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@michael-denyer michael-denyer released this 29 Sep 10:57
6139a3a

Added

  • tests/lmm_accel/test_bgen_decode_properties.py is a Hypothesis property
    test for the C BGEN layout-2 decoder. It generates truncated, padded,
    garbage and zlib-mislabelled blocks, and blocks with one header field just
    out of range, and requires the decoder to reject exactly what the NumPy
    oracle rejects and to match it bit for bit on everything else.

Changed

  • GEMMA_EQUIVALENCE.md and assumption 7 of
    GEMMA_NUMERICAL_EQUIVALENCE_BOUND.md name the jamma-lean theorems behind
    their p-value claims. GEMMA_DIVERGENCES.md §6 counts the SNPs whose lambda
    error exceeds lambda_rtol: 3 NumPy and 2 native, all at n = 30 to 100.

  • Dependency and CI-action bumps (Dependabot): google/osv-scanner-action
    2.5.1 → 2.6.0, docker/build-push-action 7.3.0 → 7.4.0,
    docker/setup-qemu-action 4.3.0 → 4.4.0, docker/setup-buildx-action
    4.3.0 → 4.4.1, build backend hatchling 1.32.0 → 1.32.3, dev dependency
    pyrefly 1.3.0 → 1.3.1, and the container's threadpoolctl 3.6.0 → 3.7.0.
    No source or numerical-result change.

Fixed

  • The BGEN decoder property test now catches a dropped B >= 1 check. It set
    the bit depth to 0 but kept the data bytes, so the size check rejected the
    block first and a decoder without the check still passed.