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Pin test GRCh38 resolution to Ensembl 81 (10.11.2) - #568
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The test reference probe accessed
EnsemblRelease.db, which can download missing reference data while checking whether a release is installed. Bare GRCh38 inputs now use the suite's existing Ensembl 81 fixture directly. This removes the installed-release scan and makes the test default independent of unrelated newer or incomplete cache entries.The change is confined to pytest configuration: explicit release numbers, release-qualified names, supplied genome objects, and other assemblies keep their existing behavior. Runtime library reference selection is unchanged. Contributor/test instructions now describe the fixed fixture and required provisioning step.
Fresh-process regressions cover empty caches, partial newer downloads, and stale index files. They intercept source acquisition and compare the complete cache contents before/after resolution. All three failed on the old code because it attempted source acquisition, and pass with this change. Alias resolution and explicit-release preservation are covered through the public reference API.
Validation:
./lint.shpassed.python -m pytest tests/test_reference_fixture.py tests/test_reference.py -q: 49 passed.TEST_SH_MAX=4 ./test.sh: 3,155 passed, 32 warnings.mkdocs build --strictpassed.Version: 10.11.2. Fixes #493. Related: openvax/pyensembl#398.
Published to PyPI from clean main after green PR CI. The deployment gate passed all 3,155 tests; wheel/sdist SHA256 hashes match the local build, and an isolated PyPI install passed the import/effect-prediction smoke test.