feat(tests): enable --doctest-modules in pytest configuration#3922
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haoyu-haoyu wants to merge 2 commits intosourmash-bio:latestfrom
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feat(tests): enable --doctest-modules in pytest configuration#3922haoyu-haoyu wants to merge 2 commits intosourmash-bio:latestfrom
haoyu-haoyu wants to merge 2 commits intosourmash-bio:latestfrom
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Add --doctest-modules to pytest addopts so doctests embedded in Python source files (e.g., sourmash/minhash.py, sourmash/lca/lca_utils.py) are executed during CI test runs alongside the existing doc/*.md doctests. Closes sourmash-bio#897
--doctest-modules only scans modules under collected paths. Without src/sourmash in testpaths, doctests in source files like minhash.py and lca/lca_utils.py would not be collected during CI runs.
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Summary
Enable automatic doctest discovery for Python source modules by adding
--doctest-modulesto pytest andsrc/sourmashtotestpaths.Changes
pyproject.toml:--doctest-modulesto[tool.pytest.ini_options] addopts"src/sourmash"totestpathsso pytest collects doctests from source filesWhy
Issue #897 noted that doctests in source files (e.g.,
sourmash/minhash.py,sourmash/lca/lca_utils.py) were never executed in CI. The existing config only testeddoc/*.mddoctests via--doctest-glob. Adding--doctest-moduleswithsrc/sourmashintestpathsensures source-level doctests are collected and run alongside unit tests.Notes
-n4parallel flag is compatible with--doctest-modules(xdist handles collection correctly)sourmashrequire the compiled Rust extension, which is available in CI but not in bare Python environmentsCloses #897