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drbergman
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Apr 4, 2025
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Looks great and straightforward. Have we been able to test on Linux and Windows? I can confirm it works on MacOS (I made sure to clear out the addons/libRoadrunner/roadrunner directory before testing).
I'm also happy to see removal of old comments :)
| else: | ||
| rrlib_dir = my_file[:-7] | ||
| rrlib_dir = my_file[:-4] | ||
| # if os_type.lower().startswith("win"): |
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can we clear out these 4 commented lines?
drbergman
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Apr 4, 2025
| print('error unzipping the file') | ||
| exit(1) | ||
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| print('Done.\n') No newline at end of file |
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Should we also clean up the downloaded zip file for the user?
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This PR is a long-overdue update to downloading and using libroadrunner in PhysiCell intracellular models. For a long time, we obtained very old libroadrunner libs and headers from a sourceforge repo that was created many years ago and not maintained. When the Mac arm64 computers came out, we had to build that lib from source. In recent discussions with Herbert Sauro's lab, we now can obtain the latest libroadrunner libs and headers from their releases (which is primarily for their Tellurium Python package) that will (now) work for C/C++/PhysiCell. Their releases are at https://github.com/sys-bio/roadrunner/releases . Look for the "Release" .zip bundles there. We have extracted a (mostly) minimal set of files from the .zip bundles there, for each OS, and host them on our own repo (https://github.com/PhysiCell-Tools/intracellular_libs/tree/main/ode). When building a libroadrunner sample project in PhysiCell, the updated
beta/setup_libroadrunner.pyscript will now download the appropriate OS-dependent bundle from our intracellular_libs repo and build the model with it.