commit.yml

name: Galaxy Tool Linting and Tests for PR
# run planemo on a git repository containing a single tool
# as a github action.
# ross lazarus august 2020
on: [pull_request,push]
env:
  GALAXY_REPO: https://github.com/galaxyproject/galaxy
  GALAXY_RELEASE: release_20.05
jobs:
  setup:
    name: setup environment and python
    runs-on: ubuntu-latest
    strategy:
      matrix:
        python-version: [3.7]
    steps:
    - name: Print github context properties
      run: |
        echo 'event: ${{ github.event_name }}'
        echo 'sha: ${{ github.sha }}'
        echo 'ref: ${{ github.ref }}'
        echo 'head_ref: ${{ github.head_ref }}'
        echo 'base_ref: ${{ github.base_ref }}'
        echo 'event.before: ${{ github.event.before }}'
        echo 'event.after: ${{ github.event.after }}'
    - uses: actions/setup-python@v1
      with:
        python-version: ${{ matrix.python-version }}
    - uses: actions/checkout@v2
      with:
    # planemo does not seem to want to install the requirement galaxyxml
    # into the venv it manages at tool testing so do it the old skool way
        repository: 'galaxyproject/galaxy'
        path: 'galaxy'
    - name: make venv ready for this galaxy and planemo
      run:  |
        python3 -m venv $GITHUB_WORKSPACE/galaxy/.venv
        . $GITHUB_WORKSPACE/galaxy/.venv/bin/activate
        pip install --upgrade pip
        pip install wheel
        pip install -r $GITHUB_WORKSPACE/galaxy/requirements.txt
    - name: Upgrade pip
      run: pip install --upgrade pip
    # Install the `wheel` package so that when installing other packages which
    # are not available as wheels, pip will build a wheel for them, which can be cached.
    - name: Install wheel
      run: pip install wheel
    - name: Install Planemo and flake8
      run: pip install planemo flake8 flake8-import-order
    # galaxyxml temporarily removed until PR accepted
    - uses: actions/checkout@v2
      with:
        fetch-depth: 1
    - name: flake8 *.py
      run: flake8 --ignore=E501,E203,W503,C901
    - name: Planemo lint
      run: planemo lint .
    - name: Planemo test tool
      run: planemo test --galaxy_root $GITHUB_WORKSPACE/galaxy --test_output tool_test_output.html --skip_venv --test_output_json tool_test_output.json --galaxy_python_version ${{ matrix.python-version }}  .
    - name: Copy artifacts into place
      run: |
        mkdir upload
        mv tool_test_output.json tool_test_output.html upload/
    - uses: actions/upload-artifact@v2.0.1
      with:
        name: 'All tool test results'
        path: upload