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Vaxrank 3.48.0

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@iskandr iskandr released this 30 Oct 01:21
· 38 commits to main since this release
v3.48.0
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Learn about vigilant mode.

Use one explicit CTA RNA restriction policy for human, dog and mouse expression inputs through the existing API and shared manifest.

  • Bind policy and supplemental RNA bounds to an exact OncoRef snapshot and complete ORFdata host inventory.
  • Check all equivalent protein occurrences, tissue coverage, independent donor/sample identities, pooling and allocation; preserve somatic counterevidence and missing-data findings.
  • Freeze the evidence and assessment for native peptide/mRNA export and offline replay.
  • Build pinned Ensembl or RefSeq host references with one species-neutral helper, total transfer budgets and no annotation indexes. Ensembl contexts bind matching variant annotations through provider metadata and exact assembly accessions.
  • Preserve predictor failure types and messages in final-product audit exports, including unsupported DLA requests.

This remains an explicit experimental research path. Existing human defaults and historical saved decisions retain their semantics. Gene RNA is not isoform abundance, and the released dog/mouse candidate facts alone do not establish a validated normal-tissue restriction panel. Mouse P1A's sequence subset is not a complete host inventory.

Reviewed in #756; closes #596, #755 and #759. ORFdata 0.42.6 supplies the pinned Ensembl builder. Install the new policy with pip install 'vaxrank[cta]', which declares its OncoRef 1.23.1 requirement. A fresh compatible environment currently selects Topiary 5.106.1. PirlyGenes pins OncoRef exactly: 6.0.18 uses 1.19.2 and the merged 6.0.19 update targets 1.23.0. Both conflict with this extra; the additional 1.23.1 coordination is tracked in pirl-unc/pirlygenes#658. Existing base installations retain their historical path.

Validation: 3,021 local tests passed with two optional skips; a normal installed wheel passed 58 targeted checks including all six species/modality CLI exports and offline replay. Full real human (245,535 proteins) and dog (63,650 proteins) references passed consumer acceptance. Release checks, GitHub CI and public-wheel receipts are verified separately.

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