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Ran 08 Jul 2026 09:32PM UTC

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Build # 28976887036

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github

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web-flow

Commit Message

Fix CI: don't depend on an uninstalled Ensembl release / alt-contig transcripts (#399)

main went red at the #396 merge because three tests required Ensembl release
115, which the openvax/ensembl-data mirror doesn't publish (it tops out at
GRCh38.95). Two fixes:

* test_frameshift_cterminus_regression.py (ATM p.F61fs, #396) skips cleanly at
  module level when release 115 isn't installed. The bug CLASS is covered on
  release 81 by test_annotator_divergence_scenarios.py and
  test_protein_diff_parity.py, so #396/#397 coverage is unaffected.

* test_timings.py used random_variants(), whose genome_name="GRCh38" default
  resolves to pyensembl's latest release (now 115). Added a backward-compatible
  ensembl= param and pinned the timing test to release 81.

* random_variants could then draw transcripts on alternate/patch scaffolds
  (CHR_HSCHR*_CTG*) that Variant rejects lazily during annotation (the contig
  check runs on .transcripts via a process-wide valid-contig cache, not in
  __init__). It now validates each variant through that exact path and skips
  un-annotatable draws, so generation is deterministic instead of flaky.

Claude-Session: https://claude.ai/code/session_01VNtZRyKZ7u9jiMGPQEbx4c

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