openvax / topiary / 34915990000-1

93%

master: 93%

Build Type

Pull #319

github

Committed by iskandr

Commit Message

Rename the ranking allele validator apart from the mhcgnomes normalizers

Three functions were called _normalize_alleles, doing two different
jobs. Two canonicalize allele names through mhcgnomes as a reader builds
a frame (io_pvacseq, io_lens). The third validates the *shape* of a
declared allele set - None, callable, Mapping or non-empty sequence with
no blank entries - and returns the names exactly as the caller spelled
them.

Verified it transforms no strings: ['HLA-A2', 'hla-a*02:01',
'HLA-A*02:01'] comes back unchanged.

That one is now _validate_declared_alleles, with a docstring saying why
it is deliberately not mhcgnomes normalization: declared alleles are
matched against whatever spelling the frame already carries, so
canonicalizing one side only would stop equal alleles comparing equal.
The shared name invited exactly the opposite conclusion - that this was
a site where the mhcnames-to-mhcgnomes migration had been missed.

Claude-Session: https://claude.ai/code/session_015pMD1uiTztbB2bTQ1FkY8m

Pull Request Pull Request #319: Make declared dependencies and exported surface match the code (#314, #315)

Coverage Stats

9 of 10 new or added lines in 5 files covered. (90.0%)

115 existing lines in 3 files now uncovered.

7118 of 7715 relevant lines covered (92.26%)

0.92 hits per line