openvax / vaxrank / 24683882380
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Configurable manufacturability rules, combined score mode, and multi-file config (#231)

* Add configurable manufacturability rules, combined score mode, and multi-file config

- Promote `manufacturability` to a top-level config section; lift nested
  `vaccine_peptides.manufacturability` with a DeprecationWarning (errors if
  both are set).
- Add a manufacturability rule registry so the lexicographic sort tuple can
  be reordered, subset, or disabled via `manufacturability.rules`. The
  default preserves the legacy 10-rule order byte-for-byte.
- Add `vaccine_peptides.combined_score_mode`
  (`sqrt_reads_times_epitope` [default/legacy], `reads_times_epitope`,
  `epitope_only`) to control how expression folds into the combined score.
- Make `--config` repeatable; later files deep-merge over earlier ones.
- Validate new knobs in `VaccineConfig` and expand config, manufacturability,
  and vaccine-peptide tests (new `tests/test_vaccine_peptide_config.py`).

* Review follow-ups: tighten configurability contract, start dataclass migration

- VaccinePeptide: decouple `expression_score` from `combined_score_mode`.
  Expression now always reports sqrt(n_alt_reads); the mode only changes
  how expression folds into `combined_score`. Keeps reports honest and
  avoids `.expression_score == 1.0` under `epitope_only`.
- VaccinePeptide: raise at __init__ on unknown `combined_score_mode`
  (defense in depth; VaccineConfig already validated, but direct
  instantiation was silently falling through to legacy behavior).
- Deduplicate `DEFAULT_COMBINED_SCORE_MODE` and `COMBINED_SCORE_MODES` —
  vaccine_peptide now imports both from vaccine_config.
- Coerce `manufacturability_rules` list → tuple in
  `extract_vaccine_config_kwargs`, matching VaccineConfig's declared type
  for direct-construction paths.
- Add end-to-end test: YAML with `manufacturability.rules` →
  `load_vaxrank_config` → `vaccine_config_from_args` → VaccineConfig
  (tuple) → VaccinePeptide, asserting the so... (continued)
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