pirl-unc / hitlist / 33447303008
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coverage: 81.148% (+0.01%) from 81.135%
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v1.53.2: make the per-peptide donor lookups public and documented (#389)

* v1.53.1: make the per-peptide donor lookups public and documented

_pmid_peptide_alleles and _pmid_peptide_per_sample_typings hold the only
evidence that narrows a peptide's candidate alleles below the study-wide
set — the curated per-peptide attributions of #45 — and were private with
a docstring that buried the one thing a caller most needs to know.

Renamed to peptide_alleles_for_pmid / peptide_typings_for_pmid, exported
from the package API, and documented in numpydoc form with the caveat
stated plainly rather than in passing: the lookup needs a
peptide_attributions CSV, only a handful of studies have one (PMID
31844290 is currently the only one), and every other study returns {}.
"No entry" means "not narrowed", never "no alleles".

That distinction is not academic — I read an empty result from this
function as evidence about a fix and drew the wrong conclusion from it.

Parameters renamed pmid_int -> pmid to match the public surface;
internal callers and the two tests that reached for the private names
updated.

Claude-Session: https://claude.ai/code/session_014cBpazLoFvftLSLavT7T9X

* Inline the body into the public function

The public name delegated to a one-line private wrapper that existed
only because I renamed around the old body instead of merging into it.
peptide_typings_for_pmid keeps its body inline, so the two were
inconsistent as well as pointlessly indirect.

Claude-Session: https://claude.ai/code/session_014cBpazLoFvftLSLavT7T9X

* v1.53.2: rebase on the 3.41.0 species-tree pin

Claude-Session: https://claude.ai/code/session_014cBpazLoFvftLSLavT7T9X

6134 of 7559 relevant lines covered (81.15%)

0.81 hits per line

Coverage Regressions

Lines Coverage ∆ File
8
93.21
 0.14% curation.py
Jobs
ID Job ID Ran Files Coverage
1 33447303008.1 30
81.15
 GitHub Action Run
Source Files on build 33447303008