Fix/remove deprecated linters #6402
Workflow file for this run
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| 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" | |
| - ".github/**" | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # 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: ${{ steps.conditions.outputs.run-tests }} | |
| # create a test matrix based on all python files in /tests | |
| list_tests: | |
| name: Get test file matrix | |
| runs-on: "ubuntu-latest" | |
| steps: | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| name: Check out source-code repository | |
| - name: List tests | |
| id: list_tests | |
| run: | | |
| echo "tests=$(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 }} | |
| # run on self-hosted runners for test_components.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default | |
| runs-on: ${{ matrix.test == 'test_components.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || '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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| name: Check out source-code repository | |
| - name: Set up Python ${{ needs.setup.outputs.python-version }} | |
| uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # 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@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # 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 ${exit_code}" | |
| exit 1 | |
| fi | |
| - name: Upload coverage | |
| uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4 | |
| with: | |
| name: coverage_${{ matrix.test }} | |
| path: .coverage | |
| coverage: | |
| needs: test | |
| # use the runner given by the input if it is dispatched manually, run on github if it is a rerun or on self-hosted by default | |
| runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }} | |
| steps: | |
| - name: go to subdirectory | |
| run: | | |
| mkdir -p pytest | |
| cd pytest | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # 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@eaceaf801fd36c7dee90939fad912460b18a1ffe # v4 | |
| - name: Run coverage | |
| run: | | |
| coverage combine --keep coverage*/.coverage* | |
| coverage report | |
| coverage xml | |
| - uses: codecov/codecov-action@e0b68c6749509c5f83f984dd99a76a1c1a231044 # v4 | |
| with: | |
| files: coverage.xml | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |