21:18:12 2025
From: noreply at github.com (alexsav815)
Date: Thu, 06 Nov 2025 20:18:12 -0800
Subject: [us-commits] [ehb54/ultrascan3] c8df9d: [15a]Prot_DEV -- [run names
 for sunsequent PDs] Pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/07982e-c8df9d@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

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

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



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From noreply at github.com  Thu Nov  6 22:18:41 2025
From: noreply at github.com (alexsav815)
Date: Thu, 06 Nov 2025 21:18:41 -0800
Subject: [us-commits] [ehb54/us3_sql] d5d2aa: [SQL for -- ] Prot_DEV -- [run
 names for sunsequen...
Message-ID: <ehb54/us3_sql/push/refs/heads/alexey-dev-for-issue608/fdece3-d5d2aa@github.com>

  Branch: refs/heads/alexey-dev-for-issue608
  Home:   https://github.com/ehb54/us3_sql
  Commit: d5d2aab313c1cfd788221a82090c53274047c859
      https://github.com/ehb54/us3_sql/commit/d5d2aab313c1cfd788221a82090c53274047c859
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M us3.sql
    M us3_autoflow_procs.sql

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



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From noreply at github.com  Thu Nov  6 22:25:03 2025
From: noreply at github.com (alexsav815)
Date: Thu, 06 Nov 2025 21:25:03 -0800
Subject: [us-commits] [ehb54/ultrascan3] c15907: [16a]Prot_DEV -- [run names
 for sunsequent PDs] Pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/c8df9d-c15907@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

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



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From noreply at github.com  Fri Nov  7 02:47:21 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 07 Nov 2025 01:47:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] cefb4f: add: cmake build update
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/deb377-fe96d5@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cefb4f09592f41675136902739310639b3013aca
      https://github.com/ehb54/ultrascan3/commit/cefb4f09592f41675136902739310639b3013aca
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    M gui/CMakeLists.txt
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_fit_meniscus/CMakeLists.txt
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/bootstrap.sh
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt
    M utils/us_defines.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  add: cmake build update


  Commit: aaeaad6c02761cee619ff74a0115ebbed284238d
      https://github.com/ehb54/ultrascan3/commit/aaeaad6c02761cee619ff74a0115ebbed284238d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    A .gitmodules

  Log Message:
  -----------
  add: vcpkg submodule


  Commit: 752239a4b3601d73dc40a986b5616f860208f51e
      https://github.com/ehb54/ultrascan3/commit/752239a4b3601d73dc40a986b5616f860208f51e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_choice.cpp
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot3d.cpp
    M gui/us_predict1.cpp
    M gui/us_project_gui.cpp
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M gui/us_widgets_dialog.h
    M programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_adv_analysis_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_plot_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.cpp
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_experiment_gui.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_convert/us_select_triples.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.cpp
    M programs/us_density_match/us_remove_models.cpp
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_exclude_profile.cpp
    M programs/us_edit/us_get_edit.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.h
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_long_messagebox.h
    M programs/us_globalequil/us_model_adpars.cpp
    M programs/us_globalequil/us_model_select.cpp
    M programs/us_integral/us_delete_models.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/dmga_worker.cpp
    M programs/us_mpi_analysis/ga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp
    M utils/us_buffer.cpp
    M utils/us_gzip.cpp
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into 534-enhancement-version-upgrade

# Conflicts:
#	gui/us_window_message.cpp
#	programs/us_rasmol_control/us_rasmol_control.cpp


  Commit: aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
      https://github.com/ehb54/ultrascan3/commit/aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-19 (Sun, 19 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    M etc/us3-splash.png
    M gui/CMakeLists.txt
    M gui/images/us3-splash.png
    M programs/CMakeLists.txt
    M programs/us/us.cpp
    M utils/us_defines.h

  Log Message:
  -----------
  add: version to splash screen


  Commit: 7f79da6635b8554a946f428c516d36f3cc0025cf
      https://github.com/ehb54/ultrascan3/commit/7f79da6635b8554a946f428c516d36f3cc0025cf
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A doc/manual/CMakeLists.txt
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h

  Log Message:
  -----------
  mod: color palette


  Commit: d396732b1811c44b0e9b297acf9dbb04b42f5b9e
      https://github.com/ehb54/ultrascan3/commit/d396732b1811c44b0e9b297acf9dbb04b42f5b9e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/UsDefinesParser.cmake
    M utils/us_defines.h

  Log Message:
  -----------
  mod: get version description for build from us_defines


  Commit: 0c3758833374f0f823c94711990117ec205ab239
      https://github.com/ehb54/ultrascan3/commit/0c3758833374f0f823c94711990117ec205ab239
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: remove OS from splash screen


  Commit: 11bbb002a0e60f0eae185c97adcae193b1ad6b40
      https://github.com/ehb54/ultrascan3/commit/11bbb002a0e60f0eae185c97adcae193b1ad6b40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/images/us3-splash.png
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: better font handling improved image


  Commit: 4375dec9c287500081a412353bd6a8d4b0dbd015
      https://github.com/ehb54/ultrascan3/commit/4375dec9c287500081a412353bd6a8d4b0dbd015
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png

  Log Message:
  -----------
  mod: update icons


  Commit: 515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
      https://github.com/ehb54/ultrascan3/commit/515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    A etc/us3-icon-128x128.xpm
    A etc/us3-icon-32x32.ico

  Log Message:
  -----------
  add: icons for all extensions


  Commit: 1f221d2f71c97c26c68d54f94c404ec7a1455bc3
      https://github.com/ehb54/ultrascan3/commit/1f221d2f71c97c26c68d54f94c404ec7a1455bc3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: remove qt4 code


  Commit: 2db3a5f9997a9b2eb153a6af2832c0b693d5e640
      https://github.com/ehb54/ultrascan3/commit/2db3a5f9997a9b2eb153a6af2832c0b693d5e640
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: format code


  Commit: 3a91742fcd41c424cda2dfa8b85cd80aadc2255b
      https://github.com/ehb54/ultrascan3/commit/3a91742fcd41c424cda2dfa8b85cd80aadc2255b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    A etc/README

  Log Message:
  -----------
  add: image readme for image conversion


  Commit: 2569ebda100a0b333a3f529881d53c8771f9aae5
      https://github.com/ehb54/ultrascan3/commit/2569ebda100a0b333a3f529881d53c8771f9aae5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M CMakeLists.txt
    M README.md
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    M admin/release/ubuntu_qt6/Dockerfile
    M doc/manual/advanced_config.body
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_passwd.cpp
    M gui/us_plot.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_table.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa_process.cpp
    M programs/us_2dsa/us_2dsa_process.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_config.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/dmga_worker.cpp
    M programs/us_mpi_analysis/ga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/parallel_masters.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/pmasters_compjob.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M utils/us_ana_profile.cpp
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 534-enhancement-version-upgrade

# Conflicts:
#	programs/us/us.cpp


  Commit: 102666e6eebaafe3144edfce3728a62e33ab053c
      https://github.com/ehb54/ultrascan3/commit/102666e6eebaafe3144edfce3728a62e33ab053c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    A programs/us_2dsa/CMakeLists.txt
    A programs/us_abde/CMakeLists.txt
    A programs/us_analysis_profile/CMakeLists.txt
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    A programs/us_audit_trail_gmp/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    A programs/us_colorgradient/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    A programs/us_convert/CMakeLists.txt
    A programs/us_dcdt/CMakeLists.txt
    A programs/us_ddist_combine/CMakeLists.txt
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    A programs/us_equiltime/CMakeLists.txt
    A programs/us_esigner_gmp/CMakeLists.txt
    A programs/us_export_legacy/CMakeLists.txt
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_ga_init/CMakeLists.txt
    A programs/us_globalequil/CMakeLists.txt
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    A programs/us_mpi_analysis/CMakeLists.txt
    A programs/us_mwl_species_sim/CMakeLists.txt
    A programs/us_mwl_spectra/CMakeLists.txt
    A programs/us_mwlr_viewer/CMakeLists.txt
    A programs/us_pcsa/CMakeLists.txt
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    A programs/us_pseudo3d_combine/CMakeLists.txt
    A programs/us_pseudo_absorbance/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    A programs/us_vhw_enhanced/CMakeLists.txt
    A programs/us_xpn_viewer/CMakeLists.txt
    M scripts/bootstrap.sh
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: simply build by adding profile config


  Commit: 18fcc684bbff2846566a57efafe210efec23cb07
      https://github.com/ehb54/ultrascan3/commit/18fcc684bbff2846566a57efafe210efec23cb07
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

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

  Log Message:
  -----------
  mod: used if-else instead of series of if statements.


  Commit: 5aae8e45629593aea0b0e007a8f2166c6f60b9c4
      https://github.com/ehb54/ultrascan3/commit/5aae8e45629593aea0b0e007a8f2166c6f60b9c4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  fix: remove mac x11 lib dependency and references to us_window_message


  Commit: d66e17404eb6616c8b39235715683f81791c61b3
      https://github.com/ehb54/ultrascan3/commit/d66e17404eb6616c8b39235715683f81791c61b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: antialiasing deprecation in qpainter


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

  Changed paths:
    M alpha/us.cpp
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_util.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

  Changed paths:
    M programs/us/us.pro

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h

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


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

  Changed paths:
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png

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


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

  Changed paths:
    M scripts/build.sh

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M gui/libus_gui.pro
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    R scripts/bootstrap.sh
    A scripts/build.sh

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

# Conflicts:
#	programs/us/us.cpp


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M .gitignore

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


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

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/Us3QrcCheck.cmake
    M admin/cmake/Us3Resources.cmake
    M admin/cmake/UsDefinesParser.cmake
    M admin/cmake/platform-config.cmake
    M doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt

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


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

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

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

597 request qt 6 migration remove qt 4 code


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/deb377ae673f...fe96d5575a8f

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From noreply at github.com  Fri Nov  7 06:20:05 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 07 Nov 2025 05:20:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4d8935: - Remove redundant `#endif`
 directive in `us_show_...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/fe96d5-8d6d6c@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4d8935a878d0e3a7a55933b8f1ac3b616f8daf6b
      https://github.com/ehb54/ultrascan3/commit/4d8935a878d0e3a7a55933b8f1ac3b616f8daf6b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp

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


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

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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/fe96d5575a8f...8d6d6c8b7f04

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From noreply at github.com  Fri Nov  7 07:55:23 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 07 Nov 2025 06:55:23 -0800
Subject: [us-commits] [ehb54/ultrascan3] 21062f: Replace
 `QRegularExpression` with `QStringLiteral`...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/8d6d6c-e1c24e@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 21062f87c59071f5d7763db68f6ee141ccb2bf99
      https://github.com/ehb54/ultrascan3/commit/21062f87c59071f5d7763db68f6ee141ccb2bf99
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp

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


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

  Changed paths:
    M gui/us_analyte_gui.cpp

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

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


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

  Changed paths:
    M gui/us_model_loader.cpp

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


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

  Changed paths:
    M gui/us_spectrodata.cpp

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


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

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

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

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


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

  Changed paths:
    M CMakeLists.txt

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/8d6d6c8b7f04...e1c24e44caea

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From noreply at github.com  Fri Nov  7 08:11:34 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 07 Nov 2025 07:11:34 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1582fd: Disable `BUILD_TESTING` by
 default in CMake config...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/e1c24e-1582fd@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1582fd4d72e144c840fd83c29710ddcca650cfea
      https://github.com/ehb54/ultrascan3/commit/1582fd4d72e144c840fd83c29710ddcca650cfea
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M CMakeLists.txt

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



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From noreply at github.com  Fri Nov  7 13:47:21 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 07 Nov 2025 12:47:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] d97b94: Refactor and optimize code
 for improved readabilit...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/1582fd-d97b94@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d97b94cfc728b74cdc4d22f4294fba7444bd03fd
      https://github.com/ehb54/ultrascan3/commit/d97b94cfc728b74cdc4d22f4294fba7444bd03fd
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

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

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

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



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From noreply at github.com  Fri Nov  7 14:41:32 2025
From: noreply at github.com (HabGab)
Date: Fri, 07 Nov 2025 13:41:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] 493670: nov 7
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/00f578-493670@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 49367092a62a7d4a77fed5442ee6884fd5c4aee1
      https://github.com/ehb54/ultrascan3/commit/49367092a62a7d4a77fed5442ee6884fd5c4aee1
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    M doc/manual/source/2dsa/index.rst
    A doc/manual/source/_static/images/data_converter.png
    A doc/manual/source/_static/images/export_leg_1.png
    A doc/manual/source/_static/images/export_leg_RA.png
    A doc/manual/source/_static/images/export_leg_RI.png
    A doc/manual/source/_static/images/export_leg_auc.png
    A doc/manual/source/_static/images/export_leg_beck.png
    M doc/manual/source/_static/images/export_legacy.png
    A doc/manual/source/export_legacy.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fe_match/fe_match_simulate.rst
    M doc/manual/source/idist_combine.rst
    M doc/manual/source/index.rst

  Log Message:
  -----------
  nov 7



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From noreply at github.com  Fri Nov  7 17:59:51 2025
From: noreply at github.com (HabGab)
Date: Fri, 07 Nov 2025 16:59:51 -0800
Subject: [us-commits] [ehb54/ultrascan3] b0cf16: nov 7 2
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/493670-b0cf16@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b0cf16b849bcaa5474ac2aac16cf3a2ea5b41056
      https://github.com/ehb54/ultrascan3/commit/b0cf16b849bcaa5474ac2aac16cf3a2ea5b41056
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-11-07 (Fri, 07 Nov 2025)

  Changed paths:
    A doc/manual/source/_static/images/us_conv-RA.png
    A doc/manual/source/_static/images/us_convert_01.png
    A doc/manual/source/_static/images/us_convert_02.png
    A doc/manual/source/_static/images/us_convert_03.png
    A doc/manual/source/_static/images/us_convert_04.png
    A doc/manual/source/_static/images/us_convert_05.png
    A doc/manual/source/_static/images/us_convert_06.png
    A doc/manual/source/_static/images/us_convert_07.png
    A doc/manual/source/_static/images/us_convert_08.png
    A doc/manual/source/_static/images/us_convert_09.png
    A doc/manual/source/_static/images/us_convert_10.png
    A doc/manual/source/_static/images/us_convert_11.png
    A doc/manual/source/_static/images/us_convert_12.png
    A doc/manual/source/_static/images/us_convert_13.png
    A doc/manual/source/_static/images/us_convert_14.png
    A doc/manual/source/_static/images/us_convert_definedscans.png
    A doc/manual/source/_static/images/us_convert_definesubset.png
    M doc/manual/source/config.rst
    A doc/manual/source/convert.rst
    M doc/manual/source/export_legacy.rst
    R doc/manual/source/import.rst
    M doc/manual/source/index.rst
    R doc/manual/source/projects/index.rst
    M doc/manual/source/solutions/index.rst
    A doc/manual/source/solutions/solution_new.rst
    A doc/manual/source/us_project.rst

  Log Message:
  -----------
  nov 7 2



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From noreply at github.com  Sat Nov  8 13:26:16 2025
From: noreply at github.com (alexsav815)
Date: Sat, 08 Nov 2025 12:26:16 -0800
Subject: [us-commits] [ehb54/ultrascan3] 7684ca: [17a]Prot_DEV -- [run names
 for sunsequent PDs] Pr...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/c15907-7684ca@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

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



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From noreply at github.com  Sat Nov  8 22:09:32 2025
From: noreply at github.com (ehb54)
Date: Sat, 08 Nov 2025 21:09:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] bad372: ubuntu24 docker images for
 usbuildtest
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/3489f2-d9428f@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: bad3722a320f36468b0f7ce1ea17191bc4264bfa
      https://github.com/ehb54/ultrascan3/commit/bad3722a320f36468b0f7ce1ea17191bc4264bfa
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

  Changed paths:
    A admin/release/testing/ubuntu24_qt6_src/Dockerfile
    A admin/release/testing/ubuntu24_qt6_src/local.pri.gui
    A admin/release/testing/ubuntu24_qt6_src/local.pri.somo

  Log Message:
  -----------
  ubuntu24 docker images for usbuildtest


  Commit: d9428f06791484625a68dd1559827a61031d01b2
      https://github.com/ehb54/ultrascan3/commit/d9428f06791484625a68dd1559827a61031d01b2
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat8_qt6_src/Dockerfile

  Log Message:
  -----------
  Merge remote-tracking branch 'refs/remotes/origin/ehb54-container-testing' into ehb54-container-testing


Compare: https://github.com/ehb54/ultrascan3/compare/3489f250bb3e...d9428f067914

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From noreply at github.com  Sun Nov  9 11:40:16 2025
From: noreply at github.com (ehb54)
Date: Sun, 09 Nov 2025 10:40:16 -0800
Subject: [us-commits] [ehb54/ultrascan3] a83947: Refactor Label class in
 qwt3d_label.cpp
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-patch-2/000000-a83947@github.com>

  Branch: refs/heads/ehb54-patch-2
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a839472cfe079feac0134e0205885649e0c8c788
      https://github.com/ehb54/ultrascan3/commit/a839472cfe079feac0134e0205885649e0c8c788
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

  Changed paths:
    M qwtplot3d/src/qwt3d_label.cpp

  Log Message:
  -----------
  Refactor Label class in qwt3d_label.cpp

Version check to 6.9 for flipped()



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From noreply at github.com  Sun Nov  9 12:04:17 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 09 Nov 2025 11:04:17 -0800
Subject: [us-commits] [ehb54/ultrascan3] 25c3b6: Add `openglwidgets` to
 project dependencies
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/d97b94-429e64@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 25c3b692febb46e387afcec3bd534dcbebe88222
      https://github.com/ehb54/ultrascan3/commit/25c3b692febb46e387afcec3bd534dcbebe88222
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

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

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

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


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

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

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

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


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

  Changed paths:
    M qwtplot3d/src/qwt3d_label.cpp

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/d97b94cfc728...429e64f9ebb3

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From noreply at github.com  Sun Nov  9 12:18:30 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 09 Nov 2025 11:18:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 535738: Add conditional
 `openglwidgets` inclusion based on...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/429e64-535738@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5357385a614755a654c3bd5aaf8e001b508a7849
      https://github.com/ehb54/ultrascan3/commit/5357385a614755a654c3bd5aaf8e001b508a7849
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-09 (Sun, 09 Nov 2025)

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

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

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



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From noreply at github.com  Sun Nov  9 17:29:31 2025
From: noreply at github.com (ehb54)
Date: Sun, 09 Nov 2025 16:29:31 -0800
Subject: [us-commits] [ehb54/ultrascan3] 41aa2d: testing dockerfile updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/d9428f-41aa2d@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 41aa2de6bd5c6be0e7ace1662b24ac04a80e021e
      https://github.com/ehb54/ultrascan3/commit/41aa2de6bd5c6be0e7ace1662b24ac04a80e021e
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-10 (Mon, 10 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat_qt6_src/Dockerfile
    M admin/release/testing/redhat_qt6_src/local.pri.gui
    M admin/release/testing/ubuntu24_qt6_src/Dockerfile

  Log Message:
  -----------
  testing dockerfile updates



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From noreply at github.com  Mon Nov 10 14:20:23 2025
From: noreply at github.com (ehb54)
Date: Mon, 10 Nov 2025 13:20:23 -0800
Subject: [us-commits] [ehb54/ultrascan3] c96c66: Update version check for
 qmake in makeall.sh
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-patch-4/000000-c96c66@github.com>

  Branch: refs/heads/ehb54-patch-4
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c96c66f46ba9f308354280592e406997830bdcd3
      https://github.com/ehb54/ultrascan3/commit/c96c66f46ba9f308354280592e406997830bdcd3
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-10 (Mon, 10 Nov 2025)

  Changed paths:
    M makeall.sh

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



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From noreply at github.com  Mon Nov 10 14:27:39 2025
From: noreply at github.com (ehb54)
Date: Mon, 10 Nov 2025 13:27:39 -0800
Subject: [us-commits] [ehb54/ultrascan3] c96c66: Update version check for
 qmake in makeall.sh
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/535738-612172@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c96c66f46ba9f308354280592e406997830bdcd3
      https://github.com/ehb54/ultrascan3/commit/c96c66f46ba9f308354280592e406997830bdcd3
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-10 (Mon, 10 Nov 2025)

  Changed paths:
    M makeall.sh

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


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

  Changed paths:
    M makeall.sh

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

Update version check for qmake in makeall.sh


Compare: https://github.com/ehb54/ultrascan3/compare/5357385a6147...61217222a10d

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From noreply at github.com  Mon Nov 10 14:27:44 2025
From: noreply at github.com (ehb54)
Date: Mon, 10 Nov 2025 13:27:44 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-patch-4/c96c66-000000@github.com>

  Branch: refs/heads/ehb54-patch-4
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Nov 10 15:26:30 2025
From: noreply at github.com (ehb54)
Date: Mon, 10 Nov 2025 14:26:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] b31976: us_branch.php updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-634/000000-b31976@github.com>

  Branch: refs/heads/ehb54-issue-634
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b319767f8ac1fd240cffc6d53d7d47e47cb80197
      https://github.com/ehb54/ultrascan3/commit/b319767f8ac1fd240cffc6d53d7d47e47cb80197
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-10 (Mon, 10 Nov 2025)

  Changed paths:
    M admin/us_branch/us_branch.php

  Log Message:
  -----------
  us_branch.php updates



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From noreply at github.com  Mon Nov 10 15:46:19 2025
From: noreply at github.com (HabGab)
Date: Mon, 10 Nov 2025 14:46:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 51a628: nov 10
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/b0cf16-51a628@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 51a628d12a19103cf0aab01c8bba71a4face8823
      https://github.com/ehb54/ultrascan3/commit/51a628d12a19103cf0aab01c8bba71a4face8823
  Author: haben <haben.gabir at uleth.ca>
  Date:   2025-11-10 (Mon, 10 Nov 2025)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_adv.rst
    M doc/manual/source/buffer/buffer_new.rst
    M doc/manual/source/buffer/buffer_settings.rst
    A doc/manual/source/colorgradient.rst
    M doc/manual/source/config.rst
    M doc/manual/source/fe_match/fe_match_main.rst
    M doc/manual/source/fit_meniscus.rst
    M doc/manual/source/ga_initialize.rst
    M doc/manual/source/pcsa/index.rst
    M doc/manual/source/solutions/solution_edit.rst
    M doc/manual/source/solutions/solution_new.rst
    M doc/manual/source/solutions/solution_select.rst
    M doc/manual/source/solutions/solution_settings.rst
    R doc/manual/source/us_project.rst
    M doc/manual/source/vhw_combine.rst
    M doc/manual/source/vhw_distrib_plot.rst
    M doc/manual/source/vhw_enhanced.rst

  Log Message:
  -----------
  nov 10



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From noreply at github.com  Tue Nov 11 13:24:50 2025
From: noreply at github.com (ehb54)
Date: Tue, 11 Nov 2025 12:24:50 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5c7ab2: us_branch.php support env
 determined checkout path
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-634/b31976-5c7ab2@github.com>

  Branch: refs/heads/ehb54-issue-634
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5c7ab2de12a14dc1e781d7cee8a27b75045ac8a1
      https://github.com/ehb54/ultrascan3/commit/5c7ab2de12a14dc1e781d7cee8a27b75045ac8a1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-11 (Tue, 11 Nov 2025)

  Changed paths:
    M admin/us_branch/us_branch.php

  Log Message:
  -----------
  us_branch.php support env determined checkout path



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From noreply at github.com  Tue Nov 11 13:29:08 2025
From: noreply at github.com (ehb54)
Date: Tue, 11 Nov 2025 12:29:08 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5990c7: us_branch.php support env
 determined checkout path
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-634-a/000000-5990c7@github.com>

  Branch: refs/heads/ehb54-issue-634-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5990c792acabee399abe6282e486ee20fd42aa3b
      https://github.com/ehb54/ultrascan3/commit/5990c792acabee399abe6282e486ee20fd42aa3b
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-11 (Tue, 11 Nov 2025)

  Changed paths:
    M admin/us_branch/us_branch.php

  Log Message:
  -----------
  us_branch.php support env determined checkout path



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From noreply at github.com  Tue Nov 11 13:44:33 2025
From: noreply at github.com (ehb54)
Date: Tue, 11 Nov 2025 12:44:33 -0800
Subject: [us-commits] [ehb54/ultrascan3] 572ca3: Update README with new
 command options
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-634-a/5990c7-572ca3@github.com>

  Branch: refs/heads/ehb54-issue-634-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 572ca3dc893cb190da1629160ce4d79aeefed4f4
      https://github.com/ehb54/ultrascan3/commit/572ca3dc893cb190da1629160ce4d79aeefed4f4
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-11 (Tue, 11 Nov 2025)

  Changed paths:
    M admin/us_branch/README.md

  Log Message:
  -----------
  Update README with new command options

Added options for enabling qt6 and non-interactive mode.



