cicd: update precommit configs #165
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| 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 . | |
| precommit_hooks: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| hook: | |
| - "end-of-file-fixer" | |
| - "trailing-whitespace" | |
| - "mixed-line-ending" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - uses: pre-commit/[email protected] | |
| with: | |
| extra_args: ${{ matrix.hook.args }} --all-files | |
| 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 |