lint_test.yml

name: Lint and test
on: ["push", "pull_request"]
jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - uses: actions/setup-python@v1
      with:
        python-version: 3.7
    - name: Install flake8
      run: pip install flake8 flake8-import-order
    - name: Flake8
      run: flake8 biomaj2galaxy test --ignore=E501,W504

  py_test:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.6, 3.7]
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - name: Python install
      run: |
        pip install -U pip setuptools nose ephemeris
        python setup.py install
    - name: Launch containers
      run: |
        export BM2G_GLOBAL_CONFIG_PATH=`pwd`/test-data/bm2g.yml
        GAL_DOCKER=$(docker run -d -p 8080:80 -e GALAXY_CONFIG_ALLOW_LIBRARY_PATH_PASTE=True -v `pwd`/test-data/:/data/ quay.io/bgruening/galaxy:20.09)
        galaxy-wait -g http://localhost:8080 --timeout 300
        docker exec -i $GAL_DOCKER install-tools /data/tools.yml
        docker exec -i $GAL_DOCKER supervisorctl restart galaxy:
        echo "-------------"
        echo "Now running tests, which are expected to fail, don't worry..."
        echo "-------------"
        python setup.py nosetests || true # it will probably fail the first time, who cares?
        docker exec -i $GAL_DOCKER supervisorctl restart galaxy:
    - name: Run tests
      run: |
        export BM2G_GLOBAL_CONFIG_PATH=`pwd`/test-data/bm2g.yml
        python setup.py nosetests

  pypi:
    runs-on: ubuntu-latest
    needs: [lint, py_test]
    name: Deploy release to Pypi
    steps:
    - name: Checkout
      uses: actions/checkout@v2
    - uses: actions/setup-python@v1
      with:
        python-version: 3.7
    - name: Python install
      run: pip install -U pip setuptools nose build
    - name: Build a binary wheel and a source tarball
      run: python -m build --sdist --wheel --outdir dist/ .
    - name: Publish distribution 📦 to PyPI
      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
      uses: pypa/gh-action-pypi-publish@master
      with:
        password: ${{ secrets.pypi_password }}