Add a BioDynaMo recipe and setup-biodynamo action. - #97
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vgvassilev merged 1 commit intoAug 13, 2026
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Every downstream simulation repo builds BioDynaMo inline on each CI run: a long build that also downloads a ~300 MB prebuilt ROOT tarball from CERN, and that needs a pyenv-managed interpreter set up beforehand. CARTopiaX carries a clone-cache-build dance plus its own pyenv step to do it. Publishing it once per cell turns that into a cache fetch. The artifact is relocatable by construction: BioDynaMo installs its own ROOT under third_party/root, and bin/thisbdm.sh derives BDMSYS from its own location, so the tree works wherever setup-recipe extracts it. build.py proves that before publishing -- it moves the install to a different path and drives a full consumer build from there. setup-biodynamo then sources thisbdm.sh and marshals the resulting environment into $GITHUB_ENV, since a composite action cannot leave a sourced shell behind and the script sets a dozen variables. Two host packages are not optional and are installed by the recipe. ROOT's PyROOT and cppyy are extension modules built against a single CPython minor, and no Ubuntu LTS ships the 3.9 the bundled ROOT wants, so it comes from deadsnakes; cling shells out to the compiler ROOT was built with to locate the standard library headers, so g++-11 has to be present or `import cppyy` dies inside libCling with a segmentation violation. The build passes -DNOPYENV=YES so the generated thisbdm.sh does not require pyenv on the consumer, which would otherwise make the published tree unsourceable.
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Every downstream simulation repo builds BioDynaMo inline on each CI run: a long build that also downloads a ~300 MB prebuilt ROOT tarball from CERN, and that needs a pyenv-managed interpreter set up beforehand. CARTopiaX carries a clone-cache-build dance plus its own pyenv step to do it.
Publishing it once per cell turns that into a cache fetch. The artifact is relocatable by construction: BioDynaMo installs its own ROOT under third_party/root, and bin/thisbdm.sh derives BDMSYS from its own location, so the tree works wherever setup-recipe extracts it. build.py proves that before publishing -- it moves the install to a different path and drives a full consumer build from there. setup-biodynamo then sources thisbdm.sh and marshals the resulting environment into $GITHUB_ENV, since a composite action cannot leave a sourced shell behind and the script sets a dozen variables.
Two host packages are not optional and are installed by the recipe. ROOT's PyROOT and cppyy are extension modules built against a single CPython minor, and no Ubuntu LTS ships the 3.9 the bundled ROOT wants, so it comes from deadsnakes; cling shells out to the compiler ROOT was built with to locate the standard library headers, so g++-11 has to be present or
import cppyydies inside libCling with a segmentation violation. The build passes -DNOPYENV=YES so the generated thisbdm.sh does not require pyenv on the consumer, which would otherwise make the published tree unsourceable.