test.yml

name: Test

on:
  - push
  - pull_request

jobs:

  test_linux_x86:
    name: Test (Linux)
    runs-on: ubuntu-latest
    env:
      OS: Linux
    strategy:
      matrix:
        include:
        - python-version: 3.7
          python-release: v3.7
          python-impl: CPython
        - python-version: 3.8
          python-release: v3.8
          python-impl: CPython
        - python-version: 3.9
          python-release: v3.9
          python-impl: CPython
        - python-version: '3.10'
          python-release: 'v3.10'
          python-impl: CPython
        - python-version: '3.11'
          python-release: 'v3.11'
          python-impl: CPython
        - python-version: pypy-3.7
          python-release: v3.7
          python-impl: PyPy
        - python-version: pypy-3.8
          python-release: v3.8
          python-impl: PyPy
        - python-version: pypy-3.9
          python-release: v3.9
          python-impl: PyPy
    steps:
    - name: Checkout code
      uses: actions/checkout@v2
      with:
        submodules: true
    - name: Cache Python requirements
      uses: actions/cache@v2
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ matrix.python-version }}
        restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}
    - name: Cache built C files
      uses: actions/cache@v2
      with:
        path: build
        key: ${{ runner.os }}-build-${{ matrix.python-version }}
        restore-keys: ${{ runner.os }}-build-${{ matrix.python-version }}
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Show Python build environment
      run: python -m sysconfig
    - name: Update pip
      run: python -m pip install -U pip wheel setuptools
    - name: Install Python requirements
      run: python -m pip install -r .github/workflows/requirements.txt
    - name: Build C extension
      run: python setup.py build_ext --inplace --debug -j0
    - name: Install test requirements
      run: python -m pip install -r pyhmmer/tests/requirements.txt
    - name: Test with coverage
      run: python -m coverage run -m unittest discover -vv
    - name: Upload to Codecov
      if: matrix.python-impl == 'CPython'
      uses: codecov/codecov-action@v3
      with:
        flags: ${{ matrix.python-release }}
        env_vars: OS
        name: test-python-${{ matrix.python-version }}
        fail_ci_if_error: false
        token: ${{ secrets.CODECOV_TOKEN }}
        verbose: true

  test_linux_arm64:
    name: Test (Linux, arm64)
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-tag:
        - cp310-manylinux_aarch64
        - cp311-manylinux_aarch64
    steps:
    - uses: actions/checkout@v3
      with:
        submodules: true
    - name: Set up QEMU
      id: qemu
      uses: docker/setup-qemu-action@v2
      with:
        platforms: all
    - name: Build manylinux wheels
      uses: pypa/cibuildwheel@v2.11.3
      env:
        CIBW_ARCHS: aarch64
        CIBW_BUILD: ${{ matrix.python-tag }}
        CIBW_BUILD_VERBOSITY: 2
        CIBW_BEFORE_BUILD: pip install cython
        CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
        CIBW_TEST_REQUIRES: importlib-resources
      with:
        output-dir: dist
    - uses: actions/upload-artifact@v3
      with:
        name: wheels
        path: dist/*

  test_osx_x86:
    name: Test (OSX)
    runs-on: macos-latest
    env:
      OS: OSX
    strategy:
      matrix:
        include:
        - python-version: 3.7
          python-release: v3.7
          python-impl: CPython
        - python-version: 3.8
          python-release: v3.8
          python-impl: CPython
        - python-version: 3.9
          python-release: v3.9
          python-impl: CPython
        - python-version: '3.10'
          python-release: 'v3.10'
          python-impl: CPython
        - python-version: '3.11'
          python-release: 'v3.11'
          python-impl: CPython
        - python-version: pypy-3.7
          python-release: v3.7
          python-impl: PyPy
        - python-version: pypy-3.8
          python-release: v3.8
          python-impl: PyPy
        - python-version: pypy-3.9
          python-release: v3.9
          python-impl: PyPy
    steps:
    - name: Checkout code
      uses: actions/checkout@v2
      with:
        submodules: true
    - name: Cache Python requirements
      uses: actions/cache@v2
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ matrix.python-version }}
        restore-keys: ${{ runner.os }}-pip-${{ matrix.python-version }}
    - name: Cache built C files
      uses: actions/cache@v2
      with:
        path: build
        key: ${{ runner.os }}-build-${{ matrix.python-version }}
        restore-keys: ${{ runner.os }}-build-${{ matrix.python-version }}
    - name: Setup Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Show Python build environment
      run: arch -x86_64 python -m sysconfig
    - name: Update pip
      run: python -m pip install -U pip wheel setuptools
    - name: Install Python requirements
      run: python -m pip install -r .github/workflows/requirements.txt
    - name: Build C extension
      run: arch -x86_64 python setup.py build_ext --inplace --debug
    - name: Install test requirements
      run: python -m pip install -r pyhmmer/tests/requirements.txt
      if: matrix.python-impl == 'CPython'
    - name: Test with coverage
      run: python -m coverage run -m unittest discover -vv
    - name: Upload to Codecov
      uses: codecov/codecov-action@v3
      if: matrix.python-impl == 'CPython'
      with:
        flags: ${{ matrix.python-release }}
        env_vars: OS
        name: test-python-${{ matrix.python-version }}
        fail_ci_if_error: false
        token: ${{ secrets.CODECOV_TOKEN }}
        codecov_curl_args: "--globoff"
        verbose: true