[us-commits] [ehb54/ultrascan3] ab214d: Fix: Calculate correct offset for omega2t if adjus...

Tue Dec 3 14:07:00 MST 2024

  Branch: refs/heads/alexey-dev-issue367
  Home:   https://github.com/ehb54/ultrascan3
  Commit: ab214dd8d0450512ee7b023f6d0658ea7c3568cc
      https://github.com/ehb54/ultrascan3/commit/ab214dd8d0450512ee7b023f6d0658ea7c3568cc
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-04 (Fri, 04 Oct 2024)

  Changed paths:
    M programs/us_convert/us_convert.cpp

  Log Message:
  -----------
  Fix: Calculate correct offset for omega2t if adjusting acceleration rate


  Commit: f08190c87108b43ff808cb692561c005f2106615
      https://github.com/ehb54/ultrascan3/commit/f08190c87108b43ff808cb692561c005f2106615
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-04 (Fri, 04 Oct 2024)

  Changed paths:
    M utils/us_simparms.cpp

  Log Message:
  -----------
  Fix: Calculate proper SimulationSpeedProfile for one timestep acceleration phases


  Commit: ac1b825ceb3133880cfbf311136c72893ecbb923
      https://github.com/ehb54/ultrascan3/commit/ac1b825ceb3133880cfbf311136c72893ecbb923
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2024-10-16 (Wed, 16 Oct 2024)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp

  Log Message:
  -----------
  us_mpi_analysis: replaced US_Tar with US_Archive


  Commit: 0c0f83844e0bbefb4d12101c1ae518f9caeb7873
      https://github.com/ehb54/ultrascan3/commit/0c0f83844e0bbefb4d12101c1ae518f9caeb7873
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2024-10-16 (Wed, 16 Oct 2024)

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

  Log Message:
  -----------
  us_archive: add an optional string list to see the extracted file


  Commit: 4906d21165b0ae14f6c4028282f0edbb06dd07a9
      https://github.com/ehb54/ultrascan3/commit/4906d21165b0ae14f6c4028282f0edbb06dd07a9
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-17 (Thu, 17 Oct 2024)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_simparms.cpp

  Log Message:
  -----------
  Prevent corrupted speed steps causing division by zero crash

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


  Commit: a7ff71ce24dcd590778b2675c593cdefd4a6ae1b
      https://github.com/ehb54/ultrascan3/commit/a7ff71ce24dcd590778b2675c593cdefd4a6ae1b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-17 (Thu, 17 Oct 2024)

  Changed paths:
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp

  Log Message:
  -----------
  Formatting

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


  Commit: 37a62fa88fbda5ae7bd77f4d701a05f1df1dc9e9
      https://github.com/ehb54/ultrascan3/commit/37a62fa88fbda5ae7bd77f4d701a05f1df1dc9e9
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-17 (Thu, 17 Oct 2024)

  Changed paths:
    M programs/us_experiment/us_experiment_gui_optima.cpp

  Log Message:
  -----------
  Remove fix because unsure if needed, added compiler warning for someone to check

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


  Commit: ebc3daaf9a59720faa1cf03861562a18feecd64b
      https://github.com/ehb54/ultrascan3/commit/ebc3daaf9a59720faa1cf03861562a18feecd64b
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-21 (Mon, 21 Oct 2024)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp

  Log Message:
  -----------
  Add low_acceleration check output to us_mpi_analysis for consistency

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


  Commit: ac611e47ae70fdd3471d67dae5d4e1b7d82263c3
      https://github.com/ehb54/ultrascan3/commit/ac611e47ae70fdd3471d67dae5d4e1b7d82263c3
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-21 (Mon, 21 Oct 2024)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp

  Log Message:
  -----------
  Fix accessing simparams for dset

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


  Commit: 014528cf370e7904c6ae1ce11e555aebf393357a
      https://github.com/ehb54/ultrascan3/commit/014528cf370e7904c6ae1ce11e555aebf393357a
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2024-10-21 (Mon, 21 Oct 2024)

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

  Log Message:
  -----------
  Add safe directory command to analyze-mpi action workflow

