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Hot fixes - #439

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migp11 wants to merge 401 commits into

MathCancer:masterfrom

PhysiCelldFBA:hot-fixes

Closed

Hot fixes#439
migp11 wants to merge 401 commits into
MathCancer:masterfrom
PhysiCelldFBA:hot-fixes

This pull request is big! We're only showing the most recent 250 commits

Commits on Oct 28, 2025
- Comment out macos appleclang GH build
  asmelko
  committed
  e68a7eb
- Rename GH Action
  asmelko
  committed
  f49b846
- Add MacOS gcc GH Actions CMake build
  asmelko
  committed
  1b665c8
- Update gcc version
  asmelko
  committed
  5c99875
- Remove macos deps steps
  asmelko
  committed
  ea63c44
- Add tests cmake GH action
  asmelko
  committed
  7d3223c
- Fix tests action
  asmelko
  committed
  54fc9e7
- Better GH action name
  asmelko
  committed
  be5b4bf
Commits on Oct 31, 2025
- Fix correct MAXNODES for physiboss sample projects
  asmelko
  committed
  7d10ed5
- Fix paths to work for windows too
  asmelko
  committed
  6433914
- Full paths to gh actions
  asmelko
  committed
  f08e98f
- Make exclusion of some tests better
  asmelko
  committed
  0d398dd
- Fix paths
  asmelko
  committed
  228fef3
- Normalize paths in testing python scripts
  asmelko
  committed
  c8ef390
- Revert "Normalize paths in testing python scripts"
  asmelko
  committed
  ced2118
- Add .exe for windows in Tests GH action
  asmelko
  committed
  aa0c359
- Add forgotten Release dir to Tests
  asmelko
  committed
  33ea67e
- FIx path again
  asmelko
  committed
  40612ed
- Final path fix
  asmelko
  committed
  0dcc50b
- Bump-up CMake minimal version as copy_directory_if_different requirement
  asmelko
  committed
  6b00c98
- improved substrate contour plot
  marcorusc
  committed
  ec2a46d
Commits on Nov 26, 2025
- General code cleaning, added function to print model for debug purpose. In intracellular.pp added more comments that refers to unit measures. In Model, swtiched from primal to dual solver, and reve…
  marcorusc
  committed
  077050f
Commits on Nov 28, 2025
- add warning message if reaction is not found
  migp11
  committed
  4ce593a
- adding the cancer_core_model
  migp11
  committed
  69f9b6c
- adding notebook fore cancer core model
  migp11
  committed
  3cb22b8
- update gitignore
  migp11
  committed
  68addeb
- Merge branch 'development' of github.com:PhysiCelldFBA/PhysiCelldFBA into development
  migp11
  committed
  192515f
- update intracellular.cpp
  migp11
  committed
  5d0911d
Commits on Dec 3, 2025
- removed printing in intracellular.cpp, added setPerturbation() in model to reduce model degeneracy and using primal if problem infeasible to make sure cell is dead
  marcorusc
  committed
  f68ac9e
- Updated windows dependencies urls
  vincent-noel
  committed
  bd78393
Commits on Dec 10, 2025
Commits on Dec 11, 2025
Commits on Dec 12, 2025
- update
  rheiland
  committed
  b88d368
Commits on Dec 15, 2025
- Use signed integers in omp pragmas to make windows openmp not complain
  asmelko
  committed
  a161bdc
- warn about is_movable
  rheiland
  committed
  068080f
- cleanup; delete confusion
  rheiland
  committed
  ae4e78e
- updated dfba configurator to use physicell-settings package
  marcorusc
  committed
  045d0f6
- updated sample project with script for nice plotting
  marcorusc
  committed
  eca0d2d
- fix bug resuming custom data
  rheiland
  committed
  27e3413
- improved resume main.cpp
  rheiland
  committed
  8361947
Commits on Dec 16, 2025
- updating MCF7 model from source
  migp11
  committed
  ba51cc0
- cleaning old files
  migp11
  committed
  01eeb42
- fix rates and inconsitent blocks
  migp11
  committed
  ffacc43
- Merge branch 'development' of github.com:PhysiCelldFBA/PhysiCelldFBA into development
  migp11
  committed
  b86846f
- XML restructuring. move sbml_filename into settings block
  migp11
  committed
  d1ccce7
- Raise error message before exit if exchange reaction cant be found in model
