25077832559
80%

Ran 28 Apr 2026 09:11PM UTC

Jobs 1

Files 25

Run time 1min

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Committed 28 Apr 2026 09:09PM UTC coverage: 69.277% (-0.002%) from 69.279%

Build # 25077832559

Build Type

push

github

Committed by

web-flow

Commit Message

v1.30.3: Inline _pack into ProteomeIndex._build hot loop (#176) (#186)

Profile run (cProfile on the full peptide_mappings build) showed
``_pack`` accounting for ~88s of runtime over 1.13B calls — pure
Python function-call overhead, since the function body is only a
shift+OR. ``_build`` itself was 79% of the 46-minute build.

Inlining the pack into the inner loop and hoisting the per-protein
``pi << _PROT_BITS`` shift out of the kmer loop drops a microbench
(500 proteins x 400aa, lengths 8-11) from ~1250ms to ~840ms — about
33% on the inner loop.

Also dropped a ``setdefault`` attempt that benchmarked ~10% slower
because the default ``[]`` argument is built on every call even on
the common key-exists path; the explicit ``raw.get`` + branch wins.

No behavioral change — packed values, index layout, and downstream
``map_peptides`` are unaffected. Existing proteome tests cover the
correctness of ``_build``.

Coverage Stats

3317 of 4788 relevant lines covered (69.28%)

0.69 hits per line

Coverage Regressions

Lines	Coverage	∆	File
14	87.8	-0.26%	proteome.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	25077832559.1	28 Apr 2026 09:11PM UTC	25	69.28	GitHub Action Run

pirl-unc / hitlist / 25077832559
80%

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