25030468362
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Ran 28 Apr 2026 02:25AM UTC

Jobs 1

Files 24

Run time 1min

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Committed 28 Apr 2026 02:23AM UTC coverage: 61.194% (-0.2%) from 61.383%

Build # 25030468362

Build Type

push

github

Committed by

web-flow

Commit Message

v1.25.0: Add hitlist qc top-level command for corpus + curation diagnostics (#167)

First step of the CLI refactor.  Adds a new top-level ``qc`` command
with three orthogonal sub-checks:

- ``hitlist qc resolution``      — histogram of (mhc_class, source,
  allele_resolution) buckets so callers know what fraction of the
  corpus is 4-digit / 2-digit / serotype / class-only.
- ``hitlist qc normalization``   — alleles in pmid_overrides whose
  ``normalize_allele`` output differs from the curated input (catches
  legacy spellings like HLA-Cw* → HLA-C*).
- ``hitlist qc cross-reference`` — alleles listed in YAML samples but
  absent from observation rows (yaml_only) and the reverse (data_only),
  so curation/data divergence surfaces explicitly.

Bare ``hitlist qc`` runs all three.

Replaces the always-green ``export alleles`` / ``export data-alleles``
mhcgnomes parsability checks with diagnostics that actually trigger on
real data.  Old subcommands stay for one release; deprecation warnings
land in the next refactor PR.

Module: ``hitlist/qc.py``.  Each function returns a DataFrame with a
``severity`` column ("info" / "warn" / "error") so a future ``hitlist
qc --strict`` can fail-on-warn from CI.

Coverage Stats

2695 of 4404 relevant lines covered (61.19%)

0.61 hits per line

Coverage Regressions

Lines	Coverage	∆	File
89	15.85	-1.26%	cli.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	25030468362.1	28 Apr 2026 02:25AM UTC	24	61.19	GitHub Action Run

pirl-unc / hitlist / 25030468362
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