  migp11
  committed
  6313439
- comment custom variable storing
  migp11
  committed
  52ffab7
- fix the use of custom variable not defined
  migp11
  committed
  edf34e4
- Update FBA xml setting file to reflect XML restructuring (sbml_filename into settings block)
  migp11
  committed
  fd1e337
- Merge pull request #4 from PhysiCelldFBA/hot-fixes
  marcorusc
  authored
  18f96ce
Commits on Dec 17, 2025
- Merge pull request #392 from asmelko/cmake
  MathCancer
  authored
  d6ebcbc
- Now using macos15-intel instead of macos-13, using g++14
  vincent-noel
  committed
  c3e82f4
- Merge pull request #400 from rheiland/resume_sim
  MathCancer
  authored
  58d091a
- update setup_tissue to use cell.csv
  migp11
  committed
  b341ec0
- Including PR#366 from Daniel
  vincent-noel
  committed
  87f3346
- Merge pull request #402 from vincent-noel/update/ci_macos
  MathCancer
  authored
  2354b24
Commits on Dec 20, 2025
- Updated MaBoSS version
  vincent-noel
  committed
  ce727e8
- Detecting MSVC and downloading a specific version of libmaboss
  vincent-noel
  committed
  3dd843e
- Updating include to reflect the new directory structure
  vincent-noel
  committed
  865f25b
- Activating physiboss on msvc workflows
  vincent-noel
  committed
  899d593
Commits on Jan 6, 2026
- working xml setting for the cancer core model
  migp11
  committed
  7231bb1
- improving path solving in dfba_configurator
  migp11
  committed
  7d71719
- adding a script to generate the yaml dfba config from a sbml model
  migp11
  committed
  408d73c
- updating oxygen and lactate bounds
  migp11
  committed
  b9a337e
- adding csv with initial cells in an spheroid of different sizes
  migp11
  committed
  8b5c5d9
- merge
  migp11
  committed
  a1c44cd
- a dfba yaml example for cancer core model
  migp11
  committed
  0a317e7
- a notebook with a prototype of the yaml crater script
  migp11
  committed
  a8fcb04
- Merge branch 'development' of github.com:PhysiCelldFBA/PhysiCelldFBA into development
  migp11
  committed
  b2f79b6
Commits on Feb 8, 2026
- fix for new .zip bundles
  rheiland
  committed
  9bb3ec4
- fix header path
  rheiland
  committed
  0953f6c
Commits on Feb 9, 2026
- Fix worms sample project
  asmelko
  committed
  1b36f6f
- Rectify test cases for worm
  asmelko
  committed
  f5a7cef
Commits on Feb 11, 2026
- Add configurable resolution variables for JPEG and GIF generation
  drbergman
  committed
  4fc426a
- movies pad jpegs to make even dims
  drbergman
  committed
  911bdd6
- update header path
  rheiland
  committed
  c0d9e4e
Commits on Feb 16, 2026
- Update max_cell_interactive_distance_in_voxel during position update
  heberlr
  committed
  502f816
- Revert "Update max_cell_interactive_distance_in_voxel during position update"
  heberlr
  committed
  337722c
Commits on Feb 17, 2026
- use manylinux
  rheiland
  committed
  5d2d591
- cleanup
  rheiland
  committed
  d7040aa
Commits on Feb 18, 2026
- Update the if-query so that it spans all possible contact with cells cases.
  elmbeech
  committed
  2cfbc80
- Merge branch 'development' into fix-division-displacement
  drbergman
  authored
  47a3768
- fix whitespace
  drbergman
  committed
  b6eceeb
Commits on Feb 19, 2026
- fix paths
  rheiland
  committed
  9443670
- create /C symlink for headers
  rheiland
  committed
  32ca016
Commits on Feb 24, 2026
- added new use case: 3D simulation of a columns of cancer cells, including python script to generate the initial positions
  marcorusc
  committed
  5bb4f5d
Commits on Feb 26, 2026
- adding diffusion steps and xml updates to cancer core model
  migp11
  committed
  26004e4
Commits on Mar 1, 2026
- update cancer column model
  migp11
  committed
  e48900b
Commits on Mar 12, 2026
- fixing solver status checks and remove debug prints
  migp11
  committed
  62df771
- update generate cell positions script
  migp11
  committed
  bcc5817
- adding otebooks and scripts for the cancer core model
  migp11
  committed
  4c2aa15
