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bioextract 0.3.0

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@FuqingZh FuqingZh released this 10 Aug 02:40
· 25 commits to main since this release
0.3.0
fa72dbb
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Learn about vigilant mode.

Highlights

  • Added GODatabase.select_ancestors() with canonical and alternate GO ID resolution, is_a/part_of ancestor traversal, optional GO slim projection, self mappings, obsolete policies, and unmatched reasons.
  • Added DuckDB query pushdown for publication-backed select_terms(), list_subsets(), and ancestor selection without temporary input tables or complete-frame materialization.
  • Preserved source/publication parity, pinned-publication identity checks, existing nine-table publication compatibility, and downstream ownership of protein membership and enrichment analysis.

Validation

  • PR #48 merged at fa72dbb after review-thread fixes.
  • Main py-ci passed on the merge head.
  • py-publish run 31350254199 passed canonical tag validation, pdm run check, distribution build, twine check, and PyPI trusted publishing.
  • Published wheel SHA-256: 2e460c53ab7cfa8ee96eb57babc259d367aa85cdd5d619d99ff7efb1579a2f72.
  • Clean-environment install verified version 0.3.0, GODatabase.select_ancestors, and removed legacy constructors.
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