24102607939
44%

Ran 07 Apr 2026 08:23PM UTC

Jobs 1

Files 15

Run time 1min

Badge

Embed ▾

Committed 07 Apr 2026 08:22PM UTC coverage: 33.52% (+0.6%) from 32.883%

Build # 24102607939

Build Type

push

github

Committed by

web-flow

Commit Message

Unified observations table: hitlist data build (#9)

* Add unified observations table: hitlist data build

New command builds a single parquet file from IEDB + CEDAR with full
source classification from YAML overrides:

  hitlist data build                    # ~4 min, cached
  hitlist data build --with-flanking    # + proteome mapping
  hitlist data build --force            # rebuild

Result: observations.parquet in ~/.hitlist/
  4,883,371 observations
  1,445,063 unique peptides
  790 unique alleles
  24 species
  36 columns (base + classification + allele metadata)
  47 MB parquet (vs 14 GB raw CSV)

New loader with filter pushdown:
  from hitlist.observations import load_observations
  df = load_observations(mhc_class="I", species="Homo sapiens")

Load time: ~2s for filtered queries on 4.88M rows.

New files:
  hitlist/builder.py — build pipeline
  hitlist/observations.py — loader with filters
  tests/test_observations.py — 7 tests (4 require built table)

* Indexer reads from observations.parquet when available

get_index() now checks if the observations table is built and derives
study/allele counts from it (no CSV re-scan needed). Falls back to
direct CSV scanning as legacy path if observations.parquet doesn't exist.

Drops ~200 lines of separate caching infrastructure (parquet index
files in ~/.hitlist/index/) — the observations table IS the index.

Coverage Stats

478 of 1426 relevant lines covered (33.52%)

0.34 hits per line

Coverage Regressions

Lines	Coverage	∆	File
70	0.0	0.0%	indexer.py
53	0.0	0.0%	cli.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	24102607939.1	07 Apr 2026 08:23PM UTC	15	33.52	GitHub Action Run

pirl-unc / hitlist / 24102607939
44%

README BADGES
x

Markdown

Textile

RDoc

HTML

Rst

Coverage Regressions

Jobs

Source Files on build 24102607939

pirl-unc / hitlist / 24102607939 44%

README BADGES x

Markdown

Textile

RDoc

HTML

Rst

Coverage Regressions

Jobs

Source Files on build 24102607939

pirl-unc / hitlist / 24102607939
44%

README BADGES
x