Support Tumor_Sample_Barcode as column name in clinical file #263
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |