Updating Pipfile and Pipfile.lock #268
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| # 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 |