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PhysiCell 1.14.1 release#343

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MathCancer merged 95 commits intomasterMathCancer/PhysiCell:masterfrom developmentMathCancer/PhysiCell:developmentCopy head branch name to clipboardDec 13, 2024

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Commits

Commits on Jul 13, 2024

• custom division, lineage

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Commits on Jul 14, 2024

• add cell_division_function

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• move the static bool BioFVM_substrates_initialized_in_dom variable out of the add_BioFVM_substrates_to_open_xml_pugi function. add a reset_BioFVM_substrates_initialized_in_dom function to reset thi…

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• move the static int max_basic_agent_ID variable out of the BioFVM::Basic_Agent function. add a BioFVM::reset_max_basic_agent_ID function to reset this variable.

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• update

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• update

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• update

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• update

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Commits on Jul 15, 2024

• incr generation for both; stochastic cell cycle

  rheiland

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Commits on Aug 15, 2024

• remove user proj

  rheiland

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• cleanup

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• cleanup

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• add custom-division-sample

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• revert to original constants code

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Commits on Aug 16, 2024

• copy cell ic file and substrate ic file to output

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Commits on Aug 17, 2024

• retrigger checks

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• Merge branch 'development' of github.com:MathCancer/PhysiCell into patch_reset_cellid

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Commits on Aug 25, 2024

• Created Cell_Asymmetric_Divisions to make those easier

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• new fix for volume

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Commits on Aug 26, 2024

• Fix convert_to_cell_definition to get volume right

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• also save geometry on convert

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Commits on Aug 29, 2024

• Replace all time checks with improved version

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• fix bug

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Commits on Sep 10, 2024

• Merge branch 'development' into standard-asym-div

  drbergman

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• protect against 0 asym div weight total

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Commits on Sep 17, 2024

• Merge branch 'MathCancer:master' into patch_reset_cellid

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• Merge branch 'MathCancer:master' into patch_save_mesh0

  elmbeech

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Commits on Sep 22, 2024

• read in attack_duration from config

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Commits on Sep 25, 2024

• Merge pull request #266 from elmbeech/patch_save_mesh0

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• Merge pull request #277 from elmbeech/patch_reset_cellid

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Commits on Sep 27, 2024

• change all rules version to 3.0; add rules_sample to tests.yml

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Commits on Sep 28, 2024

• conditional SeedRandom

  rheiland

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Commits on Oct 1, 2024

• remove parent and generation; better asym div ex

  drbergman

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• Merge branch 'development' into standard-asym-div

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Commits on Oct 2, 2024

• implement faster weighted search for possible future use

  drbergman

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Commits on Oct 11, 2024

• update asym div as per conversation

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• Removed PDFs of PhysiBoSS tutorial, added links

  vincent-noel

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• Tried to fix binary build by changing release event to 'published', bumped version in download_binary, changed physiboss repo to physiboss/physiboss

  vincent-noel

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• Merge pull request #302 from drbergman/standard-asym-div

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• Merge pull request #299 from drbergman/fix-read-attack-duration

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• Merge pull request #303 from sysbio-curie/fix/tutorial_links

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• Merge pull request #304 from sysbio-curie/fix/binaries_build

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• Merge pull request #288 from drbergman/fix-time-checks

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• Merge branch 'development' into fix-rules-versioning

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• Merge pull request #300 from drbergman/fix-rules-versioning

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• Merge pull request #301 from rheiland/fix-custom-division-seedrandom

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• Merge pull request #276 from drbergman/copy-inputs-to-output-folder

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Commits on Oct 12, 2024

• Preserve internalized substrates and custom data in Cell::convert_to_cell_definition function

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Commits on Oct 14, 2024

• Update BioFVM_basic_agent.cpp

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  MathCancer

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• Update PhysiCell_cell.cpp

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• Update PhysiCell_cell.cpp

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• Update VERSION.txt

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• more on conservation during phagocytosis

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Commits on Oct 15, 2024

• Update PhysiCell_cell.cpp

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• Update PhysiCell_cell.cpp

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• Update PhysiCell_cell.cpp

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• make output folder if it does not exist

  drbergman

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• Merge pull request #308 from MathCancer/development-paul

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• Merge pull request #307 from drbergman/fix-internalized-substrates

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• cleanup random_seed

  rheiland

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• Merge pull request #309 from drbergman/make-output-folder-finalized

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• Merge pull request #310 from rheiland/cleanup_asym_div_seed

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Commits on Oct 16, 2024

• Updated article reference with Gigabyte publication

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• Merge pull request #311 from PhysiMeSS/physimess_paper

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Commits on Oct 23, 2024

• handle abspath for output folder creation

  drbergman

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• allow windows users to do what they want

  drbergman

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Commits on Oct 24, 2024

• initialize total_attack_time at 0.0

  drbergman

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Commits on Oct 28, 2024

• add immune_test_2024 to Makefiles as immune-function-sample

  drbergman

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Commits on Nov 6, 2024

• fix buffer bug in writing coords in xml

  drbergman

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• fix bug in export rules

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  drbergman

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Commits on Nov 7, 2024

• fix bug reading large random seeds

  drbergman

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Commits on Nov 11, 2024

• write random_seed to output/random_seed.txt

  drbergman

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Commits on Nov 15, 2024

• Removed call to SeedRandom() in main of physiboss cell lines project

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• replace macos-12 with macos-13 in CI

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Commits on Nov 18, 2024

• update sample projects to 1.14.0

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Commits on Nov 21, 2024

• copying rules file(s) instead of writing new one

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Commits on Nov 27, 2024

• disallow random detachment from attack

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Commits on Dec 12, 2024

• update delete_cell() and ~Cell() using new Cell::remove_self_from_all_neighbors();

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• export parsed rules as cell_rules_parsed.csv

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• Merge pull request #340 from drbergman/fix-disallow-attack-random-detach

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• Merge pull request #342 from MathCancer/development-paul

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• Merge pull request #322 from drbergman/fix-save-random-seed-in-output

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• Merge pull request #314 from drbergman/fix-create-output-from-abspath

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• Merge pull request #319 from drbergman/fix-read-unsigned_int-random-seeds

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• Merge pull request #317 from drbergman/fix-buffer-bug

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• Merge pull request #315 from drbergman/fix-total_attack_time-initialization

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• Merge pull request #333 from drbergman/update-samples-to-1.14.0

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• Merge pull request #330 from sysbio-curie/fix/physiboss_seed_random

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• Merge pull request #316 from drbergman/add-immune-example-to-makefile

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• Merge pull request #332 from drbergman/remove-macos-12-from-ci

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• Merge pull request #318 from drbergman/fix-export-rules

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Commits on Dec 13, 2024

• Prep for 1.14.1 release: version numbers

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• Update CITATION.txt

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• Update README.md

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• update running change log

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