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From noreply at github.com  Tue Nov 11 14:03:18 2025
From: noreply at github.com (ehb54)
Date: Tue, 11 Nov 2025 13:03:18 -0800
Subject: [us-commits] [ehb54/ultrascan3] 3b5cea: testing dockerfile updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/41aa2d-3b5cea@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3b5cea33b1ad16a501b5eaacc7f53b7f1ccd0987
      https://github.com/ehb54/ultrascan3/commit/3b5cea33b1ad16a501b5eaacc7f53b7f1ccd0987
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-11 (Tue, 11 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat8_qt6_src/Dockerfile
    M admin/release/testing/redhat_qt5_qwt630/Dockerfile
    M admin/release/testing/redhat_qt6_src/Dockerfile
    M admin/release/testing/ubuntu24_qt6_src/Dockerfile

  Log Message:
  -----------
  testing dockerfile updates



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From noreply at github.com  Wed Nov 12 07:43:18 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 12 Nov 2025 06:43:18 -0800
Subject: [us-commits] [ehb54/ultrascan3] 910f23: Fix size of returned
 QByteArray for US_DB2::mysqlE...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/612172-910f23@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 910f23c2f12c7bfa2cff364725d6e6b07dc3735f
      https://github.com/ehb54/ultrascan3/commit/910f23c2f12c7bfa2cff364725d6e6b07dc3735f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-12 (Wed, 12 Nov 2025)

  Changed paths:
    M utils/us_db2.cpp

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

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



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From noreply at github.com  Wed Nov 12 08:00:24 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 12 Nov 2025 07:00:24 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-patch-2/a83947-000000@github.com>

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

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From noreply at github.com  Thu Nov 13 03:16:45 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 13 Nov 2025 02:16:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] 0587da: Refactor
 `US_SpectrogramData` and update raster ha...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/910f23-0587da@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0587da27d11a47a031a2345ea944e5b52923bd00
      https://github.com/ehb54/ultrascan3/commit/0587da27d11a47a031a2345ea944e5b52923bd00
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-13 (Thu, 13 Nov 2025)

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

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

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



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From noreply at github.com  Thu Nov 13 17:17:55 2025
From: noreply at github.com (alexsav815)
Date: Thu, 13 Nov 2025 16:17:55 -0800
Subject: [us-commits] [ehb54/ultrascan3] 49e82b: [Qt5/Qt6]GMP : 5. ANALYSIS
 -- fix 'Show oerlay' & ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/0587da-49e82b@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 49e82b3ef6a8a4567a4da2dd86bd2ea24263c28d
      https://github.com/ehb54/ultrascan3/commit/49e82b3ef6a8a4567a4da2dd86bd2ea24263c28d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-13 (Thu, 13 Nov 2025)

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

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



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From noreply at github.com  Thu Nov 13 18:28:44 2025
From: noreply at github.com (HabGab)
Date: Thu, 13 Nov 2025 17:28:44 -0800
Subject: [us-commits] [ehb54/ultrascan3] 636e2a: nov 13
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/51a628-9bfe38@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 636e2a02a3b0f15c6d3c8de0f48a6f739d8cf8a1
      https://github.com/ehb54/ultrascan3/commit/636e2a02a3b0f15c6d3c8de0f48a6f739d8cf8a1
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-11-13 (Thu, 13 Nov 2025)

  Changed paths:
    A doc/manual/source/_static/images/gmp/automation/2dsa.png
    A doc/manual/source/_static/images/gmp/automation/2dsa_it.png
    A doc/manual/source/_static/images/gmp/automation/2dsa_mc.png
    A doc/manual/source/_static/images/gmp/automation/Aprofile.png
    A doc/manual/source/_static/images/gmp/automation/analysis.png
    A doc/manual/source/_static/images/gmp/automation/auto_edit.png
    A doc/manual/source/_static/images/gmp/automation/bitmap.png
    A doc/manual/source/_static/images/gmp/automation/cells.png
    A doc/manual/source/_static/images/gmp/automation/data_viewer_rando.png
    A doc/manual/source/_static/images/gmp/automation/data_viewer_rin.png
    A doc/manual/source/_static/images/gmp/automation/data_viewer_tin.png
    A doc/manual/source/_static/images/gmp/automation/lims.png
    A doc/manual/source/_static/images/gmp/automation/main_window.png
    A doc/manual/source/_static/images/gmp/automation/man_edit.png
    A doc/manual/source/_static/images/gmp/automation/optics.png
    A doc/manual/source/_static/images/gmp/automation/pcsa.png
    A doc/manual/source/_static/images/gmp/automation/pcsa_report.png
    A doc/manual/source/_static/images/gmp/automation/plot.png
    A doc/manual/source/_static/images/gmp/automation/ranges.png
    A doc/manual/source/_static/images/gmp/automation/report_editor.png
    A doc/manual/source/_static/images/gmp/automation/rotor.png
    A doc/manual/source/_static/images/gmp/automation/solutions.png
    A doc/manual/source/_static/images/gmp/automation/speed.png
    A doc/manual/source/_static/images/gmp/automation/submit.png
    M doc/manual/source/gmp/gmp.rst
    A doc/manual/source/gmp/gmp_audit_trail.rst
    A doc/manual/source/gmp/gmp_automation.rst
    A doc/manual/source/gmp/gmp_data_acquisition/index.rst
    A doc/manual/source/gmp/gmp_protocol_development.rst
    A doc/manual/source/gmp/gmp_report_generator.rst
    A doc/manual/source/gmp/gmp_signature.rst
    M doc/manual/source/gmp/index.rst
    M doc/manual/source/index.rst
    M doc/manual/source/pcsa/pcsa_results.rst
    M doc/manual/source/start_page.rst

  Log Message:
  -----------
  nov 13


  Commit: 9bfe38fb0905a5d8502eba8ed19df1d3dba3b7ef
      https://github.com/ehb54/ultrascan3/commit/9bfe38fb0905a5d8502eba8ed19df1d3dba3b7ef
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-11-13 (Thu, 13 Nov 2025)

  Changed paths:
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_experiment.rst
    A doc/manual/source/gmp/gmp_data_acquisition/gmp_data_acquisition_gmp.rst
    M doc/manual/source/gmp/gmp_data_acquisition/index.rst
    M doc/manual/source/gmp/index.rst

  Log Message:
  -----------
  nov 13 2


Compare: https://github.com/ehb54/ultrascan3/compare/51a628d12a19...9bfe38fb0905

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From noreply at github.com  Fri Nov 14 01:26:35 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 14 Nov 2025 00:26:35 -0800
Subject: [us-commits] [ehb54/ultrascan3] 39a4c5: Refactor signal mapping
 logic in `us_autoflow_anal...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/49e82b-39a4c5@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 39a4c51ee0332b7bc85d5ad3215f311df748b287
      https://github.com/ehb54/ultrascan3/commit/39a4c51ee0332b7bc85d5ad3215f311df748b287
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

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

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



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From noreply at github.com  Fri Nov 14 11:07:45 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 14 Nov 2025 10:07:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] 33dfed: Refactor `US_Plot` and
 related classes for modern ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_plot_config/000000-33dfed@github.com>

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

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

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

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



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From noreply at github.com  Fri Nov 14 11:14:30 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 14 Nov 2025 10:14:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] ef64ca: Fix incorrect variable
 usage and remove redundant ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_plot_config/33dfed-ef64ca@github.com>

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

  Changed paths:
    M gui/us_plot.cpp

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

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



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From noreply at github.com  Fri Nov 14 16:04:21 2025
From: noreply at github.com (alexsav815)
Date: Fri, 14 Nov 2025 15:04:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] 33dfed: Refactor `US_Plot` and
 related classes for modern ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/208da0-aa4ace@github.com>

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

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

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

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


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

  Changed paths:
    M gui/us_plot.cpp

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

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


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

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

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

Fix us_plot config causing Curves to get symboles


Compare: https://github.com/ehb54/ultrascan3/compare/208da0fac807...aa4ace94a7d0

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From noreply at github.com  Fri Nov 14 21:36:02 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 14 Nov 2025 20:36:02 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/us_plot_config/ef64ca-000000@github.com>

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

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From noreply at github.com  Sat Nov 15 01:53:00 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 15 Nov 2025 00:53:00 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/tmp-main/000000-aa4ace@github.com>

  Branch: refs/heads/tmp-main
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sat Nov 15 01:55:11 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 15 Nov 2025 00:55:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] bcba62: Qt6 no longer supports the
 QString().sprintf() fun...
Message-ID: <ehb54/ultrascan3/push/refs/heads/tmp-main/aa4ace-4de7d4@github.com>

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

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

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


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

  Changed paths:
    M utils/us_dataIO.cpp

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


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

  Changed paths:
    M utils/us_gzip.cpp

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


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

  Changed paths:
    M utils/us_gzip.cpp

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


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

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

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


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

  Changed paths:
    M utils/us_local_server.h

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


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

  Changed paths:
    M utils/us_cfa_data.cpp

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


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

  Changed paths:
    M utils/us_lamm_astfvm.cpp

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


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

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

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


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

  Changed paths:
    M utils/us_ana_profile.cpp

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


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

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

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


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

  Changed paths:
    M utils/us_solve_sim.cpp

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


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

  Changed paths:
    M utils/us_solve_sim.cpp

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


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

  Changed paths:
    M utils/us_xpn_data.cpp

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


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

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

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


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

  Changed paths:
    M utils/us_crypto.cpp

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


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

  Changed paths:
    M utils/us_stiffbase.h

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


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

  Changed paths:
    M utils/us_db2.cpp

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


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

  Changed paths:
    M utils/us_buffer.cpp

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


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

  Changed paths:
    M utils/us_math2.cpp

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


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

  Changed paths:
    M utils/us_ana_profile.cpp

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


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

  Changed paths:
    M utils/us_project.cpp

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

Fixed by Lukas.

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


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

  Changed paths:
    M utils/us_report.cpp

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

fixed by Lukas.

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


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

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

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


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

  Changed paths:
    M utils/us_report.cpp

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

fixed by Lukas!

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


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

  Changed paths:
    M utils/us_report.cpp

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

fixed by Lukas

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


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

  Changed paths:
    M utils/us_report.cpp

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

fixed by Lukas!

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


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

  Changed paths:
    M utils/us_rotor.cpp

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

fixed by Lukas!

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


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

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

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


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

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

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


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

  Changed paths:
    M utils/us_util.cpp

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


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

  Changed paths:
    M utils/us_solve_sim.cpp

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


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

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

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


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

  Changed paths:
    M utils/us_analyte.cpp

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


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

  Changed paths:
    M utils/us_cfa_data.cpp

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


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

  Changed paths:
    M utils/us_xpn_data.cpp

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


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

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

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


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

  Changed paths:
    M utils/us_link_ssl.cpp

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


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

  Changed paths:
    M utils/us_xpn_data.cpp

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


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

  Changed paths:
    M utils/us_stiffbase.h

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


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

  Changed paths:
    M utils/us_hydrosim.h

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

  Changed paths:
    M admin/cmake/FindQwt.cmake

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


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

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

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

update qt6-compile


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

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

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

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


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

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

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

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


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

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

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

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


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

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

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

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


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

  Changed paths:
    M programs/CMakeLists.txt

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

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


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

  Changed paths:
    M admin/cmake/FindQwt.cmake

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

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


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

  Changed paths:
    M utils/us_util.h

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

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


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

  Changed paths:
    M utils/us_util.cpp

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

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


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

  Changed paths:
    M utils/us_db2.cpp

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

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


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

  Changed paths:
    M CMakeLists.txt

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

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


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

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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp

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


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

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

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


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

  Changed paths:
    M programs/main1.inc

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


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

  Changed paths:
    M programs/us_analysis_profile/us_analysis_profile.cpp

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


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

  Changed paths:
    M programs/us_astfem_sim/us_astfem_sim.cpp

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


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

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

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


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

  Changed paths:
    M test/utils/test_us_ana_profile.cpp

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


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

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

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


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

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us_colorgradient/us_colorgradient.cpp

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us_edit/us_edit.cpp

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


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

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

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


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

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

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


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

  Changed paths:
    M programs/us_2dsa/us_show_norm.cpp

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


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

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

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

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


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

  Changed paths:
    M gui/us_plot.cpp

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


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

  Changed paths:
    M gui/us_analyte_gui.cpp

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

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


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

  Changed paths:
    M gui/us_model_loader.cpp

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


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

  Changed paths:
    M gui/us_spectrodata.cpp

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


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

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

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

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


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

  Changed paths:
    M CMakeLists.txt

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

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


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

  Changed paths:
    M CMakeLists.txt

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


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

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

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

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


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

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

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

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


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

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

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

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


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

  Changed paths:
    M qwtplot3d/src/qwt3d_label.cpp

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

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


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

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

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

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


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

  Changed paths:
    M makeall.sh

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


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

  Changed paths:
    M makeall.sh

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

Update version check for qmake in makeall.sh


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

  Changed paths:
    M utils/us_db2.cpp

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

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


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

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

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

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


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

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

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


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

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

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

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


  Commit: 4de7d4d6d6e8449eebc38c929cf2efea19271da6
      https://github.com/ehb54/ultrascan3/commit/4de7d4d6d6e8449eebc38c929cf2efea19271da6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-15 (Sat, 15 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/FindQwt.cmake
    M gui.pri
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_csv_loader.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_util.cpp
    M gui/us_investigator.cpp
    M gui/us_license.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_mwl_data.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_plot3d.h
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_sassoc.h
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_widgets.h
    M makeall.sh
    M programs/CMakeLists.txt
    M programs/main1.inc
    M programs/us/us.cpp
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_abde_main.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_abde/us_norm_profile.h
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.h
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_buoyancy/us_buoyancy.h
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_color.cpp
    M programs/us_config/us_newxpnhost_db.cpp
    M programs/us_config/us_xpnhost_db.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_convert/us_convertio.cpp
    M programs/us_convert/us_convertio.h
    M programs/us_convert/us_experiment.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit.h
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_edit_scan.h
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_plot_control_fem.h
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.h
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_ga_init.h
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_eqmath.cpp
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_fit_worker.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_globalequil.h
    M programs/us_grid_editor/us_grid_editor.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.h
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.h
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.h
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pcsa/us_rpscan.h
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.cpp
    M programs/us_pseudo_absorbance/us_convert_scan.h
    M programs/us_pseudo_absorbance/us_pseudo_absorbance.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.cpp
    M programs/us_pseudo_absorbance/us_remove_ri.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.cpp
    M programs/us_ramp/us_experiment_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_mwlramp.cpp
    M programs/us_ramp/us_ramp.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_ramp/us_ramp_gui.h
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.h
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_spectrum/us_spectrum.h
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.h
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.h
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_io_gl2ps.h
    M qwtplot3d/include/qwt3d_openglhelper.h
    M qwtplot3d/include/qwt3d_plot.h
    M qwtplot3d/include/qwt3d_surfaceplot.h
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_io.cpp
    M qwtplot3d/src/qwt3d_io_gl2ps.cpp
    M qwtplot3d/src/qwt3d_label.cpp
    M qwtplot3d/src/qwt3d_lighting.cpp
    M qwtplot3d/src/qwt3d_movements.cpp
    M qwtplot3d/src/qwt3d_plot.cpp
    M qwtplot3d/src/qwt3d_surfaceplot.cpp
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    M utils/us_ana_profile.cpp
    M utils/us_ana_profile.h
    M utils/us_analyte.h
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_astfem_math.cpp
    M utils/us_astfem_math.h
    M utils/us_astfem_rsa.cpp
    M utils/us_astfem_rsa.h
    M utils/us_buffer.h
    M utils/us_cfa_data.cpp
    M utils/us_cfa_data.h
    M utils/us_constants.cpp
    M utils/us_constants.h
    M utils/us_crc.cpp
    M utils/us_crc.h
    M utils/us_crypto.cpp
    M utils/us_crypto.h
    M utils/us_csv_data.cpp
    M utils/us_csv_data.h
    M utils/us_dataIO.cpp
    M utils/us_dataIO.h
    M utils/us_datafiles.cpp
    M utils/us_datafiles.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_dmga_constr.cpp
    M utils/us_eprofile.h
    M utils/us_extern.h
    M utils/us_geturl.cpp
    M utils/us_geturl.h
    M utils/us_global.cpp
    M utils/us_global.h
    M utils/us_gzip.cpp
    M utils/us_gzip.h
    M utils/us_hardware.h
    M utils/us_http_post.h
    M utils/us_hydrosim.cpp
    M utils/us_hydrosim.h
    M utils/us_lamm_astfvm.cpp
    M utils/us_lamm_astfvm.h
    M utils/us_license_t.cpp
    M utils/us_license_t.h
    M utils/us_link_ssl.cpp
    M utils/us_link_ssl.h
    M utils/us_lm.cpp
    M utils/us_local_server.cpp
    M utils/us_local_server.h
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_matrix.cpp
    M utils/us_matrix.h
    M utils/us_memory.cpp
    M utils/us_memory.h
    M utils/us_model.cpp
    M utils/us_model.h
    M utils/us_noise.cpp
    M utils/us_noise.h
    M utils/us_pcsa_modelrec.cpp
    M utils/us_pcsa_modelrec.h
    M utils/us_project.cpp
    M utils/us_protocol_util.cpp
    M utils/us_protocol_util.h
    M utils/us_report.cpp
    M utils/us_report.h
    M utils/us_report_gmp.cpp
    M utils/us_rotor.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_settings.cpp
    M utils/us_settings.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_sleep.h
    M utils/us_solute.cpp
    M utils/us_solute.h
    M utils/us_solution.cpp
    M utils/us_solution.h
    M utils/us_solution_vals.h
    M utils/us_solve_sim.cpp
    M utils/us_stiffbase.cpp
    M utils/us_stiffbase.h
    M utils/us_tar.cpp
    M utils/us_tar.h
    M utils/us_time_state.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_util.cpp
    M utils/us_util.h
    A utils/us_utils_qt.h
    M utils/us_vector.cpp
    M utils/us_vector.h
    M utils/us_xpn_data.cpp
    M utils/us_xpn_data.h
    M utils/us_zsolute.cpp
    M utils/us_zsolute.h

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


Compare: https://github.com/ehb54/ultrascan3/compare/aa4ace94a7d0...4de7d4d6d6e8

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From noreply at github.com  Sat Nov 15 01:56:14 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 15 Nov 2025 00:56:14 -0800
Subject: [us-commits] [ehb54/ultrascan3] 33dfed: Refactor `US_Plot` and
 related classes for modern ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/39a4c5-57bf3b@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 33dfedcbd83e81f3116f6e0051eb43b762a00ce1
      https://github.com/ehb54/ultrascan3/commit/33dfedcbd83e81f3116f6e0051eb43b762a00ce1
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-14 (Fri, 14 Nov 2025)

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

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

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


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

  Changed paths:
    M gui/us_plot.cpp

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

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


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

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

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

Fix us_plot config causing Curves to get symboles


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/39a4c51ee033...57bf3bd1f029

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From noreply at github.com  Sat Nov 15 01:56:25 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 15 Nov 2025 00:56:25 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/tmp-main/4de7d4-000000@github.com>

  Branch: refs/heads/tmp-main
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Nov 16 02:16:00 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 01:16:00 -0800
Subject: [us-commits] [ehb54/ultrascan3] 9717b5: Replace leftRef with left
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/57bf3b-9717b5@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9717b5a3c53ea980931ab8abd9723d89c4678375
      https://github.com/ehb54/ultrascan3/commit/9717b5a3c53ea980931ab8abd9723d89c4678375
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M gui/us_plot.cpp

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



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From noreply at github.com  Sun Nov 16 07:20:16 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 06:20:16 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/000000-aa4ace@github.com>

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

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From noreply at github.com  Sun Nov 16 07:54:30 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 06:54:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4db221: issue 649,
 testing codeql qt6 build
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649/000000-4db221@github.com>

  Branch: refs/heads/ehb54-issue-649
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4db2218d24fbf448f58e228e33c6634b2ddbe429
      https://github.com/ehb54/ultrascan3/commit/4db2218d24fbf448f58e228e33c6634b2ddbe429
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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



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From noreply at github.com  Sun Nov 16 07:56:39 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 06:56:39 -0800
Subject: [us-commits] [ehb54/ultrascan3] c321e2: Update CodeQL workflow to
 use matrix containers
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/aa4ace-c321e2@github.com>

  Branch: refs/heads/lukas/codeql
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c321e21211e23831bb3cc2cc94010e79d942cc03
      https://github.com/ehb54/ultrascan3/commit/c321e21211e23831bb3cc2cc94010e79d942cc03
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Update CodeQL workflow to use matrix containers



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From noreply at github.com  Sun Nov 16 08:00:31 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 07:00:31 -0800
Subject: [us-commits] [ehb54/ultrascan3] 63ecf6: Upgrade CodeQL Action to
 version 4
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/c321e2-63ecf6@github.com>

  Branch: refs/heads/lukas/codeql
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 63ecf6e004e459935dcf5e7a472396e76a166cca
      https://github.com/ehb54/ultrascan3/commit/63ecf6e004e459935dcf5e7a472396e76a166cca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Upgrade CodeQL Action to version 4



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From noreply at github.com  Sun Nov 16 08:00:35 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 07:00:35 -0800
Subject: [us-commits] [ehb54/ultrascan3] 7efd56: issue 649,
 testing codeql qt6 build
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649/4db221-7efd56@github.com>

  Branch: refs/heads/ehb54-issue-649
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7efd56b0064621de09905cb9d76a56f0a1c83b77
      https://github.com/ehb54/ultrascan3/commit/7efd56b0064621de09905cb9d76a56f0a1c83b77
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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



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From noreply at github.com  Sun Nov 16 08:24:50 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 07:24:50 -0800
Subject: [us-commits] [ehb54/ultrascan3] 34d389: codeql qt6 updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/000000-34d389@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 34d38958b015c5ac7b1eb05fb4f5a7a380220c56
      https://github.com/ehb54/ultrascan3/commit/34d38958b015c5ac7b1eb05fb4f5a7a380220c56
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  codeql qt6 updates



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From noreply at github.com  Sun Nov 16 08:39:19 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 07:39:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 0b5dfd: codeql workflow remove
 commented section
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649/7efd56-0b5dfd@github.com>

  Branch: refs/heads/ehb54-issue-649
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0b5dfd84a4ed2f5328e79bef342f3fec70845310
      https://github.com/ehb54/ultrascan3/commit/0b5dfd84a4ed2f5328e79bef342f3fec70845310
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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



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From noreply at github.com  Sun Nov 16 08:40:18 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 07:40:18 -0800
Subject: [us-commits] [ehb54/ultrascan3] eedee9: Add changed-files job to
 CodeQL workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/63ecf6-eedee9@github.com>

  Branch: refs/heads/lukas/codeql
  Home:   https://github.com/ehb54/ultrascan3
  Commit: eedee9cfe238826f47d93dcafda227cfee29625b
      https://github.com/ehb54/ultrascan3/commit/eedee9cfe238826f47d93dcafda227cfee29625b
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Add changed-files job to CodeQL workflow



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From noreply at github.com  Sun Nov 16 09:17:41 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 08:17:41 -0800
Subject: [us-commits] [ehb54/ultrascan3] 769fa4: Fix configuration settings
 in local.pri.gui-qt6
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/34d389-769fa4@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 769fa409660d0a0f211d829375bf2ad0e5923cb9
      https://github.com/ehb54/ultrascan3/commit/769fa409660d0a0f211d829375bf2ad0e5923cb9
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Fix configuration settings in local.pri.gui-qt6



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From noreply at github.com  Sun Nov 16 09:18:18 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 08:18:18 -0800
Subject: [us-commits] [ehb54/ultrascan3] 522a7b: Remove openglwidgets from
 QT configuration
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649/0b5dfd-522a7b@github.com>

  Branch: refs/heads/ehb54-issue-649
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 522a7b53313a7a9d4d13450bbaa79b482379ab0a
      https://github.com/ehb54/ultrascan3/commit/522a7b53313a7a9d4d13450bbaa79b482379ab0a
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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



