25200317629
80%

Ran 01 May 2026 03:07AM UTC

Jobs 1

Files 27

Run time 1min

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Committed 01 May 2026 03:06AM UTC coverage: 70.945% (+0.02%) from 70.924%

Build # 25200317629

Build Type

push

github

Committed by

web-flow

Commit Message

v1.30.23: qc.proteome_coverage report (#39) (#211)

Adds qc.proteome_coverage() and a matching ``hitlist qc
proteome-coverage`` CLI subcommand that buckets observation rows by
``source_organism`` and flags species without a registered reference
proteome in SPECIES_PROTEOMES / VIRAL_PROTEOMES. Surfaces the gap
that blocks downstream features needing a per-organism proteome
(flank extraction, gene-name lookup, source-protein audits).

Implementation reuses the existing ``lookup_proteome()`` resolver --
no new registry, no downloads, no curation calls. Severity is
``warn`` when an unregistered organism has >=100 rows
(curation-priority cluster) and ``info`` for the long tail.

Real-data findings against the production parquet (8 warn-severity
gaps with >=100 rows each): AAV serotypes 2/6/9, Mycobacterium
tuberculosis (incl. H37Rv strain entry), Plasmodium falciparum --
plus 454K empty + 80K ``unidentified`` rows that can't be
proteome-resolved at all.

CLI surface:
    hitlist qc proteome-coverage --missing-only --min-rows 100
    hitlist qc proteome-coverage --severity warn --output gap.csv

Two new tests: registered/missing-with-rows/missing-long-tail
classification, and the empty-corpus schema invariant.

Coverage Stats

3709 of 5228 relevant lines covered (70.94%)

0.71 hits per line

Coverage Regressions

Lines	Coverage	∆	File
104	55.07	-0.25%	cli.py
4	92.38	-0.92%	qc.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	25200317629.1	01 May 2026 03:07AM UTC	27	70.94	GitHub Action Run

pirl-unc / hitlist / 25200317629
80%

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