Bugfix for mila code in WSL #794
Workflow file for this run
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| name: Python package | |
| on: | |
| push: | |
| branches: | |
| - master | |
| paths-ignore: | |
| - 'README.md' | |
| pull_request: | |
| paths-ignore: | |
| - 'README.md' | |
| # 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 | |
| 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 | |
| unit-tests: | |
| needs: [linting] | |
| runs-on: ${{ matrix.platform }} | |
| strategy: | |
| max-parallel: 4 | |
| matrix: | |
| platform: [ubuntu-latest, windows-latest, macos-latest] | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| env: | |
| PLATFORM: ${{ matrix.platform }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install poetry (not on MacOS) | |
| if: runner.os != 'macOS' | |
| run: pip install poetry | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: ${{ matrix.platform != 'macos-latest' && 'poetry' || '' }} | |
| - name: Install poetry (only on MacOS) | |
| if: runner.os == 'macOS' | |
| run: pip install poetry | |
| - name: Install dependencies | |
| run: poetry install --with=dev | |
| - name: Setup passwordless SSH access to localhost for tests | |
| # Adapted from https://stackoverflow.com/a/60367309/6388696 | |
| if: runner.os == 'Linux' | |
| run: | | |
| ssh-keygen -t ed25519 -f ~/.ssh/testkey -N '' | |
| cat > ~/.ssh/config <<EOF | |
| Host localhost | |
| User $USER | |
| HostName 127.0.0.1 | |
| IdentityFile ~/.ssh/testkey | |
| EOF | |
| echo -n 'from="127.0.0.1" ' | cat - ~/.ssh/testkey.pub > ~/.ssh/authorized_keys | |
| chmod og-rw ~ | |
| ssh -o 'StrictHostKeyChecking no' localhost id | |
| - name: Test with pytest | |
| run: poetry run pytest --cov=milatools --cov-report=xml --cov-append | |
| - name: Store coverage report as an artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-reports-unit-${{ matrix.platform }}-${{ matrix.python-version }} | |
| path: ./coverage.xml | |
| mock-slurm-integration-tests: | |
| name: integration tests with a mock slurm cluster | |
| needs: [unit-tests] | |
| runs-on: ${{ matrix.platform }} | |
| strategy: | |
| max-parallel: 5 | |
| matrix: | |
| platform: [ubuntu-latest] | |
| python-version: ['3.8', '3.9', '3.10', '3.11'] | |
| # For the action to work, you have to supply a mysql | |
| # service as defined below. | |
| services: | |
| mysql: | |
| image: mysql:8.0 | |
| env: | |
| MYSQL_ROOT_PASSWORD: root | |
| ports: | |
| - "8888:3306" | |
| options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # NOTE: Replacing this with our customized version of | |
| # - uses: koesterlab/setup-slurm-action@v1 | |
| - uses: ./.github/custom_setup_slurm_action | |
| timeout-minutes: 5 | |
| - name: Test if the slurm cluster is setup correctly | |
| run: srun --nodes=1 --ntasks=1 --cpus-per-task=1 --mem=1G --time=00:01:00 hostname | |
| - name: Setup passwordless SSH access to localhost for tests | |
| # Adapted from https://stackoverflow.com/a/60367309/6388696 | |
| run: | | |
| ssh-keygen -t ed25519 -f ~/.ssh/testkey -N '' | |
| cat > ~/.ssh/config <<EOF | |
| Host localhost | |
| User $USER | |
| HostName 127.0.0.1 | |
| IdentityFile ~/.ssh/testkey | |
| EOF | |
| echo -n 'from="127.0.0.1" ' | cat - ~/.ssh/testkey.pub > ~/.ssh/authorized_keys | |
| chmod og-rw ~ | |
| ssh -o 'StrictHostKeyChecking no' localhost id | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install poetry | |
| poetry install --with=dev | |
| - name: Launch integration tests | |
| run: poetry run pytest --slow --cov=milatools --cov-report=xml --cov-append -vvv --log-level=DEBUG | |
| timeout-minutes: 15 | |
| env: | |
| SLURM_CLUSTER: localhost | |
| - name: Store coverage report as an artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-reports-mock-${{ matrix.platform }}-${{ matrix.python-version }} | |
| path: ./coverage.xml | |
| real-slurm-integration-tests: | |
| name: integration tests with a real SLURM cluster | |
| needs: [mock-slurm-integration-tests] | |
| strategy: | |
| max-parallel: 1 | |
| matrix: | |
| # TODO: We should ideally also run this with Windows/Mac clients and a Linux | |
| # server. Unsure how to set that up with GitHub Actions though. | |
| python-version: ['3.11'] | |
| cluster: ['mila'] | |
| uses: ./.github/workflows/testing.yml | |
| with: | |
| cluster: ${{ matrix.cluster }} | |
| python-version: ${{ matrix.python-version }} | |
| timeout-minutes: 30 | |
| # https://about.codecov.io/blog/uploading-code-coverage-in-a-separate-job-on-github-actions/ | |
| upload-coverage-codecov: | |
| needs: [real-slurm-integration-tests] | |
| runs-on: ubuntu-latest | |
| name: Upload coverage reports to Codecov | |
| 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 }} | |
| # file: ./coverage.xml # Search for all coverage files from each workflow. | |
| # flags: integrationtests | |
| # env_vars: PLATFORM,PYTHON | |
| # name: codecov-umbrella | |
| directory: coverage_reports | |
| fail_ci_if_error: true |