28986765012
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Ran 09 Jul 2026 01:11AM UTC

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Build # 28986765012

Build Type

push

github

Committed by

web-flow

Commit Message

Switch default annotator to fast (7.0.0)

Makes `fast` (offset-arithmetic) the default effect annotator again,
while keeping `protein_diff` as the substrate for splice/germline
classification. `fast` is the more reliable annotator (see #397); this
is a major version bump because it changes default annotation behavior.

Includes:
- Default annotator flip protein_diff -> fast in the registry (7.0.0).
- Rebuilt cross-annotator parity harness (tests/test_protein_diff_parity.py)
  that compares the FULL mutant_protein_sequence, not just the class/
  short_description -- the gap that let #396 through.
- Cross-annotator parity gate in CI: the full suite is re-run under
  protein_diff on 3.11, so any bare .effects() that would diverge fails CI.
- Frameshift C-terminus divergence scenarios (forward + reverse strand).
- Docs updated to show fast as Default and opt-in examples for protein_diff.
- CI hardening: cap bare-"GRCh38" test resolution to the newest installed
  Ensembl release, and pin the remaining latest-release test genomes
  (test_variant, test_effect_classes mouse) so the suite no longer depends
  on runtime auto-download of an uninstalled release.

https://claude.ai/code/session_01VNtZRyKZ7u9jiMGPQEbx4c

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