feat: add monitoring plugin interface #6288
Workflow file for this run
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| concurrency: | |
| # Cancel concurrent flows on PRs | |
| group: ci-${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| formatting: | |
| permissions: | |
| contents: read # for actions/checkout to fetch code | |
| pull-requests: write # for marocchino/sticky-pull-request-comment to create or update PR comment | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-name: black | |
| create-args: black | |
| cache-environment: true | |
| - name: Check formatting | |
| shell: bash -el {0} | |
| run: black --check --diff . | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/sticky-pull-request-comment@v2.8.0 | |
| with: | |
| message: "Please format your code with [black](https://black.readthedocs.io): `black snakemake tests/*.py`." | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| testing: | |
| strategy: | |
| matrix: | |
| test_group: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] | |
| py_ver: ["3.11", "3.12"] | |
| runs-on: ubuntu-latest | |
| needs: formatting | |
| env: | |
| AWS_AVAILABLE: "${{ secrets.AWS_ACCESS_KEY_ID }}" | |
| GCP_AVAILABLE: "${{ secrets.GCP_SA_KEY }}" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Modify python version in test env | |
| shell: bash -el {0} | |
| run: | | |
| cp test-environment.yml test-environment-${{ matrix.py_ver }}.yml | |
| sed -E -i 's/- python.+/- python =${{ matrix.py_ver }}/' test-environment-${{ matrix.py_ver }}.yml | |
| - name: Setup snakemke environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: test-environment-${{ matrix.py_ver }}.yml | |
| environment-name: snakemake | |
| cache-environment: true | |
| - name: Install snakemake from source | |
| shell: bash -el {0} | |
| run: | | |
| conda config --set channel_priority strict | |
| pip install -e . | |
| # - name: Configure fast APT mirror | |
| # uses: vegardit/fast-apt-mirror.sh@1.0.0 | |
| - name: Setup apt dependencies | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa | |
| sudo apt-get update | |
| sudo apt install -y stress git wget openmpi-bin libopenmpi-dev apptainer | |
| - name: Test local | |
| env: | |
| CI: true | |
| ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}" | |
| #PYTHONTRACEMALLOC: 10 | |
| shell: bash -el {0} | |
| run: | | |
| pytest -v -x --show-capture=stderr \ | |
| --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration \ | |
| tests/tests.py \ | |
| tests/test_expand.py \ | |
| tests/test_io.py \ | |
| tests/test_schema.py \ | |
| tests/test_linting.py \ | |
| tests/test_executor_test_suite.py \ | |
| tests/test_api.py | |
| - name: Run tests/test_report/Snakefile to generate report | |
| shell: bash -el {0} | |
| run: | | |
| cd tests/test_report | |
| snakemake --use-conda --cores 1 --report report.zip | |
| - name: List directory structure | |
| run: | | |
| ls -R | |
| - name: Upload report | |
| if: ${{ matrix.test_group == 1 }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: report-${{ matrix.py_ver }}.zip | |
| path: tests/test_report/report.zip | |
| build-container-image: | |
| runs-on: ubuntu-latest | |
| needs: testing | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Build container image | |
| run: docker build . | |
| testing-windows: | |
| strategy: | |
| matrix: | |
| test_group: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] | |
| runs-on: windows-latest | |
| needs: formatting | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Remove unix-only dependencies | |
| shell: python | |
| run: | | |
| import fileinput | |
| excluded_on_win = ["environment-modules", "cwltool", "cwl-utils", "apptainer", "squashfuse"] | |
| for line in fileinput.input("test-environment.yml", inplace=True): | |
| if all(pkg not in line for pkg in excluded_on_win): | |
| print(line, end="") | |
| - name: Setup snakemke environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: test-environment.yml | |
| environment-name: snakemake | |
| init-shell: powershell | |
| cache-environment: true | |
| - name: Install snakemake from source | |
| run: | | |
| pip install . | |
| - name: Run tests | |
| env: | |
| CI: true | |
| ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}" | |
| run: | | |
| python -m pytest --show-capture=stderr -v -x --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration tests/tests.py |