Update README.md #521
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Python application | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| permissions: | |
| contents: read | |
| # https://stackoverflow.com/a/72408109/6388696 | |
| # https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-concurrency-to-cancel-any-in-progress-job-or-run | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| linting: | |
| name: Run linting/pre-commit checks | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - run: pip install 'pre-commit<4.0.0' | |
| - run: pre-commit --version | |
| - run: pre-commit install | |
| - run: pre-commit run --all-files --show-diff-on-failure | |
| check_docs: | |
| needs: [linting] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install the latest version of uv | |
| uses: astral-sh/setup-uv@v3 | |
| with: | |
| version: "latest" | |
| enable-cache: true | |
| # https://github.com/astral-sh/setup-uv?tab=readme-ov-file#github-authentication-token | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| cache-suffix: "3.10" | |
| - name: Install dependencies | |
| run: uv sync --frozen --extra docs | |
| - name: Build the documentation (strict mode) | |
| run: uv run mkdocs build --strict | |
| unit_tests: | |
| needs: [linting] | |
| runs-on: ${{ matrix.platform }} | |
| strategy: | |
| max-parallel: 4 | |
| matrix: | |
| platform: [ubuntu-latest, macos-latest] | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install the latest version of uv | |
| uses: astral-sh/setup-uv@v3 | |
| with: | |
| version: "latest" | |
| enable-cache: true | |
| # https://github.com/astral-sh/setup-uv?tab=readme-ov-file#github-authentication-token | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| cache-suffix: ${{ matrix.python-version }} | |
| - name: Pin python-version ${{ matrix.python-version }} | |
| run: uv python pin ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: uv sync --frozen | |
| - name: Test with pytest | |
| env: | |
| JAX_PLATFORMS: cpu | |
| run: uv run pytest -v --cov=project --cov-report=xml --cov-append --skip-if-files-missing | |
| - name: Store coverage report as an artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-reports-unit-tests-${{ matrix.platform }}-${{ matrix.python-version }} | |
| path: ./coverage.xml | |
| local_integration_tests: | |
| needs: [unit_tests, check_docs] | |
| runs-on: self-hosted | |
| timeout-minutes: 20 | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| python-version: ["3.10"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install the latest version of uv | |
| uses: astral-sh/setup-uv@v3 | |
| with: | |
| version: "latest" | |
| enable-cache: false # no need, uses the local uv cache. | |
| # https://github.com/astral-sh/setup-uv?tab=readme-ov-file#github-authentication-token | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Pin python-version ${{ matrix.python-version }} | |
| run: uv python pin ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: uv sync --all-extras --frozen | |
| - name: Test with pytest | |
| run: uv run pytest -v --cov=project --cov-report=xml --cov-append | |
| - name: Test with pytest (only slow tests) | |
| run: uv run pytest -v -m slow --slow --cov=project --cov-report=xml --cov-append | |
| - name: Store coverage report as an artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-reports-integration-tests-${{ matrix.python-version }} | |
| path: ./coverage.xml | |
| launch-slurm-actions-runner: | |
| needs: [local_integration_tests] | |
| runs-on: self-hosted | |
| timeout-minutes: 5 | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| cluster: ["mila"] #, 'narval', 'beluga'] | |
| outputs: | |
| job_id: ${{ steps.sbatch.outputs.stdout }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Copy job script to the cluster | |
| run: "scp .github/actions-runner-job.sh ${{ matrix.cluster }}:actions-runner-job.sh" | |
| - name: Launch Slurm Actions Runner | |
| id: sbatch | |
| # TODO: for DRAC clusters, the account needs to be set somehow (and obviously not be hard-coded here). | |
| # Output the job ID to a file so that the next step can use it. | |
| # NOTE: Could also use the --wait flag to wait for the job to finish (and have this run at the same time as the other step). | |
| run: | | |
| job_id=`ssh ${{ matrix.cluster }} 'cd $SCRATCH && sbatch --parsable $HOME/actions-runner-job.sh'` | |
| echo "Submitted job $job_id on the ${{ matrix.cluster }} cluster!" | |
| echo "job_id=$job_id" >> "$GITHUB_OUTPUT" | |
| # This step runs in a self-hosted Github Actions runner inside a SLURM job on the compute node of the cluster. | |
| slurm_integration_tests: | |
| name: Run integration tests on the ${{ matrix.cluster }} cluster in job ${{ needs.launch-slurm-actions-runner.outputs.job_id}} | |
| needs: [launch-slurm-actions-runner] | |
| runs-on: ${{ matrix.cluster }} | |
| timeout-minutes: 20 | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| # TODO: this should be tied to the same setting in the `launch-slurm-actions-runner` job. | |
| # cluster: ${{ needs.launch-slurm-actions-runner.strategy.matrix.cluster }} | |
| cluster: ["mila"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up the repo using the setup script | |
| run: scripts/mila_setup.sh | |
| - name: Install dependencies | |
| run: uv sync --all-extras --frozen | |
| - name: Show installed packages | |
| run: uv pip list | |
| - name: Test with pytest | |
| run: uv run pytest -v --cov=project --cov-report=xml --cov-append | |
| # TODO: Disabling full regression tests on the cluster for now, because the worker is often | |
| # interrupted and we want to avoid using the unkillable partition to not interrupt other's | |
| # work. The full regression tests are still run on the local_integration_tests job. | |
| # - name: Test with pytest (only slow tests) | |
| # run: rye run pytest -v -m slow --slow --cov=project --cov-report=xml --cov-append | |
| - name: Store coverage report as an artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-reports-slurm-integration-tests-${{ matrix.cluster }} | |
| path: ./coverage.xml | |
| # https://about.codecov.io/blog/uploading-code-coverage-in-a-separate-job-on-github-actions/ | |
| upload-coverage-codecov: | |
| needs: [local_integration_tests, slurm_integration_tests] | |
| runs-on: ubuntu-latest | |
| name: Upload coverage reports to Codecov | |
| timeout-minutes: 5 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Download artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| pattern: coverage-reports-* | |
| merge-multiple: false | |
| # download all the artifacts in this directory (each .coverage.xml will be in a subdirectory) | |
| # Next step if this doesn't work would be to give the coverage files a unique name and use merge-multiple: true | |
| path: coverage_reports | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| directory: coverage_reports | |
| fail_ci_if_error: true |