Merge pull request #599 from UW-GAC/feature/dbgap-application-views-f… #1185
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: CI | |
| # Enable Buildkit and let compose use it to speed up image building | |
| env: | |
| DOCKER_BUILDKIT: 1 | |
| COMPOSE_DOCKER_CLI_BUILD: 1 | |
| on: | |
| pull_request: | |
| branches: [ "main" ] | |
| paths-ignore: [ "docs/**" ] | |
| push: | |
| branches: [ "main" ] | |
| paths-ignore: [ "docs/**" ] | |
| concurrency: | |
| group: ${{ github.head_ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8] | |
| backend: ["sqlite", "mariadb"] | |
| mariadb-version: ["10.4"] | |
| include: | |
| - python-version: 3.12 # Possible future version. | |
| backend: "mariadb" | |
| mariadb-version: "10.5" | |
| pip-recompile: true | |
| - python-version: 3.12 # Possible future version. | |
| backend: "mariadb" | |
| mariadb-version: "10.11" | |
| pip-recompile: true | |
| name: "py${{ matrix.python-version }}-${{ matrix.backend }}-${{ matrix.mariadb-version }}" | |
| services: | |
| mysql: | |
| # Always start mariadb, even if we are testing with the mysql backend. | |
| # Github actions do not allow conditional services yet. | |
| image: mariadb:${{ matrix.mariadb-version }} | |
| ports: | |
| - 3306:3306 | |
| env: | |
| MYSQL_ROOT_PASSWORD: root | |
| options: --tmpfs /var/lib/mysql | |
| env: | |
| PYTEST_ADDOPTS: "--maxfail=20" # Stop testing after too many failures. | |
| # Conditionally set the database url based on the backend. | |
| DATABASE_URL: ${{ matrix.backend == 'sqlite' && 'sqlite:///db.sqlite3' || 'mysql://root:[email protected]:3306/mysql' }} | |
| steps: | |
| - name: Checkout Code Repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| cache-dependency-path: | | |
| requirements/requirements.txt | |
| requirements/test-requirements.txt | |
| - name: Ensure pip is installed | |
| run: | | |
| python -m ensurepip --upgrade | |
| python -m pip install --upgrade pip | |
| # Upgrade setup tools | |
| python -m pip install --upgrade setuptools | |
| - name: Install piptools | |
| run: python -m pip install pip-tools | |
| - name: Recompile pip files if requested | |
| if: matrix.pip-recompile | |
| run: | | |
| pip-compile -v requirements/requirements.in | |
| pip-compile -v requirements/test-requirements.in | |
| # Print out changes. | |
| git diff | |
| - name: Install Dependencies | |
| run: | | |
| pip-sync requirements/requirements.txt requirements/test-requirements.txt | |
| - name: Collect staticfiles | |
| run: python manage.py collectstatic --noinput --settings=config.settings.test | |
| - name: Run tests | |
| run: | | |
| pytest --cov=primed -n auto | |
| mv .coverage .coverage-${{ strategy.job-index }} | |
| - name: List files for debugging purposes | |
| run: ls -lhta | |
| - name: Upload coverage data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-data-${{ strategy.job-index }} | |
| path: .coverage-${{ strategy.job-index }} | |
| coverage: | |
| needs: | |
| - test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out the repo | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --upgrade coverage "django<4" django-coverage-plugin | |
| - name: Download coverage data | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: ./artifacts/ | |
| - name: Merge coverage files | |
| run: | | |
| python -m coverage combine ./artifacts/coverage-data*/.coverage-* | |
| python -m coverage xml | |
| ls -la .coverage* | |
| - name: Report coverage | |
| run: | | |
| python -m coverage report | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |