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Download and cache HGNC aliases in one call - #441
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Human alias lookup required visiting HGNC and manually downloading a TSV before calling PyEnsembl. Add
GeneNameAliases.download_hgnc()to download the complete set once and return a usable alias mapping. Later calls reuse the cached snapshot without network access.Reuse PyEnsembl's atomic download/provenance path under
aliases/homo_sapiens/hgnc. Separate sources by URL so archived snapshots and mirrors with identical filenames cannot collide. Support a custom cache directory, source URL and explicitoverwrite=Truerefresh. Preservefrom_hgnc(path)for selected local snapshots; detect gzip from its contents so compressed URLs also work with query strings or extensionless endpoints. Ordinary gene queries retain their existing behavior.The alias guide now starts with the one-call workflow and an actual p53 result, followed by offline reuse, refresh, pinned snapshots and custom mappings.
Validation: ./lint.sh and TEST_SH_MAX=2 ./test.sh passed (538 passed, 1 opt-in benchmark skipped). Real local-HTTP tests cover acquisition, offline reuse, refresh, source separation, gzip, cache placement, failed refresh preservation and invalid URLs. ./docs.sh passed with complete API coverage, and all five home/query examples matched their documented output. The official HGNC complete set loaded 98,547 names and resolved p53 to TP53 / ENSG00000141510 against installed human release 93. Version: 2.23.0.
Closes #440.
Cross-version validation: lint, the complete suite (538 passed, one opt-in benchmark skipped), and all five documented examples passed in separate local environments for Python 3.9, 3.10, 3.11, 3.12, 3.13 and 3.14. GitHub's strict documentation build passed; its test matrix is delayed by the ongoing https://www.githubstatus.com/ Actions hosted-runner assignment incident. No required status check is configured on main. Clean-main deployment will run the ordinary lint/test gates.
Release: merged at 85bb9b6 and published as 2.23.0 on PyPI (wheel and source archive verified). Clean-main ./deploy.sh passed lint and 538 tests, one opt-in benchmark skipped, and pushed v2.23.0. The final main documentation build passed on GitHub and locally. Its hosted publish job remained queued, so the same validated site was pushed with ghp-import to gh-pages at 3fbd3e8. GitHub Pages deployment completed successfully on 2026-10-06 after rerunning https://github.com/openvax/pyensembl/actions/runs/37369599482. Verified the public home/examples, cached HGNC guide and API, and both old tutorial fragments in the browser.