4 Commits

Include renames

Author	SHA1	Message	Date
kemal	da61c7b9fd	Prepare for public release on Gitea: simurgarray package names, community files, Gitea templates, pseudonymised P6 probe names	2026-09-30 12:09:13 +01:00
kemal	7f3cd96fc4	Release 1.1.0: compiled kernels (P9) and packaging (P10)	2026-09-28 23:56:39 +01:00
kemal	1f2abcbdba	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.	2026-09-28 22:41:56 +01:00
kemal	b0494be576	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).	2026-09-28 21:28:55 +01:00