EVA-3696 - Processing via a scanner and new brokering method #1071
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: Python package | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9] | |
| nextflow-version: [21.10.5, 22.10.7] | |
| java-version: [11] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Java ${{ matrix.java-version }} | |
| uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '${{ matrix.java-version }}' | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies ${{ matrix.nextflow-version }} | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| python setup.py install | |
| # Install Nextflow | |
| mkdir /tmp/nextflow && cd /tmp/nextflow | |
| wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v${{ matrix.nextflow-version }}/nextflow-${{ matrix.nextflow-version }}-all | bash | |
| echo "/tmp/nextflow" >> $GITHUB_PATH | |
| cd - | |
| # Build java dependencies | |
| tests/nextflow-tests/build_tests.sh | |
| - 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: | | |
| # reduce the default SSL security level to get around a misconfiguration in the Ensembl server | |
| # https://github.com/Ensembl/ensembl-rest/issues/427 | |
| # See https://askubuntu.com/a/1233456 | |
| sed 's/DEFAULT@SECLEVEL=2/DEFAULT@SECLEVEL=1/' /usr/lib/ssl/openssl.cnf > openssl_sec1.cnf | |
| export OPENSSL_CONF=openssl_sec1.cnf | |
| PYTHONPATH=. pytest tests | |
| - name: Test nextflow workflows | |
| run: | | |
| # Run nextflow tests | |
| tests/nextflow-tests/run_tests_validation.sh | |
| tests/nextflow-tests/run_tests_prep_brokering.sh | |
| tests/nextflow-tests/run_tests_accession_and_variant_load.sh | |
| tests/nextflow-tests/run_tests_accession_and_variant_load_human.sh | |
| tests/nextflow-tests/run_tests_clustering.sh | |
| tests/nextflow-tests/run_tests_remapping_clustering.sh |