Load vcf bgz #158
Workflow file for this run
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| # This workflow will build a Java project with Maven | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven | |
| # | |
| # Notes: | |
| # - we need to install pypandoc first as it is needed by pyspark setup | |
| # - using python 3.7 because platform specific wheel for pandas 0.23.x required | |
| # by hail is not available for python 3.8 | |
| # | |
| name: Verify | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - branch-* | |
| pull_request: | |
| branches: | |
| - master | |
| - branch-* | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| BUILD_TYPE: issue | |
| steps: | |
| - name: Extract version from branch name (for release branches) | |
| if: startsWith(github.event.pull_request.head.ref, 'release/') | |
| run: | | |
| BRANCH_NAME="${{ github.event.pull_request.head.ref }}" | |
| VERSION=${BRANCH_NAME#release/} | |
| echo "BUILD_VERSION=$VERSION" >> $GITHUB_ENV | |
| echo "BUILD_TYPE=release" >> $GITHUB_ENV | |
| - uses: actions/checkout@v2 | |
| - name: Set up JDK 1.8 | |
| uses: actions/setup-java@v1 | |
| with: | |
| java-version: 1.8 | |
| - name: Cache Maven packages | |
| uses: actions/cache@v2 | |
| with: | |
| path: ~/.m2 | |
| key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }} | |
| restore-keys: ${{ runner.os }}-m2 | |
| - name: Set up Python 3.7 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: Cache Python packages | |
| uses: actions/cache@v2 | |
| id: pythoncache | |
| with: | |
| path: /home/runner/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('dev/dev-requirements.txt') }} | |
| restore-keys: ${{ runner.os }}-pip | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip cache dir | |
| pip install pypandoc==1.5 | |
| if [ -f dev/dev-requirements.txt ]; then pip install -r dev/dev-requirements.txt; fi | |
| - name: Validate Python code | |
| run: pylint --max-line-length=140 python/varspark --rcfile python/pylintrc | |
| - name: Build with Maven | |
| run: mvn -Dbuild.type=${BUILD_TYPE} -B package --file pom.xml | |
| - name: Test with pytest | |
| run: | | |
| dev/py-test.sh |