ci.yml

name: CI
on:
  push:
    branches: [main, "perf/**"]
  pull_request:

jobs:
  test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: ["3.11"]
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install
        run: |
          pip install numpy==2.4.6 Cython==3.2.5 pytest==9.1.1 pydivsufsort==0.0.20
      - name: Build native extensions
        run: |
          python -c "
          from setuptools import setup, Extension
          from Cython.Build import cythonize
          import numpy as np
          ext=[Extension('bwtandem._accelerators',['bwtandem/_accelerators.pyx'],include_dirs=[np.get_include()])]
          setup(script_args=['build_ext','--inplace'], ext_modules=cythonize(ext, compiler_directives={'language_level':'3'}))
          "
          python bwtandem/c_extensions/build.py
      - name: Deposited-evidence hashes verify
        # a results/ file edited after hashing shipped once (e178707):
        # every clone must be able to verify the deposit as advertised
        run: sha256sum -c results/manifest.sha256 --quiet
      - name: Test (native)
        run: python -m pytest tests/ -q
      - name: Test (pure-Python fallback parity)
        run: BWT_DISABLE_NATIVE=1 python -m pytest tests/test_accel_parity.py tests/test_ambiguous_native_paths.py -q
      - name: CLI smoke
        run: |
          python -m bwtandem.main arabadopsis_chrs/test_seq1.fa --tiers tier1 --format bed -o /tmp/smoke -v
          test -s /tmp/smoke.bed

  install:
    # The in-place build above cannot detect a wheel that ships without the
    # native extension (that exact defect shipped as a py3-none-any wheel).
    # This job installs the wheel into a clean environment, runs the declared
    # entry point from outside the checkout, and asserts the accelerator
    # actually loaded from the installed package as a compiled extension.
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-python@v5
        with:
          python-version: "3.11"
      - name: Build and install wheel
        run: |
          pip install build
          python -m build --wheel
          pip install dist/*.whl numpy==2.4.6 pydivsufsort==0.0.20
      - name: Entry point + native import from outside the checkout
        run: |
          FIXTURE=$PWD/arabadopsis_chrs/test_seq1.fa
          cd /tmp
          bwtandem --help
          python -c "
          import bwtandem._accelerators as a
          assert a.__file__.endswith(('.so', '.pyd')), a.__file__
          assert 'site-packages' in a.__file__, a.__file__
          # the ctypes C sources must ship in the wheel: build.py compiles
          # them at first import, and without them the fast C paths silently
          # fall back to Python (that exact defect shipped once)
          import glob, os
          import bwtandem.c_extensions.build as b
          cs = glob.glob(os.path.join(os.path.dirname(b.__file__), '*.c'))
          assert len(cs) == 4, cs
          "
          bwtandem "$FIXTURE" --tiers tier1 --format bed -o /tmp/inst_smoke
          test -s /tmp/inst_smoke.bed