Remove nfcore_external_java_deps.jar from lib directory in pipeline template #6065
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
| name: Python tests | |
| # This workflow is triggered on pushes and PRs to the repository. | |
| # Only run if we changed a Python file | |
| on: | |
| push: | |
| branches: | |
| - dev | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| pull_request: | |
| paths-ignore: | |
| - "docs/**" | |
| - "CHANGELOG.md" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| # Cancel if a newer run with the same workflow name is queued | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| setup: | |
| runs-on: "ubuntu-latest" | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.11"] | |
| runner: ["ubuntu-latest"] | |
| include: | |
| - python-version: "3.8" | |
| runner: "ubuntu-20.04" | |
| steps: | |
| - name: Check conditions | |
| id: conditions | |
| run: echo "run-tests=${{ github.ref == 'refs/heads/master' || (matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8') }}" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| python-version: ${{ matrix.python-version }} | |
| runner: ${{ matrix.runner }} | |
| run-tests: ${{ steps.conditions.outputs.run-tests }} | |
| # create a test matrix based on all python files in /tests | |
| list_tests: | |
| name: Get test file matrix | |
| runs-on: "ubuntu-latest" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| name: Check out source-code repository | |
| - name: List tests | |
| id: list_tests | |
| run: | | |
| echo "tests=$(find tests/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT | |
| outputs: | |
| tests: ${{ steps.list_tests.outputs.tests }} | |
| test: | |
| name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }} | |
| needs: [setup, list_tests] | |
| if: ${{ needs.setup.outputs.run-tests }} | |
| runs-on: self-hosted | |
| strategy: | |
| matrix: ${{ fromJson(needs.list_tests.outputs.tests) }} | |
| fail-fast: false # run all tests even if one fails | |
| steps: | |
| - name: go to subdirectory and change nextflow workdir | |
| run: | | |
| mkdir -p pytest | |
| cd pytest | |
| export NXF_WORK=$(pwd) | |
| - uses: actions/checkout@v4 | |
| name: Check out source-code repository | |
| - name: Set up Python ${{ needs.setup.outputs.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ needs.setup.outputs.python-version }} | |
| cache: "pip" | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip -r requirements-dev.txt | |
| pip install -e . | |
| - name: Downgrade git to the Ubuntu official repository's version | |
| if: ${{ needs.setup.outputs.runner == 'ubuntu-20.04' && needs.setup.outputs.python-version == '3.8' }} | |
| run: | | |
| sudo apt update | |
| sudo apt remove -y git git-man | |
| sudo add-apt-repository --remove ppa:git-core/ppa | |
| sudo apt install -y git | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +'%Y-%m')" >> $GITHUB_ENV | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Look if nf-test is already installed and write to env variable | |
| id: check-nftest | |
| run: | | |
| if [ -f /usr/local/bin/nf-test ]; then | |
| echo "nftest_installed=true" >> $GITHUB_ENV | |
| else | |
| echo "nftest_installed=false" >> $GITHUB_ENV | |
| fi | |
| - name: Cache nf-test installation | |
| if: env.nftest_installed != 'true' | |
| id: cache-software | |
| uses: actions/cache@13aacd865c20de90d75de3b17ebe84f7a17d57d2 # v4 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-nftest-${{ env.date }} | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' && env.nftest_installed != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: move coveragerc file up | |
| run: | | |
| mv .github/.coveragerc . | |
| - name: Test with pytest | |
| run: | | |
| python3 -m pytest tests/${{matrix.test}} --color=yes --cov --durations=0 && exit_code=0|| exit_code=$? | |
| # don't fail if no tests were collected, e.g. for test_licence.py | |
| if [ "${exit_code}" -eq 5 ]; then | |
| echo "No tests were collected" | |
| exit 0 | |
| elif [ "${exit_code}" -ne 0 ]; then | |
| echo "Tests failed with exit code ${exit_code}" | |
| exit 1 | |
| fi | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage_${{ matrix.test }} | |
| path: .coverage | |
| coverage: | |
| needs: test | |
| runs-on: self-hosted | |
| steps: | |
| - name: go to subdirectory | |
| run: | | |
| mkdir -p pytest | |
| cd pytest | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| env: | |
| AGENT_TOOLSDIRECTORY: /opt/actions-runner/_work/tools/tools/ | |
| with: | |
| python-version: 3.11 | |
| cache: "pip" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip -r requirements-dev.txt | |
| pip install -e . | |
| - name: move coveragerc file up | |
| run: | | |
| mv .github/.coveragerc . | |
| - name: Download all artifacts | |
| uses: actions/download-artifact@v4 | |
| - name: Run coverage | |
| run: | | |
| coverage combine --keep coverage*/.coverage* | |
| coverage report | |
| coverage xml | |
| - uses: codecov/codecov-action@v3 | |
| with: | |
| files: coverage.xml | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |