pirl-unc / tsarina

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• close-tsarina-4-via-load-all-evidence
• consolidate-iedb-drop-netmhcpan-shim
• fix/curation-audit-fixes
• hitlist-1.6.0-integration
• main
• ms-curation
• simplify-species-kwargs-for-hitlist-1.9
• warn-binding-assays-on-cached-path

Build # 24607455020

Build Type

push

github

Committed by web-flow

Commit Message

v0.7.0: --include-binding-assays actually works (closes #4) (#10)

hitlist 1.10.0 shipped load_all_evidence() — union of observations +
binding parquet with an evidence_kind column.  Wiring tsarina's cached
path through it so --include-binding-assays stops being a warn-and-noop
and actually returns binding rows.

Changes:

- cli_hits.py: when --include-binding-assays is set on the cached path,
  call load_all_evidence(gene_name=, mhc_class=, species=); otherwise
  stay on load_observations().  The old "warn and drop" branch is gone.
- cli_hits.py: --help text for --include-binding-assays updated to
  describe the union + evidence_kind behavior.  No more "no-op"
  language.
- pyproject.toml: hitlist pin >=1.9.0 → >=1.10.0 (required for
  load_all_evidence).
- version.py: 0.6.2 → 0.7.0 (minor bump; user-visible behavior change
  for a flag that was previously silently wrong).

Tests:

- test_hits_help_describes_include_binding_assays_union (replaces the
  old no-op help-text assertion).
- test_include_binding_assays_routes_to_load_all_evidence — when the
  flag is set, load_all_evidence is called, load_observations isn't.
- test_default_cached_path_uses_load_observations_not_union —
  regression guard for the without-flag path.

146 passing (was 148 — old warning test + old help-text test replaced
by two new routing tests; net same coverage on this flag).

Closes #4.

Coverage Stats

606 of 1741 relevant lines covered (34.81%)

0.35 hits per line