openvax / topiary / 24489771087

88%

master: 90%

Build Type

Pull #138

github

Committed by iskandr

Commit Message

Rename scope= → include= + add scope='protected_tissues'

Renames the public API parameter from `scope=` (abstract jargon) to
`include=` (reads naturally at the call site):

  SelfProteome.from_ensembl(include="non_cta")
  SelfProteome.from_ensembl(include="protected_tissues")
  SelfProteome.from_ensembl(include="all")
  SelfProteome.from_ensembl(include=lambda gene_id: ...)

Adds include="protected_tissues" — filters the reference proteome to
genes expressed in named tissues.  Multi-species safe:

- Human default: pirlygenes/HPA expression data, curated vital-organ
  tissue list (heart, lung, liver, kidney, cerebral cortex).
- Any species with explicit data: tissue_gene_ids={gene_ids} bypasses
  pirlygenes entirely.
- Non-human without tissue_gene_ids: raises ValueError with actionable
  message directing users to supply their own data.

4 new tests + all existing tests updated for the parameter rename.
29 self_proteome tests pass, lint clean.

Pull Request Pull Request #138: SelfProteome scope="protected_tissues" — multi-species (part B of #124)

Coverage Stats

29 of 30 new or added lines in 1 file covered. (96.67%)

12 existing lines in 1 file now uncovered.

3618 of 4100 relevant lines covered (88.24%)

2.65 hits per line