pirl-unc / hitlist / 33586433548
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coverage: 81.118%. Remained the same
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v1.55.2: make DEFAULT_FLANK actually decide the stored flank width (#401)

#398 introduced DEFAULT_FLANK = 15 and wired it into
`ProteomeIndex.map_peptides`, and every docstring and the PR body said flanks
were now 15 residues. They were not. `build_peptide_mappings` -- the function
that writes peptide_mappings.parquet -- kept its own hardcoded
`flank: int = 10`, and `builder.py` calls it without passing the argument, so
the signature default that actually governed the artifact was the one nobody
updated.

Caught by measuring the rebuilt parquet rather than trusting the change:
23,513,320 of the stored n_flanks were exactly 10 residues, max 10.

The constant existed and looked authoritative, which is precisely why nothing
noticed a second literal sitting behind it. So the fix is not only to point
`build_peptide_mappings` at DEFAULT_FLANK but to make a competing literal fail
the suite: three tests assert that both entry points' defaults resolve to the
constant, and that no module in the package hardcodes a numeric flank default
at all. The last one is verified non-vacuous -- it matches `flank: int = 10`
and `flank=10` while ignoring `flank: int = DEFAULT_FLANK` and
`seq[pos - flank : pos]`.

Also drops a stale `flank=5` from a module docstring example, which advertised
a third width that was never the default.

peptide_mappings.parquet needs rebuilding again for the flanks to widen; the
class II coverage from #398 is already in the current artifact and unaffected.

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

6139 of 7568 relevant lines covered (81.12%)

0.81 hits per line

Jobs
ID Job ID Ran Files Coverage
1 33586433548.1 30
81.12
 GitHub Action Run
Source Files on build 33586433548