27800559606
80%

Ran 19 Jun 2026 01:58AM UTC

Jobs 1

Files 29

Run time 1min

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Committed 19 Jun 2026 01:52AM UTC coverage: 80.435% (+0.07%) from 80.37%

Build # 27800559606

Build Type

push

github

Committed by

web-flow

Commit Message

Friendlier CLI + accurate docs + curated top-level API (#345)

Friendliness:
- Stale deprecation targets: every "Run: hitlist data build" /
  "data fetch-proteomes" error + help string (qc, observations, mappings,
  builder, cli, bulk_proteomics) now points at the canonical
  `hitlist build observations` / `build proteomes` instead of the commands the
  tool itself disowns.
- `data remove <typo>` no longer claims success: remove() returns whether a
  dataset existed; the CLI warns + exits 1 when nothing was registered.

Docs / API:
- Curated top-level API: `from hitlist import build_observations,
  load_ms_observations, ProteomeIndex, fetch, VersionedDatasetRegistry, ...`
  now works (lazy PEP-562 resolution so import stays fast), discoverable via
  dir(hitlist)/__all__. Previously only __version__ was exported.
- generate_ms_observations_table forwarded only a subset of params — restore the
  6 dropped filters (source, peptide, length_min/max, the exclude_* flags) so
  the README-advertised entry point isn't a capability regression.
- README: fix the deprecated quickstart command, the phantom `data index`
  command, the deprecated export-alias table, and `explode_mappings` ->
  `map_source_proteins`.
- load_supplementary_manifest docstring: `label` -> `study_label` (the real key).

Bumps 1.43.1 -> 1.44.0.

Coverage Stats

5879 of 7309 relevant lines covered (80.44%)

0.8 hits per line

Coverage Regressions

Lines	Coverage	∆	File
117	51.72	-0.13%	cli.py
110	84.44	0.0%	export.py
36	72.19	0.0%	mappings.py
11	73.56	0.92%	downloads.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	27800559606.1	19 Jun 2026 01:58AM UTC	29	80.44	GitHub Action Run

pirl-unc / hitlist / 27800559606
80%

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pirl-unc / hitlist / 27800559606 80%

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pirl-unc / hitlist / 27800559606
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