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v0.7.0

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@github-actions github-actions released this 28 Sep 00:28
· 87 commits to main since this release
45fc514
  • Add bioevidence review (check, agreement, adjudication-sheet, score, freeze)
    implementing the gold-standard protocol: strict annotation checks, Krippendorff's α with
    bootstrap interval and Cohen's κ (both cross-checked against reference implementations),
    adjudication of disagreements, scoring on the test split with hash-bound joins, and frozen
    manifests. It never produces labels.
  • Add a blinded ClinVar expert-review kit (evaluation/clinvar_review/): all 95 variants where
    the validator and NCBI disagree plus 95 stratum-matched controls, an Excel workbook with
    dropdowns, a reviewer rubric, a private key, and an importer into the protocol format.
  • CI runs ruff and mypy, and enforces a 95% test-coverage minimum (currently 98%).
  • Add CONTRIBUTING, CODE_OF_CONDUCT (Contributor Covenant 2.1), SECURITY, issue forms and a
    pull request template.
  • Add community/profiles/: contributed domain profiles whose example cases are built,
    validated and checked against expected outcomes in CI; _template/ to copy.
  • Add a documentation site (MkDocs, strict link checking) published to GitHub Pages.
  • The canine 0.3 implementation is also preserved at the canine-0.3 tag.
  • No change to validation decisions or report format; both benchmarks reproduce 0.6.0 exactly
    apart from validator_version.

Also in this release: 0.6.0 (not published separately)

0.6.0 was never released on its own, so upgrading from 0.5.0 also brings:

  • A second real-data case, ClinVar germline classifications: 5,026 variants from the 2023-09 release validated with a ClinVar-style profile, compared with NCBI's own review status (98–99% agreement) and with 2026-09 outcomes. Where the validator is stricter, classifications were about 4–5× more likely to be reclassified or in conflict three years later (1★ and 2★).
  • docs/STANDARDS.md mapping the record model to ECO, Biolink 4.4.4, GA4GH VA-Spec 1.0.1 and PROV-O; ECO meanings on ExtractionMethod in the LinkML schema.

See the CHANGELOG for details.