refactor: resolve Pylance warnings (#366) #139
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: Tests | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| db_url: ["http://localhost:8000", "postgres://postgres:postgres@localhost:5432/gene_normalizer_test"] | |
| python-version: ["3.10", "3.11", "3.12"] | |
| services: | |
| postgres: | |
| image: postgres:14 | |
| env: | |
| POSTGRES_USER: 'postgres' | |
| POSTGRES_DB: 'gene_normalizer_test' | |
| POSTGRES_PASSWORD: 'postgres' | |
| ports: | |
| - 5432:5432 | |
| 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 | |
| GENE_NORM_DB_URL: ${{ matrix.db_url }} | |
| GENE_TEST: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install DynamoDB dependencies | |
| if: ${{ env.GENE_NORM_DB_URL == 'http://localhost:8000' }} | |
| run: python3 -m pip install ".[etl,test]" | |
| - name: Install PG dependencies | |
| if: ${{ env.GENE_NORM_DB_URL != 'http://localhost:8000' }} | |
| run: python3 -m pip install ".[pg,etl,test]" | |
| - name: Build local DynamoDB | |
| if: ${{ env.GENE_NORM_DB_URL == 'http://localhost:8000' }} | |
| run: | | |
| chmod +x ./tests/unit/dynamodb_build.bash | |
| ./tests/unit/dynamodb_build.bash | |
| - name: Run tests | |
| run: python3 -m pytest | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: python3 -m pip install ".[dev]" | |
| - name: Check style | |
| run: python3 -m ruff check . && python3 -m ruff format --check . | |
| docs: | |
| runs-on: ubuntu-latest | |
| env: | |
| SPHINX_GITHUB_CHANGELOG_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.11 | |
| - name: Install dependencies | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| python3 -m pip install '.[docs,pg,etl]' | |
| - name: Attempt docs build | |
| working-directory: ./docs | |
| run: make html |