openvax / vaxrank / 25819186559
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Score expressions are the single source of truth (3.1.0) (#291)

Three layers of "default lives in two places" collapsed to one DSL
expression per layer. No code path silently runs a hardcoded Python
formula while a user expression governs elsewhere.

Layer 3 — Combined score:
- Delete ``combined_score_mode`` enum and the three legacy modes.
- ``VaccineConfig.combined_score_expr: str`` defaults to
  ``DEFAULT_COMBINED_SCORE_EXPR = "sqrt(n_alt_reads) * target_epitope_score"``.
- ``__post_init__`` always pre-parses the expression; ``combined_score``
  always evaluates the AST. No mode branch, no fallback.

Layer 2 — Per-epitope total:
- New ``CandidateEpitope.per_allele_scores`` (dict[allele -> score])
  populated at predict time. ``epitope_score`` property sums it.
- ``target_epitope_score`` / ``self_epitope_score`` now read
  ``e.epitope_score`` directly. No re-scoring inside VaccinePeptide.
- ``_legacy_score_one`` deleted from production. Test-only oracle
  moved to ``tests/_legacy_score_reference.py`` for parity assertions.

Layer 1 — Per-(peptide, allele) score:
- Delete ``_default_score_node`` Python builder.
- Two string templates (``DEFAULT_AFFINITY_SCORE_EXPR_TEMPLATE`` /
  ``DEFAULT_PERCENTILE_SCORE_EXPR_TEMPLATE``) formatted against the
  scalar thresholds in ``EpitopeConfig`` and parsed via the topiary
  DSL. ``build_score_node`` always parses a string.
- ``predict_epitopes`` writes the DSL-computed score onto each
  CandidateEpitope's ``per_allele_scores`` so VaccinePeptide can read
  it back without recomputation.

Verified byte-identical rank table on the HCC1395 smoke run vs 3.0.2;
830 tests pass.

Breaking config change: YAML files setting
``vaccine_peptides.combined_score_mode`` no longer parse — switch to
``combined_score_expr`` with one of:
- ``"target_epitope_score"``             (was ``epitope_only``)
- ``"n_alt_reads * target_epitope_score"`` (was ``reads_times_epitope``)
- ``"sqrt(n_alt_reads) * target_epitope_score"`` (default, ... (continued)
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