Add option to include descriptions & Add additional columns when annotating genomic change #253
Workflow file for this run
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Run all python tests | |
| on: | |
| push: | |
| branches: [ master, next-minor-release ] | |
| pull_request: | |
| branches: [ master, next-minor-release ] | |
| jobs: | |
| lint: | |
| name: Linting using flake8 | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.9" | |
| - name: Run flake8 | |
| uses: julianwachholz/flake8-action@v2 | |
| with: | |
| checkName: "Python Lint" | |
| path: . | |
| config: flake8.ini | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| pytest: | |
| needs: lint | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest ] | |
| python-version: [ '3.7','3.8','3.9','3.10','3.11' ] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| env: | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest | |
| if [[ $PYTHON_VERSION =~ ^2\.[0-9]+$ ]]; then pip install -r requirements/common.txt -r requirements/pip2.7.txt; fi | |
| if [[ $PYTHON_VERSION =~ ^3\.[0-9]+$ ]]; then pip install -r requirements/common.txt -r requirements/pip3.txt; fi | |
| - name: Test with pytest | |
| env: | |
| ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }} | |
| run: | | |
| pytest | |
| build-in-windows: | |
| needs: lint | |
| runs-on: windows-latest | |
| strategy: | |
| matrix: | |
| python-version: [ '3.7','3.8','3.9','3.10','3.11' ] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| env: | |
| PYTHON_VERSION: ${{ matrix.python-version }} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install pytest | |
| if ( $env:PYTHON_VERSION -match '^2\.[0-9]+$' ) | |
| { | |
| pip install -r requirements/common.txt -r requirements/pip2.7.txt | |
| } | |
| if ( $env:PYTHON_VERSION -match '^3\.[0-9]+$' ) | |
| { | |
| pip install -r requirements/common.txt -r requirements/pip3.txt | |
| } | |
| - name: Test with pytest | |
| env: | |
| ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }} | |
| run: | | |
| pytest |