Preserve complete gene-query results in exports - #431
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Coverage Report for CI Build 34115961327Coverage increased (+0.2%) to 83.258%Details
Uncovered ChangesNo uncovered changes found. Coverage Regressions110 previously-covered lines in 2 files lost coverage.
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An export such as
gene=["PRAME", "ENSG00000198681"]could drop both genes because names and IDs were intersected. MS, binding, and training exports now select the union of the gene alternatives and preserve it through source-protein expansion. Mappings matching both identifiers are deduplicated; unrelated genes sharing a peptide remain excluded. Explicit peptide filters narrow the union, and the low-level loaders retain their existing column-filter conjunctions.Empty gene matches also exposed an untyped empty peptide predicate that raised a PyArrow type error. Peptide filters now carry a string-typed value set, so empty queries return zero rows. Version: 1.58.2.
Validation: format and lint pass;
./test.shpasses 1,232 tests; targeted export/loader tests pass 201 tests. New cases cover mixed/duplicate/unknown identifiers, compact and expanded training for all evidence modes, shared peptides, large mapping selections, and empty intersections.Closes #425.
Closes #430.