New:
- Ship vaxrank/config/default.yaml — every YAML knob documented in one
place with comments + DSL examples. Users bootstrap their own config:
vaxrank --print-default-config > my-config.yaml - New CLI flag --print-default-config writes the bundled YAML to stdout.
- vaccine_peptides.require_mutant_epitopes_in_variant (default true,
legacy behavior). Set false to keep every variant for which a vaccine
peptide could be assembled — useful when the vaxrank report is
downstream input for an independent predictor.
Schema:
- epitopes.default_methods (added in 2.7.0) is now wired into
EpitopesConfigSchema, so YAML use is no longer rejected by
forbid_unknown_fields. Users hitting that error in 2.7.0 should
re-run on 2.8.0.
Closes the last hardcoded scoring/ranking item from #199 (variant
'drop if zero epitope-bearing peptides' filter at core_logic.py:150).
All other items from that issue's status comment had already shipped.
PR: #240