chore(deps): depend on bbi-variant-annotation from PyPI and bump to 2026.3.1

[bencap]

Summary

poetry publish for 2026.3.0 failed because PyPI rejects packages whose metadata names a git dependency, and the server extra pinned variant-annotation to a git tag. variant-annotation is now on PyPI as bbi-variant-annotation 1.2.0b3, so this depends on it from there and bumps the version so the release can be published.

Changes

• pyproject.toml: bbi-variant-annotation = { version = "1.2.0b3", optional = true } replaces the git pin, in both the dependency and the server extras list; version 2026.3.1.
• poetry.lock: re-locked. The only package change is variant-annotation 1.2.0-beta.1 (git) → bbi-variant-annotation 1.2.0b3 (PyPI).
• src/mavedb/__init__.py: __version__ = "2026.3.1".

bbi-variant-annotation 1.2.0b3 is built from bbi-lab/variant-annotation v1.2.0-beta.3, whose library code is identical to v1.2.0-beta.1; only its packaging changed (the git-only mapping extra was dropped, and PyPI refused variant-annotation as too similar to the existing variantannotation). It still imports as variant_annotation, so no code changes here.

Testing

• pytest -m "not network and not slow": 5,399 passed, 22 skipped.
• ruff check, ruff format --check and mypy src are clean.
• docker build --platform linux/amd64 succeeds; inside the image mavedb.__version__ is 2026.3.1 and bbi-variant-annotation 1.2.0b3 is installed and imports.

After merge: poetry publish --build from main publishes mavedb 2026.3.1.

[coveralls]

Coverage Report for CI Build 38979824049

Coverage decreased (-0.06%) to 90.343%

Details

• Coverage decreased (-0.06%) from the base build.
• Patch coverage: 1 of 1 lines across 1 file are fully covered (100%).
• 12 coverage regressions across 3 files.

Uncovered Changes

No uncovered changes found.

Coverage Regressions

12 previously-covered lines in 3 files lost coverage.

File	Lines Losing Coverage	Coverage
src/mavedb/lib/clinvar/utils.py	6	90.91%
src/mavedb/worker/jobs/external_services/clinvar.py	4	96.97%
src/mavedb/lib/mondo_ols.py	2	96.92%

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Coverage Stats

Relevant Lines:	19157
Covered Lines:	17307
Line Coverage:	90.34%
Coverage Strength:	0.9 hits per line

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💛 - Coveralls