feat!: support PostgreSQL as optional storage backend #230
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: checks | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| name: test py${{ matrix.python-version }} ${{ matrix.db_url }} | |
| runs-on: ubuntu-latest | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.DUMMY_AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.DUMMY_AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: us-east-2 | |
| AWS_DEFAULT_OUTPUT: text | |
| THERAPY_NORM_DB_URL: ${{ matrix.db_url }} | |
| THERAPY_TEST: true | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10'] | |
| db_url: ['http://localhost:8002', 'postgresql://postgres:postgres@localhost:5432/therapy_normalizer_test'] | |
| services: | |
| postgres: | |
| image: postgres:14 | |
| env: | |
| POSTGRES_USER: 'postgres' | |
| POSTGRES_DB: 'therapy_normalizer_test' | |
| POSTGRES_PASSWORD: 'postgres' | |
| ports: | |
| - 5432:5432 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Build local DynamoDB | |
| if: ${{ env.THERAPY_NORM_DB_URL == 'http://localhost:8002' }} | |
| run: | | |
| chmod +x ./tests/scripts/dynamodb_run.sh | |
| ./tests/scripts/dynamodb_run.sh | |
| - name: Install DynamoDB dependencies | |
| if: ${{ env.THERAPY_NORM_DB_URL == 'http://localhost:8002' }} | |
| run: python3 -m pip install ".[etl,test]" | |
| - name: Run DDB tests | |
| if: ${{ env.THERAPY_NORM_DB_URL == 'http://localhost:8002' }} | |
| run: python3 -m pytest | |
| - name: Install PG dependencies | |
| if: ${{ env.THERAPY_NORM_DB_URL == 'postgresql://postgres:postgres@localhost:5432/therapy_normalizer_test' }} | |
| run: python3 -m pip install ".[pg,etl,test]" | |
| - name: Run PG tests | |
| if: ${{ env.THERAPY_NORM_DB_URL == 'postgresql://postgres:postgres@localhost:5432/therapy_normalizer_test' }} | |
| env: | |
| DISEASE_NORM_DB_URL: postgresql://postgres:postgres@localhost:5432/therapy_normalizer_test | |
| run: python3 -m pytest | |
| lint: | |
| name: lint py${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| env: | |
| AWS_ACCESS_KEY_ID: ${{ secrets.DUMMY_AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.DUMMY_AWS_SECRET_ACCESS_KEY }} | |
| AWS_DEFAULT_REGION: us-east-2 | |
| AWS_DEFAULT_OUTPUT: text | |
| strategy: | |
| matrix: | |
| python-version: ['3.8', '3.9', '3.10'] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: python3 -m pip install ".[dev]" | |
| - name: Check style | |
| run: python3 -m flake8 therapy/ tests/ setup.py | |
| - name: Check type correctness | |
| if: ${{ always() }} | |
| run: python3 -m mypy --ignore-missing-imports therapy/ |