- update exchange fluxes in custom variables
  migp11
  committed
  85d441a
- fix z-slide for SVG plotting
  migp11
  committed
  b801ddb
- adding Zelinsky model data
  migp11
  committed
  9125704
- add the proper xml for the cancer core model
  migp11
  committed
  35174f7
- update gitignore
  migp11
  committed
  00dfb43
- tiny XML config (deprecated)
  migp11
  committed
  75a2168
Commits on Mar 18, 2026
- Creating baterial-colony project
  migp11
  committed
  22dd5a3
- update Makefile to include bacterial colony model
  migp11
  committed
  04a9e84
- fix details in cancer.core model
  migp11
  committed
  34e6cc6
- sbatch script to run in slurm cluster
  migp11
  committed
  8305cdd
- commenting debug prints in dfba model creation
  migp11
  committed
  1367904
- update script for creating cell positions bacterial colony
  migp11
  committed
  77eb2b4
Commits on Mar 20, 2026
- updated ecoli acetic switch example: xml files now match the settings used for generating the figures for the publication; added scripts for analysis; improved jupyter notebooks for image generatio…
  marcorusc
  committed
  4ccbab7
Commits on Mar 21, 2026
- add contact_with_built_in variable and change the code accordingly.
  elmbeech
  committed
  5eef794
Commits on Apr 9, 2026
- update bacterial colony model
  migp11
  committed
  70aef96
- scripts for bacterial colony model
  migp11
  committed
  60553f4
- Merge branch 'development' of github.com:PhysiCelldFBA/PhysiCelldFBA into development
  migp11
  committed
  8a6cd83
Commits on Apr 10, 2026
Commits on Apr 14, 2026
Commits on May 18, 2026
- Add trim_cr utility function and apply it to CSV parsing in multiple files
  drbergman
  committed
  018d6a5
Commits on May 20, 2026
- improved use case of metabolic-driven motility with configuration files and scripts to replicate the manuscript images
  marcorusc
  committed
  aff4be5
- corrected and updated notebook for analysis of the unit test. Corrected error in the config file of the Unit test (misplacement of the SBML model path)
  marcorusc
  committed
  cb9b89b
Commits on Jun 16, 2026
- Improved final plots for the unit test
  marcorusc
  committed
  2b34f1f
Commits on Jul 6, 2026
- Updated crossfeeding model
  othmya
  committed
  8ffcbb4
- Update Makefile to include crossfeeding model
  othmya
  committed
  c710aa7
- fixed correct Makefile, custom cpp for crossfeeding
  othmya
  committed
  171e256
- Fixed crossfeeding custom CPP
  othmya
  committed
  202f096
- Removed non-used config files to clean up crossfeeding model
  othmya
  committed
  23a0d43
- Fixed crossfeeding config file
  othmya
  committed
  51d5a37
Commits on Jul 10, 2026
- Updated unit test plot, harmonized both plots and changed axis. Updated .ipynb that generates the plot
  othmya
  committed
  99021ea
- Updated motility figure generation script
  othmya
  committed
  ae0cc04
Commits on Jul 15, 2026
- Clean up crossfeeding config files
  othmya
  committed
  a86de4b
Commits on Jul 16, 2026
Commits on Jul 17, 2026
- removed ecoli acetic switch test. Added mass conversion unit test.
  marcorusc
  committed
  fafa24f
Commits on Jul 21, 2026
- Restored original order of container update: first advance secretion and then intracellular update
  marcorusc
  committed
  31c4dc8
Commits on Jul 22, 2026
Commits on Jul 23, 2026
- Updated config and csv for motility example
  othmya
  committed
  e19da28
Commits on Jul 24, 2026
- Skip processing of blank lines in CSV input and ensure minimum column count
  drbergman
  committed
  abc005b
Commits on Jul 27, 2026
- New metabolic-driven-motility simulation with multiple sources
  marcorusc
  committed
  d711b79
Commits on Jul 28, 2026
- Updated cancer core example config and script generation
  othmya
  committed
  e509d5b
Commits on Jul 31, 2026
- small config fixes and updated scripts for cancer core metabolism model
  othmya
  committed
  de5f218
Commits on Aug 6, 2026
- Make the attack link symmetric, following spring-attachment semantics
  
