pysam/.github/workflows/ci.yaml at d7315358ab2a1cee2c5c3db6eca757197aeb3060 · pysam-developers/pysam · GitHub

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name: CI

on: [push, pull_request]

jobs:
  direct:
    runs-on: ${{ matrix.os }}-latest
    strategy:
      matrix:
        os: [ubuntu, macos]
        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13', '3.14']
        exclude:
          # Avoid spurious "upgrade pip" error annotation
          - os: macos
            python-version: 3.8

    steps:
      - name: Checkout pysam
        uses: actions/checkout@v6

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install prerequisite Python libraries
        run:  pip install Cython mypy pytest setuptools

      - name: Install Linux build prerequisites
        if:   runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -q --no-install-recommends --no-install-suggests libbz2-dev libcurl4-openssl-dev liblzma-dev

      - name: Update macOS build prerequisites
        if:   runner.os == 'macOS'
        run: |
          brew unlink xz || true  # Remove brewed liblzma as it is not multiarch

      - name: Build (directly from checkout)
        run:  python setup.py build

      - name: Install test prerequisites
        run: |
          case $RUNNER_OS in
          Linux)
              sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix
              ;;
          macOS)
              brew install -q samtools bcftools
              ;;
          esac

      - name: Run tests
        run: |
          export PYTHONPATH=$(echo $GITHUB_WORKSPACE/build/lib.*)
          export REF_PATH=':'
          pytest


  system:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        include:
          - os: freebsd
            version: "15.0"
            python-version: "3.11"

          - os: netbsd
            version: "10.1"
            python-version: "3.14"

    steps:
      - name: Checkout pysam
        uses: actions/checkout@v6

      - name: Build and test on ${{ matrix.os }}
        uses: cross-platform-actions/action@v1
        env:
          MAKE: "gmake"
          PYSAM_FIX_CFLAGS: "1"
          python: "python${{ matrix.python-version }}"
          pytest: "pytest-${{ matrix.python-version }}"
        with:
          operating_system: ${{ matrix.os }}
          version: ${{ matrix.version }}
          environment_variables: MAKE PYSAM_FIX_CFLAGS python pytest
          run: |
            sudo devtools/install-prerequisites.sh $PWD/devtools/emulate-tools.py /usr/local/bin
            $python setup.py build
            PYTHONPATH="$(echo $PWD/build/lib.*)" REF_PATH=":" $pytest


  sdist:
    runs-on: ${{ matrix.os }}-latest
    strategy:
      matrix:
        os: [ubuntu, macos]
        python-version: ['3.14']

    steps:
      - name: Checkout pysam
        uses: actions/checkout@v6

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v6
        with:
          python-version: ${{ matrix.python-version }}

      - name: Install prerequisite Python libraries
        run:  pip install Cython mypy pytest setuptools

      - name: Install build prerequisites
        if:   runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -q --no-install-recommends --no-install-suggests libbz2-dev libcurl4-openssl-dev liblzma-dev

      - name: Create source distribution
        run:  python setup.py sdist --owner=root --group=root

      - name: Build (via sdist tarball)
        run:  pip install --verbose --no-deps --no-binary=':all:' pysam-*.tar.gz
        working-directory: dist

      - name: Install test prerequisites
        run: |
          case $RUNNER_OS in
          Linux)
              sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix
              ;;
          macOS)
              brew install -q samtools bcftools
              ;;
          esac

      - name: Run tests
        run:  REF_PATH=':' pytest

      - name: Upload sdist tarball
        if:   runner.os == 'Linux'
        uses: actions/upload-artifact@v7
        with:
          name: sdist
          path: dist/pysam-*.tar.gz
          retention-days: 14


  conda:
    timeout-minutes: 20
    runs-on: ${{ matrix.os }}-latest
    strategy:
      matrix:
        os: [ubuntu]
        python-version: ['3.13']
    defaults:
      run:
        shell: bash -el {0}  # needed for conda activation
    env:
      HTSLIB_CONFIGURE_OPTIONS: "--disable-libcurl"

    steps:
      - name: Checkout pysam
        uses: actions/checkout@v6

      - name: Set up Conda and Python ${{ matrix.python-version }}
        uses: conda-incubator/setup-miniconda@v3
        with:
          channels: conda-forge,bioconda
          channel-priority: strict
          conda-remove-defaults: true
          python-version: ${{ matrix.python-version }}
          environment-file: devtools/environment-dev.yaml

      - name: Build (directly from checkout)
        run:  python setup.py install

      - name: Install test prerequisites via Conda
        run:  conda install "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11" pytest

      - name: Run tests
        run:  REF_PATH=':' pytest