Merge pull request #2423 from mahesh-panchal/update_gitpod_profile #345
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] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| jobs: | |
| pytest: | |
| runs-on: ${{ matrix.runner }} | |
| strategy: | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| runner: ["ubuntu-latest"] | |
| include: | |
| - runner: "ubuntu-20.04" | |
| python-version: "3.8" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| name: Check out source-code repository | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install python 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: ${{ matrix.runner == 'ubuntu-20.04' && matrix.python-version == '3.8' }} | |
| run: | | |
| sudo apt update | |
| sudo apt remove git git-man | |
| sudo add-apt-repository --remove ppa:git-core/ppa | |
| sudo apt install git | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "latest-everything" | |
| - name: Test with pytest | |
| run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core | |
| - uses: codecov/codecov-action@v1 | |
| name: Upload code coverage report | |
| with: | |
| if: success() | |
| token: ${{ secrets.CODECOV_TOKEN }} |