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From noreply at github.com  Sun Nov 16 09:39:28 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 08:39:28 -0800
Subject: [us-commits] [ehb54/ultrascan3] e3cc16: add mpich to usbuildtest
 dockerfiles, remove +open...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/3b5cea-e3cc16@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e3cc16934de3f025cd5f450e4ead7817c83ea564
      https://github.com/ehb54/ultrascan3/commit/e3cc16934de3f025cd5f450e4ead7817c83ea564
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat8_qt6_src/Dockerfile
    M admin/release/testing/redhat_qt5_qwt630/Dockerfile
    M admin/release/testing/redhat_qt6_src/Dockerfile
    M admin/release/testing/ubuntu24_qt6_src/Dockerfile
    M admin/release/testing/ubuntu24_qt6_src/local.pri.gui

  Log Message:
  -----------
  add mpich to usbuildtest dockerfiles, remove +openglwidgets from local.pri.gui



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From noreply at github.com  Sun Nov 16 09:59:23 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 08:59:23 -0800
Subject: [us-commits] [ehb54/ultrascan3] 7ac7f3: Update `value` method to
 return default `QVariant`
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/9717b5-7ac7f3@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7ac7f3643ac686e016a4c0bda79f188aefc06933
      https://github.com/ehb54/ultrascan3/commit/7ac7f3643ac686e016a4c0bda79f188aefc06933
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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

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



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From noreply at github.com  Sun Nov 16 10:35:24 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 09:35:24 -0800
Subject: [us-commits] [ehb54/ultrascan3] 85d4b1: Refine CodeQL analysis
 configuration and containers
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/eedee9-85d4b1@github.com>

  Branch: refs/heads/lukas/codeql
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 85d4b14481d93682abbc2910e156cf20b2e112ca
      https://github.com/ehb54/ultrascan3/commit/85d4b14481d93682abbc2910e156cf20b2e112ca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Refine CodeQL analysis configuration and containers



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From noreply at github.com  Sun Nov 16 10:45:39 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 09:45:39 -0800
Subject: [us-commits] [ehb54/ultrascan3] 603179: Update CodeQL workflow
 containers and paths
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/85d4b1-603179@github.com>

  Branch: refs/heads/lukas/codeql
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 603179fb6f6dbe18e771a67d99080367459254d1
      https://github.com/ehb54/ultrascan3/commit/603179fb6f6dbe18e771a67d99080367459254d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Update CodeQL workflow containers and paths



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From noreply at github.com  Sun Nov 16 11:46:50 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 10:46:50 -0800
Subject: [us-commits] [ehb54/ultrascan3] a45a52: Update CodeQL workflow for
 changed files and conta...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/603179-a45a52@github.com>

  Branch: refs/heads/lukas/codeql
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a45a5216aa76e722e1277db65aa46d0f5f0c9c66
      https://github.com/ehb54/ultrascan3/commit/a45a5216aa76e722e1277db65aa46d0f5f0c9c66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Update CodeQL workflow for changed files and containers



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From noreply at github.com  Sun Nov 16 12:05:09 2025
From: noreply at github.com (Lukas Dobler)
Date: Sun, 16 Nov 2025 11:05:09 -0800
Subject: [us-commits] [ehb54/ultrascan3] 2edff6: Update CodeQL analysis
 workflow to use latest action
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/a45a52-2edff6@github.com>

  Branch: refs/heads/lukas/codeql
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 2edff65d3dbb994738f689da9f7a500b9d262815
      https://github.com/ehb54/ultrascan3/commit/2edff65d3dbb994738f689da9f7a500b9d262815
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

  Log Message:
  -----------
  Update CodeQL analysis workflow to use latest action



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From noreply at github.com  Sun Nov 16 12:17:41 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 11:17:41 -0800
Subject: [us-commits] [ehb54/ultrascan3] dc8509: updated testing dockerfiles,
 local.pri.mpi for mpi...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/e3cc16-dc8509@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: dc85092ff0b3a0b57debf1341ff19f4407dce2a6
      https://github.com/ehb54/ultrascan3/commit/dc85092ff0b3a0b57debf1341ff19f4407dce2a6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat8_qt6_src/Dockerfile
    A admin/release/testing/redhat8_qt6_src/local.pri.mpi
    M admin/release/testing/redhat_qt5_qwt630/Dockerfile
    A admin/release/testing/redhat_qt5_qwt630/local.pri.mpi
    M admin/release/testing/redhat_qt5_qwt630/local.pri.somo
    M admin/release/testing/redhat_qt6_src/Dockerfile
    A admin/release/testing/redhat_qt6_src/local.pri.mpi
    A admin/release/testing/ubuntu22_qt5_src/Dockerfile
    A admin/release/testing/ubuntu22_qt5_src/local.pri.gui
    A admin/release/testing/ubuntu22_qt5_src/local.pri.mpi
    A admin/release/testing/ubuntu22_qt5_src/local.pri.somo
    M admin/release/testing/ubuntu24_qt6_src/Dockerfile
    A admin/release/testing/ubuntu24_qt6_src/local.pri.mpi

  Log Message:
  -----------
  updated testing dockerfiles, local.pri.mpi for mpi tests



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From noreply at github.com  Sun Nov 16 16:18:19 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 15:18:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 49edbb: testing dockerfile updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/dc8509-49edbb@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 49edbb26942d965b51daedf68614b8a775eeb24f
      https://github.com/ehb54/ultrascan3/commit/49edbb26942d965b51daedf68614b8a775eeb24f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat8_qt6_src/Dockerfile
    M admin/release/testing/redhat8_qt6_src/local.pri.mpi
    M admin/release/testing/redhat_qt5_qwt630/Dockerfile
    M admin/release/testing/redhat_qt5_qwt630/local.pri.mpi
    M admin/release/testing/redhat_qt6_src/Dockerfile
    M admin/release/testing/redhat_qt6_src/local.pri.mpi

  Log Message:
  -----------
  testing dockerfile updates



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From noreply at github.com  Sun Nov 16 21:20:31 2025
From: noreply at github.com (alexsav815)
Date: Sun, 16 Nov 2025 20:20:31 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue650/000000-aa4ace@github.com>

  Branch: refs/heads/alexey-dev-issue650
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sun Nov 16 22:57:42 2025
From: noreply at github.com (alexsav815)
Date: Sun, 16 Nov 2025 21:57:42 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5e08ea: GMP [dataDisk]: 1. EXP. --
 init. steps for dealing...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue650/aa4ace-5e08ea@github.com>

  Branch: refs/heads/alexey-dev-issue650
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
      https://github.com/ehb54/ultrascan3/commit/5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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



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From noreply at github.com  Sun Nov 16 23:15:31 2025
From: noreply at github.com (ehb54)
Date: Sun, 16 Nov 2025 22:15:31 -0800
Subject: [us-commits] [ehb54/ultrascan3] a00ab6: build test containers,
 further updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-container-testing/49edbb-a00ab6@github.com>

  Branch: refs/heads/ehb54-container-testing
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a00ab61f9c5620e17e0853ce401ad483698b5ea1
      https://github.com/ehb54/ultrascan3/commit/a00ab61f9c5620e17e0853ce401ad483698b5ea1
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M admin/release/testing/redhat8_qt6_src/Dockerfile
    M admin/release/testing/redhat8_qt6_src/local.pri.gui
    M admin/release/testing/redhat_qt5_qwt630/local.pri.gui
    M admin/release/testing/redhat_qt6_src/local.pri.gui
    M admin/release/testing/ubuntu24_qt6_src/local.pri.gui

  Log Message:
  -----------
  build test containers, further updates



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From noreply at github.com  Sun Nov 16 23:39:45 2025
From: noreply at github.com (alexsav815)
Date: Sun, 16 Nov 2025 22:39:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] 637512: GMP [dataDisk]: 1. EXP. --
 [MODS to generated prto...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue650/5e08ea-637512@github.com>

  Branch: refs/heads/alexey-dev-issue650
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 637512db487f7224a48db9fddadac0121cd0ec6e
      https://github.com/ehb54/ultrascan3/commit/637512db487f7224a48db9fddadac0121cd0ec6e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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



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From noreply at github.com  Mon Nov 17 02:36:33 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 17 Nov 2025 01:36:33 -0800
Subject: [us-commits] [ehb54/ultrascan3] 6334d8: Uncomment `column_indexes`
 calls in `us_xpn_data.c...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/7ac7f3-6334d8@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6334d8a547ec98d53ccca0926c511a7554263428
      https://github.com/ehb54/ultrascan3/commit/6334d8a547ec98d53ccca0926c511a7554263428
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M utils/us_xpn_data.cpp

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



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From noreply at github.com  Mon Nov 17 03:17:43 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 17 Nov 2025 02:17:43 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/000000-aa4ace@github.com>

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

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From noreply at github.com  Mon Nov 17 03:26:56 2025
From: noreply at github.com (Lukas Dobler)
Date: Mon, 17 Nov 2025 02:26:56 -0800
Subject: [us-commits] [ehb54/ultrascan3] 31bffc: Update unit-tests.yml to
 include additional paths
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/aa4ace-31bffc@github.com>

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

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

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



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From noreply at github.com  Mon Nov 17 12:05:05 2025
From: noreply at github.com (alexsav815)
Date: Mon, 17 Nov 2025 11:05:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] 72306f: GMP : 2.LIVE_UPDATE --
 check for positiveness of t...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/6334d8-72306f@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 72306fcec7a1e4c91c96c06a871d7f0478ac8964
      https://github.com/ehb54/ultrascan3/commit/72306fcec7a1e4c91c96c06a871d7f0478ac8964
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

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

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



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From noreply at github.com  Mon Nov 17 16:44:00 2025
From: noreply at github.com (alexsav815)
Date: Mon, 17 Nov 2025 15:44:00 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/000000-aa4ace@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Nov 18 10:06:21 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 09:06:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] 7ac7f3: Update `value` method to
 return default `QVariant`
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/769fa4-bfdd41@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 7ac7f3643ac686e016a4c0bda79f188aefc06933
      https://github.com/ehb54/ultrascan3/commit/7ac7f3643ac686e016a4c0bda79f188aefc06933
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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

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


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

  Changed paths:
    M utils/us_xpn_data.cpp

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


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

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

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


  Commit: bfdd414e2645c7d5d437bc9b52fcdda2bf03e8c0
      https://github.com/ehb54/ultrascan3/commit/bfdd414e2645c7d5d437bc9b52fcdda2bf03e8c0
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.h
    M utils/us_db2.cpp
    M utils/us_db2.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge pull request #317 from ehb54/lukas/qt6-compile

Lukas/qt6 compile


Compare: https://github.com/ehb54/ultrascan3/compare/769fa409660d...bfdd414e2645

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From noreply at github.com  Tue Nov 18 10:41:11 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 09:41:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] b191a0: codeql updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/bfdd41-b191a0@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b191a0d821f00fc197a91730689f726709d0d6b6
      https://github.com/ehb54/ultrascan3/commit/b191a0d821f00fc197a91730689f726709d0d6b6
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  codeql updates



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From noreply at github.com  Tue Nov 18 10:47:01 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 09:47:01 -0800
Subject: [us-commits] [ehb54/ultrascan3] c0e8db: codeql updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/b191a0-c0e8db@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c0e8db64a14dc4dc1aa413b99675382f23f473f5
      https://github.com/ehb54/ultrascan3/commit/c0e8db64a14dc4dc1aa413b99675382f23f473f5
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  codeql updates



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From noreply at github.com  Tue Nov 18 10:48:51 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 18 Nov 2025 09:48:51 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5e08ea: GMP [dataDisk]: 1. EXP. --
 init. steps for dealing...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/aa4ace-17ce4b@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
      https://github.com/ehb54/ultrascan3/commit/5e08ea6d12eced7c9aafcaeb63be2b6fc7fd227e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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


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

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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


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

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

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

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


Compare: https://github.com/ehb54/ultrascan3/compare/aa4ace94a7d0...17ce4b6fb272

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From noreply at github.com  Tue Nov 18 10:48:58 2025
From: noreply at github.com (Borries Demeler)
Date: Tue, 18 Nov 2025 09:48:58 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue650/637512-000000@github.com>

  Branch: refs/heads/alexey-dev-issue650
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Nov 18 10:51:02 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 09:51:02 -0800
Subject: [us-commits] [ehb54/ultrascan3] 3ef376: codeql updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/c0e8db-3ef376@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3ef37661aefaa8ed21730949183459b186c66f63
      https://github.com/ehb54/ultrascan3/commit/3ef37661aefaa8ed21730949183459b186c66f63
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  codeql updates



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From noreply at github.com  Tue Nov 18 10:55:53 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 09:55:53 -0800
Subject: [us-commits] [ehb54/ultrascan3] 9d976f: codeql updates
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/3ef376-9d976f@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 9d976f3c9d1a6518edd80e6ae247102605d4d862
      https://github.com/ehb54/ultrascan3/commit/9d976f3c9d1a6518edd80e6ae247102605d4d862
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  codeql updates



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From noreply at github.com  Tue Nov 18 12:14:14 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 11:14:14 -0800
Subject: [us-commits] [ehb54/ultrascan3] b0f38f: GMP : 6.REPORTER -- ranges
 for CG-models...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/aa4ace-b0f38f@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

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



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From noreply at github.com  Tue Nov 18 12:24:32 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 11:24:32 -0800
Subject: [us-commits] [ehb54/ultrascan3] 508b55: codeql updates,
 +manual-build.yml
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/9d976f-508b55@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 508b558aec2c51180653bf5c7c551eb1393f8e87
      https://github.com/ehb54/ultrascan3/commit/508b558aec2c51180653bf5c7c551eb1393f8e87
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  codeql updates, +manual-build.yml



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From noreply at github.com  Tue Nov 18 12:32:23 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 11:32:23 -0800
Subject: [us-commits] [ehb54/ultrascan3] cefb4f: add: cmake build update
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/7684ca-6c646f@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: cefb4f09592f41675136902739310639b3013aca
      https://github.com/ehb54/ultrascan3/commit/cefb4f09592f41675136902739310639b3013aca
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    M gui/CMakeLists.txt
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_fit_meniscus/CMakeLists.txt
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/bootstrap.sh
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt
    M utils/us_defines.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  add: cmake build update


  Commit: aaeaad6c02761cee619ff74a0115ebbed284238d
      https://github.com/ehb54/ultrascan3/commit/aaeaad6c02761cee619ff74a0115ebbed284238d
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    A .gitmodules

  Log Message:
  -----------
  add: vcpkg submodule


  Commit: 752239a4b3601d73dc40a986b5616f860208f51e
      https://github.com/ehb54/ultrascan3/commit/752239a4b3601d73dc40a986b5616f860208f51e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-18 (Sat, 18 Oct 2025)

  Changed paths:
    M gui/CMakeLists.txt
    M gui/us_abstractrotor_gui.cpp
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_associations_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_choice.cpp
    M gui/us_csv_loader.cpp
    M gui/us_data_loader.cpp
    M gui/us_editor.h
    M gui/us_editor_gui.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_investigator.cpp
    M gui/us_license.h
    M gui/us_load_auc.cpp
    M gui/us_loadable_noise.cpp
    M gui/us_minimize.cpp
    M gui/us_model_gui.cpp
    M gui/us_model_loader.cpp
    M gui/us_noise_loader.cpp
    M gui/us_passwd.h
    M gui/us_plot.cpp
    M gui/us_plot3d.cpp
    M gui/us_predict1.cpp
    M gui/us_project_gui.cpp
    M gui/us_properties.cpp
    M gui/us_report_gui.cpp
    M gui/us_resids_bitmap.cpp
    M gui/us_rotor_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.h
    M gui/us_select_edits.cpp
    M gui/us_select_item.cpp
    M gui/us_select_runs.cpp
    M gui/us_solution_gui.cpp
    M gui/us_table.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M gui/us_widgets_dialog.h
    M programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_adv_analysis_2d.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_plot_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_astfem_sim.h
    M programs/us_astfem_sim/us_clipdata.cpp
    M programs/us_astfem_sim/us_clipdata.h
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_colorgradient/us_colorgradient.h
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_combine_models/us_combine_models.cpp
    M programs/us_config/us_admin.h
    M programs/us_config/us_advanced.h
    M programs/us_config/us_color.cpp
    M programs/us_config/us_color.h
    M programs/us_config/us_config.h
    M programs/us_config/us_font.h
    M programs/us_config/us_xpnhost.h
    M programs/us_config/us_xpnhost_db.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_experiment_gui.cpp
    M programs/us_convert/us_get_run.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_convert/us_select_triples.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_density_match/us_model_params.cpp
    M programs/us_density_match/us_remove_models.cpp
    M programs/us_dmga_init/us_constraints_edit.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_exclude_profile.cpp
    M programs/us_edit/us_get_edit.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_advanced_fem.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_plot_control_fem.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.h
    M programs/us_globalequil/us_eqmodel_control.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_globalequil/us_long_messagebox.h
    M programs/us_globalequil/us_model_adpars.cpp
    M programs/us_globalequil/us_model_select.cpp
    M programs/us_integral/us_delete_models.cpp
    M programs/us_manage_data/us_data_model.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/dmga_worker.cpp
    M programs/us_mpi_analysis/ga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwl_spectra/us_mwls_pltctl.cpp
    M programs/us_mwlr_viewer/us_mwl_pltctrl.cpp
    M programs/us_mwlr_viewer/us_mwl_run.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_analysis_control_pc.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_mrecs_loader.cpp
    M programs/us_pcsa/us_plot_control_pc.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo3d_combine/us_remove_distros.cpp
    M programs/us_ramp/us_experiment_gui_ra.cpp
    M programs/us_ramp/us_get_dbrun_ra.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_select_triples_ra.cpp
    M programs/us_reporter/us_sync_db.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_rotor_calibration/us_get_dbexp.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_combine/us_vhwc_pltctl.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_run_auc.cpp
    M programs/us_xpn_viewer/us_xpn_run_raw.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M us_somo/develop/3dplot/lightingdlgbase.h
    M us_somo/develop/src/us_hydrodyn.cpp
    M utils/us_buffer.cpp
    M utils/us_gzip.cpp
    M utils/us_lamm_astfvm.cpp
    M utils/us_license_t.cpp
    M utils/us_matrix.cpp
    M utils/us_pcsa_modelrec.cpp
    M utils/us_project.cpp
    M utils/us_run_protocol.cpp
    M utils/us_run_protocol.h
    M utils/us_simparms.cpp
    M utils/us_simparms.h
    M utils/us_solve_sim.cpp
    M utils/us_tar.cpp
    M utils/us_time_state.cpp
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/master' into 534-enhancement-version-upgrade

# Conflicts:
#	gui/us_window_message.cpp
#	programs/us_rasmol_control/us_rasmol_control.cpp


  Commit: aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
      https://github.com/ehb54/ultrascan3/commit/aa011c07ff3e7a68fbec50f20b6e6b54dd9bc28e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-19 (Sun, 19 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    M etc/us3-splash.png
    M gui/CMakeLists.txt
    M gui/images/us3-splash.png
    M programs/CMakeLists.txt
    M programs/us/us.cpp
    M utils/us_defines.h

  Log Message:
  -----------
  add: version to splash screen


  Commit: 7f79da6635b8554a946f428c516d36f3cc0025cf
      https://github.com/ehb54/ultrascan3/commit/7f79da6635b8554a946f428c516d36f3cc0025cf
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    A doc/manual/CMakeLists.txt
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M programs/us/us.cpp
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h

  Log Message:
  -----------
  mod: color palette


  Commit: d396732b1811c44b0e9b297acf9dbb04b42f5b9e
      https://github.com/ehb54/ultrascan3/commit/d396732b1811c44b0e9b297acf9dbb04b42f5b9e
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    A admin/cmake/UsDefinesParser.cmake
    M utils/us_defines.h

  Log Message:
  -----------
  mod: get version description for build from us_defines


  Commit: 0c3758833374f0f823c94711990117ec205ab239
      https://github.com/ehb54/ultrascan3/commit/0c3758833374f0f823c94711990117ec205ab239
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: remove OS from splash screen


  Commit: 11bbb002a0e60f0eae185c97adcae193b1ad6b40
      https://github.com/ehb54/ultrascan3/commit/11bbb002a0e60f0eae185c97adcae193b1ad6b40
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-20 (Mon, 20 Oct 2025)

  Changed paths:
    M gui/images/us3-splash.png
    M programs/us/us.cpp

  Log Message:
  -----------
  mod: better font handling improved image


  Commit: 4375dec9c287500081a412353bd6a8d4b0dbd015
      https://github.com/ehb54/ultrascan3/commit/4375dec9c287500081a412353bd6a8d4b0dbd015
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png

  Log Message:
  -----------
  mod: update icons


  Commit: 515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
      https://github.com/ehb54/ultrascan3/commit/515eaaf6649d633f2f1ebe08fa6e6d17166ab7af
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-27 (Mon, 27 Oct 2025)

  Changed paths:
    A etc/us3-icon-128x128.xpm
    A etc/us3-icon-32x32.ico

  Log Message:
  -----------
  add: icons for all extensions


  Commit: 1f221d2f71c97c26c68d54f94c404ec7a1455bc3
      https://github.com/ehb54/ultrascan3/commit/1f221d2f71c97c26c68d54f94c404ec7a1455bc3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: remove qt4 code


  Commit: 2db3a5f9997a9b2eb153a6af2832c0b693d5e640
      https://github.com/ehb54/ultrascan3/commit/2db3a5f9997a9b2eb153a6af2832c0b693d5e640
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

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

  Log Message:
  -----------
  mod: format code


  Commit: 3a91742fcd41c424cda2dfa8b85cd80aadc2255b
      https://github.com/ehb54/ultrascan3/commit/3a91742fcd41c424cda2dfa8b85cd80aadc2255b
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    A etc/README

  Log Message:
  -----------
  add: image readme for image conversion


  Commit: 2569ebda100a0b333a3f529881d53c8771f9aae5
      https://github.com/ehb54/ultrascan3/commit/2569ebda100a0b333a3f529881d53c8771f9aae5
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-28 (Tue, 28 Oct 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml
    M CMakeLists.txt
    M README.md
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M admin/release/buildpkg.pl
    M admin/release/centos7/Dockerfile
    M admin/release/redhat/Dockerfile
    M admin/release/ubuntu/Dockerfile
    M admin/release/ubuntu_qt6/Dockerfile
    M doc/manual/advanced_config.body
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_failed_gmp_run_gui.cpp
    M gui/us_passwd.cpp
    M gui/us_plot.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_table.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets.h
    M gui/us_widgets_dialog.cpp
    M programs/us/us.cpp
    M programs/us/us.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_2dsa_process.cpp
    M programs/us_2dsa/us_2dsa_process.h
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_audit_trail_gmp/us_audit_trail_gmp.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_colorgradient/us_colorgradient.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_config.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_select_rundd.cpp
    M programs/us_density_match/us_density_match.cpp
    M programs/us_dmga_init/us_dmga_init.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_select_lambdas.cpp
    M programs/us_esigner_gmp/us_esigner_gmp.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_dmga_mc_stats.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_ga_init/us_solutedata.cpp
    M programs/us_ga_init/us_solutedata.h
    M programs/us_globalequil/us_eqreporter.cpp
    M programs/us_globalequil/us_long_messagebox.cpp
    M programs/us_helpdaemon/us_helpdaemon.cpp
    M programs/us_integral/us_integral.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_manage_data.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mpi_analysis/2dsa_master.cpp
    M programs/us_mpi_analysis/dmga_master.cpp
    M programs/us_mpi_analysis/dmga_worker.cpp
    M programs/us_mpi_analysis/ga_master.cpp
    M programs/us_mpi_analysis/ga_worker.cpp
    M programs/us_mpi_analysis/parallel_masters.cpp
    M programs/us_mpi_analysis/pcsa_master.cpp
    M programs/us_mpi_analysis/pmasters_compjob.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mpi_analysis/us_mpi_parse.cpp
    M programs/us_mwl_species_fit/us_mwl_sf_plot3d.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.h
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_adv_analysis_pc.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_pcsa_process.cpp
    M programs/us_pcsa/us_pcsa_process.h
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_pseudo_absorbance/us_add_refScan.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_reporter/us_reporter.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_vhw_combine/us_select_runid.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/qwtplot3d.pro
    M qwtplot3d/src/qwt3d_mousekeyboard.cpp
    M test/modelbuilder/us_modelbuilder.cpp
    M us_somo/develop/src/qwt/scrollzoomer.cpp
    M us_somo/develop/src/us_dirhist.cpp
    M us_somo/develop/src/us_editor.cpp
    M us_somo/develop/src/us_hydrodyn.cpp
    M us_somo/develop/src/us_hydrodyn_batch.cpp
    M us_somo/develop/src/us_hydrodyn_bd.cpp
    M us_somo/develop/src/us_hydrodyn_comparative.cpp
    M us_somo/develop/src/us_hydrodyn_saxs.cpp
    M utils/us_ana_profile.cpp
    M utils/us_crypto.cpp
    M utils/us_db2.cpp
    M utils/us_hardware.cpp
    M utils/us_hydrosim.h
    M utils/us_link_ssl.cpp
    M utils/us_math2.cpp
    M utils/us_math2.h
    M utils/us_timer.cpp
    M utils/us_timer.h
    M utils/us_xpn_data.cpp

  Log Message:
  -----------
  Merge remote-tracking branch 'origin/main' into 534-enhancement-version-upgrade

# Conflicts:
#	programs/us/us.cpp


  Commit: 102666e6eebaafe3144edfce3728a62e33ab053c
      https://github.com/ehb54/ultrascan3/commit/102666e6eebaafe3144edfce3728a62e33ab053c
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M CMakeLists.txt
    M admin/test/docker/Dockerfile
    M gui/CMakeLists.txt
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    A programs/us_2dsa/CMakeLists.txt
    A programs/us_abde/CMakeLists.txt
    A programs/us_analysis_profile/CMakeLists.txt
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    A programs/us_audit_trail_gmp/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    A programs/us_colorgradient/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    A programs/us_convert/CMakeLists.txt
    A programs/us_dcdt/CMakeLists.txt
    A programs/us_ddist_combine/CMakeLists.txt
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    A programs/us_equiltime/CMakeLists.txt
    A programs/us_esigner_gmp/CMakeLists.txt
    A programs/us_export_legacy/CMakeLists.txt
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    A programs/us_ga_init/CMakeLists.txt
    A programs/us_globalequil/CMakeLists.txt
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    A programs/us_mpi_analysis/CMakeLists.txt
    A programs/us_mwl_species_sim/CMakeLists.txt
    A programs/us_mwl_spectra/CMakeLists.txt
    A programs/us_mwlr_viewer/CMakeLists.txt
    A programs/us_pcsa/CMakeLists.txt
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    A programs/us_pseudo3d_combine/CMakeLists.txt
    A programs/us_pseudo_absorbance/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    A programs/us_vhw_enhanced/CMakeLists.txt
    A programs/us_xpn_viewer/CMakeLists.txt
    M scripts/bootstrap.sh
    M test-docker.sh
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt

  Log Message:
  -----------
  mod: simply build by adding profile config


  Commit: 18fcc684bbff2846566a57efafe210efec23cb07
      https://github.com/ehb54/ultrascan3/commit/18fcc684bbff2846566a57efafe210efec23cb07
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

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

  Log Message:
  -----------
  mod: used if-else instead of series of if statements.


