Fixing flaky tests #497
Workflow file for this run
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| name: "CI" | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| schedule: | |
| # At 07:00 UTC on Monday and Thursday. | |
| - cron: "0 7 * * *" | |
| workflow_dispatch: | |
| defaults: | |
| run: | |
| shell: bash -leo pipefail {0} | |
| jobs: | |
| tests: | |
| runs-on: ${{ matrix.os}} | |
| name: "💻-${{matrix.os }} 🐍-${{ matrix.python-version }}" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| python-version: | |
| - "3.11" | |
| - "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +%Y-%m-%d)" >> "${GITHUB_OUTPUT}" | |
| - name: "Setup Micromamba" | |
| uses: mamba-org/setup-micromamba@v2 | |
| with: | |
| environment-file: environment.yml | |
| environment-name: openfe_analysis_env | |
| cache-environment: true | |
| cache-downloads: true | |
| cache-environment-key: environment-${{ steps.date.outputs.date }} | |
| cache-downloads-key: downloads-${{ steps.date.outputs.date }} | |
| create-args: >- | |
| python=${{ matrix.python-version }} | |
| init-shell: bash | |
| - name: "Download Zenodo data" | |
| run: | | |
| python - <<'EOF' | |
| import pooch | |
| from pathlib import Path | |
| cache = Path(pooch.os_cache("openfe_analysis")) | |
| cache.mkdir(parents=True, exist_ok=True) | |
| # Files to download: direct Zenodo URLs + MD5 hashes | |
| files = { | |
| "openfe_analysis_simulation_output.tar.gz": ( | |
| "https://zenodo.org/records/17916322/files/openfe_analysis_simulation_output.tar.gz", | |
| "09752f2c4e5b7744d8afdee66dbd1414" | |
| ), | |
| "openfe_analysis_skipped.tar.gz": ( | |
| "https://zenodo.org/records/17916322/files/openfe_analysis_skipped.tar.gz", | |
| "3840d044299caacc4ccd50e6b22c0880" | |
| ), | |
| } | |
| # Download and untar each file | |
| for fname, (url, md5) in files.items(): | |
| pooch.retrieve( | |
| url=url, | |
| fname=fname, | |
| path=cache, | |
| known_hash=f"md5:{md5}", | |
| processor=pooch.Untar() | |
| ) | |
| EOF | |
| - name: "Install" | |
| run: | | |
| python -m pip install --no-deps . | |
| - name: "Test imports" | |
| run: | | |
| python -Ic "import openfe_analysis; print(openfe_analysis.__version__)" | |
| - name: "Run tests" | |
| run: | | |
| pytest -n auto -v --cov=openfe_analysis --cov-report=xml --durations=10 | |
| - name: codecov | |
| if: ${{ github.repository == 'OpenFreeEnergy/openfe_analysis' | |
| && github.event_name == 'pull_request' }} | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: coverage.xml | |
| fail_ci_if_error: false | |
| verbose: true |