  drbergman
  and
  claude
  committed
  0493418
- Fix rules engine treating behavior/signal synonyms as separate entries
  
  heberlr
  and
  claude
  committed
  04c06f3
Commits on Aug 7, 2026
- Address review: attacked_by races, and restore the spring on resume
  
  drbergman
  and
  claude
  committed
  7a81b97
- Fix a typo in an adjacent comment
  
  drbergman
  and
  claude
  committed
  12720aa
- Read pAttackTarget once in the effector-attack block
  
  drbergman
  and
  claude
  committed
  6c79881
- Generate header dependencies so header edits trigger a rebuild
  
  drbergman
  and
  claude
  committed
  47692be
- Defer teardown out of the mechanics parallel-for
  
  drbergman
  and
  claude
  committed
  9fbd031
Commits on Aug 8, 2026
- Correct a comment the teardown deferral invalidated
  
  drbergman
  and
  claude
  committed
  649dc13
Commits on Aug 9, 2026
- Take spring attachments under the lock before iterating them
  
  drbergman
  and
  claude
  committed
  b995db6
Commits on Aug 14, 2026
Commits on Aug 15, 2026
Commits on Aug 17, 2026
- check is_movable in add_potential function: avoid update velocity
  
  heberlr
  authored and
  vincent-noel
  committed
  6f08abd
- Updated mechano test results
  vincent-noel
  committed
  cc596ef
Commits on Aug 19, 2026
- Figure and config fixes
  othmya
  committed
  5e05779
- Initialize loop counter in intialize_hypothesis_rulesets
  
  drbergman
  and
  claude
  committed
  c00f424
- Compare neighbor type against diff_type, not the running counter
  
  drbergman
  and
  claude
  committed
  6b0aa2b
Commits on Aug 24, 2026
- harmonizing XMls
  othmya
  committed
  3360ebb
Commits on Sep 15, 2026
- Not checking mechano tests results anymore
  vincent-noel
  committed
  e81f443
Commits on Sep 24, 2026
- Merge pull request #430 from vincent-noel/fix/heberlr/pr-neighbor-list-for-non-movable-cells
  vincent-noel
  authored
  167c817
- Update max cell interactive distance in voxel during position update
  
  heberlr
  authored and
  vincent-noel
  committed
  6f8fec7
- Refactor max cell interactive distance update to occur after voxel index assignment
  
  heberlr
  authored and
  vincent-noel
  committed
  2c9ef67
- update max_cell_interactive_distance_in_voxel if cell changed voxel
  
  heberlr
  authored and
  vincent-noel
  committed
  15841f4
- Updated worm and virus-macrophage test results
  vincent-noel
  committed
  be087a2
- Not checking virus-macrophage tests results anymore
  vincent-noel
  committed
  5a11815
- Merge pull request #429 from vincent-noel/fix/heberlr/pr-bug-neighbors
  vincent-noel
  authored
  4950735
Commits on Oct 2, 2026
- Merge pull request #434 from drbergman/fix-interaction-sample-diff-type
  drbergman
  authored
  ca1877e
- Merge pull request #433 from drbergman/fix-uninitialized-ruleset-loop-counter
  drbergman
  authored
  49d7cc5
Commits on Oct 9, 2026
- Remove redundant per-solve bookkeeping from dFBAModel::optimize
  
  migp11
  and
  claude
  committed
  b780351
- Fix silent custom_data corruption from undeclared names
  
  migp11
  and
  claude
  committed
  f13357e
- Merge hotfix/optimize-bookkeeping
  migp11
  committed
  3e65b8d
- Add parsimonious FBA to dFBAModel
  migp11
  committed
  7b00fc4
- Do not track dFBA test binaries or generated dumps
  migp11
  committed
  06d252f
- Expose pFBA from configuration and wire it into dFBAIntracellular
  migp11
  committed
  12e6856
- Add a benchmark showing the LP is warm-started between timesteps
  migp11
  committed
  fdc159e
- Track header dependencies so a header edit rebuilds its dependents
  
  migp11
  and
  claude
  committed
  87210db
- Merge hotfix/makefile-header-deps
  
  migp11
  and
  claude
  committed
  5a26dae
- Merge development into feature/pfba
  migp11
  committed
  17a2b2f
- Run both pFBA stages inside optimize(), and fix two second-stage defects
  migp11
  committed
  f5e2073
Commits on Oct 10, 2026
- Add the reviewer-response figures, and track the FVA analysis code
  migp11
  committed
  74eabcc
Commits on Oct 11, 2026
- Add a failing test: uptake cap lets a voxel's substrate go negative
  
  migp11
  and
  claude
  committed
  aa530d4
- Fix the unit conversion in the uptake cap (multiply -> divide by 1e15)
  
  migp11
  and
  claude
  committed
  948c95f
- Share a voxel's substrate between the cells that draw on it
  
  migp11
  and
  claude
  committed
  d496cc6
Commits on Oct 13, 2026
Commits on Oct 14, 2026
Commits on Oct 15, 2026
- Clean BACTERIAL-COLONY unused files and scripts
  migp11
  committed
  66b125b
- Fix BACTERIAL-COLONY params
  migp11
  committed
  dccde49
- Clean CANCER-CORE unused xml and csv files
  migp11
  committed
  9d49392
Commits on Oct 16, 2026
- Merge LP column-order validation into development-based review branch
  marcorusc
  committed
  09c058a
- Merge pFBA into development-based review branch
  marcorusc
  committed
  b5f4510
Commits on Oct 19, 2026

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Commits on Oct 28, 2025

Commits on Oct 31, 2025

Commits on Nov 26, 2025

Commits on Nov 28, 2025

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Commits on Dec 15, 2025

Commits on Dec 16, 2025

Commits on Dec 17, 2025

Commits on Dec 20, 2025

Commits on Jan 6, 2026

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Commits on Feb 16, 2026

Commits on Feb 17, 2026

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Commits on Mar 18, 2026