  Commit: 5aae8e45629593aea0b0e007a8f2166c6f60b9c4
      https://github.com/ehb54/ultrascan3/commit/5aae8e45629593aea0b0e007a8f2166c6f60b9c4
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M gui/libus_gui.pro

  Log Message:
  -----------
  fix: remove mac x11 lib dependency and references to us_window_message


  Commit: d66e17404eb6616c8b39235715683f81791c61b3
      https://github.com/ehb54/ultrascan3/commit/d66e17404eb6616c8b39235715683f81791c61b3
  Author: aaron <aaron at aucsolutions.com>
  Date:   2025-10-31 (Fri, 31 Oct 2025)

  Changed paths:
    M programs/us/us.cpp

  Log Message:
  -----------
  fix: antialiasing deprecation in qpainter


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

  Changed paths:
    M alpha/us.cpp
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_util.cpp
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    M programs/us_abde/us_norm_profile.cpp
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_buoyancy/us_buoyancy.cpp
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_config/us_color.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    M programs/us_dcdt/us_dcdt.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    M programs/us_equiltime/us_equiltime.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_proto_ranges.cpp
    M programs/us_export_legacy/us_export.cpp
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    M programs/us_ga_init/us_ga_init.cpp
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    M programs/us_modelmetrics/us_modelmetrics.cpp
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    M programs/us_second_moment/us_second_moment.cpp
    M programs/us_spectrum/us_spectrum.cpp
    M programs/us_vhw_combine/us_vhw_combine.cpp
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

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

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


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

  Changed paths:
    M programs/us/us.pro

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M programs/us/us.h

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


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

  Changed paths:
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png

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


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

  Changed paths:
    M scripts/build.sh

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


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

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

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


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M .gitignore
    M CMakeLists.txt
    M admin/cmake/GenerateVersion.cmake
    R etc/README
    M etc/us3-GMP-icon-128x128.ico
    M etc/us3-GMP-icon-128x128.png
    M etc/us3-GMP-icon-128x128.xpm
    M etc/us3-GMP-icon-32x32.ico
    M etc/us3-GMP-icon-32x32.png
    M etc/us3-GMP-icon-32x32.xpm
    M etc/us3-GMP-icon-48x48.ico
    M etc/us3-GMP-icon-48x48.png
    M etc/us3-GMP-icon-48x48.xpm
    M etc/us3-icon-128x128.ico
    M etc/us3-icon-128x128.png
    R etc/us3-icon-128x128.xpm
    R etc/us3-icon-32x32.ico
    M etc/us3-icon-32x32.png
    M etc/us3-icon-32x32.xpm
    M etc/us3-icon-48x48.ico
    M etc/us3-icon-48x48.png
    M etc/us3-icon-48x48.xpm
    M etc/us3-icon.icns
    M etc/us3-splash.png
    M gui/images/check.png
    M gui/images/us3-icon-128x128.png
    M gui/images/us3-icon-16x16.png
    M gui/images/us3-icon-256x256.png
    M gui/images/us3-icon-32x32.png
    M gui/images/us3-icon-48x48.png
    M gui/images/us3-icon-512x512.png
    M gui/images/us3-icon-64x64.png
    M gui/images/us3-splash.png
    M gui/libus_gui.pro
    M programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    R scripts/bootstrap.sh
    A scripts/build.sh

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

# Conflicts:
#	programs/us/us.cpp


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

  Changed paths:
    M programs/us/us.cpp

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


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

  Changed paths:
    M .gitignore

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


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

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M admin/cmake/GenerateVersion.cmake
    M admin/cmake/Us3QrcCheck.cmake
    M admin/cmake/Us3Resources.cmake
    M admin/cmake/UsDefinesParser.cmake
    M admin/cmake/platform-config.cmake
    M doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M qwtplot3d/CMakeLists.txt
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M utils/CMakeLists.txt

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


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

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

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

597 request qt 6 migration remove qt 4 code


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

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

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

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


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

  Changed paths:
    M gui/us_plot.cpp

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

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


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

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

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

Fix us_plot config causing Curves to get symboles


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

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

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


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

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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


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

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

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

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


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

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

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


Compare: https://github.com/ehb54/ultrascan3/compare/7684ca675c73...6c646f633296

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From noreply at github.com  Tue Nov 18 12:35:18 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 11:35:18 -0800
Subject: [us-commits] [ehb54/ultrascan3] 8908ee: manual-build.yml - add
 workflow_dispatch
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/508b55-8908ee@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8908ee3dc8f751db88b258efaa804a196277133d
      https://github.com/ehb54/ultrascan3/commit/8908ee3dc8f751db88b258efaa804a196277133d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  manual-build.yml - add workflow_dispatch



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From noreply at github.com  Tue Nov 18 12:39:56 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 11:39:56 -0800
Subject: [us-commits] [ehb54/ultrascan3] f40add: manual-build.yml - add
 workflow_dispatch
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/8908ee-f40add@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f40add00ca6220f6398e4b540a64c98a8881e8b4
      https://github.com/ehb54/ultrascan3/commit/f40add00ca6220f6398e4b540a64c98a8881e8b4
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  manual-build.yml - add workflow_dispatch



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From noreply at github.com  Tue Nov 18 13:11:00 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 12:11:00 -0800
Subject: [us-commits] [ehb54/ultrascan3] 285695: manual-build.yml now
 doc-build.yml; added to schedule
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/f40add-285695@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 285695164a89bd05f579e274f471da513e387bc3
      https://github.com/ehb54/ultrascan3/commit/285695164a89bd05f579e274f471da513e387bc3
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/doc-build.yml
    R .github/workflows/manual-build.yml

  Log Message:
  -----------
  manual-build.yml now doc-build.yml; added to schedule



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From noreply at github.com  Tue Nov 18 13:12:30 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 12:12:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 14525b: manual-build.yml now
 doc-build.yml; added to schedule
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/285695-14525b@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 14525b330657a37cdfe481761a97e39dce1c3e37
      https://github.com/ehb54/ultrascan3/commit/14525b330657a37cdfe481761a97e39dce1c3e37
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

  Log Message:
  -----------
  manual-build.yml now doc-build.yml; added to schedule



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From noreply at github.com  Tue Nov 18 14:40:27 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 13:40:27 -0800
Subject: [us-commits] [ehb54/ultrascan3] 0ebfc3: GMP-PROT.DEV -- extend the
 case of re-processing d...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/6c646f-0ebfc3@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

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



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From noreply at github.com  Tue Nov 18 14:49:13 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 13:49:13 -0800
Subject: [us-commits] [ehb54/ultrascan3] b08b1c: codeql updates to main
 branch
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649/522a7b-b08b1c@github.com>

  Branch: refs/heads/ehb54-issue-649
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b08b1c4672f375b1df4d08eb2e61fd656c9d406d
      https://github.com/ehb54/ultrascan3/commit/b08b1c4672f375b1df4d08eb2e61fd656c9d406d
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

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

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



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From noreply at github.com  Tue Nov 18 15:16:03 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 14:16:03 -0800
Subject: [us-commits] [ehb54/ultrascan3] 71e029: [1]GMP-PROT.DEV -- extend
 the case of re-processin...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/0ebfc3-71e029@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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



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From noreply at github.com  Tue Nov 18 15:35:18 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 14:35:18 -0800
Subject: [us-commits] [ehb54/ultrascan3] f49d8c: [2]GMP-PROT.DEV -- extend
 the case of re-processin...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/71e029-f49d8c@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

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



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From noreply at github.com  Tue Nov 18 15:40:47 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 14:40:47 -0800
Subject: [us-commits] [ehb54/ultrascan3] 8f6a93: [3]GMP-PROT.DEV -- extend
 the case of re-processin...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/f49d8c-8f6a93@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

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



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From noreply at github.com  Tue Nov 18 15:44:57 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 18 Nov 2025 14:44:57 -0800
Subject: [us-commits] [ehb54/us3lims_dbinst]
Message-ID: <ehb54/us3lims_dbinst/push/refs/heads/codeql/000000-82c80d@github.com>

  Branch: refs/heads/codeql
  Home:   https://github.com/ehb54/us3lims_dbinst

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From noreply at github.com  Tue Nov 18 15:53:10 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 14:53:10 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649-a/14525b-000000@github.com>

  Branch: refs/heads/ehb54-issue-649-a
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Nov 18 15:59:43 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 14:59:43 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-649/b08b1c-000000@github.com>

  Branch: refs/heads/ehb54-issue-649
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Nov 18 15:59:40 2025
From: noreply at github.com (ehb54)
Date: Tue, 18 Nov 2025 14:59:40 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4db221: issue 649,
 testing codeql qt6 build
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/17ce4b-0cd115@github.com>

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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

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

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

issue 649, testing codeql qt6 build


Compare: https://github.com/ehb54/ultrascan3/compare/17ce4b6fb272...0cd1156f3fea

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From noreply at github.com  Tue Nov 18 16:01:37 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 18 Nov 2025 15:01:37 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4db221: issue 649,
 testing codeql qt6 build
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/72306f-9d2cd0@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4db2218d24fbf448f58e228e33c6634b2ddbe429
      https://github.com/ehb54/ultrascan3/commit/4db2218d24fbf448f58e228e33c6634b2ddbe429
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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


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

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

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

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


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

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

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


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

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

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

issue 649, testing codeql qt6 build


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

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

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

Update lukas/qt6-compile with main


Compare: https://github.com/ehb54/ultrascan3/compare/72306fcec7a1...9d2cd0b12aa0

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From noreply at github.com  Tue Nov 18 16:04:10 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 18 Nov 2025 15:04:10 -0800
Subject: [us-commits] [ehb54/ultrascan3] 1687a5: CodeQl action: Add qt6
 containers for gui and mpi
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/9d2cd0-1687a5@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 1687a57993f87b8937fdcf06045e10225b504ca6
      https://github.com/ehb54/ultrascan3/commit/1687a57993f87b8937fdcf06045e10225b504ca6
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

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

Updated branches for pull requests and enabled additional Qt6 containers.



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

From noreply at github.com  Tue Nov 18 20:01:44 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 19:01:44 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4db221: issue 649,
 testing codeql qt6 build
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/b0f38f-540061@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4db2218d24fbf448f58e228e33c6634b2ddbe429
      https://github.com/ehb54/ultrascan3/commit/4db2218d24fbf448f58e228e33c6634b2ddbe429
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-16 (Sun, 16 Nov 2025)

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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


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

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

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

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


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

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

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


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

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

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

issue 649, testing codeql qt6 build


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

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

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

add main stuff to alexey-dev-issue651


Compare: https://github.com/ehb54/ultrascan3/compare/b0f38f43b87f...5400614d6c78

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From noreply at github.com  Wed Nov 19 00:21:49 2025
From: noreply at github.com (alexsav815)
Date: Tue, 18 Nov 2025 23:21:49 -0800
Subject: [us-commits] [ehb54/ultrascan3] d40493: GMP 6. REPORT -- for runs
 based on Custom-Grid mod...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/540061-d40493@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

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

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



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From noreply at github.com  Wed Nov 19 01:24:02 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 00:24:02 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/codeql/2edff6-000000@github.com>

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

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From noreply at github.com  Wed Nov 19 01:24:10 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 00:24:10 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/597-request-qt-6-migration-remove-qt-4-code/13f85d-000000@github.com>

  Branch: refs/heads/597-request-qt-6-migration-remove-qt-4-code
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Nov 19 01:24:15 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 00:24:15 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/534-enhancement-version-upgrade/95598e-000000@github.com>

  Branch: refs/heads/534-enhancement-version-upgrade
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Nov 19 01:25:45 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 00:25:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4db221: issue 649,
 testing codeql qt6 build
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/31bffc-8f3452@github.com>

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

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

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


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

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

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


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

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

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


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

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

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


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

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

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


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

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

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


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

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

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

Alexey dev issue650: dataDisk submission with arbitrary selection of channels


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

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

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


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

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

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

issue 649, testing codeql qt6 build


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

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

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

update to main


Compare: https://github.com/ehb54/ultrascan3/compare/31bffce6f225...8f345295dc58

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From noreply at github.com  Wed Nov 19 03:26:31 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 02:26:31 -0800
Subject: [us-commits] [ehb54/ultrascan3] 129b8d: Refactor CodeQL workflow
 for improved caching and ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/8f3452-129b8d@github.com>

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

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

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



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From noreply at github.com  Wed Nov 19 03:28:58 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 02:28:58 -0800
Subject: [us-commits] [ehb54/ultrascan3] 793e12: Simplify build step in
 CodeQL analysis workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/129b8d-793e12@github.com>

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

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

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

Removed ccache setup and git configuration from the build step.



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From noreply at github.com  Wed Nov 19 05:40:10 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 04:40:10 -0800
Subject: [us-commits] [ehb54/ultrascan3] 0f76a4: Refactor CodeQL analysis
 workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/793e12-0f76a4@github.com>

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

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

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

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



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From noreply at github.com  Wed Nov 19 05:50:17 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 04:50:17 -0800
Subject: [us-commits] [ehb54/ultrascan3] 6c8077: Refactor CodeQL workflow to
 simplify caching and b...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/0f76a4-6c8077@github.com>

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

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

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

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



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From noreply at github.com  Wed Nov 19 07:22:03 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 06:22:03 -0800
Subject: [us-commits] [ehb54/ultrascan3] 27c760: Update unit-tests.yml to
 remove path filters for push
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/6c8077-27c760@github.com>

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

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

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

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



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From noreply at github.com  Wed Nov 19 07:22:43 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 06:22:43 -0800
Subject: [us-commits] [ehb54/ultrascan3] 246540: Update static analysis
 workflow trigger paths
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/27c760-246540@github.com>

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

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

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

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



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From noreply at github.com  Wed Nov 19 07:44:10 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 06:44:10 -0800
Subject: [us-commits] [ehb54/ultrascan3] c1ac9c: Document CMake formatter
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/246540-c1ac9c@github.com>

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

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

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



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From noreply at github.com  Wed Nov 19 08:13:43 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 07:13:43 -0800
Subject: [us-commits] [ehb54/ultrascan3] 391ac4: Updating nproc
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/c1ac9c-391ac4@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 391ac4d011a289eafa902e9d56eb4382491f0b66
      https://github.com/ehb54/ultrascan3/commit/391ac4d011a289eafa902e9d56eb4382491f0b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Updating nproc



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From noreply at github.com  Wed Nov 19 08:17:05 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 07:17:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] ea7559: Fix minor comments
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/391ac4-ea7559@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ea7559d6bcd810ed7a176871e33f0d36b49152e2
      https://github.com/ehb54/ultrascan3/commit/ea7559d6bcd810ed7a176871e33f0d36b49152e2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/unit-tests.yml
    M admin/linting/cmake/.cmake-format.yaml
    M admin/linting/cmake/README.md

  Log Message:
  -----------
  Fix minor comments



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From noreply at github.com  Wed Nov 19 08:28:05 2025
From: noreply at github.com (Borries Demeler)
Date: Wed, 19 Nov 2025 07:28:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] b91982: Prot_DEV -- dataDisk type
 of data to reuse in Prot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/0cd115-6e9473@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [1]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [2]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  [4]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h

  Log Message:
  -----------
  [55]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [6]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [7]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [8]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [9]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [11a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [12a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [13a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  [15a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [16a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [17a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 6c646f633296c0b2cdf20178c282494f364c1846
      https://github.com/ehb54/ultrascan3/commit/6c646f633296c0b2cdf20178c282494f364c1846
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project_academic/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    M programs/us_config/us_color.cpp
    A programs/us_convert/CMakeLists.txt
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    A programs/us_pcsa/CMakeLists.txt
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_vhw_combine.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt
    M utils/us_defines.h
    M utils/us_run_protocol.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue608


  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [2]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 6e94734ca883da80e058cf4e51dee4474e9863e5
      https://github.com/ehb54/ultrascan3/commit/6e94734ca883da80e058cf4e51dee4474e9863e5
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #305 from ehb54/alexey-dev-issue608

Alexey dev issue608: Prot. Dev. for DataDisk data types


Compare: https://github.com/ehb54/ultrascan3/compare/0cd1156f3fea...6e94734ca883

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From noreply at github.com  Wed Nov 19 08:28:07 2025
From: noreply at github.com (Borries Demeler)
Date: Wed, 19 Nov 2025 07:28:07 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue608/8f6a93-000000@github.com>

  Branch: refs/heads/alexey-dev-issue608
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Nov 19 08:29:33 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 07:29:33 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5ff2d2: Update checkout action
 version
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/ea7559-5ff2d2@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5ff2d239588616635adbdfaf775949a91f5d7565
      https://github.com/ehb54/ultrascan3/commit/5ff2d239588616635adbdfaf775949a91f5d7565
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update checkout action version



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From noreply at github.com  Wed Nov 19 08:31:00 2025
From: noreply at github.com (Lukas Dobler)
Date: Wed, 19 Nov 2025 07:31:00 -0800
Subject: [us-commits] [ehb54/ultrascan3] 321b58: fix branches
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/5ff2d2-321b58@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
      https://github.com/ehb54/ultrascan3/commit/321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  fix branches



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From noreply at github.com  Wed Nov 19 20:01:25 2025
From: noreply at github.com (aaron-auc)
Date: Wed, 19 Nov 2025 19:01:25 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/653-bug-unit-tests-failed-on-a-main-branch-pr-action-logs-provide-insufficient-details/000000-6e9473@github.com>

  Branch: refs/heads/653-bug-unit-tests-failed-on-a-main-branch-pr-action-logs-provide-insufficient-details
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Wed Nov 19 22:02:06 2025
From: noreply at github.com (alexsav815)
Date: Wed, 19 Nov 2025 21:02:06 -0800
Subject: [us-commits] [ehb54/ultrascan3] aad9ec: [also aspect ratio of the
 plots]GMP 6. REPORT -- f...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/d40493-aad9ec@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...



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From noreply at github.com  Thu Nov 20 01:00:54 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 20 Nov 2025 00:00:54 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-fixes/000000-6e9473@github.com>

  Branch: refs/heads/lukas/cmake-fixes
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Nov 20 06:17:18 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 20 Nov 2025 05:17:18 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5c92b7: Move general code used by
 multiple programs to lib...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-fixes/6e9473-5c92b7@github.com>

  Branch: refs/heads/lukas/cmake-fixes
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly



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From noreply at github.com  Thu Nov 20 06:56:21 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 20 Nov 2025 05:56:21 -0800
Subject: [us-commits] [ehb54/ultrascan3] 22b358: - Add `US3_BUILD_PROGRAMS`
 flag to disable program...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-fixes/5c92b7-eed161@github.com>

  Branch: refs/heads/lukas/cmake-fixes
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


Compare: https://github.com/ehb54/ultrascan3/compare/5c92b751327d...eed16179a882

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From noreply at github.com  Thu Nov 20 07:08:16 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 20 Nov 2025 06:08:16 -0800
Subject: [us-commits] [ehb54/ultrascan3] 342c57: Fix typos
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-fixes/eed161-342c57@github.com>

  Branch: refs/heads/lukas/cmake-fixes
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos



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From noreply at github.com  Thu Nov 20 07:11:14 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 20 Nov 2025 06:11:14 -0800
Subject: [us-commits] [ehb54/ultrascan3] 8ec561: - Apply `const QString&` to
 parameters in `readLeg...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-fixes/342c57-8ec561@github.com>

  Branch: refs/heads/lukas/cmake-fixes
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_convert.cpp
    M utils/us_convert.h

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging



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From noreply at github.com  Thu Nov 20 08:19:00 2025
From: noreply at github.com (ehb54)
Date: Thu, 20 Nov 2025 07:19:00 -0800
Subject: [us-commits] [ehb54/ultrascan3] 941a03: add comment
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/000000-941a03@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 941a0388f62a7d77b83111dec187f42c78603cc9
      https://github.com/ehb54/ultrascan3/commit/941a0388f62a7d77b83111dec187f42c78603cc9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  add comment



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From noreply at github.com  Thu Nov 20 08:25:45 2025
From: noreply at github.com (ehb54)
Date: Thu, 20 Nov 2025 07:25:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] a1e640: comment 2
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/941a03-a1e640@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a1e64084cc68a813d8f0f9bdea45043df1977f01
      https://github.com/ehb54/ultrascan3/commit/a1e64084cc68a813d8f0f9bdea45043df1977f01
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  comment 2



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From noreply at github.com  Thu Nov 20 10:06:37 2025
From: noreply at github.com (ehb54)
Date: Thu, 20 Nov 2025 09:06:37 -0800
Subject: [us-commits] [ehb54/ultrascan3] ebd0fe: comment 2
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/a1e640-ebd0fe@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ebd0fea4759a30412ac4f92f12a9e84179488916
      https://github.com/ehb54/ultrascan3/commit/ebd0fea4759a30412ac4f92f12a9e84179488916
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  comment 2



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From noreply at github.com  Thu Nov 20 10:18:39 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 20 Nov 2025 09:18:39 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5cf422: Refactor CodeQL analysis
 workflow conditions
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/321b58-5cf422@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5cf42202af6d7f5544a2cf1111d44f5f1a232777
      https://github.com/ehb54/ultrascan3/commit/5cf42202af6d7f5544a2cf1111d44f5f1a232777
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL analysis workflow conditions

Removed specific file paths from pull request triggers and updated conditions for CodeQL analysis steps.



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From noreply at github.com  Thu Nov 20 10:34:30 2025
From: noreply at github.com (Lukas Dobler)
Date: Thu, 20 Nov 2025 09:34:30 -0800
Subject: [us-commits] [ehb54/ultrascan3] 3f486a: Rename analysis job for GUI
 programs
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/5cf422-3f486a@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 3f486acaa2a2e5b708f257acf949e90d1b042bbc
      https://github.com/ehb54/ultrascan3/commit/3f486acaa2a2e5b708f257acf949e90d1b042bbc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Rename analysis job for GUI programs



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From noreply at github.com  Thu Nov 20 12:03:19 2025
From: noreply at github.com (alexsav815)
Date: Thu, 20 Nov 2025 11:03:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] a81ad0: [remove x_min/max from
 global settings]GMP 6. REPO...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/aad9ec-a81ad0@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...



