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Finish release warning cleanup (5.88.1) - #440
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coverage: 93.387% (+0.02%) from 93.366% — fix/release-warnings into master |
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The release gate still emitted predictor API deprecations, a Polars deprecation, and unasserted scientific diagnostics. Treating all warnings as errors also exposed unclosed predictor log streams and a test input file.
Use the current predictor DataFrame API for cache misses while retaining legacy-only predictors; require GTFParse >=2.8.1 and mhctools >=3.45.1 for the upstream fixes; close the test file; and assert the intentionally emitted diagnostics. Every unexpected warning now fails the suite. Bumps Topiary to 5.88.1.
Closes #432. Upstream fixes: openvax/mhctools#478 and #477.
Validation:
./lint.shpasses.PYTHON=$PWD/.venv/bin/python TEST_SH_MAX=1 ./test.sh -q -xpasses all 4,864 tests with zero failures, skips, or warnings and 94% coverage. Both current and legacy-only cache fallbacks are covered. All GitHub CI gates pass, including core Python 3.10–3.12, both Isovar versions, PirlyGenes, packaging, and the released Vaxrank consumer workflow.Released: https://pypi.org/project/topiary/5.88.1/. The final clean-master deploy gate also passed all 4,864 tests with zero failures, skips, or warnings (94% coverage). Both published artifact hashes match the build, and tag v5.88.1 points to merge b8e9cad. The merged branch was removed; only master remains locally and on GitHub.