biodbs 0.4.0¶
Released: 2026-07-05
0.4.0 expands biodbs to cover the reference databases supported by the QIIME 2 plugin RESCRIPt, and hardens live-API reliability.
Highlights¶
- Added PR2 (Protist Ribosomal Reference) support via the GitHub Releases API.
- Added GreenGenes support for release-directory browsing and file downloads.
- Added EUKARYOME support for eukaryote-wide rRNA (SSU/LSU/ITS/longread) archives.
- Added MIDORI2 support for QIIME-formatted mitochondrial reference files.
- Added UNITE support, resolving fungal/eukaryote ITS releases through the PlutoF DOI API.
- Added GTDB and HOMD database support.
- Shipped offline (mocked) unit tests, live integration tests, and documentation for each new database.
- Routed PubChem requests through the shared rate-limited request path so the configured per-host rate limit and retry backoff take effect.
CI Reliability¶
This release added the new databases' live suites to the integration matrix and made the integration jobs rerun only failed tests to absorb third-party API throttling of CI IP ranges. A guard test now asserts that biodbs.__version__ matches the packaged version so the runtime version cannot drift from the release.
Not Yet Included¶
BOLD is deferred: its legacy public API endpoint has been retired and the current Portal API requires a multi-step token flow with no RESCRIPt precedent. It is tracked in docs/dev/rescript-parity-plan.md.
Upgrade¶
No API migration is required for users upgrading from 0.3.1.