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mcvickerlab / GenVarLoader Public

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test: coverage initiative — kernels, readers, with_* API#195

Merged

d-laub merged 56 commits into

mainmcvickerlab/GenVarLoader:mainfrom

worktree-test-coverage-initiativemcvickerlab/GenVarLoader:worktree-test-coverage-initiativeCopy head branch name to clipboard

May 27, 2026

Conversation Commits56 (56)Checks Files changed

Merged

test: coverage initiative — kernels, readers, with_* API#195
d-laub merged 56 commits into
mainfrom
worktree-test-coverage-initiative

Commits

Commits on May 25, 2026

docs(spec): test coverage initiative
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docs(plan): test coverage implementation plan
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test(kernels): extend reconstruct_haplotype case matrix
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test(kernels): add get_diffs_sparse behavior tests
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test(kernels): add filter_af coverage across input layouts
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test(kernels): fill choose_exonic_variants scenario gaps
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test(kernels): add intervals_to_tracks behavior tests
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test(fasta): cover missing contig, protocol attrs, zero-length
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test(bigwig): cover read smoke path, protocol attrs, missing file
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test(bigwig): tighten missing-path raises to RuntimeError
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test(torch): cover get_dataloader/get_sampler smoke paths
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test(torch): drop unused numpy import
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test(torch): re-add numpy import before torch (ABI workaround)
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test(dataset): cover with_* method matrix

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test(open): cover error paths on Dataset.open

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test(indexing): cover negative, oob, boolean-mask, empty selections

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chore(cov): exclude numba modules from coverage gate

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docs(cov): regenerate baseline with full test data accessible
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test(torch): noqa E402 for imports after importorskip
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style: ruff format pass
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Commits on May 26, 2026

fix: inline offset computation in filter_af 2-D path; reorder test_torch imports
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docs(spec): test coverage deeper initiative
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docs(plan): test coverage deeper implementation plan
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test(parity): oracle parity for annotated and reference output modes
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test(parity): cross-mode equivalence (VCF/PGEN/SVAR, Ragged/Array, name/int)
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test(kernels): cross-check fast/slow paths and 1d/2d layouts agree
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test(determinism): same seed/jitter -> identical output; seeded dataloader reproducible
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test(determinism): xfail capture for with_settings(rng=...) bug
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test(query): cover filter combinations and empty-result behavior
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test(ragged): cover public utilities in _ragged
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test(ragged): xfail capture for to_padded numeric branch bug
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test(sitesonly): fill INFO-field and empty-region gaps
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test(dataset-utils): cover public helpers in _dataset/_utils
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test(torch): cover return_indices and transform paths
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test(filter_af): pin down NaN handling contract
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test(shapes): single-region, single-sample, empty subset
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test(write): round-trip on empty BED, overlapping regions, missing contig
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style(tests): remove unused polars import in test_dataset_utils

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claude
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docs(cov): new baseline after deeper coverage initiative
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style(tests): ruff format

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fix(dataset): with_settings(rng=...) maps to _rng dataclass field
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fix(torch): forward generator from DataLoader through to RandomSampler for reproducible shuffle
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fix(ragged): to_padded numeric branch handles clip=True RegularArray output
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fix(sitesonly): use correct genoray VCF.get_record_info kwargs (fields= not attrs=)
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test(boundary): contig-end region pads with N on read
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test(boundary): spanning deletion at region/contig boundary
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docs(cov): rebaseline after bug fixes and boundary tests
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style: ruff format pass
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test(with-methods): self-build tracks-enabled dataset; don't rely on data-gen tracks
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style: ruff format pass
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test(with-methods): use bigwig-backed tracks fixture to avoid polars_bio state issue
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Commits on May 27, 2026

test(tracks): skip polars-bio Table tests on py3.12 to avoid segfault

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claude
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docs(spec): CI hg38 reference cache design
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docs(plan): CI hg38 reference cache implementation plan
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ci: cache hg38 reference to skip repeated 1GB download
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docs: note CI cache key must be bumped if hg38 reference changes
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committed

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