fix: [#256] adapt check_local for cancer and pull_sheets fix #351
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| jobs: | |
| cancel-previous: | |
| runs-on: ubuntu-latest | |
| if: github.ref != 'refs/heads/main' | |
| steps: | |
| - uses: khan/[email protected] | |
| with: | |
| workflows: "main.yml" | |
| env: | |
| GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
| linting: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.12" | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Install system dependencies | |
| run: sudo apt-get install -y libbz2-dev liblzma-dev | |
| - name: Setup environment variables | |
| run: echo "GIT_LFS_SKIP_SMUDGE=1" >> $GITHUB_ENV | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge,bioconda,nodefaults | |
| environment-file: 'environment.yaml' | |
| # overriding the python-version here seems to break due to issues with strings/quotes, see https://github.com/bihealth/cubi-tk/actions/runs/13308587922/job/37169672255?pr=258#step:5:386 | |
| # python-version: ${{ matrix.python-version }} | |
| - name: Set up Python | |
| run: uv python install ${{ matrix.python-version }} | |
| - name: Install the project | |
| run: uv sync --all-extras --dev | |
| - name: Run linting tools | |
| run: | | |
| make lint | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/[email protected] | |
| with: | |
| message: 'Please check your code via `make lint`.' | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| testing: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.12" | |
| needs: linting | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| with: | |
| lfs: true | |
| - name: Install system dependencies | |
| run: sudo apt-get install -y libbz2-dev liblzma-dev | |
| - name: Setup environment variables | |
| run: echo "GIT_LFS_SKIP_SMUDGE=1" >> $GITHUB_ENV | |
| - name: Setup conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge,bioconda,nodefaults | |
| environment-file: 'environment.yaml' | |
| # see above | |
| # python-version: ${{ matrix.python-version }} | |
| - name: Set up Python | |
| run: uv python install ${{ matrix.python-version }} | |
| - name: Install the project | |
| run: uv sync --all-extras --dev | |
| - name: Run tests | |
| run: uv run pytest | |
| - uses: codecov/codecov-action@v3 |