PhysiCell 1.14.1 release #343
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…t of the add_BioFVM_substrates_to_open_xml_pugi function. add a reset_BioFVM_substrates_initialized_in_dom function to reset this variable.
…sic_Agent function. add a BioFVM::reset_max_basic_agent_ID function to reset this variable.
keep the basename the same, i.e. do not change to path/to/output/cells.csv also, remove unreachable lines
1. Assign weights for transformation of daughter cells to new cell type for asymmetric division.
2. Weights are converted to probabilities at division to allow for rules to be applied to weights.
3. Add the following element to phenotypes (such as right after cell_transformations)
<cell_asymmetric_divisions>
<asymmetric_division_weights>
<asymmetric_division_weight name="stem" units="dimensionless">0.0</asymmetric_division_weight>
<asymmetric_division_weight name="progenitor_1" units="dimensionless">1.0</asymmetric_division_weight>
<asymmetric_division_weight name="progenitor_2" units="dimensionless">0.0</asymmetric_division_weight>
</asymmetric_division_weights>
</cell_asymmetric_divisions>
4. Add the new sample project `make asymmetric-division-sample` to try out the new feature
Previous version immediately gave new cell type volume instead of letting it grow to that size.
Specifically, any time check I found (searching the codebase for uses of `fabs`), I replaced with the form: ``` current_time > next_event_time - 0.5 * diffusion_dt ``` Assuming diffusion_dt really is the smallest time step, this will evaluate true at the time step closest to next_event_time. Importantly, this will never accumulate floating point errors to the point where the check fails. This has happened with the save checks: ``` abs( current_time - next_save_time ) < 0.01 * diffusion_dt ``` Finally, this is ever so slightly more robust than a user's suggestion to convert save times to integers as this does not rely on time steps being multiples of one another.
add reset function for mesh.mat file generation.
add reset function for Cell ID.
- record the value of applies_to_dead - use v3 for export (to make sharing easier)
gh actions deprecation upcoming silence gcc@13 warnings in build binaries
FOR EACH `project` IN `sample_projects`:
- `make project`
- `python path/to/studio.py -c ./config/PhysiCell_settings.xml` # studio v2.40.0 used
- IF ERROR; CONTINUE # errors came from hierarchical configs
- DELETE `random_seed` FROM `user_parameters`
- SAVE `PhysiCell_settings.xml` TO `project/config/`
- do not let random detachment occur when one cell is attacking another - this could result in the detachment occuring while the attack continues - an alternative solution is to say that detachment necessarily ends the attack
…_neighbors(); update delete_cell(int) and ~Cell() so that if the cell is deleted, it removes itself from all its neighbors' neighbor lists.
disallow random detachment from attack
bugfix: if cell dies, must remove self from neighbors (to avoid interactions with deleted cells).
write random_seed to output/random_seed.txt
handle abspath for output folder creation
…eeds fix bug reading large random seeds
fix buffer bug in writing coords in xml
…zation initialize total_attack_time to 0.0
update sample projects to 1.14.0
Removed call to SeedRandom() in main of physiboss cell lines project
add immune_test_2024 to Makefiles as immune-function-sample
remove macos-12 from ci
fix bug in export rules
update version to 1.14.1, cleanup.
update version in CITATION.txt
update readme / release notes for upcoming 1.14.1 release.
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