Run snakemake -n in CI
#26
Workflow file for this run
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| name: legend-dataflow | |
| on: | |
| workflow_dispatch: | |
| pull_request: | |
| push: | |
| branches: | |
| - main | |
| - "releases/**" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| FORCE_COLOR: 3 | |
| jobs: | |
| unit-tests: | |
| name: Run legend-dataflow unit tests | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| os: [ubuntu-latest, macos-13] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Get dependencies and install legend-dataflow | |
| run: | | |
| python -m pip install --upgrade pip wheel setuptools | |
| python -m pip install --upgrade .[test] | |
| - name: Run unit tests | |
| run: | | |
| python -m pytest | |
| run-dataflow: | |
| if: github.event.pull_request.head.repo.fork == false | |
| name: Run the Snakemake workflow | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.11", "3.12"] | |
| os: [ubuntu-latest, macos-13] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set LEGEND_METADATA variable | |
| run: | | |
| echo "LEGEND_METADATA=$GITHUB_WORKSPACE/inputs" >> $GITHUB_ENV | |
| - name: Clone legend-metadata | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: legend-exp/legend-metadata | |
| fetch-depth: 0 | |
| submodules: recursive | |
| token: ${{ secrets.CLONE_LEGEND_METADATA }} | |
| path: ${{ env.LEGEND_METADATA }} | |
| - name: Get dependencies and install legend-dataflow | |
| run: | | |
| python -m pip install --upgrade uv | |
| python -m uv pip install --upgrade .[runprod] | |
| - name: Set the PRODENV variable | |
| run: | | |
| echo "PRODENV=$(realpath $GITHUB_WORKSPACE/..)" >> $GITHUB_ENV | |
| - name: test prodenv scripts | |
| run: | | |
| cp .github/dataflow-config-ci.yaml ./dataflow-config.yaml | |
| python -m uv run dataprod -v install dataflow-config.yaml | |
| - name: run workflows in dry-run mode | |
| run: | | |
| snakemake --workflow-profile workflow/profiles/lngs-build-raw -n all-*-daq.gen | |
| snakemake --workflow-profile workflow/profiles/lngs-build-raw -n all-*-raw.gen | |
| test-coverage: | |
| name: Calculate and upload test coverage | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 2 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Generate Report | |
| run: | | |
| python -m pip install --upgrade pip wheel setuptools | |
| python -m pip install --upgrade .[test] | |
| python -m pytest --cov=legenddataflow --cov-report=xml | |
| - name: Upload Coverage to codecov.io | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |