24118351081
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Ran 08 Apr 2026 05:03AM UTC

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Build # 24118351081

Build Type

push

github

Committed by

iskandr

Commit Message

Use Topiary as upstream epitope prediction engine

Replace direct mhctools predict_subsequences call with Topiary's
TopiaryPredictor.predict_from_named_sequences(). This enables
support for multiple prediction kinds (presentation, stability,
processing) in addition to IC50 affinity, while preserving
vaxrank's unique value: WT epitope comparison, reference proteome
checking, vaccine peptide ranking, and manufacturability scoring.

The predict_epitopes() function now accepts either a TopiaryPredictor
or a bare mhctools BasePredictor (auto-wrapped in TopiaryPredictor).

Also bumps mhctools requirement to >=3.0.0 and adds topiary>=4.2.0.

Part of the plan for #209 (decouple MHC prediction tools).

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