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From noreply at github.com  Thu Nov 20 16:24:35 2025
From: noreply at github.com (Borries Demeler)
Date: Thu, 20 Nov 2025 15:24:35 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5c92b7: Move general code used by
 multiple programs to lib...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/6e9473-1e8120@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_convert.cpp
    M utils/us_convert.h

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


Compare: https://github.com/ehb54/ultrascan3/compare/6e94734ca883...1e8120944857

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From noreply at github.com  Thu Nov 20 16:24:44 2025
From: noreply at github.com (Borries Demeler)
Date: Thu, 20 Nov 2025 15:24:44 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/cmake-fixes/8ec561-000000@github.com>

  Branch: refs/heads/lukas/cmake-fixes
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Thu Nov 20 17:30:06 2025
From: noreply at github.com (alexsav815)
Date: Thu, 20 Nov 2025 16:30:06 -0800
Subject: [us-commits] [ehb54/ultrascan3] b91982: Prot_DEV -- dataDisk type
 of data to reuse in Prot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/a81ad0-9317a3@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [1]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [2]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  [4]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h

  Log Message:
  -----------
  [55]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [6]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [7]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [8]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [9]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [11a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [12a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [13a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  [15a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [16a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [17a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 6c646f633296c0b2cdf20178c282494f364c1846
      https://github.com/ehb54/ultrascan3/commit/6c646f633296c0b2cdf20178c282494f364c1846
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project_academic/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    M programs/us_config/us_color.cpp
    A programs/us_convert/CMakeLists.txt
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    A programs/us_pcsa/CMakeLists.txt
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_vhw_combine.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt
    M utils/us_defines.h
    M utils/us_run_protocol.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue608


  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [2]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 6e94734ca883da80e058cf4e51dee4474e9863e5
      https://github.com/ehb54/ultrascan3/commit/6e94734ca883da80e058cf4e51dee4474e9863e5
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #305 from ehb54/alexey-dev-issue608

Alexey dev issue608: Prot. Dev. for DataDisk data types


  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_convert.cpp
    M utils/us_convert.h

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


Compare: https://github.com/ehb54/ultrascan3/compare/a81ad04f934c...9317a33dcf14

To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications

From noreply at github.com  Fri Nov 21 02:36:11 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 21 Nov 2025 01:36:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] b91982: Prot_DEV -- dataDisk type
 of data to reuse in Prot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/3f486a-02ab6c@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [1]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [2]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  [4]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h

  Log Message:
  -----------
  [55]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [6]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [7]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [8]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [9]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [11a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [12a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [13a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  [15a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [16a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [17a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 6c646f633296c0b2cdf20178c282494f364c1846
      https://github.com/ehb54/ultrascan3/commit/6c646f633296c0b2cdf20178c282494f364c1846
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project_academic/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    M programs/us_config/us_color.cpp
    A programs/us_convert/CMakeLists.txt
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    A programs/us_pcsa/CMakeLists.txt
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_vhw_combine.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt
    M utils/us_defines.h
    M utils/us_run_protocol.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue608


  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [2]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 6e94734ca883da80e058cf4e51dee4474e9863e5
      https://github.com/ehb54/ultrascan3/commit/6e94734ca883da80e058cf4e51dee4474e9863e5
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #305 from ehb54/alexey-dev-issue608

Alexey dev issue608: Prot. Dev. for DataDisk data types


  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_convert.cpp
    M utils/us_convert.h

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


  Commit: 02ab6c663335530dbf4295161c2f68c1043b3874
      https://github.com/ehb54/ultrascan3/commit/02ab6c663335530dbf4295161c2f68c1043b3874
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


Compare: https://github.com/ehb54/ultrascan3/compare/3f486acaa2a2...02ab6c663335

To unsubscribe from these emails, change your notification settings at https://github.com/ehb54/ultrascan3/settings/notifications

From noreply at github.com  Fri Nov 21 05:19:19 2025
From: noreply at github.com (ehb54)
Date: Fri, 21 Nov 2025 04:19:19 -0800
Subject: [us-commits] [ehb54/ultrascan3] 5c92b7: Move general code used by
 multiple programs to lib...
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/ebd0fe-1266be@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_convert.cpp
    M utils/us_convert.h

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


  Commit: 1266be2b9bea8dfeef9b35c56fee9c2bf78d423b
      https://github.com/ehb54/ultrascan3/commit/1266be2b9bea8dfeef9b35c56fee9c2bf78d423b
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-test-commit


Compare: https://github.com/ehb54/ultrascan3/compare/ebd0fea4759a...1266be2b9bea

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From noreply at github.com  Fri Nov 21 05:27:44 2025
From: noreply at github.com (ehb54)
Date: Fri, 21 Nov 2025 04:27:44 -0800
Subject: [us-commits] [ehb54/ultrascan3] f858b5: comment 4
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/1266be-f858b5@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f858b50eb0149b4eb8b0eb5158c40a0078ed51cf
      https://github.com/ehb54/ultrascan3/commit/f858b50eb0149b4eb8b0eb5158c40a0078ed51cf
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  comment 4



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From noreply at github.com  Fri Nov 21 07:29:36 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 21 Nov 2025 06:29:36 -0800
Subject: [us-commits] [ehb54/ultrascan3] 013afa: Refactor GitHub Actions
 workflows to enhance modul...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/02ab6c-2574c2@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 013afa9051723a54ff17a3431895f0e6aa65eebc
      https://github.com/ehb54/ultrascan3/commit/013afa9051723a54ff17a3431895f0e6aa65eebc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Refactor GitHub Actions workflows to enhance modularity and efficiency
- Introduce `changed-files` job to conditionally trigger workflows based on file changes.
- Add status-checking jobs for Documentation, CodeQL analysis, and Static Analysis builds.
- Improve concurrency management and file fetch depth.
- Optimize CI Docker containers and cleanup processes.
- Streamline conditional checks and matrix configurations.


  Commit: 2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
      https://github.com/ehb54/ultrascan3/commit/2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    A .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add `unit-tests-v2.yml` GitHub Actions workflow

- Introduce a new workflow for unit testing with support for configurable test filters and debug mode.
- Add a `changed-files` job to detect relevant file modifications and conditionally trigger tests.
- Implement improved concurrency management and result-checking mechanisms.
- Streamline test setup, build process, and log management for enhanced clarity and efficiency.
- Enable artifact uploads for detailed test results and logs.


Compare: https://github.com/ehb54/ultrascan3/compare/02ab6c663335...2574c202cf8e

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From noreply at github.com  Fri Nov 21 07:34:28 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 21 Nov 2025 06:34:28 -0800
Subject: [us-commits] [ehb54/ultrascan3] e2a9b2: Normalize glob patterns in
 GitHub Actions workflows
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/2574c2-e2a9b2@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e2a9b2acaeeeac868cf1d55f459225e683e37d11
      https://github.com/ehb54/ultrascan3/commit/e2a9b2acaeeeac868cf1d55f459225e683e37d11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Normalize glob patterns in GitHub Actions workflows



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From noreply at github.com  Fri Nov 21 07:37:48 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 21 Nov 2025 06:37:48 -0800
Subject: [us-commits] [ehb54/ultrascan3] 037064: Fix incorrect
 `CMAKE_MODULE_PATH` to use absolute ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/e2a9b2-037064@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 037064b1d8968578fcb9a42ba07e275c96b38a8c
      https://github.com/ehb54/ultrascan3/commit/037064b1d8968578fcb9a42ba07e275c96b38a8c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Fix incorrect `CMAKE_MODULE_PATH` to use absolute path in `unit-tests-v2.yml` workflow



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From noreply at github.com  Fri Nov 21 07:51:11 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 21 Nov 2025 06:51:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] 4c0538: Enhance `unit-tests.yml`
 workflow with dynamic fil...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/037064-12e9e1@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 4c0538dff646603c4258628a076f9807a29af7c3
      https://github.com/ehb54/ultrascan3/commit/4c0538dff646603c4258628a076f9807a29af7c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Enhance `unit-tests.yml` workflow with dynamic file change detection and improved concurrency management

- Add `changed-files` job to detect relevant modifications and conditionally trigger unit tests.
- Introduce concurrency control to prevent duplicate runs.
- Expand artifacts to include additional logs for better debugging.
- Add status-checking job to validate unit testing outcomes.
- Refactor workflow for clarity and streamlined test execution.


  Commit: 12e9e1fd701da2b201e7d47b3cb642812813e4e7
      https://github.com/ehb54/ultrascan3/commit/12e9e1fd701da2b201e7d47b3cb642812813e4e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Enhance `static-analysis.yml` workflow with CPP file-specific change detection

- Add outputs and environment variables to track `.cpp` and `.h` file changes.
- Update `changed-files` step to simplify logic and rely on filtered outputs.
- Streamline file detection for first commits and pull requests.


Compare: https://github.com/ehb54/ultrascan3/compare/037064b1d896...12e9e1fd701d

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From noreply at github.com  Fri Nov 21 07:54:31 2025
From: noreply at github.com (Lukas Dobler)
Date: Fri, 21 Nov 2025 06:54:31 -0800
Subject: [us-commits] [ehb54/ultrascan3] e94063: Normalize glob pattern
 syntax in `unit-tests.yml` ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/12e9e1-158b85@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e94063c15730a822262820f18c468a429ac4c374
      https://github.com/ehb54/ultrascan3/commit/e94063c15730a822262820f18c468a429ac4c374
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Normalize glob pattern syntax in `unit-tests.yml` workflow


  Commit: 158b855316998f18924177b91ad5cb81e696ad53
      https://github.com/ehb54/ultrascan3/commit/158b855316998f18924177b91ad5cb81e696ad53
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update static-analysis workflow to use latest `us3comp` container image


Compare: https://github.com/ehb54/ultrascan3/compare/12e9e1fd701d...158b85531699

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From noreply at github.com  Fri Nov 21 13:58:13 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 12:58:13 -0800
Subject: [us-commits] [ehb54/ultrascan3] e90b56: GMP 6. REPORT --
 [single-point data] add debug sta...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/9317a3-e90b56@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...



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From noreply at github.com  Fri Nov 21 14:03:06 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 13:03:06 -0800
Subject: [us-commits] [ehb54/ultrascan3] fe4173: [1]GMP 6. REPORT --
 [single-point data] add debug ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/e90b56-fe4173@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...



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From noreply at github.com  Fri Nov 21 14:09:10 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 13:09:10 -0800
Subject: [us-commits] [ehb54/ultrascan3] dc717a: [2]GMP 6. REPORT --
 [single-point data] add debug ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/fe4173-dc717a@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...



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From noreply at github.com  Fri Nov 21 14:15:28 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 13:15:28 -0800
Subject: [us-commits] [ehb54/ultrascan3] f27c85: [3]GMP 6. REPORT --
 [single-point data] add debug ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/dc717a-f27c85@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...



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From noreply at github.com  Fri Nov 21 14:21:28 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 13:21:28 -0800
Subject: [us-commits] [ehb54/ultrascan3] 48cb1f: [4]GMP 6. REPORT --
 [single-point data] add debug ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/f27c85-48cb1f@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...



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From noreply at github.com  Fri Nov 21 15:46:45 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 14:46:45 -0800
Subject: [us-commits] [ehb54/ultrascan3] 74a2a0: PROT_DEV: run_selector --
 order in reverse chronol...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/48cb1f-74a2a0@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...



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From noreply at github.com  Fri Nov 21 19:17:05 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 18:17:05 -0800
Subject: [us-commits] [ehb54/ultrascan3] b0f38f: GMP : 6.REPORTER -- ranges
 for CG-models...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/1e8120-350edc@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP : 6.REPORTER -- ranges for CG-models...


  Commit: 5400614d6c78af525f22b1f858362a99edc462a1
      https://github.com/ehb54/ultrascan3/commit/5400614d6c78af525f22b1f858362a99edc462a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #319 from ehb54/main

add main stuff to alexey-dev-issue651


  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...


  Commit: 350edcd3194656d020a571d45cbe1dd872d041e2
      https://github.com/ehb54/ultrascan3/commit/350edcd3194656d020a571d45cbe1dd872d041e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #322 from ehb54/alexey-dev-issue651

Alexey dev issue651: Ind. & Combined Plots in GMP Rpeorts: CG-model-based runs (ranges), Plot Aspect Ratios, "Combined Plots" section title


Compare: https://github.com/ehb54/ultrascan3/compare/1e8120944857...350edcd31946

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From noreply at github.com  Fri Nov 21 19:38:31 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 18:38:31 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue631/000000-350edc@github.com>

  Branch: refs/heads/alexey-dev-issue631
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Fri Nov 21 19:49:17 2025
From: noreply at github.com (alexsav815)
Date: Fri, 21 Nov 2025 18:49:17 -0800
Subject: [us-commits] [ehb54/ultrascan3] 05f602: GMP 6. REPORT -- generate
 correct build number in ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue631/350edc-05f602@github.com>

  Branch: refs/heads/alexey-dev-issue631
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...



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From noreply at github.com  Sat Nov 22 04:12:51 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 22 Nov 2025 03:12:51 -0800
Subject: [us-commits] [ehb54/ultrascan3] e1ce70: Update file patterns for
 static analysis
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/158b85-e1ce70@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: e1ce700f61527eedba262f237e41dbcc16de6de7
      https://github.com/ehb54/ultrascan3/commit/e1ce700f61527eedba262f237e41dbcc16de6de7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update file patterns for static analysis



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From noreply at github.com  Sat Nov 22 04:20:51 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 22 Nov 2025 03:20:51 -0800
Subject: [us-commits] [ehb54/ultrascan3] aebbdd: Update CodeQL workflow to
 ignore specific files
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/e1ce70-aebbdd@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: aebbdda924bca0630a6b1b50f5110f340c8804aa
      https://github.com/ehb54/ultrascan3/commit/aebbdda924bca0630a6b1b50f5110f340c8804aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Update CodeQL workflow to ignore specific files

Ignore changes in us_mpi_analysis directory during file checks and update build commands.



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From noreply at github.com  Sat Nov 22 04:49:59 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 22 Nov 2025 03:49:59 -0800
Subject: [us-commits] [ehb54/ultrascan3] a4a655: Exclude us_mpi_analysis
 from CodeQL analysis gui
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/aebbdd-a4a655@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a4a655d619279b7bb59e01ee82fce46e875eebca
      https://github.com/ehb54/ultrascan3/commit/a4a655d619279b7bb59e01ee82fce46e875eebca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Exclude us_mpi_analysis from CodeQL analysis gui



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From noreply at github.com  Sat Nov 22 04:53:17 2025
From: noreply at github.com (Lukas Dobler)
Date: Sat, 22 Nov 2025 03:53:17 -0800
Subject: [us-commits] [ehb54/ultrascan3] 14ba4d: Fix syntax for exclusion in
 CodeQL workflow
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/a4a655-14ba4d@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 14ba4d63b16861ed659ae0c204b0ee3f54589432
      https://github.com/ehb54/ultrascan3/commit/14ba4d63b16861ed659ae0c204b0ee3f54589432
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Fix syntax for exclusion in CodeQL workflow



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From noreply at github.com  Sat Nov 22 08:54:33 2025
From: noreply at github.com (Borries Demeler)
Date: Sat, 22 Nov 2025 07:54:33 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue651/74a2a0-000000@github.com>

  Branch: refs/heads/alexey-dev-issue651
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Sat Nov 22 09:14:33 2025
From: noreply at github.com (Borries Demeler)
Date: Sat, 22 Nov 2025 08:14:33 -0800
Subject: [us-commits] [ehb54/ultrascan3] 05f602: GMP 6. REPORT -- generate
 correct build number in ...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/350edc-770769@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...


  Commit: 770769aa570aae22f64b5b817de2320ab1b070e3
      https://github.com/ehb54/ultrascan3/commit/770769aa570aae22f64b5b817de2320ab1b070e3
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #326 from ehb54/alexey-dev-issue631

GMP 6. REPORT -- generate correct build number in the header...


Compare: https://github.com/ehb54/ultrascan3/compare/350edcd31946...770769aa570a

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From noreply at github.com  Sat Nov 22 09:14:34 2025
From: noreply at github.com (Borries Demeler)
Date: Sat, 22 Nov 2025 08:14:34 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue631/05f602-000000@github.com>

  Branch: refs/heads/alexey-dev-issue631
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Nov 24 10:02:09 2025
From: noreply at github.com (ehb54)
Date: Mon, 24 Nov 2025 09:02:09 -0800
Subject: [us-commits] [ehb54/ultrascan3] b0f38f: GMP : 6.REPORTER -- ranges
 for CG-models...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/gh_actions/14ba4d-3f56d2@github.com>

  Branch: refs/heads/lukas/gh_actions
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP : 6.REPORTER -- ranges for CG-models...


  Commit: 5400614d6c78af525f22b1f858362a99edc462a1
      https://github.com/ehb54/ultrascan3/commit/5400614d6c78af525f22b1f858362a99edc462a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #319 from ehb54/main

add main stuff to alexey-dev-issue651


  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...


  Commit: 350edcd3194656d020a571d45cbe1dd872d041e2
      https://github.com/ehb54/ultrascan3/commit/350edcd3194656d020a571d45cbe1dd872d041e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #322 from ehb54/alexey-dev-issue651

Alexey dev issue651: Ind. & Combined Plots in GMP Rpeorts: CG-model-based runs (ranges), Plot Aspect Ratios, "Combined Plots" section title


  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...


  Commit: 770769aa570aae22f64b5b817de2320ab1b070e3
      https://github.com/ehb54/ultrascan3/commit/770769aa570aae22f64b5b817de2320ab1b070e3
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #326 from ehb54/alexey-dev-issue631

GMP 6. REPORT -- generate correct build number in the header...


  Commit: 3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
      https://github.com/ehb54/ultrascan3/commit/3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


Compare: https://github.com/ehb54/ultrascan3/compare/14ba4d63b168...3f56d29bde0a

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From noreply at github.com  Mon Nov 24 12:52:11 2025
From: noreply at github.com (ehb54)
Date: Mon, 24 Nov 2025 11:52:11 -0800
Subject: [us-commits] [ehb54/ultrascan3] 31bffc: Update unit-tests.yml to
 include additional paths
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/770769-c088a8@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 31bffce6f2258893d277cf9e2ab6b5a2290acd70
      https://github.com/ehb54/ultrascan3/commit/31bffce6f2258893d277cf9e2ab6b5a2290acd70
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update unit-tests.yml to include additional paths


  Commit: 8f345295dc5803000521a47ad53aa246df51eff7
      https://github.com/ehb54/ultrascan3/commit/8f345295dc5803000521a47ad53aa246df51eff7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #320 from ehb54/main

update to main


  Commit: 129b8d9184d5cab1189cca7b84574bf7e97dca76
      https://github.com/ehb54/ultrascan3/commit/129b8d9184d5cab1189cca7b84574bf7e97dca76
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL workflow for improved caching and builds


  Commit: 793e12c735495da5c5b6deed3355e2428e6c2a16
      https://github.com/ehb54/ultrascan3/commit/793e12c735495da5c5b6deed3355e2428e6c2a16
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Simplify build step in CodeQL analysis workflow

Removed ccache setup and git configuration from the build step.


  Commit: 0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
      https://github.com/ehb54/ultrascan3/commit/0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL analysis workflow

Refactor CodeQL analysis workflow to improve target calculation and build steps.


  Commit: 6c80777b7287a29fe978526475e6f099ca3ef827
      https://github.com/ehb54/ultrascan3/commit/6c80777b7287a29fe978526475e6f099ca3ef827
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL workflow to simplify caching and builds

Removed caching steps for ccache, utils, qwtplot3d, and gui. Added build steps for utils, qwtplot3d, and gui using qmake.


  Commit: 27c760f8c268e77d5038469cfd40243fb274f2d1
      https://github.com/ehb54/ultrascan3/commit/27c760f8c268e77d5038469cfd40243fb274f2d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update unit-tests.yml to remove path filters for push

Removed specific path filters for push events in unit-tests workflow.


  Commit: 2465409a96b820d237f9bf0c3b09b12f859060d7
      https://github.com/ehb54/ultrascan3/commit/2465409a96b820d237f9bf0c3b09b12f859060d7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update static analysis workflow trigger paths

Removed specific path triggers for push events in static analysis workflow.


  Commit: c1ac9c0b43cdde1480834d2fb742344b9649144f
      https://github.com/ehb54/ultrascan3/commit/c1ac9c0b43cdde1480834d2fb742344b9649144f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Document CMake formatter


  Commit: 391ac4d011a289eafa902e9d56eb4382491f0b66
      https://github.com/ehb54/ultrascan3/commit/391ac4d011a289eafa902e9d56eb4382491f0b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Updating nproc


  Commit: ea7559d6bcd810ed7a176871e33f0d36b49152e2
      https://github.com/ehb54/ultrascan3/commit/ea7559d6bcd810ed7a176871e33f0d36b49152e2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/unit-tests.yml
    M admin/linting/cmake/.cmake-format.yaml
    M admin/linting/cmake/README.md

  Log Message:
  -----------
  Fix minor comments


  Commit: 5ff2d239588616635adbdfaf775949a91f5d7565
      https://github.com/ehb54/ultrascan3/commit/5ff2d239588616635adbdfaf775949a91f5d7565
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update checkout action version


  Commit: 321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
      https://github.com/ehb54/ultrascan3/commit/321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  fix branches


  Commit: 5cf42202af6d7f5544a2cf1111d44f5f1a232777
      https://github.com/ehb54/ultrascan3/commit/5cf42202af6d7f5544a2cf1111d44f5f1a232777
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL analysis workflow conditions

Removed specific file paths from pull request triggers and updated conditions for CodeQL analysis steps.


  Commit: 3f486acaa2a2e5b708f257acf949e90d1b042bbc
      https://github.com/ehb54/ultrascan3/commit/3f486acaa2a2e5b708f257acf949e90d1b042bbc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Rename analysis job for GUI programs


  Commit: 02ab6c663335530dbf4295161c2f68c1043b3874
      https://github.com/ehb54/ultrascan3/commit/02ab6c663335530dbf4295161c2f68c1043b3874
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


  Commit: 013afa9051723a54ff17a3431895f0e6aa65eebc
      https://github.com/ehb54/ultrascan3/commit/013afa9051723a54ff17a3431895f0e6aa65eebc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Refactor GitHub Actions workflows to enhance modularity and efficiency
- Introduce `changed-files` job to conditionally trigger workflows based on file changes.
- Add status-checking jobs for Documentation, CodeQL analysis, and Static Analysis builds.
- Improve concurrency management and file fetch depth.
- Optimize CI Docker containers and cleanup processes.
- Streamline conditional checks and matrix configurations.


  Commit: 2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
      https://github.com/ehb54/ultrascan3/commit/2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    A .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add `unit-tests-v2.yml` GitHub Actions workflow

- Introduce a new workflow for unit testing with support for configurable test filters and debug mode.
- Add a `changed-files` job to detect relevant file modifications and conditionally trigger tests.
- Implement improved concurrency management and result-checking mechanisms.
- Streamline test setup, build process, and log management for enhanced clarity and efficiency.
- Enable artifact uploads for detailed test results and logs.


  Commit: e2a9b2acaeeeac868cf1d55f459225e683e37d11
      https://github.com/ehb54/ultrascan3/commit/e2a9b2acaeeeac868cf1d55f459225e683e37d11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Normalize glob patterns in GitHub Actions workflows


  Commit: 037064b1d8968578fcb9a42ba07e275c96b38a8c
      https://github.com/ehb54/ultrascan3/commit/037064b1d8968578fcb9a42ba07e275c96b38a8c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Fix incorrect `CMAKE_MODULE_PATH` to use absolute path in `unit-tests-v2.yml` workflow


  Commit: 4c0538dff646603c4258628a076f9807a29af7c3
      https://github.com/ehb54/ultrascan3/commit/4c0538dff646603c4258628a076f9807a29af7c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Enhance `unit-tests.yml` workflow with dynamic file change detection and improved concurrency management

- Add `changed-files` job to detect relevant modifications and conditionally trigger unit tests.
- Introduce concurrency control to prevent duplicate runs.
- Expand artifacts to include additional logs for better debugging.
- Add status-checking job to validate unit testing outcomes.
- Refactor workflow for clarity and streamlined test execution.


