cibuildwheel.yml

name: Build Wheels

on: [push, pull_request]

jobs:
  build_wheels:
    name: Build wheels on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        # macos-13 is an intel runner, macos-14 is apple silicon
        os: [ubuntu-20.04, windows-2019, macos-13, macos-14]
    env:
      # Seems to have trouble parsing our setup.py, thus:
      CIBW_PROJECT_REQUIRES_PYTHON: ">=3.9"
      # Install numpy with a wheel (do NOT compile it):
      CIBW_BEFORE_BUILD: "pip install --only-binary :all: -r requirements.txt"
      # There are/were no numpy wheels for these:
      CIBW_SKIP: pp37-* pp38-* pp39-* pp310-* cp39-manylinux_i686 cp310-manylinux_i686 cp311-manylinux_i686 cp312-manylinux_i686 *-musllinux_*
      # configure cibuildwheel to build native arch & aarch64 too
      CIBW_ARCHS_LINUX: auto aarch64
      # Quick test with C code using NumPy C API:
      CIBW_TEST_COMMAND: "python {package}/Tests/test_Cluster.py"

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0  # Optional
          submodules: true  # Optional, use if you have submodules

      - name: Set up QEMU
        if: runner.os == 'Linux'
        uses: docker/setup-qemu-action@v3
        with:
          platforms: all

      - name: Checkout tag/commit
        run: |
          git submodule update --init biopython
          cd biopython
          # Use commit hash if tag is still pending:
          # This is some commits after Biopython 1.84 but before 1.85, to test a CPython 3.13 fix:
          git checkout 22ebf951e736bd44f04e3552a4a39723ccb3c219
          cd ..

      - name: Build wheels
        uses: pypa/cibuildwheel@v2.20.0
        with:
          package-dir: biopython
          output-dir: wheelhouse

      - uses: actions/upload-artifact@v4
        with:
          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
          path: ./wheelhouse/*.whl