4 Commits

Include renames

Author	SHA1	Message	Date
kemal	7cffb67e18	Guard against committed credentials: ignore secret files, secret scan in CI	2026-09-30 08:37:18 +01:00
kemal	97cb24ebb5	CI: fix the Install step (setup-uv already creates .venv) and make sure a C linker exists for the Rust build	2026-09-30 08:29:58 +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
kemal	368c97b9aa	P0: project setup (packaging, CI, licences, data/oracle scripts) ... - pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE, THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf) - CI workflow for Gitea/GitHub Actions: lint, type check, unit tests - fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36" bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug - make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs - plan §17: corrected P0 dataset table	2026-09-27 16:56:39 +01:00