feat: Add periods to patient addresses (#3041) #939
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: Test record-linkage Container | |
| on: | |
| pull_request: | |
| branches: | |
| - "**" | |
| paths: | |
| - containers/record-linkage/** | |
| merge_group: | |
| types: | |
| - checks_requested | |
| push: | |
| branches: | |
| - main | |
| paths-ignore: | |
| - pyproject.toml | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| TEST_RUNNER_PYTHON_VERSION: 3.11 | |
| CONTAINER: record-linkage | |
| jobs: | |
| python-linting: | |
| uses: ./.github/workflows/linting-python.yaml | |
| with: | |
| python_runner_version: 3.11 # must be hardcoded; cannot pass in from env | |
| unit-test-python-containers: | |
| runs-on: ubuntu-latest | |
| services: | |
| test-db: | |
| image: postgres:13-alpine3.16 | |
| env: | |
| POSTGRES_PASSWORD: pw | |
| POSTGRES_DB: testdb | |
| POSTGRES_USER: postgres | |
| # Set health checks to wait until postgres has started | |
| options: >- | |
| --health-cmd pg_isready | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| --name testdb | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Setup python ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{env.TEST_RUNNER_PYTHON_VERSION}} | |
| cache: pip | |
| - name: Install pytest and pytest-cov | |
| run: pip install pytest pytest-cov | |
| - name: Install dependencies | |
| working-directory: ./containers/${{env.CONTAINER}} | |
| run: | | |
| commit_hash=$(git rev-parse HEAD) | |
| find ./ -name requirements.txt -exec sed -i -e "s/phdi@main/phdi@${commit_hash}/g" {} \; | |
| pip install -r requirements.txt | |
| if [ -f dev-requirements.txt ]; then | |
| pip install -r dev-requirements.txt | |
| fi | |
| - name: Run unit tests for container with coverage | |
| working-directory: ./containers/${{env.CONTAINER}} | |
| run: | | |
| python -m pytest --cov-report xml --cov=. -m "not integration" tests/ | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| flags: ${{ env.CONTAINER }} | |
| build-container: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Build ${{ env.CONTAINER }} Container | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: ./containers/${{ env.CONTAINER }} | |
| push: false | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max |