kemal
6524a6d1b0
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).
25 lines
818 B
Python
25 lines
818 B
Python
"""Optional compiled kernels (``rust/simurg-core``, plan §18 P9).
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``core`` is the ``simurg_core`` extension module when it is installed, else ``None``; every caller keeps a pure
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Python/NumPy path with bit-identical results. ``SIMURG_PURE_PYTHON=1`` forces the pure paths (tests, debugging).
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"""
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from __future__ import annotations
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import os
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from types import ModuleType
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core: ModuleType | None
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if os.environ.get("SIMURG_PURE_PYTHON", "") not in ("", "0"):
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core = None
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else:
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try:
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import simurg_core as core # type: ignore[no-redef]
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except ImportError: # pragma: no cover - depends on the installation
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core = None
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def backend() -> str:
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"""``"rust <version>"`` or ``"python"`` (recorded in run manifests)."""
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return f"rust {core.__version__}" if core is not None else "python"
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