25143627132
80%

Ran 30 Apr 2026 02:07AM UTC

Jobs 1

Files 25

Run time 1min

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Committed 30 Apr 2026 02:06AM UTC coverage: 69.733% (+0.007%) from 69.726%

Build # 25143627132

Build Type

push

github

Committed by

web-flow

Commit Message

v1.30.6: Cluster canonicals by FASTA in build_peptide_mappings (#107) (#190)

Closes #107.

The cProfile run from #176 showed ``ProteomeIndex.from_fasta`` hitting
the LRU cache 78% of the time (683 hits / 868 calls). The remaining
22% is mostly LRU eviction from interleaved build order:
``build_peptide_mappings`` iterated canonicals alphabetically, but
strain variants that share one underlying FASTA (LCMV / SARS-CoV-2 /
EBV / etc.) aren't always alphabetically adjacent, and the cache
(maxsize=4 since v1.19.2 for memory bounds) holds at most one
canonical's worth of (path, length) entries.

Sort canonicals by ``(group_key, canonical)`` instead, where
``group_key`` is the UniProt ``proteome_id`` for FASTA-backed entries
and the species name for ensembl entries. Same-FASTA strain variants
now land adjacently, so the second through Nth member of a group hits
the cache for all 4 lengths in a row.

No memory cost — cache size unchanged at maxsize=4. The build is
deterministic (within-group ordering is alphabetical by canonical).
Ensembl entries don't share the from_fasta cache so the ordering
benefit only applies to FASTA-backed species, which is the
22%-miss-rate set we care about.

Tests pin the bucketing rules (uniprot proteome_id clusters, ensembl
sorts before uniprot, end-to-end adjacency on a synthetic mixed list).

Coverage Stats

3419 of 4903 relevant lines covered (69.73%)

0.7 hits per line

Coverage Regressions

Lines	Coverage	∆	File
69	27.11	2.34%	mappings.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	25143627132.1	30 Apr 2026 02:07AM UTC	25	69.73	GitHub Action Run

pirl-unc / hitlist / 25143627132
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