Replace the two _sliced_fields methods with one slice_fields helper - #314
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HaplotypeMatrix and GenotypeMatrix each carried an identical _sliced_fields method that read self.fields and self._accessible_idx and switched on a 'view' | 'underlying' string. One module-level slice_fields in accessible.py takes the accessible index explicitly instead: view callers pass self._accessible_idx, filter() passes nothing because its index already addresses the underlying array. Closes #313
nspope
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Sep 23, 2026
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Looks good, much tidier.
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Closes #313.
HaplotypeMatrix._sliced_fieldsandGenotypeMatrix._sliced_fieldswere the same function line for line. Both readself.fieldsandself._accessible_idx, and both switched on aspace='view' | 'underlying'string to decide whether to compose through the accessible index.This replaces them with one module-level
slice_fields(fields, keep_idx, accessible_idx=None)inpg_gpu/accessible.py. The accessible index is passed explicitly: view callers hand inself._accessible_idx, and the twofilter()callers pass nothing because their index already addresses the underlying array. Both matrix modules already import fromaccessible.py, so no new import edge.All eight call sites are updated and both methods are deleted.
grep -rn "_sliced_fields\|space=" pg_gpu/returns nothing.No new tests. The masked-field tests from #307 cover every call site:
tests/test_haplotype_matrix.py::test_variant_subset_methods_preserve_fields_under_accessible_masktests/test_haplotype_matrix.py::test_exclude_missing_sites_preserves_fields_under_accessible_masktests/test_genotype_matrix_coverage.py::TestFieldsUnderAccessibleMasktests/test_qc_fields.py::TestHaplotypeMatrixFilterFull non-slow suite passes locally on an A100 (1816 passed, 80 skipped, 19 xfailed). Ruff is clean.