Migrate the GVL core to Rust (Phases 0–5): numba-free, byte-identical, cargo-standalone#262

Merged

d-laub merged 213 commits into

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Jun 27, 2026

Commits on Jun 24, 2026

docs(spec): Phase 2 rust migration — genotype assembly + variant gather design

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docs(plan): Phase 2 rust migration implementation plan

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test(parity): tuple-aware kernel parity helper for Phase 2 kernels

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perf(genotypes): port get_diffs_sparse numba->rust (parity-gated)

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perf(genotypes): port choose_exonic_variants numba->rust (parity-gated)

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refactor(genotypes): delete dead filter_af kernel + its dead test (superseded by inline numpy)

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perf(variants): port _gather_v_idxs(+_ss) numba->rust as gather_rows (parity)

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perf(variants): port _gather_alleles numba->rust (parity-gated)

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fix(variants): gather_rows must preserve data dtype (dosage/custom fields)

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perf(variants): port _compact_keep numba->rust (i32/f32, dtype-preserving)

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perf(variants): port _fill_empty_scalar + _fill_empty_fixed numba->rust (dtype-preserving)

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perf(variants): port _fill_empty_seq numba->rust (u8/i32, dtype-preserving)

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test(parity): variants-mode dataset backstop (spy-guarded, byte-identical)

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fix(test): update stale _gather_v_idxs_ss import after Task 5 rename; lint/docstring cleanup

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docs(roadmap): Phase 2 parity-verified; switch to persistent rust-migration branch

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test(parity): narrow AF-backstop except to KeyError (fail loudly on real errors)

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docs(spec): Phase 3 reconstruction + track realignment design

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docs(plan): Phase 3 reconstruction + track realignment implementation plan

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perf(reference): port padded_slice numba->rust core (cargo-tested)
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perf(reference): port get_reference numba->rust (parity, default rust)

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fix(reference): revert padded_slice leniency — mirror numba's loud failure for start>=clen (parity twin)

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test(parity): reference-mode + spliced dataset backstop (spy-guarded)

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test(parity): add rust-spy-wiring guard + silence no-op with_tracks warning (review fixes)

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perf(reconstruct): port reconstruct_haplotype_from_sparse core (cargo-tested)

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test(reconstruct): cover allele_start_idx==v_len, skip-variant, and keep-mask branches
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perf(reconstruct): port reconstruct_haplotypes_from_sparse batch (parity, default rust)

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fix(reconstruct): clamp writable_ref when ref_idx past contig end; skip numba annotated flake

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fix(reconstruct): strengthen SAFETY comments; rename batch test to match serial-only impl

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fix(reconstruct): guard non-annotated parity test against numba SystemError; correct rayon-deferral comment

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test(parity): haplotypes + annotated-haps dataset backstop (spy-guarded)

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perf(tracks): port xorshift64/hash4 PRNG (direct numba parity)

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perf(tracks): port apply_insertion_fill (4 strategies) core (cargo-tested)

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docs(tracks): correct REPEAT_5P_NORM precision comment (numba divides in f64; f32-direct safe only for division)
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perf(tracks): port shift_and_realign_tracks_sparse (parity, default rust)

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fix(tracks): clamp writable_ref when deletion extends past track end

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test(tracks): raise shift_and_realign parity to 500 examples (harden Interpolate/FlankSample float paths in CI)
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perf(intervals): port tracks_to_intervals RLE numba->rust (parity, default rust)

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Commits on Jun 25, 2026

Commits on Jun 26, 2026

Commits on Jun 27, 2026