Preserve species-filter parity across evidence exports - #435
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Coverage Report for CI Build 34152991955Coverage increased (+0.2%) to 83.456%Details
Uncovered ChangesNo uncovered changes found. Coverage Regressions205 previously-covered lines in 3 files lost coverage.
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Evidence exports could not select source or host species or exclude chimeric systems, although their raw loaders supported those filters. MS (including the compatibility wrapper), binding, training, peptide summaries, and all corresponding CLI commands now forward the three independent filters. Existing positional arguments and default evidence selection are preserved.
The parity regressions also exposed #434: system flags ignored the raw source-species fallback used by source filtering. A shared coalescing helper now supplies the existing classifiers in loaders and exports, retaining primary-source precedence and the raw annotations.
Validation: 109 new regressions cover exact evidence identities, independent/combined axes, aliases, lists, empty results, projections, summaries, CLI, and fallback classification. The targeted suite passes 162 tests; format and lint pass;
./test.shpasses 1,389 tests with one expected warning. A streaming audit of all 4,439,643 MS and 891,885 binding rows found zero chimeric-classification changes in the current corpus. Version: 1.58.5.Closes #386. Closes #434.