  Commit: 12e9e1fd701da2b201e7d47b3cb642812813e4e7
      https://github.com/ehb54/ultrascan3/commit/12e9e1fd701da2b201e7d47b3cb642812813e4e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Enhance `static-analysis.yml` workflow with CPP file-specific change detection

- Add outputs and environment variables to track `.cpp` and `.h` file changes.
- Update `changed-files` step to simplify logic and rely on filtered outputs.
- Streamline file detection for first commits and pull requests.


  Commit: e94063c15730a822262820f18c468a429ac4c374
      https://github.com/ehb54/ultrascan3/commit/e94063c15730a822262820f18c468a429ac4c374
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Normalize glob pattern syntax in `unit-tests.yml` workflow


  Commit: 158b855316998f18924177b91ad5cb81e696ad53
      https://github.com/ehb54/ultrascan3/commit/158b855316998f18924177b91ad5cb81e696ad53
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update static-analysis workflow to use latest `us3comp` container image


  Commit: e1ce700f61527eedba262f237e41dbcc16de6de7
      https://github.com/ehb54/ultrascan3/commit/e1ce700f61527eedba262f237e41dbcc16de6de7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update file patterns for static analysis


  Commit: aebbdda924bca0630a6b1b50f5110f340c8804aa
      https://github.com/ehb54/ultrascan3/commit/aebbdda924bca0630a6b1b50f5110f340c8804aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Update CodeQL workflow to ignore specific files

Ignore changes in us_mpi_analysis directory during file checks and update build commands.


  Commit: a4a655d619279b7bb59e01ee82fce46e875eebca
      https://github.com/ehb54/ultrascan3/commit/a4a655d619279b7bb59e01ee82fce46e875eebca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Exclude us_mpi_analysis from CodeQL analysis gui


  Commit: 14ba4d63b16861ed659ae0c204b0ee3f54589432
      https://github.com/ehb54/ultrascan3/commit/14ba4d63b16861ed659ae0c204b0ee3f54589432
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Fix syntax for exclusion in CodeQL workflow


  Commit: 3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
      https://github.com/ehb54/ultrascan3/commit/3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


  Commit: c088a80976663c552cffec04fcb0cfe084922560
      https://github.com/ehb54/ultrascan3/commit/c088a80976663c552cffec04fcb0cfe084922560
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Merge pull request #321 from ehb54/lukas/gh_actions

Lukas/gh actions


Compare: https://github.com/ehb54/ultrascan3/compare/770769aa570a...c088a8097666

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From noreply at github.com  Mon Nov 24 13:33:39 2025
From: noreply at github.com (alexsav815)
Date: Mon, 24 Nov 2025 12:33:39 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue657/000000-c088a8@github.com>

  Branch: refs/heads/alexey-dev-issue657
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Nov 24 13:40:37 2025
From: noreply at github.com (alexsav815)
Date: Mon, 24 Nov 2025 12:40:37 -0800
Subject: [us-commits] [ehb54/ultrascan3] 70cf96: GMP 5. ANALYSIS -- added
 more processEvens() for p...
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue657/c088a8-70cf96@github.com>

  Branch: refs/heads/alexey-dev-issue657
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 70cf969d22c8ecb1892bcb7a3301d101bca7aa55
      https://github.com/ehb54/ultrascan3/commit/70cf969d22c8ecb1892bcb7a3301d101bca7aa55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...



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From noreply at github.com  Mon Nov 24 16:37:29 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 24 Nov 2025 15:37:29 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/alexey-dev-issue657/70cf96-000000@github.com>

  Branch: refs/heads/alexey-dev-issue657
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Mon Nov 24 16:37:26 2025
From: noreply at github.com (Borries Demeler)
Date: Mon, 24 Nov 2025 15:37:26 -0800
Subject: [us-commits] [ehb54/ultrascan3] 70cf96: GMP 5. ANALYSIS -- added
 more processEvens() for p...
Message-ID: <ehb54/ultrascan3/push/refs/heads/main/c088a8-815465@github.com>

  Branch: refs/heads/main
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 70cf969d22c8ecb1892bcb7a3301d101bca7aa55
      https://github.com/ehb54/ultrascan3/commit/70cf969d22c8ecb1892bcb7a3301d101bca7aa55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 815465ed2b2679fbcf4cda7c076dda6fdc89f322
      https://github.com/ehb54/ultrascan3/commit/815465ed2b2679fbcf4cda7c076dda6fdc89f322
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Merge pull request #327 from ehb54/alexey-dev-issue657

GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in FITME_AUTO & View Overlay


Compare: https://github.com/ehb54/ultrascan3/compare/c088a8097666...815465ed2b26

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From noreply at github.com  Mon Nov 24 20:19:37 2025
From: noreply at github.com (ehb54)
Date: Mon, 24 Nov 2025 19:19:37 -0800
Subject: [us-commits] [ehb54/ultrascan3] 31bffc: Update unit-tests.yml to
 include additional paths
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/f858b5-f34431@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 31bffce6f2258893d277cf9e2ab6b5a2290acd70
      https://github.com/ehb54/ultrascan3/commit/31bffce6f2258893d277cf9e2ab6b5a2290acd70
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update unit-tests.yml to include additional paths


  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP : 6.REPORTER -- ranges for CG-models...


  Commit: 5400614d6c78af525f22b1f858362a99edc462a1
      https://github.com/ehb54/ultrascan3/commit/5400614d6c78af525f22b1f858362a99edc462a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #319 from ehb54/main

add main stuff to alexey-dev-issue651


  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 8f345295dc5803000521a47ad53aa246df51eff7
      https://github.com/ehb54/ultrascan3/commit/8f345295dc5803000521a47ad53aa246df51eff7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #320 from ehb54/main

update to main


  Commit: 129b8d9184d5cab1189cca7b84574bf7e97dca76
      https://github.com/ehb54/ultrascan3/commit/129b8d9184d5cab1189cca7b84574bf7e97dca76
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL workflow for improved caching and builds


  Commit: 793e12c735495da5c5b6deed3355e2428e6c2a16
      https://github.com/ehb54/ultrascan3/commit/793e12c735495da5c5b6deed3355e2428e6c2a16
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Simplify build step in CodeQL analysis workflow

Removed ccache setup and git configuration from the build step.


  Commit: 0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
      https://github.com/ehb54/ultrascan3/commit/0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL analysis workflow

Refactor CodeQL analysis workflow to improve target calculation and build steps.


  Commit: 6c80777b7287a29fe978526475e6f099ca3ef827
      https://github.com/ehb54/ultrascan3/commit/6c80777b7287a29fe978526475e6f099ca3ef827
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL workflow to simplify caching and builds

Removed caching steps for ccache, utils, qwtplot3d, and gui. Added build steps for utils, qwtplot3d, and gui using qmake.


  Commit: 27c760f8c268e77d5038469cfd40243fb274f2d1
      https://github.com/ehb54/ultrascan3/commit/27c760f8c268e77d5038469cfd40243fb274f2d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update unit-tests.yml to remove path filters for push

Removed specific path filters for push events in unit-tests workflow.


  Commit: 2465409a96b820d237f9bf0c3b09b12f859060d7
      https://github.com/ehb54/ultrascan3/commit/2465409a96b820d237f9bf0c3b09b12f859060d7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update static analysis workflow trigger paths

Removed specific path triggers for push events in static analysis workflow.


  Commit: c1ac9c0b43cdde1480834d2fb742344b9649144f
      https://github.com/ehb54/ultrascan3/commit/c1ac9c0b43cdde1480834d2fb742344b9649144f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Document CMake formatter


  Commit: 391ac4d011a289eafa902e9d56eb4382491f0b66
      https://github.com/ehb54/ultrascan3/commit/391ac4d011a289eafa902e9d56eb4382491f0b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Updating nproc


  Commit: ea7559d6bcd810ed7a176871e33f0d36b49152e2
      https://github.com/ehb54/ultrascan3/commit/ea7559d6bcd810ed7a176871e33f0d36b49152e2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/unit-tests.yml
    M admin/linting/cmake/.cmake-format.yaml
    M admin/linting/cmake/README.md

  Log Message:
  -----------
  Fix minor comments


  Commit: 5ff2d239588616635adbdfaf775949a91f5d7565
      https://github.com/ehb54/ultrascan3/commit/5ff2d239588616635adbdfaf775949a91f5d7565
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update checkout action version


  Commit: 321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
      https://github.com/ehb54/ultrascan3/commit/321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  fix branches


  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 5cf42202af6d7f5544a2cf1111d44f5f1a232777
      https://github.com/ehb54/ultrascan3/commit/5cf42202af6d7f5544a2cf1111d44f5f1a232777
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL analysis workflow conditions

Removed specific file paths from pull request triggers and updated conditions for CodeQL analysis steps.


  Commit: 3f486acaa2a2e5b708f257acf949e90d1b042bbc
      https://github.com/ehb54/ultrascan3/commit/3f486acaa2a2e5b708f257acf949e90d1b042bbc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Rename analysis job for GUI programs


  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


  Commit: 02ab6c663335530dbf4295161c2f68c1043b3874
      https://github.com/ehb54/ultrascan3/commit/02ab6c663335530dbf4295161c2f68c1043b3874
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


  Commit: 013afa9051723a54ff17a3431895f0e6aa65eebc
      https://github.com/ehb54/ultrascan3/commit/013afa9051723a54ff17a3431895f0e6aa65eebc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Refactor GitHub Actions workflows to enhance modularity and efficiency
- Introduce `changed-files` job to conditionally trigger workflows based on file changes.
- Add status-checking jobs for Documentation, CodeQL analysis, and Static Analysis builds.
- Improve concurrency management and file fetch depth.
- Optimize CI Docker containers and cleanup processes.
- Streamline conditional checks and matrix configurations.


  Commit: 2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
      https://github.com/ehb54/ultrascan3/commit/2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    A .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add `unit-tests-v2.yml` GitHub Actions workflow

- Introduce a new workflow for unit testing with support for configurable test filters and debug mode.
- Add a `changed-files` job to detect relevant file modifications and conditionally trigger tests.
- Implement improved concurrency management and result-checking mechanisms.
- Streamline test setup, build process, and log management for enhanced clarity and efficiency.
- Enable artifact uploads for detailed test results and logs.


  Commit: e2a9b2acaeeeac868cf1d55f459225e683e37d11
      https://github.com/ehb54/ultrascan3/commit/e2a9b2acaeeeac868cf1d55f459225e683e37d11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Normalize glob patterns in GitHub Actions workflows


  Commit: 037064b1d8968578fcb9a42ba07e275c96b38a8c
      https://github.com/ehb54/ultrascan3/commit/037064b1d8968578fcb9a42ba07e275c96b38a8c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Fix incorrect `CMAKE_MODULE_PATH` to use absolute path in `unit-tests-v2.yml` workflow


  Commit: 4c0538dff646603c4258628a076f9807a29af7c3
      https://github.com/ehb54/ultrascan3/commit/4c0538dff646603c4258628a076f9807a29af7c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Enhance `unit-tests.yml` workflow with dynamic file change detection and improved concurrency management

- Add `changed-files` job to detect relevant modifications and conditionally trigger unit tests.
- Introduce concurrency control to prevent duplicate runs.
- Expand artifacts to include additional logs for better debugging.
- Add status-checking job to validate unit testing outcomes.
- Refactor workflow for clarity and streamlined test execution.


  Commit: 12e9e1fd701da2b201e7d47b3cb642812813e4e7
      https://github.com/ehb54/ultrascan3/commit/12e9e1fd701da2b201e7d47b3cb642812813e4e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Enhance `static-analysis.yml` workflow with CPP file-specific change detection

- Add outputs and environment variables to track `.cpp` and `.h` file changes.
- Update `changed-files` step to simplify logic and rely on filtered outputs.
- Streamline file detection for first commits and pull requests.


  Commit: e94063c15730a822262820f18c468a429ac4c374
      https://github.com/ehb54/ultrascan3/commit/e94063c15730a822262820f18c468a429ac4c374
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Normalize glob pattern syntax in `unit-tests.yml` workflow


  Commit: 158b855316998f18924177b91ad5cb81e696ad53
      https://github.com/ehb54/ultrascan3/commit/158b855316998f18924177b91ad5cb81e696ad53
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update static-analysis workflow to use latest `us3comp` container image


  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...


  Commit: 350edcd3194656d020a571d45cbe1dd872d041e2
      https://github.com/ehb54/ultrascan3/commit/350edcd3194656d020a571d45cbe1dd872d041e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #322 from ehb54/alexey-dev-issue651

Alexey dev issue651: Ind. & Combined Plots in GMP Rpeorts: CG-model-based runs (ranges), Plot Aspect Ratios, "Combined Plots" section title


  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...


  Commit: e1ce700f61527eedba262f237e41dbcc16de6de7
      https://github.com/ehb54/ultrascan3/commit/e1ce700f61527eedba262f237e41dbcc16de6de7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update file patterns for static analysis


  Commit: aebbdda924bca0630a6b1b50f5110f340c8804aa
      https://github.com/ehb54/ultrascan3/commit/aebbdda924bca0630a6b1b50f5110f340c8804aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Update CodeQL workflow to ignore specific files

Ignore changes in us_mpi_analysis directory during file checks and update build commands.


  Commit: a4a655d619279b7bb59e01ee82fce46e875eebca
      https://github.com/ehb54/ultrascan3/commit/a4a655d619279b7bb59e01ee82fce46e875eebca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Exclude us_mpi_analysis from CodeQL analysis gui


  Commit: 14ba4d63b16861ed659ae0c204b0ee3f54589432
      https://github.com/ehb54/ultrascan3/commit/14ba4d63b16861ed659ae0c204b0ee3f54589432
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Fix syntax for exclusion in CodeQL workflow


  Commit: 770769aa570aae22f64b5b817de2320ab1b070e3
      https://github.com/ehb54/ultrascan3/commit/770769aa570aae22f64b5b817de2320ab1b070e3
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #326 from ehb54/alexey-dev-issue631

GMP 6. REPORT -- generate correct build number in the header...


  Commit: 3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
      https://github.com/ehb54/ultrascan3/commit/3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


  Commit: c088a80976663c552cffec04fcb0cfe084922560
      https://github.com/ehb54/ultrascan3/commit/c088a80976663c552cffec04fcb0cfe084922560
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Merge pull request #321 from ehb54/lukas/gh_actions

Lukas/gh actions


  Commit: 70cf969d22c8ecb1892bcb7a3301d101bca7aa55
      https://github.com/ehb54/ultrascan3/commit/70cf969d22c8ecb1892bcb7a3301d101bca7aa55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 815465ed2b2679fbcf4cda7c076dda6fdc89f322
      https://github.com/ehb54/ultrascan3/commit/815465ed2b2679fbcf4cda7c076dda6fdc89f322
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Merge pull request #327 from ehb54/alexey-dev-issue657

GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in FITME_AUTO & View Overlay


  Commit: f34431b433cbbb8b1ea9d3a18572183b63518f0e
      https://github.com/ehb54/ultrascan3/commit/f34431b433cbbb8b1ea9d3a18572183b63518f0e
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-test-commit


Compare: https://github.com/ehb54/ultrascan3/compare/f858b50eb014...f34431b433cb

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From noreply at github.com  Tue Nov 25 03:16:53 2025
From: noreply at github.com (Lukas Dobler)
Date: Tue, 25 Nov 2025 02:16:53 -0800
Subject: [us-commits] [ehb54/ultrascan3] b91982: Prot_DEV -- dataDisk type
 of data to reuse in Prot...
Message-ID: <ehb54/ultrascan3/push/refs/heads/lukas/qt6-compile/1687a5-06815f@github.com>

  Branch: refs/heads/lukas/qt6-compile
  Home:   https://github.com/ehb54/ultrascan3
  Commit: b91982360f02fc7d35efdbb917d2e08596c14560
      https://github.com/ehb54/ultrascan3/commit/b91982360f02fc7d35efdbb917d2e08596c14560
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 04ac91d9174e6d65816307faf1663175f2de6e72
      https://github.com/ehb54/ultrascan3/commit/04ac91d9174e6d65816307faf1663175f2de6e72
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [1]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: a107deb079b8089a73b101015763d8462f3aa43c
      https://github.com/ehb54/ultrascan3/commit/a107deb079b8089a73b101015763d8462f3aa43c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [2]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 77345534ee55741a3995fabe13f6faf8e1c5f881
      https://github.com/ehb54/ultrascan3/commit/77345534ee55741a3995fabe13f6faf8e1c5f881
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-03 (Mon, 03 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [3]Prot_DEV -- dataDisk type of data to reuse in Prot Dev....


  Commit: 7fc94237d997b68034bf17cbc314276cab5bc394
      https://github.com/ehb54/ultrascan3/commit/7fc94237d997b68034bf17cbc314276cab5bc394
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h

  Log Message:
  -----------
  [4]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: cff3d662e38213f7cc385ca99277c08dec6b43aa
      https://github.com/ehb54/ultrascan3/commit/cff3d662e38213f7cc385ca99277c08dec6b43aa
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h

  Log Message:
  -----------
  [55]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c280a617392dd55877185f3ece5a41202145aa63
      https://github.com/ehb54/ultrascan3/commit/c280a617392dd55877185f3ece5a41202145aa63
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [6]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1e35e7a3947fa08e0fd5e651641d80217b2f5337
      https://github.com/ehb54/ultrascan3/commit/1e35e7a3947fa08e0fd5e651641d80217b2f5337
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [7]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 86e9df690a84fc07f0443a794532a3a16247575b
      https://github.com/ehb54/ultrascan3/commit/86e9df690a84fc07f0443a794532a3a16247575b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-04 (Tue, 04 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [8]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 47aced1a7b9dd464c9e3233c131bffd2e5a43590
      https://github.com/ehb54/ultrascan3/commit/47aced1a7b9dd464c9e3233c131bffd2e5a43590
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [9]Prot_DEV -- Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
      https://github.com/ehb54/ultrascan3/commit/bf902b2991efbb3e2fc1009ef6800c635b5e7ea0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: d24d57352af04940c3cf6e6d3c87044a795c1f32
      https://github.com/ehb54/ultrascan3/commit/d24d57352af04940c3cf6e6d3c87044a795c1f32
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [10a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 21d57858d1f94bc1c02fbb7004faa197e3e44d77
      https://github.com/ehb54/ultrascan3/commit/21d57858d1f94bc1c02fbb7004faa197e3e44d77
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  [11a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 1b35ec93929d2ec945666589dfacd9390605a4c1
      https://github.com/ehb54/ultrascan3/commit/1b35ec93929d2ec945666589dfacd9390605a4c1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h

  Log Message:
  -----------
  [12a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 07982e368feea4dc848c21cf3ef6300332da9eb9
      https://github.com/ehb54/ultrascan3/commit/07982e368feea4dc848c21cf3ef6300332da9eb9
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-05 (Wed, 05 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [13a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c8df9d077992267f115dc3a8c6d6c57928fcb568
      https://github.com/ehb54/ultrascan3/commit/c8df9d077992267f115dc3a8c6d6c57928fcb568
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  [15a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: c1590729931d88a83cc57cdd346ccb2ee12835b4
      https://github.com/ehb54/ultrascan3/commit/c1590729931d88a83cc57cdd346ccb2ee12835b4
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-06 (Thu, 06 Nov 2025)

  Changed paths:
    M programs/us_edit/us_edit.cpp

  Log Message:
  -----------
  [16a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 7684ca675c735b07511e83617000346fe1a4731c
      https://github.com/ehb54/ultrascan3/commit/7684ca675c735b07511e83617000346fe1a4731c
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-08 (Sat, 08 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  [17a]Prot_DEV -- [run names for sunsequent PDs] Prep. steps for dealing with dataDisk vs. Instrument sources of data to reuse in Prot Dev; some fixes for Vel. vs. ABDE types....


  Commit: 31bffce6f2258893d277cf9e2ab6b5a2290acd70
      https://github.com/ehb54/ultrascan3/commit/31bffce6f2258893d277cf9e2ab6b5a2290acd70
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-17 (Mon, 17 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update unit-tests.yml to include additional paths


  Commit: b0f38f43b87f21495a47b399bf731e3b11812b15
      https://github.com/ehb54/ultrascan3/commit/b0f38f43b87f21495a47b399bf731e3b11812b15
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP : 6.REPORTER -- ranges for CG-models...


