24735655636
72%

Ran 21 Apr 2026 05:04PM UTC

Jobs 1

Files 32

Run time 1min

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Committed 21 Apr 2026 05:03PM UTC coverage: 47.415% (+1.8%) from 45.592%

Build # 24735655636

Build Type

push

github

Committed by

web-flow

Commit Message

v1.0.1: unify k-mer enumeration behind _proteome_kmers (#25)

Collapses the three ad-hoc proteome-walk loops (peptides._non_cta_proteome_kmers,
viral._human_proteome_kmers, and the two inline walks in
viral.cancer_specific_viral_peptides) into a single cached primitive:
peptides._proteome_kmers(release, lengths, gene_ids=None).

Outcomes:

- Three inner-loop copies -> one. Net -60 lines across peptides.py +
  viral.py.
- cancer_specific_viral_peptides was previously un-cached; now shares
  the v0.10.1 fast path that cta_exclusive_peptides and
  human_exclusive_viral_peptides already enjoyed. Same ~10-60s -> sub-ms
  win for repeat calls.
- Cross-function cache sharing: running cta_exclusive_peptides then
  cancer_specific_viral_peptides in one process now builds the non-CTA
  k-mer set exactly once.
- No public API or output schema change.

When hitlist ships the proteome_kmer_set primitive (hitlist#99), the
tsarina call sites collapse to a one-line delegate without any other
change.

193 passed (was 189).

Closes #19.

Coverage Stats

917 of 1934 relevant lines covered (47.41%)

0.47 hits per line

Coverage Regressions

Lines	Coverage	∆	File
43	48.45	12.31%	peptides.py
17	61.29	22.05%	viral.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	24735655636.1	21 Apr 2026 05:04PM UTC	32	47.41	GitHub Action Run

pirl-unc / tsarina / 24735655636
72%

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