vcell-fenics

FEniCSx (DOLFINx) backend for Virtual Cell models and a VCell solver: a VCell SimulationTask in, a VTU + zarr results bundle out. Orientation: docs/overview.md; the container: docker/README.md; the release contract: SOLVER-RELEASE.md.

Releases

A release is a tag vX.Y.Z on main; the artifacts are the container images (no archives).

1. In a PR, set the version in both pyproject.toml ([project].version) and src/vcell_fenics/__init__.py (__version__) — tests/test_version.py checks they agree — and merge it.

2. Tag the merge commit on main and push the tag:

   git fetch origin && git tag -a vX.Y.Z origin/main -m "vcell-fenics X.Y.Z" && git push origin vX.Y.Z

3. The container workflow runs on the tag. It fails at once if the tag is not v<package version> or not on main, builds and smoke-tests the image and SIF (checking both report X.Y.Z), then publishes ghcr.io/virtualcell/vcell-fenics:X.Y.Z (and :vX.Y.Z, multi-arch) and oras://ghcr.io/virtualcell/vcell-fenics_singularity:X.Y.Z (and :vX.Y.Z, amd64), and creates the GitHub Release with notes. latest keeps following main.

A mistaken tag is fixed by bumping the version and tagging again — never by moving a published tag.