openvax / vaxrank / 25405745710
96%
master: 88%

LAST BUILD BRANCH: v3.1.8
DEFAULT BRANCH: master
Ran
Jobs 0
Files 0
Run time –
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
25405745710

push

github

web-flow 
Phase 2 of #273: extract ManufacturabilityConfig struct (#276)

Manufacturability config moves off ``VaccineConfig`` onto its own
struct (peptide-only, threaded into the ranker as a separate
parameter). YAML and CLI surfaces unchanged from Phase 1.

In-code split:

- New ``vaxrank/manufacturability_config.py`` with
  ``ManufacturabilityConfig`` (msgspec.Struct, frozen): fields are
  the four GRAVY thresholds + the rules tuple, plus a
  ``thresholds_dict()`` convenience for the VaccinePeptide kwarg
  shape.
- ``VaccineConfig`` no longer carries
  ``max_c_terminal_hydropathy`` / ``min_kmer_hydropathy`` /
  ``max_kmer_hydropathy_low_priority`` /
  ``max_kmer_hydropathy_high_priority`` /
  ``manufacturability_rules``. Validation of unknown rule names
  also moved (now on ManufacturabilityConfig).
- ``run_vaxrank``, ``create_vaccine_peptides_dict``,
  ``vaccine_peptides_for_variant``,
  ``vaccine_peptides_from_epitopes`` all gain a
  ``manufacturability_config: Optional[ManufacturabilityConfig]``
  parameter. ``None`` falls back to ``ManufacturabilityConfig()``
  defaults — preserves the old "no override → built-in defaults"
  behavior.
- Loader: ``_VACCINE_CONFIG_MAPPING`` no longer includes the
  manufacturability fields. New
  ``_MANUFACTURABILITY_CONFIG_MAPPING`` reads from
  ``peptide.manufacturability.*`` and feeds into a new
  ``extract_manufacturability_config_kwargs()`` helper.
- New ``manufacturability_config_from_args()`` CLI helper
  alongside the existing ``vaccine_config_from_args``.

Auto-skip when peptide isn't an active modality:

- ``run_vaxrank_from_parsed_args`` only builds a
  ManufacturabilityConfig when ``'peptide' in --vaccine-type``;
  otherwise passes ``None``. The ``manufacturability`` sentinel
  inside ``ranking_rules`` then tie-breaks against
  ``ManufacturabilityConfig()`` defaults rather than against
  user-overridden thresholds that don't apply to mRNA-only runs.

Tests:

- Updated tests that constructed ``VaccineConfig`` wi... (continued)
Source Files on build 25405745710
Detailed source file information is not available for this build.