2 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	92416397fe	P10 (WIP): release build script, Dockerfile, conda recipes, fresh-VM acceptance task ... scripts/build_dist.sh: sdist + pure wheel + manylinux_2_28 kernel wheels (maturin --zig, both architectures). Dockerfile (multi-stage, kernels included, non-root user). packaging/conda/{simurg,simurg-core}. scripts/p10/digest.py: platform-independent content digests of GTC/VCF/summary outputs. Cloud task p10 installs the artifacts on a fresh Ubuntu VM and runs the tutorial with pip, Docker and conda installs. trial.sh picks the arm64/amd64 image from the instance type and can run instances in parallel (PARALLEL=1). Licence files ship in both wheels; Rust crate notices added. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 22:41:56 +01:00
kemalandClaude Opus 5.5	5bdd41b048	P9 (WIP): compiled kernels (rust/simurg-core, PyO3) with bit-identical pure-Python fallback ... Rust ports of the hot paths found by profiling: fused per-locus GenCall calling and scoring, BAF/LRR, libm maps with CPython math semantics, both nearest-neighbour searches of the normalization fit, and the BPM LocusEntry parser. Address coverage is memoised per IDAT layout. SIMURG_PURE_PYTHON=1 forces the pure paths. On the Pi: genotype_sample 3.4 s -> 1.1 s, 36-sample GSA run 131 s -> 46 s, BPM read 4x faster; 36 GSA + 6 Omni2.5 GTCs and QC tables byte-identical to the pure path; tests/unit/test_core_kernels.py checks every kernel on edge cases. bench/profile_genotype.py, bench/scaling.py, cloud task p9 (thread scaling). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 21:28:55 +01:00