Model 00023 #274
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
| # This GitHub Action workflow will | |
| # - Format code using Black | |
| # - Build project with all dependencies | |
| # - Check code with flake8 linter | |
| # - Run tests with pytest | |
| # ubuntu-latest has 7GB RAM and 14GB SSD. macos-latest has 14GB RAM and 14GB SSD. Using macos assuming more RAM -> faster tests -> less timeouts | |
| # Nonetheless, our tests seem to need >10 GB RAM and >16,7 GB SSD Space. Test refactoring needed. | |
| # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
| name: Build and test | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| formatting: | |
| outputs: | |
| new_sha: ${{ steps.sha.outputs.SHA }} | |
| runs-on: macos-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} # ${{ github.event.pull_request.head.sha }} | |
| - name: Setup Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.8" | |
| cache: 'pip' | |
| - name: Setup isort and Black | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install isort black | |
| - name: Run isort | |
| run: | | |
| isort --profile black . | |
| - name: Run Black formatter | |
| run: | | |
| black . | |
| - name: Commit changes | |
| uses: EndBug/add-and-commit@v8 | |
| with: | |
| message: 'Fix styling' | |
| add: '*.py' | |
| - name: Get commit hash | |
| id: sha | |
| run: | | |
| sha_new=$(git rev-parse HEAD) | |
| echo $sha_new | |
| echo "::set-output name=SHA::$sha_new" | |
| build: | |
| if: always() | |
| needs: formatting | |
| runs-on: macos-latest | |
| steps: | |
| - name: Checkout to latest changes | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ needs.formatting.outputs.new_sha }} | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.8" | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest pytest-cov pytest-github-actions-annotate-failures | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip install -e . | |
| - name: Install model dependencies | |
| run: | | |
| python src/medigan/execute_model/install_model_dependencies.py | |
| lint: | |
| needs: build | |
| runs-on: macos-latest | |
| steps: | |
| - name: Checkout to latest changes | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ needs.formatting.outputs.new_sha }} | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.8" | |
| cache: 'pip' | |
| - name: Install cached dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip install flake8 | |
| pip install -e . | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --max-line-length=88 --extend-ignore=E203,E501 | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=88 --extend-ignore=E203,E501 --statistics | |
| test: | |
| needs: build | |
| runs-on: macos-latest #windows-latest | |
| steps: | |
| - name: Checkout to latest changes | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ needs.formatting.outputs.new_sha }} | |
| fetch-depth: 0 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.8" | |
| cache: 'pip' | |
| - name: Install cached dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip install pytest pytest-cov pytest-github-actions-annotate-failures | |
| pip install -e . | |
| python src/medigan/execute_model/install_model_dependencies.py | |
| # for windows: pip install -r requirements.txt | |
| # for mac/linux: if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Test with pytest | |
| run: | | |
| pytest tests -W ignore::DeprecationWarning --verbose --failed-first --log-cli-level=INFO #--cov=. --cov-report html #--capture=tee-sys |