24667809737

Ran 20 Apr 2026 01:03PM UTC

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Build # 24667809737

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push

github

Committed by

web-flow

Commit Message

Use varcode's default (fast) annotator and pin to 4.x (#230)

varcode 4 exposes a registered annotator API with "fast" as the
process-wide default. Drop the explicit coupling to protein_diff:
- Import apply_variant_to_transcript from its canonical home in
  varcode.mutant_transcript instead of re-export via
  varcode.annotators.protein_diff.
- Bump the varcode pin to >=4.0.0,<5.0.0 so the new registry is
  available and fast is the default for variant.effects().
- Update AGENTS.md domain note to reflect the new default.

No runtime behaviour change for effect classification: variant.effects()
already used the registry default under the hood; vaxrank was never
calling set_default_annotator("protein_diff"). This PR just removes a
stale protein_diff-specific import.

Bumps to 2.4.2.

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