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


  Commit: 3fd930c4bcb884dc6edb01065052a79f82fbc4d9
      https://github.com/ehb54/ultrascan3/commit/3fd930c4bcb884dc6edb01065052a79f82fbc4d9
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2024-10-31 (Thu, 31 Oct 2024)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_archive.cpp
    M utils/us_archive.h

  Log Message:
  -----------
  Merge pull request #143 from samo38/us_issue_375

Us issue 375


  Commit: 56e22ba731537a2b7c1328c14503c8ff160accc0
      https://github.com/ehb54/ultrascan3/commit/56e22ba731537a2b7c1328c14503c8ff160accc0
  Author: doluk <69309597+doluk at users.noreply.github.com>
  Date:   2024-11-11 (Mon, 11 Nov 2024)

  Changed paths:
    M gui/us_predict1.cpp
    M gui/us_predict1.h

  Log Message:
  -----------
  Add apparent s and D as column, properly label columns as apparent and standardized s and D

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


  Commit: b0cf8f1efbd20ca56fe6981d6cd49855ace930f5
      https://github.com/ehb54/ultrascan3/commit/b0cf8f1efbd20ca56fe6981d6cd49855ace930f5
  Author: Lukas Dobler <69309597+doluk at users.noreply.github.com>
  Date:   2024-11-11 (Mon, 11 Nov 2024)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_simparms.cpp

  Log Message:
  -----------
  Merge pull request #138 from ehb54/Lukas-low-speed-convert

low acceleration rate conversion


  Commit: c3461c1abef0d1f6bd573ca6ff040a5225decc98
      https://github.com/ehb54/ultrascan3/commit/c3461c1abef0d1f6bd573ca6ff040a5225decc98
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2024-11-13 (Wed, 13 Nov 2024)

  Changed paths:
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_data_tree.h

  Log Message:
  -----------
  GMP : Manage Data -- prevent data {edit,models,noise} deletion if they were generated/required by GMP framework...


  Commit: 4674c49901490a2149b2c2146aec046393b0b688
      https://github.com/ehb54/ultrascan3/commit/4674c49901490a2149b2c2146aec046393b0b688
  Author: samo38 <saeed.mortezazadeh25 at gmail.com>
  Date:   2024-11-15 (Fri, 15 Nov 2024)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  us_convert_gui.cpp :: take out referecne data for each channel separately when the wavelengths differ even if each channel has only one triple


  Commit: 419c03d7424b0157e6bbb28aa253cf90af611ad0
      https://github.com/ehb54/ultrascan3/commit/419c03d7424b0157e6bbb28aa253cf90af611ad0
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2024-11-20 (Wed, 20 Nov 2024)

  Changed paths:
    M programs/us_convert/us_convert_gui.cpp

  Log Message:
  -----------
  Merge pull request #153 from samo38/issue_309

RIProfile issue with multi-wavelength runs


  Commit: cd9f7a39b2fbeca119107837e0e5aca4aba85c73
      https://github.com/ehb54/ultrascan3/commit/cd9f7a39b2fbeca119107837e0e5aca4aba85c73
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2024-11-20 (Wed, 20 Nov 2024)

  Changed paths:
    M gui/us_predict1.cpp
    M gui/us_predict1.h

  Log Message:
  -----------
  Merge pull request #152 from ehb54/us_predict1_bugfix

Improve us_predict1 by providing apparent and standardized s and D


  Commit: 93316649875f323b60d0a5c034fa42f472ab0dec
      https://github.com/ehb54/ultrascan3/commit/93316649875f323b60d0a5c034fa42f472ab0dec
  Author: ehb54 <brookes at uthscsa.edu>
  Date:   2024-11-21 (Thu, 21 Nov 2024)

  Changed paths:
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php

  Log Message:
  -----------
  us_branch initlal commit


  Commit: 28db369ade10d36ff248ced336037abb95650274
      https://github.com/ehb54/ultrascan3/commit/28db369ade10d36ff248ced336037abb95650274
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2024-11-21 (Thu, 21 Nov 2024)

  Changed paths:
    A admin/us_branch/README.md

  Log Message:
  -----------
  Create README.md


  Commit: 51d4e32f29d0bc9acf1ad7fd12b45021c72e8693
      https://github.com/ehb54/ultrascan3/commit/51d4e32f29d0bc9acf1ad7fd12b45021c72e8693
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2024-11-21 (Thu, 21 Nov 2024)

