kemal
b0494be576
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).
32 lines
1.0 KiB
YAML
32 lines
1.0 KiB
YAML
# Runs on Gitea Actions (reads .github/workflows) and GitHub Actions.
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name: ci
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on:
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push:
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pull_request:
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jobs:
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test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python: ["3.12", "3.13"]
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steps:
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- uses: actions/checkout@v4
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- uses: astral-sh/setup-uv@v5
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with:
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python-version: ${{ matrix.python }}
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- name: Install
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run: uv venv && uv pip install -e ".[dev]"
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- name: Lint
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run: uv run ruff check src tests && uv run ruff format --check src tests
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- name: Type check
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run: uv run mypy
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- name: Unit tests (no downloaded data needed)
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run: uv run pytest tests/unit -q
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- name: Build the compiled kernels (rust/simurg-core)
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run: |
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curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y --profile minimal
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PATH="$HOME/.cargo/bin:$PATH" uv pip install ./rust/simurg-core
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- name: Unit tests with the compiled kernels (must equal the pure-Python results)
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run: uv run pytest tests/unit -q
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