ci: install test job env via micromamba (refs #279)#910
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Replace pip-based setup in the test matrix with mamba-org/setup-micromamba
consuming the autogenerated environment.yml, so PyMC comes from
conda-forge in CI.
- Pin setup-micromamba to v3.0.0 by SHA, matching the security style
of the rest of the workflow.
- Add `defaults.run.shell: bash -el {0}` so the activated env persists
across steps.
- Pass python plus the missing test extras (pytest, pytest-cov,
papermill) via `create-args`, since environment.yml is generated
from the dev extras and does not include them.
- Install the local package with `pip install --no-deps -e .` so pip
cannot pull pip-built pymc/pytensor on top of the conda ones.
- Drop 3.11 from the matrix because environment.yml pins
`python>=3.12`. New matrix is ["3.12", "3.14"].
Probe for pymc-labs#279, kept on a feature branch for validation.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #910 +/- ##
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Coverage 95.07% 95.07%
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anevolbap
changed the title
Add `-e test` to the pyproject2conda invocation in .pre-commit-config.yaml and the check-environment-yml job in ci.yml. Regenerate environment.yml so it now includes pytest, pytest-cov, and papermill. Drop those three deps from the test job's create-args, since they now flow through environment.yml. Keeps that file as the single dependency source per pymc-labs#713 and removes the cache-key divergence introduced by passing test deps through create-args.
Header-only change so the file matches what the pyproject2conda-yaml prek hook produces. The body is identical to the previous commit. Restores pre-commit.ci to green.
anevolbap
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juanitorduz
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May 11, 2026
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thanks @anevolbap !
@drbenvincent can you take a look as this one is key ;) ?
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Thanks for all these. I'm a bit behind on causal reviews - bear with me and I'll attempt to catch up |
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Refs #279.
The CI
testmatrix still installs PyMC via pip. #304 moved local dev to a conda install but explicitly scoped out CI. Earlier attempts at the CI half stalled (#281 conda-lock, #412 pixi). #713 has since madeenvironment.ymlan autogenerated artifact synced withpyproject.toml, which makes a clean swap straightforward.What this PR does
Switches the
testmatrix in.github/workflows/ci.ymlfrompip install -e .[test]tomamba-org/setup-micromambaconsuming the autogeneratedenvironment.yml, so PyMC comes fromconda-forgein CI.setup-micromambato v3.0.0 by SHA, matching the security style of the rest of the workflow.defaults.run.shell: bash -el {0}so the activated env persists across steps.pytest,pytest-cov,papermill) fromenvironment.ymlby adding-e testto thepyproject2condainvocation in.pre-commit-config.yamland thecheck-environment-ymljob. Keepsenvironment.ymlas the single source of truth.pip install --no-deps -e .so pip cannot pull pip-builtpymc/pytensoron top of the conda ones.Open question: Python 3.11 in CI
The matrix changed from
["3.11", "3.14"]to["3.12", "3.14"], becauseenvironment.ymlis generated with--python-include "python>=3.12"and the 3.11 leg would not solve. The package itself still claims 3.11 support (requires-python = ">=3.11",Programming Language :: Python :: 3.11classifier). Two paths forward, neither taken in this PR:requires-pythonto>=3.12and drop the 3.11 classifier.--python-includein thepyproject2condainvocation topython>=3.11so the 3.11 leg can solve, then re-add it to the matrix.Happy to take direction on which one you prefer.
CI runtime impact
The
testmatrix went from ~3-5 min (pip) to roughly 5-8 min (conda) on the first run.cache-environmentshould bring subsequent runs closer to the pip baseline as long asenvironment.ymldoes not change.Verification
pymc,pytensor,numpy,scipyall fromconda-forgewith MKL BLAS,blas_ldflagsreferences the conda env'slib, nopytensor.tensor.blasnumpy-fallback warning. Doctests 35 passed / 11 skipped, extra tests 2 passed, full suite 936 passed / 17 skipped, coverage 94.97% in 3m27s.test (3.12)andtest (3.14)pass. TheShow environmentstep in each test job's log confirmspymcis installed fromconda-forgeandblas_ldflagsreferences the conda env'slib.Out of scope
release.yml,test_notebook.yml, anduml.ymlworkflows also pip-install PyMC (transitively viacausalpy[docs]etc.). They are in the spirit of install pymc in the recommended manner for remote workflows #279 but a separate change.prekjob or thecheck-environment-ymljob beyond the-e testaddition above.Reviewed with Claude Opus 4.7 (adversarial review pass).