fix(docker): repair the Dockerfile as a legacy BNG2.pl image (#414)#445
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The runtime stage ran `pip install` on the PyBNF wheel WITHOUT --no-deps, so pip re-resolved the full dependency set including `bngsim>=0.5.0,<1` -- a private, macOS-only wheel with no public Linux build. The image could not build end-to-end on Linux. Direction A (legacy BNG2.pl image, works today): - Install PyBNF's public runtime deps explicitly, then `pip install --no-deps` the wheel, mirroring .github/actions/setup-pybnf. bngsim is intentionally omitted; PyBNF imports cleanly without it and uses the BNG2.pl backend. - Replace the from-source BioNetGen compile with the official prebuilt Linux tarball (BNG2.pl + bundled run_network/NFsim binaries) -- faster, no autoconf/cmake/ninja toolchain. - Default to Python 3.13 (now supported). - Document the image's backend (legacy BNG2.pl) in the header; drop the stale bngsim private-index escape hatch. Add .github/workflows/docker.yml to build and smoke-test the image (on demand, and on Dockerfile/pyproject changes) so it can't rot silently again. Closes #414
`bash -lc` re-sources /etc/profile, which resets PATH to the Debian default and drops the image's BNGPATH entry, so `command -v BNG2.pl` failed even though BNG2.pl (0755) is correctly installed and on PATH. Use a non-login `bash -c` that inherits the container's ENV PATH.
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Summary
Fixes the broken/stale
Dockerfile(#414) via Direction A — a legacy BNG2.pl image that builds end-to-end on Linux today.What was broken
The runtime stage ran
pip installon the PyBNF wheel without--no-deps, so pip re-resolved PyBNF's full dependency set — includingbngsim>=0.5.0,<1, a private macOS-only wheel with no public Linux build. The image could not build on Linux.Changes
pip install --no-depsthe wheel — mirroring.github/actions/setup-pybnf.bngsimis intentionally omitted; PyBNF imports cleanly without it and falls back to the BNG2.pl backend.make_dist.pl --build) with the official prebuilt Linux tarball (BioNetGen-2.9.3-linux.tar.gz: BNG2.pl + bundledrun_network/NFsim). Faster, no autoconf/cmake/ninja toolchain..github/workflows/docker.ymlbuilds + smoke-tests the image (on demand, and onDockerfile/pyproject.tomlchanges) so it can't rot silently again.Acceptance criteria (#414)
docker buildsucceeds end-to-end on Linux (no dependency on a nonexistent bngsim Linux wheel) — verified by thedockerworkflow on this PR.Closes #414