Randy Heiland

distinguishing extensions: addons vs. plugins

2

We want to have a community discussion about future extensions to PhysiCell. We begin by discussing the existing "addons" extension for intracellular models and then discuss a possible "plugins" extension....

Users have reported getting a strange compilation error after they updated their macOS to 12.6. Running `make` would end in: ``` ld: Assertion failed: (_file->_atomsArrayCount == computedAtomCount && "more atoms...

make reset - avoid "rm *.cpp"?

7

Could we possibly *not* have `make reset` do a `rm *.cpp`? Just wondering what the danger is in having them? I've been bitten by this on multiple occasions. I make...

suspicious that custom data conserved attribute not being set

2

https://github.com/MathCancer/PhysiCell/blob/master/core/PhysiCell_cell.cpp#L3039

A reminder that we still have some hierarchical config files, rather than the "flattened" syntax that the Studio requires. At least these, it seems: ``` ~/dev/PhysiCell_v1.12.0/sample_projects$ grep parent */config/*.xml cancer_immune/config/PhysiCell_settings.xml:...

PhyisiCell_rules typo in some Makefiles

1

* sample_projects/Makefile-default * sample_projects_intracellular/ode/test_sbml1/Makefile * do a global search for others

https://github.com/MathCancer/PhysiCell/blob/master/sample_projects/rules_sample/config/cell_rules.csv#L27 and https://github.com/MathCancer/PhysiCell/blob/master/sample_projects/rules_sample/config/cell_rules.csv#L32 need a comma after "decreases"

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 );

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.