Skip to content

biodbs 0.3.1

Released: 2026-06-19

0.3.1 is a stabilization release focused on making the test suite reliable offline, separating live API checks from normal CI, and raising coverage to 85%.

Highlights

  • Raised package coverage from 75% to 85% with offline tests for QuickGO, HPA, PubChem, Reactome, BioMart, KEGG, NCBI, and convenience fetch functions.
  • Moved live KEGG and QuickGO fetcher checks behind the integration marker.
  • Added mocked KEGG REST coverage for URL construction and parser behavior.
  • Replaced broad JSON parsing exception handlers with explicit decode-related exceptions.
  • Added a ruff check . baseline and contributor guidance for offline and integration test gates.

CI Reliability

Normal CI should use the offline gate:

pytest -m "not integration"

Live-service checks remain available when needed:

pytest -m integration

The live KEGG list/organism endpoint was removed from integration assertions after returning validation errors in CI. The tests now use a stable human pathway list endpoint while still covering the same tabular data behavior.

EnrichR ORA integration tests now skip on API rate limits, matching the existing behavior for unavailable remote services.

Verification

Validated before release:

pytest -q -m "not integration" --cov=biodbs --cov-report=term --maxfail=1
uv run ruff check .
uv build

Final coverage result:

TOTAL 85%

Upgrade

pip install --upgrade biodbs==0.3.1

No API migration is required for users upgrading from 0.3.0.