  Commit: 6c646f633296c0b2cdf20178c282494f364c1846
      https://github.com/ehb54/ultrascan3/commit/6c646f633296c0b2cdf20178c282494f364c1846
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M .gitignore
    A .gitmodules
    M CMakeLists.txt
    A CMakePresets.json
    A admin/cmake/GenerateVersion.cmake
    A admin/cmake/Us3QrcCheck.cmake
    A admin/cmake/Us3Resources.cmake
    A admin/cmake/UsDefinesParser.cmake
    A admin/cmake/platform-config.cmake
    A admin/cmake/triplets/x64-osx-dynamic.cmake
    R admin/cmake/us_version.h.in
    M admin/test/docker/Dockerfile
    M alpha/us.cpp
    A buildsys/vcpkg/overlay-ports/qwt/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwt/vcpkg.json
    A buildsys/vcpkg/overlay-ports/qwtplot3d/portfile.cmake
    A buildsys/vcpkg/overlay-ports/qwtplot3d/qwtplot3d-config.cmake.in
    A buildsys/vcpkg/overlay-ports/qwtplot3d/vcpkg.json
    A doc/manual/CMakeLists.txt
    M gui/CMakeLists.txt
    M gui/libus_gui.pro
    M gui/us_analysis_base2.cpp
    M gui/us_analyte_gui.cpp
    M gui/us_buffer_gui.cpp
    M gui/us_combined_plots_parms_gui.cpp
    M gui/us_edit_spectrum.cpp
    M gui/us_extinctfitter_gui.cpp
    M gui/us_extinction_gui.cpp
    M gui/us_gui_settings.cpp
    M gui/us_gui_settings.h
    M gui/us_gui_util.cpp
    R gui/us_mac_utils.c
    R gui/us_mac_utils.h
    M gui/us_new_spectrum.cpp
    M gui/us_plot.cpp
    M gui/us_plot.h
    M gui/us_plot3d.cpp
    M gui/us_report_general_gui.cpp
    M gui/us_report_gui.cpp
    M gui/us_run_details2.cpp
    M gui/us_sassoc.cpp
    M gui/us_scan_excl_gui.cpp
    M gui/us_sim_params_gui.cpp
    M gui/us_solution_gui.cpp
    M gui/us_spectrodata.cpp
    M gui/us_spectrodata.h
    M gui/us_tmst_plot.cpp
    M gui/us_widgets.cpp
    M gui/us_widgets_dialog.cpp
    R gui/us_win_utils.c
    R gui/us_win_utils.h
    R gui/us_window_message.cpp
    R gui/us_window_message.h
    R gui/us_x11_utils.c
    R gui/us_x11_utils.h
    M programs/CMakeLists.txt
    A programs/us/CMakeLists.txt
    M programs/us/revision.sh
    M programs/us/us.cpp
    M programs/us/us.pro
    M programs/us/us_win_data.cpp
    A programs/us/us_win_data.h
    A programs/us_2dplot/CMakeLists.txt
    M programs/us_2dplot/us_2dplot.cpp
    M programs/us_2dplot/us_2dplot.h
    A programs/us_2dsa/CMakeLists.txt
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_2dsa/us_analysis_control_2d.cpp
    M programs/us_2dsa/us_resplot_2d.cpp
    M programs/us_2dsa/us_show_norm.cpp
    A programs/us_abde/CMakeLists.txt
    M programs/us_abde/us_norm_profile.cpp
    A programs/us_analysis_profile/CMakeLists.txt
    M programs/us_analysis_profile/us_analysis_profile.cpp
    M programs/us_analysis_profile/us_anapro_utils.cpp
    A programs/us_analyte/CMakeLists.txt
    A programs/us_assign_reviewers_gmp/CMakeLists.txt
    A programs/us_astfem_sim/CMakeLists.txt
    M programs/us_astfem_sim/us_astfem_sim.cpp
    M programs/us_astfem_sim/us_clipdata.h
    A programs/us_audit_trail_gmp/CMakeLists.txt
    M programs/us_autoflow_analysis/CMakeLists.txt
    A programs/us_buffer/CMakeLists.txt
    A programs/us_buoyancy/CMakeLists.txt
    M programs/us_buoyancy/us_buoyancy.cpp
    A programs/us_colorgradient/CMakeLists.txt
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project_gui.cpp
    M programs/us_com_project_academic/CMakeLists.txt
    A programs/us_combine_models/CMakeLists.txt
    A programs/us_config/CMakeLists.txt
    M programs/us_config/us_color.cpp
    A programs/us_convert/CMakeLists.txt
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_intensity.cpp
    A programs/us_dcdt/CMakeLists.txt
    M programs/us_dcdt/us_dcdt.cpp
    A programs/us_ddist_combine/CMakeLists.txt
    M programs/us_ddist_combine/us_ddist_combine.cpp
    A programs/us_density_match/CMakeLists.txt
    A programs/us_dmga_init/CMakeLists.txt
    A programs/us_edit/CMakeLists.txt
    M programs/us_edit/us_edit.cpp
    M programs/us_edit/us_edit_scan.cpp
    M programs/us_edit/us_ri_noise.cpp
    A programs/us_equiltime/CMakeLists.txt
    M programs/us_equiltime/us_equiltime.cpp
    A programs/us_esigner_gmp/CMakeLists.txt
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_experiment/us_proto_ranges.cpp
    A programs/us_export_legacy/CMakeLists.txt
    M programs/us_export_legacy/us_export.cpp
    A programs/us_extinction/CMakeLists.txt
    A programs/us_fds_filemanager/CMakeLists.txt
    M programs/us_fds_filemanager/us_fds_filemanager.cpp
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_adv_dmgamc.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_fematch/us_resplot_fem.cpp
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_fit_meniscus/us_fit_meniscus.cpp
    A programs/us_ga_init/CMakeLists.txt
    M programs/us_ga_init/us_ga_init.cpp
    A programs/us_globalequil/CMakeLists.txt
    M programs/us_globalequil/us_eqfit_control.cpp
    M programs/us_globalequil/us_eqhistogram.cpp
    M programs/us_globalequil/us_globalequil.cpp
    A programs/us_grid_editor/CMakeLists.txt
    A programs/us_helpdaemon/CMakeLists.txt
    A programs/us_integral/CMakeLists.txt
    A programs/us_investigator/CMakeLists.txt
    A programs/us_legacy_converter/CMakeLists.txt
    A programs/us_license/CMakeLists.txt
    A programs/us_manage_data/CMakeLists.txt
    A programs/us_model_gui/CMakeLists.txt
    A programs/us_modelmetrics/CMakeLists.txt
    M programs/us_modelmetrics/us_modelmetrics.cpp
    A programs/us_mpi_analysis/CMakeLists.txt
    M programs/us_mwl_species_fit/CMakeLists.txt
    M programs/us_mwl_species_fit/us_mwl_species_fit.cpp
    A programs/us_mwl_species_sim/CMakeLists.txt
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    A programs/us_mwl_spectra/CMakeLists.txt
    M programs/us_mwl_spectra/us_mwl_spectra.cpp
    A programs/us_mwlr_viewer/CMakeLists.txt
    M programs/us_mwlr_viewer/us_mwlr_viewer.cpp
    A programs/us_pcsa/CMakeLists.txt
    M programs/us_pcsa/us_mlplot.cpp
    M programs/us_pcsa/us_pcsa.cpp
    M programs/us_pcsa/us_resplot_pc.cpp
    M programs/us_pcsa/us_rpscan.cpp
    A programs/us_predict1/CMakeLists.txt
    A programs/us_predict2/CMakeLists.txt
    A programs/us_project/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    A programs/us_pseudo3d_combine/CMakeLists.txt
    M programs/us_pseudo3d_combine/us_pseudo3d_combine.cpp
    A programs/us_pseudo_absorbance/CMakeLists.txt
    M programs/us_query_rmsd/CMakeLists.txt
    A programs/us_ramp/CMakeLists.txt
    M programs/us_ramp/us_intensity_ra.cpp
    M programs/us_ramp/us_ramp_gui.cpp
    R programs/us_rasmol_control/us_rasmol_control.cpp
    R programs/us_rasmol_control/us_rasmol_control.h
    R programs/us_rasmol_control/us_rasmol_control.pro
    A programs/us_reassign_reviewers_gmp/CMakeLists.txt
    A programs/us_reporter/CMakeLists.txt
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    A programs/us_rotor/CMakeLists.txt
    A programs/us_rotor_calibration/CMakeLists.txt
    M programs/us_rotor_calibration/us_rotor_calibration.cpp
    A programs/us_sassoc/CMakeLists.txt
    A programs/us_second_moment/CMakeLists.txt
    M programs/us_second_moment/us_second_moment.cpp
    A programs/us_solution/CMakeLists.txt
    A programs/us_spectrum/CMakeLists.txt
    M programs/us_spectrum/us_spectrum.cpp
    A programs/us_tmst_viewer/CMakeLists.txt
    A programs/us_vhw_combine/CMakeLists.txt
    M programs/us_vhw_combine/us_vhw_combine.cpp
    A programs/us_vhw_enhanced/CMakeLists.txt
    M programs/us_vhw_enhanced/us_distrib_plot.cpp
    M programs/us_vhw_enhanced/us_vhw_enhanced.cpp
    A programs/us_xpn_viewer/CMakeLists.txt
    M programs/us_xpn_viewer/us_xpn_viewer_gui.cpp
    M qwtplot3d/CMakeLists.txt
    M qwtplot3d/include/qwt3d_openglhelper.h
    A scripts/build.sh
    M test-docker.sh
    M test/CMakeLists.txt
    M test/utils/CMakeLists.txt
    M test/utils/test_us_ana_profile.cpp
    M utils/CMakeLists.txt
    M utils/us_defines.h
    M utils/us_run_protocol.h
    A vcpkg
    A vcpkg-configuration.json
    A vcpkg.json

  Log Message:
  -----------
  Merge branch 'main' into alexey-dev-issue608


  Commit: 0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
      https://github.com/ehb54/ultrascan3/commit/0ebfc3ee220014a56edc62db5dfdb61cdf14cc37
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 71e029d4b0191c6f9e49f61052bb4994b733a90e
      https://github.com/ehb54/ultrascan3/commit/71e029d4b0191c6f9e49f61052bb4994b733a90e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_experiment/us_exp_utils.cpp

  Log Message:
  -----------
  [1]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: f49d8cf364400df6d8104e5fd915d79df22d8638
      https://github.com/ehb54/ultrascan3/commit/f49d8cf364400df6d8104e5fd915d79df22d8638
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [2]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 8f6a939aba51bb5c70c66d760e2242304e659c0f
      https://github.com/ehb54/ultrascan3/commit/8f6a939aba51bb5c70c66d760e2242304e659c0f
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [3]GMP-PROT.DEV -- extend the case of re-processing dataDisk runs for arbitrary channels chases...


  Commit: 5400614d6c78af525f22b1f858362a99edc462a1
      https://github.com/ehb54/ultrascan3/commit/5400614d6c78af525f22b1f858362a99edc462a1
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-18 (Tue, 18 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #319 from ehb54/main

add main stuff to alexey-dev-issue651


  Commit: d40493020d965b05f43ed5c8a2eb1daaf5166a48
      https://github.com/ehb54/ultrascan3/commit/d40493020d965b05f43ed5c8a2eb1daaf5166a48
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 8f345295dc5803000521a47ad53aa246df51eff7
      https://github.com/ehb54/ultrascan3/commit/8f345295dc5803000521a47ad53aa246df51eff7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    A .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    A .github/workflows/doc-build.yml
    M admin/codeql/docker/local.pri.gui
    M admin/codeql/docker/local.pri.mpi
    M admin/codeql/docker/local.pri.somo
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M utils/us_run_protocol.h

  Log Message:
  -----------
  Merge pull request #320 from ehb54/main

update to main


  Commit: 129b8d9184d5cab1189cca7b84574bf7e97dca76
      https://github.com/ehb54/ultrascan3/commit/129b8d9184d5cab1189cca7b84574bf7e97dca76
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL workflow for improved caching and builds


  Commit: 793e12c735495da5c5b6deed3355e2428e6c2a16
      https://github.com/ehb54/ultrascan3/commit/793e12c735495da5c5b6deed3355e2428e6c2a16
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Simplify build step in CodeQL analysis workflow

Removed ccache setup and git configuration from the build step.


  Commit: 0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
      https://github.com/ehb54/ultrascan3/commit/0f76a4bf8a6ae54cd386ba2a645b0994b3b8b8b5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL analysis workflow

Refactor CodeQL analysis workflow to improve target calculation and build steps.


  Commit: 6c80777b7287a29fe978526475e6f099ca3ef827
      https://github.com/ehb54/ultrascan3/commit/6c80777b7287a29fe978526475e6f099ca3ef827
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL workflow to simplify caching and builds

Removed caching steps for ccache, utils, qwtplot3d, and gui. Added build steps for utils, qwtplot3d, and gui using qmake.


  Commit: 27c760f8c268e77d5038469cfd40243fb274f2d1
      https://github.com/ehb54/ultrascan3/commit/27c760f8c268e77d5038469cfd40243fb274f2d1
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update unit-tests.yml to remove path filters for push

Removed specific path filters for push events in unit-tests workflow.


  Commit: 2465409a96b820d237f9bf0c3b09b12f859060d7
      https://github.com/ehb54/ultrascan3/commit/2465409a96b820d237f9bf0c3b09b12f859060d7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update static analysis workflow trigger paths

Removed specific path triggers for push events in static analysis workflow.


  Commit: c1ac9c0b43cdde1480834d2fb742344b9649144f
      https://github.com/ehb54/ultrascan3/commit/c1ac9c0b43cdde1480834d2fb742344b9649144f
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Document CMake formatter


  Commit: 391ac4d011a289eafa902e9d56eb4382491f0b66
      https://github.com/ehb54/ultrascan3/commit/391ac4d011a289eafa902e9d56eb4382491f0b66
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Updating nproc


  Commit: ea7559d6bcd810ed7a176871e33f0d36b49152e2
      https://github.com/ehb54/ultrascan3/commit/ea7559d6bcd810ed7a176871e33f0d36b49152e2
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/unit-tests.yml
    M admin/linting/cmake/.cmake-format.yaml
    M admin/linting/cmake/README.md

  Log Message:
  -----------
  Fix minor comments


  Commit: 6e94734ca883da80e058cf4e51dee4474e9863e5
      https://github.com/ehb54/ultrascan3/commit/6e94734ca883da80e058cf4e51dee4474e9863e5
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_convert/us_convert_gui.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #305 from ehb54/alexey-dev-issue608

Alexey dev issue608: Prot. Dev. for DataDisk data types


  Commit: 5ff2d239588616635adbdfaf775949a91f5d7565
      https://github.com/ehb54/ultrascan3/commit/5ff2d239588616635adbdfaf775949a91f5d7565
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Update checkout action version


  Commit: 321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
      https://github.com/ehb54/ultrascan3/commit/321b58c1347db9be2b3ef6cbb24e94e5e4119dfa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M .github/workflows/doc-build.yml

  Log Message:
  -----------
  fix branches


  Commit: aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
      https://github.com/ehb54/ultrascan3/commit/aad9ec569ffb658a9035b4b0f5c75d8fc050fa1b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-19 (Wed, 19 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  [also aspect ratio of the plots]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 5c92b751327dc3f2908415ade46f68cc6ae21f7f
      https://github.com/ehb54/ultrascan3/commit/5c92b751327dc3f2908415ade46f68cc6ae21f7f
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Move general code used by multiple programs to libraries. Update CMakeLists.txt and *.pro files accordingly


  Commit: 22b358bc7c50111c979137831392022b5920ece3
      https://github.com/ehb54/ultrascan3/commit/22b358bc7c50111c979137831392022b5920ece3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M test-docker.sh

  Log Message:
  -----------
  - Add `US3_BUILD_PROGRAMS` flag to disable program builds in docker tests
- Redirect build output to `tee build.log` for better log visibility
- Ensure consistent newline at end of script


  Commit: eed16179a8828fcdad33d10893011f872744078a
      https://github.com/ehb54/ultrascan3/commit/eed16179a8828fcdad33d10893011f872744078a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M programs/us_fit_meniscus/CMakeLists.txt
    M utils/CMakeLists.txt

  Log Message:
  -----------
  - Fix variable mismatches in `BUILD_TESTING` conditions across CMakeLists.
- Disable `US3_BUILD_PROGRAMS` in `TEST` profile to align with expected behavior.
- Update logging for `BUILD_TESTING` status in CMake output.
- Remove redundant `US3_BUILD_TESTS` conditions for cleaner logic.


  Commit: 342c572ec5c13739d56e6a45922eeddd2168d777
      https://github.com/ehb54/ultrascan3/commit/342c572ec5c13739d56e6a45922eeddd2168d777
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_convert_gui.cpp
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M test-docker.sh

  Log Message:
  -----------
  Fix typos


  Commit: 8ec56186a4b601669d87ed939d3ac1f4e7057561
      https://github.com/ehb54/ultrascan3/commit/8ec56186a4b601669d87ed939d3ac1f4e7057561
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_convert.cpp
    M utils/us_convert.h

  Log Message:
  -----------
  - Apply `const QString&` to parameters in `readLegacyData` for efficiency
- Remove unused `mixed_type` variable and redundant assignment of `runType`
- Clean up debug statements for clearer logging


  Commit: 5cf42202af6d7f5544a2cf1111d44f5f1a232777
      https://github.com/ehb54/ultrascan3/commit/5cf42202af6d7f5544a2cf1111d44f5f1a232777
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Refactor CodeQL analysis workflow conditions

Removed specific file paths from pull request triggers and updated conditions for CodeQL analysis steps.


  Commit: 3f486acaa2a2e5b708f257acf949e90d1b042bbc
      https://github.com/ehb54/ultrascan3/commit/3f486acaa2a2e5b708f257acf949e90d1b042bbc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Rename analysis job for GUI programs


  Commit: a81ad04f934cbf1c4a0983859a74441fa4aaae0e
      https://github.com/ehb54/ultrascan3/commit/a81ad04f934cbf1c4a0983859a74441fa4aaae0e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [remove x_min/max from global settings]GMP 6. REPORT -- for runs based on Custom-Grid model, use correct ranges for ind. and combined distributions...


  Commit: 1e81209448574c4a6b3bf57955a2aed48a70cca2
      https://github.com/ehb54/ultrascan3/commit/1e81209448574c4a6b3bf57955a2aed48a70cca2
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #323 from ehb54/lukas/cmake-fixes

Fix failing Unittests and cmake build


  Commit: 9317a33dcf14a74c7ca9e145158c539dc3c10be3
      https://github.com/ehb54/ultrascan3/commit/9317a33dcf14a74c7ca9e145158c539dc3c10be3
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge pull request #325 from ehb54/main

Include main into alexey-dev-issue651


  Commit: 02ab6c663335530dbf4295161c2f68c1043b3874
      https://github.com/ehb54/ultrascan3/commit/02ab6c663335530dbf4295161c2f68c1043b3874
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


  Commit: 013afa9051723a54ff17a3431895f0e6aa65eebc
      https://github.com/ehb54/ultrascan3/commit/013afa9051723a54ff17a3431895f0e6aa65eebc
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Refactor GitHub Actions workflows to enhance modularity and efficiency
- Introduce `changed-files` job to conditionally trigger workflows based on file changes.
- Add status-checking jobs for Documentation, CodeQL analysis, and Static Analysis builds.
- Improve concurrency management and file fetch depth.
- Optimize CI Docker containers and cleanup processes.
- Streamline conditional checks and matrix configurations.


  Commit: 2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
      https://github.com/ehb54/ultrascan3/commit/2574c202cf8e3a25d12efaf4dd85cbfcf4cce419
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    A .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Add `unit-tests-v2.yml` GitHub Actions workflow

- Introduce a new workflow for unit testing with support for configurable test filters and debug mode.
- Add a `changed-files` job to detect relevant file modifications and conditionally trigger tests.
- Implement improved concurrency management and result-checking mechanisms.
- Streamline test setup, build process, and log management for enhanced clarity and efficiency.
- Enable artifact uploads for detailed test results and logs.


  Commit: e2a9b2acaeeeac868cf1d55f459225e683e37d11
      https://github.com/ehb54/ultrascan3/commit/e2a9b2acaeeeac868cf1d55f459225e683e37d11
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Normalize glob patterns in GitHub Actions workflows


  Commit: 037064b1d8968578fcb9a42ba07e275c96b38a8c
      https://github.com/ehb54/ultrascan3/commit/037064b1d8968578fcb9a42ba07e275c96b38a8c
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests-v2.yml

  Log Message:
  -----------
  Fix incorrect `CMAKE_MODULE_PATH` to use absolute path in `unit-tests-v2.yml` workflow


  Commit: 4c0538dff646603c4258628a076f9807a29af7c3
      https://github.com/ehb54/ultrascan3/commit/4c0538dff646603c4258628a076f9807a29af7c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Enhance `unit-tests.yml` workflow with dynamic file change detection and improved concurrency management

- Add `changed-files` job to detect relevant modifications and conditionally trigger unit tests.
- Introduce concurrency control to prevent duplicate runs.
- Expand artifacts to include additional logs for better debugging.
- Add status-checking job to validate unit testing outcomes.
- Refactor workflow for clarity and streamlined test execution.


  Commit: 12e9e1fd701da2b201e7d47b3cb642812813e4e7
      https://github.com/ehb54/ultrascan3/commit/12e9e1fd701da2b201e7d47b3cb642812813e4e7
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Enhance `static-analysis.yml` workflow with CPP file-specific change detection

- Add outputs and environment variables to track `.cpp` and `.h` file changes.
- Update `changed-files` step to simplify logic and rely on filtered outputs.
- Streamline file detection for first commits and pull requests.


  Commit: e94063c15730a822262820f18c468a429ac4c374
      https://github.com/ehb54/ultrascan3/commit/e94063c15730a822262820f18c468a429ac4c374
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/unit-tests.yml

  Log Message:
  -----------
  Normalize glob pattern syntax in `unit-tests.yml` workflow


  Commit: 158b855316998f18924177b91ad5cb81e696ad53
      https://github.com/ehb54/ultrascan3/commit/158b855316998f18924177b91ad5cb81e696ad53
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update static-analysis workflow to use latest `us3comp` container image


  Commit: e90b563926591d47a67070f0413d64f995ed47a0
      https://github.com/ehb54/ultrascan3/commit/e90b563926591d47a67070f0413d64f995ed47a0
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: fe4173f931d8dff6fa90b5ac68584d7288da6e44
      https://github.com/ehb54/ultrascan3/commit/fe4173f931d8dff6fa90b5ac68584d7288da6e44
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [1]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: dc717ab5d9685a48525ee315d3f4bffe9dec806e
      https://github.com/ehb54/ultrascan3/commit/dc717ab5d9685a48525ee315d3f4bffe9dec806e
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [2]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: f27c85345e2838e5372ad69873016bc574f4b005
      https://github.com/ehb54/ultrascan3/commit/f27c85345e2838e5372ad69873016bc574f4b005
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [3]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
      https://github.com/ehb54/ultrascan3/commit/48cb1fa84db559ebdc58a2b9c4b7e7c00ff9cb5b
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_ddist_combine/us_ddist_combine.cpp

  Log Message:
  -----------
  [4]GMP 6. REPORT -- [single-point data] add debug stats...


  Commit: 74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
      https://github.com/ehb54/ultrascan3/commit/74a2a0309cbf2e06fe514e02ea2cc40874cf4f25
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp

  Log Message:
  -----------
  PROT_DEV: run_selector -- order in reverse chronological order...


  Commit: 350edcd3194656d020a571d45cbe1dd872d041e2
      https://github.com/ehb54/ultrascan3/commit/350edcd3194656d020a571d45cbe1dd872d041e2
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge pull request #322 from ehb54/alexey-dev-issue651

Alexey dev issue651: Ind. & Combined Plots in GMP Rpeorts: CG-model-based runs (ranges), Plot Aspect Ratios, "Combined Plots" section title


  Commit: 05f602b3975c9e9cfbbeb21813b637046978d65a
      https://github.com/ehb54/ultrascan3/commit/05f602b3975c9e9cfbbeb21813b637046978d65a
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  GMP 6. REPORT -- generate correct build number in the header...


  Commit: e1ce700f61527eedba262f237e41dbcc16de6de7
      https://github.com/ehb54/ultrascan3/commit/e1ce700f61527eedba262f237e41dbcc16de6de7
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/static-analysis.yml

  Log Message:
  -----------
  Update file patterns for static analysis


  Commit: aebbdda924bca0630a6b1b50f5110f340c8804aa
      https://github.com/ehb54/ultrascan3/commit/aebbdda924bca0630a6b1b50f5110f340c8804aa
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Update CodeQL workflow to ignore specific files

Ignore changes in us_mpi_analysis directory during file checks and update build commands.


  Commit: a4a655d619279b7bb59e01ee82fce46e875eebca
      https://github.com/ehb54/ultrascan3/commit/a4a655d619279b7bb59e01ee82fce46e875eebca
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Exclude us_mpi_analysis from CodeQL analysis gui


  Commit: 14ba4d63b16861ed659ae0c204b0ee3f54589432
      https://github.com/ehb54/ultrascan3/commit/14ba4d63b16861ed659ae0c204b0ee3f54589432
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M .github/workflows/codeql-analysis.yml

  Log Message:
  -----------
  Fix syntax for exclusion in CodeQL workflow


  Commit: 770769aa570aae22f64b5b817de2320ab1b070e3
      https://github.com/ehb54/ultrascan3/commit/770769aa570aae22f64b5b817de2320ab1b070e3
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-22 (Sat, 22 Nov 2025)

  Changed paths:
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Merge pull request #326 from ehb54/alexey-dev-issue631

GMP 6. REPORT -- generate correct build number in the header...


  Commit: 3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
      https://github.com/ehb54/ultrascan3/commit/3f56d29bde0ad6a71c607a8bcfb56bc7caca4961
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/gh_actions


  Commit: c088a80976663c552cffec04fcb0cfe084922560
      https://github.com/ehb54/ultrascan3/commit/c088a80976663c552cffec04fcb0cfe084922560
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml

  Log Message:
  -----------
  Merge pull request #321 from ehb54/lukas/gh_actions

Lukas/gh actions


  Commit: 70cf969d22c8ecb1892bcb7a3301d101bca7aa55
      https://github.com/ehb54/ultrascan3/commit/70cf969d22c8ecb1892bcb7a3301d101bca7aa55
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in (1) FITMEN_AUTO stage, and (2) View Overlay while simulating data -- may have caused stoppage in updating main GUI after completion of these stages...


