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• add-load-all-evidence
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Build # 26997363926

Build Type

push

github

Committed by web-flow

Commit Message

v1.30.65: CI coverage for the peptide_mappings build, offline (#176/#63) (#276)

Closes the last 'not covered in CI' gap from #275: the proteome-dependent
mapping build now runs in CI with no network.

fetch_species_proteome uses an already-cached FASTA if one is on disk, so
pre-placing a tiny synthetic FASTA at a UniProt-registry species'
(Sarcophilus harrisii) cache path lets the full mapping pipeline run
offline: source-organism -> lookup_proteome -> from_fasta -> the
int-encoded ProteomeIndex (#250/#273) -> map_peptides -> peptide_mappings
.parquet. HITLIST_BUILD_WORKERS=1 forces the sequential path (no
ProcessPoolExecutor in the test).

New test asserts only the 3 FASTA-substring peptides map (NOTINPROT
dropped), the full sidecar schema, and correct positions against the
source protein — exercising the #250/#273 redesign end-to-end in CI for
the first time. ~11s for both build tests combined.

Verified: pytest -m integration -n 2 -> 22 passed, 1 skipped.

Coverage Stats

5055 of 6290 relevant lines covered (80.37%)

0.8 hits per line