  Changed paths:
    A admin/us_branch/README.md
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php

  Log Message:
  -----------
  Merge pull request #154 from ehb54/ehb54-issue-296

Ehb54 issue 296 - us_branch.php utility program


  Commit: 7e7d1d0eec6365a62504dc752e14f9e4aae8072d
      https://github.com/ehb54/ultrascan3/commit/7e7d1d0eec6365a62504dc752e14f9e4aae8072d
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2024-11-21 (Thu, 21 Nov 2024)

  Changed paths:
    M programs/us_manage_data/us_data_tree.cpp

  Log Message:
  -----------
  GMP : Manage Data -- prevent data {edit,models,noise} deletion if they were generated/required by GMP framework -- including 2DSA, -FM models & associated noises (even though they are not required by GMP report)...


  Commit: dee661fe1c3202eb4e1e685b3d30d07d6de3c863
      https://github.com/ehb54/ultrascan3/commit/dee661fe1c3202eb4e1e685b3d30d07d6de3c863
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2024-11-21 (Thu, 21 Nov 2024)

  Changed paths:
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_archive.cpp
    M utils/us_archive.h

  Log Message:
  -----------
  Merge pull request #155 from ehb54/samo38-issue-375

Samo38 issue 375


  Commit: c610cf5b6ca9788984d2c6e52c5274d2bf57bfc7
      https://github.com/ehb54/ultrascan3/commit/c610cf5b6ca9788984d2c6e52c5274d2bf57bfc7
  Author: ehb54 <ehb54 at users.noreply.github.com>
  Date:   2024-11-21 (Thu, 21 Nov 2024)

  Changed paths:
    A admin/us_branch/README.md
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M utils/us_archive.cpp
    M utils/us_archive.h

  Log Message:
  -----------
  Merge pull request #156 from ehb54/master

merge master to 373


  Commit: a60fcd2bb823d492aaea28b47b2cfc260f66d95f
      https://github.com/ehb54/ultrascan3/commit/a60fcd2bb823d492aaea28b47b2cfc260f66d95f
  Author: Borries Demeler <7659499+demeler at users.noreply.github.com>
  Date:   2024-11-22 (Fri, 22 Nov 2024)

  Changed paths:
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_data_tree.h

  Log Message:
  -----------
  Merge pull request #157 from ehb54/alexey-dev-issue373

Alexey dev issue373


  Commit: e95a6d93273e6511bebe28af72c76887a6df3434
      https://github.com/ehb54/ultrascan3/commit/e95a6d93273e6511bebe28af72c76887a6df3434
  Author: alexsav815 <alexsav.science at gmail.com>
  Date:   2024-12-03 (Tue, 03 Dec 2024)

  Changed paths:
    M .github/workflows/codeql-analysis.yml
    A admin/us_branch/README.md
    A admin/us_branch/us_branch.php
    A admin/us_branch/utility.php
    M gui/us_predict1.cpp
    M gui/us_predict1.h
    M programs/us_2dsa/us_2dsa.cpp
    M programs/us_autoflow_analysis/us_autoflow_analysis.cpp
    M programs/us_convert/us_convert.cpp
    M programs/us_convert/us_convert_gui.cpp
    M programs/us_experiment/us_experiment_gui_optima.cpp
    M programs/us_fematch/us_fematch.cpp
    M programs/us_manage_data/us_data_tree.cpp
    M programs/us_manage_data/us_data_tree.h
    M programs/us_mpi_analysis/us_mpi_analysis.cpp
    M programs/us_mwl_species_sim/us_mwl_species_sim.cpp
    M programs/us_reporter_gmp/us_reporter_gmp.cpp
    M utils/us_archive.cpp
    M utils/us_archive.h
    M utils/us_simparms.cpp

  Log Message:
  -----------
  Merge pull request #160 from ehb54/master

Bring branch alexey-dev-issue367 to the current master state for testing


Compare: https://github.com/ehb54/ultrascan3/compare/bcc3770dbb0f...e95a6d93273e

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