kemalandClaude Opus 5.5
5bdd41b048
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
15 lines
370 B
TOML
15 lines
370 B
TOML
[build-system]
|
|
requires = ["maturin>=1.7,<2"]
|
|
build-backend = "maturin"
|
|
|
|
[project]
|
|
name = "simurg-core"
|
|
description = "Compiled kernels for SimurgArray (optional; the pure-Python paths give identical results)"
|
|
requires-python = ">=3.12"
|
|
license = { text = "MIT" }
|
|
dependencies = ["numpy>=1.26"]
|
|
dynamic = ["version"]
|
|
|
|
[tool.maturin]
|
|
features = ["pyo3/extension-module"]
|