EVA-3322 - Use new version of pyutils #23
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: Python package | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.6, 3.8] | |
| java-version: [1.8] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Setup Java JDK # Nextflow relies on JDK | |
| uses: actions/setup-java@v1.4.3 | |
| # The Java version to make available on the path. Takes a whole or semver Java version, or 1.x syntax (e.g. 1.8 => Java 8.x). Early access versions can be specified in the form of e.g. 14-ea, 14.0.0-ea, or 14.0.0-ea.28 | |
| with: | |
| java-version: ${{ matrix.java-version }} | |
| - name: Set up Nextflow | |
| run: | | |
| sudo bash -c "export JAVA_CMD="$(which java)" && cd /usr/bin && (curl -s https://get.nextflow.io | bash) && chmod 755 nextflow" | |
| /usr/bin/nextflow -version | |
| - name: Set up BCFtools | |
| run: | | |
| sudo apt update | |
| sudo apt -y install samtools bcftools tabix | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| python setup.py install | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| PYTHONPATH=. pytest tests |