PhysiCell

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saving rules v1 instead of v2 to /output

3

https://github.com/MathCancer/PhysiCell/blob/master/core/PhysiCell_rules.cpp#L2356 setup_cell_rules() is calling export_rules_csv_v1( rules_file );

rheiland

MultiCellDS saves `elapsed_time_in_phase` twice?

1

As best I can tell, `elapsed_time_in_phase` is being saved twice: 1. https://github.com/MathCancer/PhysiCell/blob/3d7051f167b6b3551296a4b6d93db742dc532ee6/modules/PhysiCell_MultiCellDS.cpp#L1769 2. https://github.com/MathCancer/PhysiCell/blob/3d7051f167b6b3551296a4b6d93db742dc532ee6/modules/PhysiCell_MultiCellDS.cpp#L1807 Note: these two are appended to the list of labels in the output xml here: 1....

drbergman

disable_bugfix did not update based on the value of legacy_cell_defaults_copy previously. This fixes that for anyone still using the old, buggy version.

drbergman

getter functions for lists of dying and dividing cells

5

I realize there are other ways to figure this out, but it might be very convenient to access the list of cells that are going to divide or die in...

josephabrams

Clarifying attack/damage rates

1

# Motivating question If `cd8` attacks `tumor` with `attack_rate("tumor") = 1.0` and the `damage_rate` for `cd8` is `1.0`, how much damage do we expect a `tumor` agent to accumulate per...

drbergman

Define damage rate as damage/attack. See #223.

drbergman

updated scripts to build, run, test all sample projects

7

* this bash script compiles all (non-intracellular) sample projects and creates user_projects of each, preparing for the next step of running (brief) simulations of each.

rheiland

PhysiCell::Cell_Definition possibly memory leaking

2

I get a `Segmentation fault (core dumped)`, if I try to generate a second instance of a Cell_Definition. Reading up on this, this potentially points to a memory leaking. Minimal...

elmbeech

To make PhysiBoSS export in MultiCellDS work, we need to setup the Makefile so that ADDON_PHYSIBOSS is defined. I did it for the model I used to develop the functionality,...

vincent-noel

I wrote a simpler version of the GitHub actions, using what's called a matrix: https://docs.github.com/en/actions/using-jobs/using-a-matrix-for-your-jobs We define the list of projects to run like this: ``` projects: [ {project: "virus-macrophage-sample",...

vincent-noel