pirl-unc / hitlist / 27321728378
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Files 29
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coverage: 79.788% (-0.1%) from 79.898%
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v1.40.1: ship packaged ENSG→symbol map; fill 98% of blank gene_names offline (#336)

* v1.40.1: ship packaged ENSG→symbol map; fill 98% of blank gene_names offline

The line_expression gene_name fill previously relied entirely on a live
pyensembl lookup, which needs release data installed (`pyensembl install
--release 112`) and only resolved ~85% of the blank ENSG IDs. Pre-resolve
the full set offline (Ensembl 75 → 112 → 90, mygene.info for the tail) and
ship the result as a packaged CSV so the build fills 9,127/9,287 (98%) of
the blanks with no release data required.

- hitlist/data/line_expression/ensembl_gene_id_symbol.csv: 9,127-row
  gene_id → HGNC symbol map (160 IDs remain truly unmappable: retired
  ENSG IDs with no current symbol in any release or mygene).
- _fill_gene_names_from_csv(): primary, portable fill source.
  _fill_gene_names_via_ensembl() now a fallback for IDs absent from the
  CSV (e.g. future additions).
- pyproject.toml: ship data/line_expression/*.csv in the wheel.
- tests: CSV fill + packaged-map well-formedness.

* fix: stub is_built() in species-filter test so it passes without a built corpus

test_pmhc_forwards_source_and_host_species_filters monkeypatched
load_observations but not the is_built() guard query() runs first, so it
only passed where observations.parquet already existed on disk. CI builds
the corpus on a single Python version (.github/workflows/tests.yml), so the
test had been failing on 3.9/3.10/3.12 since #329 — the sole red check on
main. Stub is_built() too.

5570 of 6981 relevant lines covered (79.79%)

0.8 hits per line

Coverage Regressions

Lines Coverage ∆ File
121
51.08
 -0.01% cli.py
115
76.26
 -0.77% builder.py
107
62.02
 0.35% downloads.py
51
91.03
 -0.12% pmhc_query.py
40
79.17
 -0.18% scanner.py
32
84.22
 0.04% export.py
Jobs
ID Job ID Ran Files Coverage
1 27321728378.1 29
79.79
 GitHub Action Run
Source Files on build 27321728378