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Make source distributions reproduce the full test suite - #572
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The source archive shipped test modules without their helpers or fixtures, so consumers could not reproduce the suite from the published artifact. Include the complete test package and bounded data tree, together with the docs, executable examples, scripts and configuration the tests read. Runtime wheel contents stay unchanged apart from the version.
Add a reviewed SHA256 inventory and fixture provenance notes. All 38 pre-existing data/provenance files retain their exact bytes; the larger RNA bundle and reference datasets remain external through the documented setup. A regression builds an sdist and checks that all test support files are present and unchanged. CI now installs and runs the full suite and parity checks from the unpacked archive outside the checkout, on Python 3.9/3.10/3.11.
Validation:
./lint.sh,./test.sh(3,195 passed) andmkdocs build --strictpass.twine check --strict; the sdist is approximately 4.4 MB and the wheel contains only runtime files and package metadata.Version 10.11.4. Closes #509. Missing upstream acquisition records for some legacy fixtures are documented honestly and tracked separately in #571; this PR preserves their bytes and does not change scientific expectations.
Published 10.11.4 from merged commit
57447d08b91ae26c5771ed4355e4c23d17dd270c; the pushedv10.11.4tag targets that commit. Deployment reran all 3,195 tests successfully. Downloaded both public artifacts and matched their SHA256 hashes against the original release files:2573b8fc3a91a9008fc89f70c27ca356377424394a2ff980318071c5ac5ff8e27a20c372f3471fa0665e34f8641960596c71e9e56ee9d6df526a1ac258dd7f34Installed the downloaded wheel in the isolated environment and unpacked the public source tarball outside any checkout: 138 tests passed covering archive contents, fixture hashes, VCF/MAF/spec/caller fixtures, the bundled Osteosarc snapshot, and executable documentation.
Post-merge verification: archive-based Python matrix, documentation deployment.