  Commit: 815465ed2b2679fbcf4cda7c076dda6fdc89f322
      https://github.com/ehb54/ultrascan3/commit/815465ed2b2679fbcf4cda7c076dda6fdc89f322
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp

  Log Message:
  -----------
  Merge pull request #327 from ehb54/alexey-dev-issue657

GMP 5. ANALYSIS -- added more processEvens() for progressDialogs in FITME_AUTO & View Overlay


  Commit: 06815f05ab2f337ae26ce8382ddaf80069e0e931
      https://github.com/ehb54/ultrascan3/commit/06815f05ab2f337ae26ce8382ddaf80069e0e931
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    M CMakeLists.txt
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    M gui/libus_gui.pro
    M gui/us_combined_plots_parms_gui.cpp
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_edit/us_edit.cpp
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_exp_utils.cpp
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into lukas/qt6-compile


Compare: https://github.com/ehb54/ultrascan3/compare/1687a57993f8...06815f05ab2f

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From noreply at github.com  Tue Nov 25 09:40:40 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 08:40:40 -0800
Subject: [us-commits] [ehb54/ultrascan3] 6e0a4e: commit to force somo
 recompile
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/f34431-6e0a4e@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 6e0a4e0c05af1607a1f13f9280d07b1df3b63075
      https://github.com/ehb54/ultrascan3/commit/6e0a4e0c05af1607a1f13f9280d07b1df3b63075
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp

  Log Message:
  -----------
  commit to force somo recompile



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From noreply at github.com  Tue Nov 25 09:47:27 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 08:47:27 -0800
Subject: [us-commits] [ehb54/ultrascan3] a0b589: add
 reviews-requested-approved.yml
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/6e0a4e-a0b589@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: a0b5895c531258602d00f0cb6c6f84be16cc9c47
      https://github.com/ehb54/ultrascan3/commit/a0b5895c531258602d00f0cb6c6f84be16cc9c47
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    A .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  add reviews-requested-approved.yml



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From noreply at github.com  Tue Nov 25 09:49:54 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 08:49:54 -0800
Subject: [us-commits] [ehb54/ultrascan3] c12437: reviews-requested-approved
 fix
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/a0b589-c12437@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: c12437ef4270788d9e516c26e0b0370c3f22286a
      https://github.com/ehb54/ultrascan3/commit/c12437ef4270788d9e516c26e0b0370c3f22286a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  reviews-requested-approved fix



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From noreply at github.com  Tue Nov 25 09:52:12 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 08:52:12 -0800
Subject: [us-commits] [ehb54/ultrascan3] 782867: reviews-requested-approved
 fix
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/c12437-782867@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 782867c5e963efad09ea7b4a9cfb9c6149d6852f
      https://github.com/ehb54/ultrascan3/commit/782867c5e963efad09ea7b4a9cfb9c6149d6852f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  reviews-requested-approved fix



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From noreply at github.com  Tue Nov 25 10:01:26 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 09:01:26 -0800
Subject: [us-commits] [ehb54/ultrascan3] 396795: reviews-requested-approved
 fix
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/782867-396795@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 396795f6a4219e6dcd6365dac17a808f9bb278df
      https://github.com/ehb54/ultrascan3/commit/396795f6a4219e6dcd6365dac17a808f9bb278df
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  reviews-requested-approved fix



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From noreply at github.com  Tue Nov 25 11:56:03 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 10:56:03 -0800
Subject: [us-commits] [ehb54/ultrascan3] d2ad9f: restore modified code files
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/396795-d2ad9f@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3
  Commit: d2ad9fa01092f723f4f3404fe82e8bc481920924
      https://github.com/ehb54/ultrascan3/commit/d2ad9fa01092f723f4f3404fe82e8bc481920924
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp
    M utils/us_extern.h

  Log Message:
  -----------
  restore modified code files



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From noreply at github.com  Tue Nov 25 12:02:09 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 11:02:09 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-test-commit/d2ad9f-000000@github.com>

  Branch: refs/heads/ehb54-test-commit
  Home:   https://github.com/ehb54/ultrascan3

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From noreply at github.com  Tue Nov 25 12:02:09 2025
From: noreply at github.com (ehb54)
Date: Tue, 25 Nov 2025 11:02:09 -0800
Subject: [us-commits] [ehb54/ultrascan3] 941a03: add comment
Message-ID: <ehb54/ultrascan3/push/refs/heads/ehb54-issue-659/000000-d2ad9f@github.com>

  Branch: refs/heads/ehb54-issue-659
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 941a0388f62a7d77b83111dec187f42c78603cc9
      https://github.com/ehb54/ultrascan3/commit/941a0388f62a7d77b83111dec187f42c78603cc9
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  add comment


  Commit: a1e64084cc68a813d8f0f9bdea45043df1977f01
      https://github.com/ehb54/ultrascan3/commit/a1e64084cc68a813d8f0f9bdea45043df1977f01
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  comment 2


  Commit: ebd0fea4759a30412ac4f92f12a9e84179488916
      https://github.com/ehb54/ultrascan3/commit/ebd0fea4759a30412ac4f92f12a9e84179488916
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-20 (Thu, 20 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  comment 2


  Commit: 1266be2b9bea8dfeef9b35c56fee9c2bf78d423b
      https://github.com/ehb54/ultrascan3/commit/1266be2b9bea8dfeef9b35c56fee9c2bf78d423b
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M gui/libus_gui.pro
    A gui/us_convert_gui.cpp
    A gui/us_convert_gui.h
    A gui/us_experiment_gui.cpp
    A gui/us_experiment_gui.h
    A gui/us_get_run.cpp
    A gui/us_get_run.h
    A gui/us_intensity.cpp
    A gui/us_intensity.h
    A gui/us_select_triples.cpp
    A gui/us_select_triples.h
    A gui/us_selectbox.cpp
    A gui/us_selectbox.h
    M programs/us_autoflow_analysis/CMakeLists.txt
    M programs/us_autoflow_analysis/us_autoflow_analysis.h
    M programs/us_autoflow_analysis/us_autoflow_analysis.pro
    M programs/us_com_project/CMakeLists.txt
    M programs/us_com_project/us_com_project.pro
    M programs/us_com_project/us_com_project_gui.h
    M programs/us_com_project_academic/CMakeLists.txt
    M programs/us_com_project_academic/us_com_project_academic.pro
    M programs/us_convert/CMakeLists.txt
    R programs/us_convert/us_convert.cpp
    R programs/us_convert/us_convert.h
    M programs/us_convert/us_convert.pro
    R programs/us_convert/us_convert_gui.cpp
    R programs/us_convert/us_convert_gui.h
    R programs/us_convert/us_convertio.cpp
    R programs/us_convert/us_convertio.h
    R programs/us_convert/us_experiment.cpp
    R programs/us_convert/us_experiment.h
    R programs/us_convert/us_experiment_gui.cpp
    R programs/us_convert/us_experiment_gui.h
    R programs/us_convert/us_get_run.cpp
    R programs/us_convert/us_get_run.h
    R programs/us_convert/us_intensity.cpp
    R programs/us_convert/us_intensity.h
    R programs/us_convert/us_select_triples.cpp
    R programs/us_convert/us_select_triples.h
    R programs/us_convert/us_selectbox.cpp
    R programs/us_convert/us_selectbox.h
    M programs/us_experiment/CMakeLists.txt
    M programs/us_experiment/us_experiment.pro
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_experiment/us_experiment_gui_optima.h
    M programs/us_fematch/CMakeLists.txt
    M programs/us_fematch/us_fematch.pro
    M programs/us_fit_meniscus/CMakeLists.txt
    M programs/us_legacy_converter/CMakeLists.txt
    M programs/us_legacy_converter/us_legacy_converter.cpp
    M programs/us_legacy_converter/us_legacy_converter.h
    M programs/us_legacy_converter/us_legacy_converter.pro
    M programs/us_protocol_dev/CMakeLists.txt
    M programs/us_protocol_dev/us_protocol_dev.pro
    M programs/us_protocol_dev/us_protocol_dev_gui.h
    M programs/us_query_rmsd/CMakeLists.txt
    M programs/us_query_rmsd/us_query_rmsd.pro
    M programs/us_reporter_gmp/CMakeLists.txt
    M programs/us_reporter_gmp/us_reporter_gmp.pro
    M programs/us_xpn_viewer/us_xpn_viewer.pro
    M test-docker.sh
    M utils/CMakeLists.txt
    M utils/libus_utils.pro
    A utils/us_convert.cpp
    A utils/us_convert.h
    A utils/us_convertio.cpp
    A utils/us_convertio.h
    A utils/us_experiment.cpp
    A utils/us_experiment.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-test-commit


  Commit: f858b50eb0149b4eb8b0eb5158c40a0078ed51cf
      https://github.com/ehb54/ultrascan3/commit/f858b50eb0149b4eb8b0eb5158c40a0078ed51cf
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-21 (Fri, 21 Nov 2025)

  Changed paths:
    M utils/us_extern.h

  Log Message:
  -----------
  comment 4


  Commit: f34431b433cbbb8b1ea9d3a18572183b63518f0e
      https://github.com/ehb54/ultrascan3/commit/f34431b433cbbb8b1ea9d3a18572183b63518f0e
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2025-11-24 (Mon, 24 Nov 2025)

  Changed paths:
    R .github/workflows/.yamllint.yml
    M .github/workflows/codeql-analysis.yml
    M .github/workflows/doc-build.yml
    M .github/workflows/static-analysis.yml
    A .github/workflows/unit-tests-v2.yml
    M .github/workflows/unit-tests.yml
    A admin/linting/cmake/.cmake-format.yaml
    A admin/linting/cmake/README.md
    A admin/linting/yaml/.yamllint.yml
    M gui/us_combined_plots_parms_gui.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_ddist_combine/us_ddist_combine.cpp
    M programs/us_ddist_combine/us_ddist_combine.h
    M programs/us_protocol_dev/us_protocol_dev_gui.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.h

  Log Message:
  -----------
  Merge branch 'main' into ehb54-test-commit


  Commit: 6e0a4e0c05af1607a1f13f9280d07b1df3b63075
      https://github.com/ehb54/ultrascan3/commit/6e0a4e0c05af1607a1f13f9280d07b1df3b63075
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp

  Log Message:
  -----------
  commit to force somo recompile


  Commit: a0b5895c531258602d00f0cb6c6f84be16cc9c47
      https://github.com/ehb54/ultrascan3/commit/a0b5895c531258602d00f0cb6c6f84be16cc9c47
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    A .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  add reviews-requested-approved.yml


  Commit: c12437ef4270788d9e516c26e0b0370c3f22286a
      https://github.com/ehb54/ultrascan3/commit/c12437ef4270788d9e516c26e0b0370c3f22286a
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  reviews-requested-approved fix


  Commit: 782867c5e963efad09ea7b4a9cfb9c6149d6852f
      https://github.com/ehb54/ultrascan3/commit/782867c5e963efad09ea7b4a9cfb9c6149d6852f
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  reviews-requested-approved fix


  Commit: 396795f6a4219e6dcd6365dac17a808f9bb278df
      https://github.com/ehb54/ultrascan3/commit/396795f6a4219e6dcd6365dac17a808f9bb278df
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M .github/workflows/reviews-requested-approved.yml

  Log Message:
  -----------
  reviews-requested-approved fix


  Commit: d2ad9fa01092f723f4f3404fe82e8bc481920924
      https://github.com/ehb54/ultrascan3/commit/d2ad9fa01092f723f4f3404fe82e8bc481920924
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M us_somo/develop/src/us_hydrodyn.cpp
    M utils/us_extern.h

  Log Message:
  -----------
  restore modified code files


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Subject: [us-commits] [ehb54/ultrascan3] ef1d9f: nov 25
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/9bfe38-ef1d9f@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ef1d9fdfacb60f6f6ee4143fc57f73cc7167d7a2
      https://github.com/ehb54/ultrascan3/commit/ef1d9fdfacb60f6f6ee4143fc57f73cc7167d7a2
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-11-25 (Tue, 25 Nov 2025)

  Changed paths:
    M doc/manual/source/2dsa/2dsa_adv.rst
    A doc/manual/source/_static/images/UltraScan-logo.png
    R doc/manual/source/_static/images/colorgrad.png
    A doc/manual/source/_static/images/colorgradient/colorgrad.png
    A doc/manual/source/_static/images/colorgradient/colorgradient_main.png
    M doc/manual/source/colorgradient.rst
    M doc/manual/source/index.rst

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From: noreply at github.com (aaron-auc)
Date: Thu, 27 Nov 2025 16:41:32 -0800
Subject: [us-commits] [ehb54/us3_sql] 4455db: add: version file and workflow
Message-ID: <ehb54/us3_sql/push/refs/heads/versioning/6ffbfa-4455db@github.com>

  Branch: refs/heads/versioning
  Home:   https://github.com/ehb54/us3_sql
  Commit: 4455dbb5cc62bb5159c6488f35eff29f97fc6519
      https://github.com/ehb54/us3_sql/commit/4455dbb5cc62bb5159c6488f35eff29f97fc6519
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-27 (Thu, 27 Nov 2025)

  Changed paths:
    A .github/workflows/release.yml
    A VERSION
    A gfac/gfac.sql
    A newus3/newus3.sql
    A us3_notice/us3_notice.sql
    A uslims3_global/global.sql

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From noreply at github.com  Thu Nov 27 18:43:31 2025
From: noreply at github.com (aaron-auc)
Date: Thu, 27 Nov 2025 17:43:31 -0800
Subject: [us-commits] [ehb54/us3_sql] dc18ee: mod: use callable action
Message-ID: <ehb54/us3_sql/push/refs/heads/versioning/4455db-dc18ee@github.com>

  Branch: refs/heads/versioning
  Home:   https://github.com/ehb54/us3_sql
  Commit: dc18ee3e9ed645cd2927766e6789d5f5cc461afe
      https://github.com/ehb54/us3_sql/commit/dc18ee3e9ed645cd2927766e6789d5f5cc461afe
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-27 (Thu, 27 Nov 2025)

  Changed paths:
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  mod: use callable action



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From noreply at github.com  Fri Nov 28 00:59:22 2025
From: noreply at github.com (HabGab)
Date: Thu, 27 Nov 2025 23:59:22 -0800
Subject: [us-commits] [ehb54/ultrascan3] dc778a: nov27
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/ef1d9f-dc778a@github.com>

  Branch: refs/heads/haben-Dev
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  Commit: dc778acf5259399b68c8f3a88623c1a99d827787
      https://github.com/ehb54/ultrascan3/commit/dc778acf5259399b68c8f3a88623c1a99d827787
  Author: Haben <gabirh at myumanitoba.ca>
  Date:   2025-11-28 (Fri, 28 Nov 2025)

  Changed paths:
    M doc/manual/source/_static/css/custom.css
    M doc/manual/source/colorgradient.rst

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  nov27



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From noreply at github.com  Fri Nov 28 11:22:59 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 28 Nov 2025 10:22:59 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/653-bug-unit-tests-failed-on-a-main-branch-pr-action-logs-provide-insufficient-details/6e9473-000000@github.com>

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From noreply at github.com  Fri Nov 28 11:23:27 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 28 Nov 2025 10:23:27 -0800
Subject: [us-commits] [ehb54/ultrascan3]
Message-ID: <ehb54/ultrascan3/push/refs/heads/370-request-email-address-maintenance/adc6c2-000000@github.com>

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From noreply at github.com  Fri Nov 28 15:11:46 2025
From: noreply at github.com (aaron-auc)
Date: Fri, 28 Nov 2025 14:11:46 -0800
Subject: [us-commits] [ehb54/ultrascan3] 75dc17: fix: version check for
 notices
Message-ID: <ehb54/ultrascan3/push/refs/heads/notices-fix/000000-75dc17@github.com>

  Branch: refs/heads/notices-fix
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 75dc17665cd257146092a569f966700373e3c0b3
      https://github.com/ehb54/ultrascan3/commit/75dc17665cd257146092a569f966700373e3c0b3
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-28 (Fri, 28 Nov 2025)

  Changed paths:
    M CMakeLists.txt
    M CMakePresets.json
    M programs/us/CMakeLists.txt
    M programs/us/us.cpp
    M scripts/build.sh

  Log Message:
  -----------
  fix: version check for notices



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From noreply at github.com  Sat Nov 29 09:24:55 2025
From: noreply at github.com (HabGab)
Date: Sat, 29 Nov 2025 08:24:55 -0800
Subject: [us-commits] [ehb54/ultrascan3] 544fb2: Nov 29
Message-ID: <ehb54/ultrascan3/push/refs/heads/haben-Dev/dc778a-85ec26@github.com>

  Branch: refs/heads/haben-Dev
  Home:   https://github.com/ehb54/ultrascan3
  Commit: 544fb2f3526fae2609d113bfa9e5972b87d34a60
      https://github.com/ehb54/ultrascan3/commit/544fb2f3526fae2609d113bfa9e5972b87d34a60
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-11-29 (Sat, 29 Nov 2025)

  Changed paths:
    R doc/manual/2dsa/2dsa.body
    R doc/manual/2dsa/2dsa_advan.body
    R doc/manual/2dsa/2dsa_analvv.body
    R doc/manual/2dsa/2dsa_analys.body
    R doc/manual/experiment/experiment_cells.body
    R doc/manual/experiment/experiment_general.body
    R doc/manual/experiment/experiment_photomult.body
    R doc/manual/experiment/experiment_rotor.body
    R doc/manual/experiment/experiment_solutions.body
    R doc/manual/experiment/experiment_speeds.body
    R doc/manual/experiment/experiment_upload.body
    R doc/manual/fe_match/fe_match.body
    R doc/manual/fe_match/fe_match_adv.body
    R doc/manual/fe_match/fe_match_controls.body
    R doc/manual/fe_match/fe_match_lddat.body
    R doc/manual/fe_match/fe_match_simulate.body
    R doc/manual/gmp/gmp.body
    R doc/manual/gmp/gmp_audit_trail.body
    R doc/manual/gmp/gmp_data_acquisition.body
    R doc/manual/gmp/gmp_data_acquisition_experiment.body
    R doc/manual/gmp/gmp_data_acquisition_gmp.body
    R doc/manual/gmp/gmp_protocol_development.body
    R doc/manual/gmp/gmp_report_generator.body
    R doc/manual/gmp/gmp_signature.body
    R doc/manual/images/2dsa_3dplot.png
    R doc/manual/images/2dsa_advan.png
    R doc/manual/images/2dsa_analvv.png
    R doc/manual/images/2dsa_analys.png
    R doc/manual/images/2dsa_main-c.png
    R doc/manual/images/2dsa_main-o.png
    R doc/manual/images/2dsa_resplot.png
    R doc/manual/images/advanced_config.png
    R doc/manual/images/analyte_details.png
    R doc/manual/images/analytes.png
    R doc/manual/images/associations.png
    R doc/manual/images/astfem_sim.png
    R doc/manual/images/buffer_edit.png
    R doc/manual/images/buffer_info.png
    R doc/manual/images/buffer_new.png
    R doc/manual/images/buffer_select.png
    R doc/manual/images/buffer_settings.png
    R doc/manual/images/cfa_view-loadauc.png
    R doc/manual/images/cfa_view-loadraw.png
    R doc/manual/images/cfa_view-main.png
    R doc/manual/images/cfa_view-statsauc.png
    R doc/manual/images/cfa_view-statsraw.png
    R doc/manual/images/color-1.png
    R doc/manual/images/color-2.png
    R doc/manual/images/color-a.png
    R doc/manual/images/color-b.png
    R doc/manual/images/colorgrad.png
    R doc/manual/images/colorgrad1.png
    R doc/manual/images/combine_models-idedit.png
    R doc/manual/images/combine_models-save.png
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    R doc/manual/images/components.png
    R doc/manual/images/config.png
    R doc/manual/images/config1.png
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    R doc/manual/images/convert-RIdata.png
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    R doc/manual/images/convert-experiment.png
    R doc/manual/images/convert-mwl.png
    R doc/manual/images/convert-seltrip.png
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    R doc/manual/images/convert.png
    R doc/manual/images/data_loader-edits.png
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    R doc/manual/images/database.png
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    R doc/manual/images/densmatch_main.png
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    R doc/manual/images/experiment_upload.png
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    R doc/manual/images/fe_match.png
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    R html/_static/images/gmp/vhw_distribution.png
    R html/_static/images/grid_editor.png
    R html/_static/images/grid_editor_multi_grids.png
    R html/_static/images/grid_editor_multi_grids_sed.png
    R html/_static/images/grid_editor_mw_view.png
    R html/_static/images/grid_editor_subgrid1-bad.png
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    R html/_static/images/grid_editor_subgrid2-bad.png
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    R html/_static/images/grid_editor_subgrid3-bad.png
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    R html/_static/images/idist_comb_selPre.png
    R html/_static/images/idist_comb_seldis.png
    R html/_static/images/idist_combine.png
    R html/_static/images/load_auc-search.png
    R html/_static/images/load_auc-trips.png
    R html/_static/images/load_auc.png
    R html/_static/images/load_colormap.png
    R html/_static/images/load_model_dis-MID.png
    R html/_static/images/load_model_distrib.png
    R html/_static/images/load_noise.png
    R html/_static/images/load_noise_details.png
    R html/_static/images/manage_data.png
    R html/_static/images/manage_data_bhide.png
    R html/_static/images/manage_data_bshow.png
    R html/_static/images/manage_data_cmenu-1.png
    R html/_static/images/manage_data_cmenu-2.png
    R html/_static/images/manage_data_conf.png
    R html/_static/images/manage_data_exp.png
    R html/_static/images/manage_data_pasw.png
    R html/_static/images/manage_data_sync.png
    R html/_static/images/manage_data_thelp-1.png
    R html/_static/images/manage_data_thelp-2.png
    R html/_static/images/master-pw.png
    R html/_static/images/model_editor.png
    R html/_static/images/mwlr_view_3dplot.png
    R html/_static/images/mwlr_view_load.png
    R html/_static/images/mwlr_view_pltctrl.png
    R html/_static/images/mwlr_viewer.png
    R html/_static/images/mwlr_viewer_xwavl.png
    R html/_static/images/optima_config_edit.png
    R html/_static/images/optima_config_new.png
    R html/_static/images/optima_host_config.png
    R html/_static/images/pcsa_3dplot.png
    R html/_static/images/pcsa_analys-line.png
    R html/_static/images/pcsa_analys-sigm.png
    R html/_static/images/pcsa_main-c.png
    R html/_static/images/pcsa_mlines-line1.png
    R html/_static/images/pcsa_mlines-line2.png
    R html/_static/images/pcsa_mlines-sigm1.png
    R html/_static/images/pcsa_mlines-sigm2.png
    R html/_static/images/pcsa_resplot.png
    R html/_static/images/pcsa_rpscan-auto.png
    R html/_static/images/pcsa_rpscan-select.png
    R html/_static/images/plot_controls.png
    R html/_static/images/predict1.png
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    R html/_static/images/print.png
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    R html/_static/images/pseudo3d_comb_rmv.png
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    R html/_static/images/register.png
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    R html/_static/images/rotor-add.png
    R html/_static/images/rotor-save-calibration.png
    R html/_static/images/rotor.png
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    R html/_static/images/sequence.png
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    R html/_static/images/us_buffer_spect.png
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    R html/_static/images/us_edit_mwl.png
    R html/_static/images/us_equiltime.png
    R html/_static/images/us_fds_filemanager-0.png
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    R html/_static/images/vhw_combine-combo.png
    R html/_static/images/vhw_combine-envel.png
    R html/_static/images/vhw_combine-selrun.png
    R html/_static/images/vhw_combine.png
    R html/_static/images/vhw_distribution.png
    R html/_static/images/vhw_enh_groups.png
    R html/_static/images/vhw_enh_groups.png6-33-11.png
    R html/_static/images/vhw_enh_groups_res.png
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    R html/_static/minus.png
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    R html/_static/searchtools.js
    R html/_static/sphinx_highlight.js
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    R html/buffer.html
    R html/combine_models.html
    R html/common_dialogs.html
    R html/config.html
    R html/custom_grid.html
    R html/ddist_combine.html
    R html/dens_match.html
    R html/fe_match.html
    R html/fe_match_simulate.html
    R html/fit_meniscus.html
    R html/ga_initialize.html
    R html/genindex.html
    R html/gmp.html
    R html/idist_combine.html
    R html/import.html
    R html/index.html
    R html/objects.inv
    R html/pseudo3d.html
    R html/rmsd_query.html
    R html/run_details.html
    R html/search.html
    R html/searchindex.js
    R html/second_moment.html
    R html/start_page.html
    R html/time_derivative.html
    R html/us_edit.html
    R html/us_investigator.html
    R html/us_modelmetrics.html
    R html/vhw_combine.html
    R html/vhw_distrib_plot.html
    R html/vhw_enhanced.html

  Log Message:
  -----------
  Nov 29


  Commit: 85ec263cd82116c207e80ce69daab402a4db07aa
      https://github.com/ehb54/ultrascan3/commit/85ec263cd82116c207e80ce69daab402a4db07aa
  Author: Haben Gabir <haben.gabir at uleth.ca>
  Date:   2025-11-29 (Sat, 29 Nov 2025)

  Changed paths:
    M doc/manual/source/_static/css/custom.css
    M doc/manual/source/colorgradient.rst

  Log Message:
  -----------
  Merge branch 'haben-Dev' of github.com:ehb54/ultrascan3 into haben-Dev


Compare: https://github.com/ehb54/ultrascan3/compare/dc778acf5259...85ec263cd821

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From noreply at github.com  Sat Nov 29 20:58:50 2025
From: noreply at github.com (aaron-auc)
Date: Sat, 29 Nov 2025 19:58:50 -0800
Subject: [us-commits] [ehb54/us3_sql] 39f9f2: add: metascheduler column to
 gfac
Message-ID: <ehb54/us3_sql/push/refs/heads/versioning/dc18ee-39f9f2@github.com>

  Branch: refs/heads/versioning
  Home:   https://github.com/ehb54/us3_sql
  Commit: 39f9f230e6b116d08d9c35cc7e6fac040f11113d
      https://github.com/ehb54/us3_sql/commit/39f9f230e6b116d08d9c35cc7e6fac040f11113d
  Author: aaron-auc <aaron at aucsolutions.com>
  Date:   2025-11-29 (Sat, 29 Nov 2025)

  Changed paths:
    M gfac/gfac.sql

  Log Message:
  -----------
  add: metascheduler column to gfac



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