test_cpac.yml

# This workflows will upload a Python Package using Twine when a release is created
# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries

name: Test cpac

on:
  push:
    paths-ignore:
    - README.rst
  pull_request:

jobs:
  test_cpac:

    runs-on: ubuntu-latest
    env:
      SINGULARITY_CACHEDIR: $GITHUB_WORKSPACE/.singularity/cache
      SINGULARITY_TMPDIR: $GITHUB_WORKSPACE/.singularity/tmp

    strategy:
      max-parallel: 1  # This'll slow it down but increase stability
      matrix:
        platform: [docker]
        tag: [nightly] # latest
        go: [1.14]
        python: [3.7, 3.8, 3.9, "3.10", 3.11]
        singularity: [3.6.4]

    steps:
    - name: Maximize space
      uses: easimon/maximize-build-space@v8
      with:
        remove-dotnet: 'true'
        remove-android: 'true'
        remove-haskell: 'true'
        remove-docker-images: 'false'
    - uses: actions/checkout@v3
    - name: Set up Go
      uses: actions/setup-go@v4
      with:
        go-version: ${{ matrix.go }}
    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python }}
    - name: Install --upgrade pip setuptools wheel
      run: python -m pip install --upgrade pip setuptools wheel
    - name: Set up Singularity
      if: ${{ matrix.platform == 'singularity' }}
      uses: eWaterCycle/setup-singularity@v7
      with:
        singularity-version: ${{ matrix.singularity }}
    - name: Prepare Singularity cache and tmp directories
      if: ${{ matrix.platform == 'singularity' }}
      run: mkdir -p ${SINGULARITY_CACHEDIR} && mkdir -p ${SINGULARITY_TMPDIR}
    - name: Install dependencies
      run: |
        sudo apt-get install libffi-dev \
                             flawfinder \
                             libgpgme11-dev \
                             libseccomp-dev \
                             squashfs-tools \
                             libssl1.1 libssl-dev \
                             libuuid1 uuid-dev
        pip install -r requirements.txt
        pip install -r requirements-dev.txt
        pip install coverage coveralls nipype
    - name: Install cpac
      run: cd $GITHUB_WORKSPACE && pip install -e .
    - name: Test cpac, platform and tag specified
      run: |
        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} --tag ${{ matrix.tag }} .
        coverage report -m
    - name: Test cpac, platform specified, tag unspecified
      if: ${{ matrix.tag == 'latest' }}
      run: |
        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --platform ${{ matrix.platform }} .
        coverage report -m
    - name: Test cpac, platform unspecified, tag specified
      if: ${{ matrix.platform == 'docker' }}
      run: |
        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules --tag ${{ matrix.tag }} .
        coverage report -m
    - name: Test cpac, platform and tag unspecified
      if: ${{ matrix.platform == 'docker' }} && ${{ matrix.tag }} == 'latest'
      run: |
        coverage run --append -m pytest --basetemp=${PWD}/tmp --doctest-modules .
        coverage report -m
    - name: Report coverage
      uses: AndreMiras/coveralls-python-action@v20201129
      with:
        parallel: True
        flag-name: Test cpac ${{ matrix.platform }} with Python ${{ matrix.python }}
      continue-on-error: true
  finalize_coverage-report:
    needs: 
      - test_cpac
    runs-on: ubuntu-latest
    steps:
    - name: Finalize coverage report
      uses: AndreMiras/coveralls-python-action@v20201129
      with:
        parallel-finished: true
      continue-on-error: true
  update_README:
    # Only update README if tests succeed
    needs:
      - test_cpac
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 0
    - name: Install cpac
      run: |
        export DEB_PYTHON_INSTALL_LAYOUT=deb_system
        cd $GITHUB_WORKSPACE
        pip install .
    - name: Configure Git credentials
      uses: oleksiyrudenko/gha-git-credentials@v2.1
      with:
        global: true
        token: ${{ secrets.GITHUB_TOKEN }}
    - name: Update README
      run: |
        (head -n $(read -d : <<< $(less README.rst | grep ".. BEGIN USAGE" -n); expr $REPLY + 1) README.rst; \
        printf ".. code-block:: shell\n\n    cpac --help\n"; \
        cpac --help | sed 's/^/    /'; \
        tail --lines=+$(read -d : <<< $(less README.rst | grep ".. END USAGE" -n); expr $REPLY - 1) README.rst\
        ) > tempREADME &&
        mv tempREADME README.rst &
        wait %1
        if [[ $(git diff --numstat README.rst) ]]; then
            git add README.rst
            git commit -m ":memo: Update usage from helpstring"
            git push origin HEAD:${GITHUB_REF}
        fi
      shell: bash