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…n-20261021 Fix dual-use V allele aliases and prepare 0.6.2
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🟢 Approved
The narrow resolver change preserves existing safeguards, includes regression coverage, and has no identified blocking issues.
No open issues 🎉
What changed in this PR
Releases VDJmatch 0.6.2 with model-backed _DV alias support for V-loop lookup, preserving allele identity and submitted calls.
Changes:
- Adds underscore aliases to the shared resolver.
- Adds human and mouse regression cases.
- Updates documentation and release metadata.
| File | Description |
|---|---|
| tests/unit/test_geometry.py | Adds underscore-alias regression cases. |
| src/vdjmatch/match/geometry.py | Recognizes model-backed _DV spellings. |
| skills/vdjmatch/SKILL.md | Documents alias and allele preservation. |
| README.md | Explains supported dual-use spellings. |
| pyproject.toml | Bumps version to 0.6.2. |
| docs/cli.rst | Clarifies alias resolution requirements. |
| CHANGELOG.md | Records the release fix. |
Review effort: Balanced
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Resolve model-backed underscore TRAV/DV spellings before V-loop lookup, preserving allele identity and submitted metadata. For example, TRAV14_DV401 now resolves to TRAV14/DV401 instead of being treated as missing. Scoring formulas, exact-hit behavior and calibrated defaults are unchanged.
Updates README, CLI documentation, the vdjmatch skill and release metadata. Human and mouse regression cases cover the shared resolver. Validation: 1,531 non-slow tests passed in 87.34 s; strict Sphinx build passed; clean wheel installation, CLI import, exact alias geometry and serial/parallel equality passed. No private data or analysis outputs are included.