openvax / vaxrank / 24344953695
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Integrate topiary 5.0 DSL for epitope filtering and ranking (#223)

* Integrate topiary 5.0 DSL for epitope filtering and ranking (#216)

Replaces the per-row EpitopePrediction.logistic_epitope_score call in
predict_epitopes with a topiary DSLNode pipeline: optional apply_filter
up front, then a single score_node.eval pass indexed by
(source_sequence_name, peptide, peptide_offset, allele). Users can now
configure filtering/ranking via ``filter_expr`` / ``score_expr`` on
EpitopeConfig; when unset, nodes are synthesized from the scalar fields.

The synthesized affinity-mode score node divides by 1/(1+exp(-mid/width))
so its output matches the legacy scorer byte-for-byte — topiary's
LogisticExpr does not apply that normalizer. Default path has no
filter_node so legacy "min_epitope_score=0 keeps everything" semantics
are preserved; the score node's (Affinity < cutoff) mask + min-score
gate reproduces the old behavior.

Other logistic_epitope_score callers (VaccinePeptide, report, epitope_io)
are unchanged and will migrate in a follow-up.

Deps bumped: topiary>=5.0.0, varcode>=2.1.0, mhctools>=3.7.0 (topiary 5.0
requires >=3.7.0).

* Review follow-ups for topiary 5.0 DSL integration

- Eager-validate EpitopeConfig.filter_expr / score_expr in __post_init__
  so malformed YAML DSL strings fail at config load, not mid-pipeline.
- Drop the dead 0.0 fallback in score_series.get(); reindex+fillna
  upstream already guarantee every group tuple is present.
- Add a multi-allele parity test over distinct (peptide, allele) groups.
- Document the multi-method ambiguity behavior (default affinity raises
  when multiple prediction_method_name values are present; qualify via
  affinity['modelname'] to disambiguate) with two new tests.
- README: add a dedicated section on filter_expr / score_expr with a
  working YAML example, plus rows for both fields in the EpitopeConfig
  reference table. Use column(ident) — the form topiary's parser
  accepts — rather than column('str... (continued)
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