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Install Windows CI dependencies with pip instead of conda, test 3.12 too - #1344
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conda was only used on Windows because msprime had no Windows wheels; it now ships them for Python 3.11 through 3.14. The conda-forge solve recently started pulling in both MKL (libiomp) and llvm-openmp (libomp), which makes threadpoolctl raise a RuntimeWarning in test_genee and fails the run because warnings are errors. Using pip for everything avoids the mixed OpenMP runtimes and removes the setup-miniconda step.
This was referenced Sep 3, 2026
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Matches the Build workflow, which already covers 3.11 and 3.12.
Billyzhang1229
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Billyzhang1229
marked this pull request as ready for review
September 3, 2026 16:21
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This seems like a straightforward win, merging |
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The Windows workflow started failing in
test_geneewith warnings treated as errors:conda install msprimeon conda-forge now resolves to MKL (libiomp) plusllvm-openmp(libomp), while the pip-installed scientific stack brings its own OpenMP, so threadpoolctl sees both runtimes. I confirmed the failure is independent of thesetup-minicondaversion by running the same job with v2 and v4.conda was only used on Windows because msprime had no Windows wheels at the time. It now publishes them for Python 3.11 through 3.14, so this switches the job to
setup-python+ pip like the other workflows and drops the miniconda step entirely.Second commit adds Python 3.12 to the matrix so Windows covers the same versions as the Build workflow.
Verified green on my fork