24736095121
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Ran 21 Apr 2026 05:18PM UTC

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Build # 24736095121

Build Type

push

github

Committed by

web-flow

Commit Message

Expose vaccine_peptides.ranking_rules in YAML config (Phase 2 of #199) (#237)

Builds on #235 (Phase 1 refactor). Adds a `ranking_rules` YAML key under
`vaccine_peptides:` that flows through the schema, loader mapping,
`VaccineConfig`, and `VaccinePeptide.lexicographic_sort_key`.

- `VaxrankConfigSchema.vaccine_peptides.ranking_rules: list[str]`
- `VaccineConfig.ranking_rules: Optional[tuple[str, ...]]` with
  post-init validation against `RANKING_RULE_REGISTRY`.
- `extract_vaccine_config_kwargs` now coerces both `manufacturability_rules`
  and `ranking_rules` from list to tuple via a small shared loop.
- `VaccinePeptide.ranking_rules: Optional[tuple]` threads into
  `compute_ranking_tuple`; `to_dict` emits it only when non-default,
  matching the `manufacturability_rules` precedent.
- `core_logic.vaccine_peptides_from_epitopes` passes
  `vaccine_config.ranking_rules` into each constructed VaccinePeptide.

Tests:
- End-to-end YAML -> VaccineConfig -> VaccinePeptide covering the
  `manufacturability` sentinel expansion.
- Tuple coercion invariant.
- Unknown ranking rule rejected at VaccineConfig construction.
- to_dict roundtrip coverage (including the "omit when default" branch
  for ranking_rules).

Default behavior unchanged; all 378 tests pass locally.

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