copy id_rsa wsl to windows
#800
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: ['3.9', '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 |