feat: --accession flag for direct NCBI assembly downloads #61
This file contains hidden or 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 | |
| on: | |
| push: | |
| branches: [main, develop] | |
| pull_request: | |
| branches: [main, develop] | |
| jobs: | |
| test: | |
| name: Test Python ${{ matrix.python-version }} (${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.9", "3.11", "3.12"] | |
| include: | |
| - os: macos-latest | |
| python-version: "3.12" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e .[dev] | |
| - name: Run tests | |
| run: pytest -v | |
| - name: Lint (Python 3.11 only) | |
| if: matrix.python-version == '3.11' | |
| run: | | |
| black --check nanopore_simulator/ tests/ | |
| flake8 nanopore_simulator/ | |
| mypy nanopore_simulator/ | |
| - name: Security scan (Python 3.11 only) | |
| if: matrix.python-version == '3.11' | |
| run: | | |
| pip install bandit pip-audit | |
| bandit -r nanopore_simulator/ -c pyproject.toml || bandit -r nanopore_simulator/ -s B101 | |
| pip-audit |