Smaller fixes and adding tests #1
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| name: MetaQuest CI | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| workflow_dispatch: # Allows manual triggering | |
| jobs: | |
| lint: | |
| name: Code Quality | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 mypy pytest black | |
| pip install -e ".[dev]" | |
| - name: Check code formatting with Black | |
| run: black --check --diff metaquest | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 metaquest --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings | |
| flake8 metaquest --count --exit-zero --max-complexity=10 --max-line-length=100 --statistics | |
| - name: Type check with mypy | |
| run: mypy --ignore-missing-imports metaquest | |
| test: | |
| name: Test Python ${{ matrix.python-version }} | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| 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 pytest pytest-cov | |
| pip install -e ".[dev]" | |
| - name: Test with pytest | |
| run: | | |
| pytest tests/ --cov=metaquest --cov-report=xml | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| file: ./coverage.xml | |
| fail_ci_if_error: false | |
| build: | |
| name: Build and verify package | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| cache: 'pip' | |
| - name: Install build dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build twine check-wheel-contents | |
| - name: Build package | |
| run: python -m build | |
| - name: Check wheel contents | |
| run: check-wheel-contents dist/*.whl | |
| - name: Check distribution with twine | |
| run: twine check dist/* | |
| - name: Test installation | |
| run: | | |
| pip install dist/*.whl | |
| python -c "import metaquest; print(metaquest.__version__)" | |
| - name: Archive distribution packages | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| integration: | |
| name: Integration Test | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| cache: 'pip' | |
| - name: Download distribution packages | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: dist | |
| path: dist/ | |
| - name: Install package | |
| run: pip install dist/*.whl | |
| - name: Install test dependencies | |
| run: pip install pytest | |
| - name: Download test genome | |
| run: | | |
| mkdir -p test_data | |
| metaquest download_test_genome --output-folder test_data | |
| - name: Run basic CLI commands | |
| run: | | |
| metaquest --help | |
| metaquest --version | |
| - name: Verify integration | |
| run: | | |
| # Add verification steps here | |
| test -f test_data/GCF_000008985.1.fasta && echo "Test genome downloaded successfully" || exit 1 |