Code Quality Tools¶

Genalyzer uses automated linting and formatting tools to maintain consistent code quality across both C++ and Python codebases. These checks run automatically in CI on every push and pull request.

C++ Formatting: clang-format¶

All C and C++ source files are formatted with clang-format using the project’s .clang-format configuration. The configuration is based on the LLVM style with project-specific customizations including tab-based indentation and C++20 language standard.

Running locally¶

# Check formatting (dry run)
find include/ src/ bindings/c/ -name '*.hpp' -o -name '*.h' -o -name '*.cpp' -o -name '*.c' | xargs clang-format --dry-run --Werror

# Apply formatting
find include/ src/ bindings/c/ -name '*.hpp' -o -name '*.h' -o -name '*.cpp' -o -name '*.c' | xargs clang-format -i

Pre-commit hook¶

clang-format also runs as a pre-commit hook. Install the hooks with:

pip install pre-commit
pre-commit install

After installation, clang-format runs automatically on staged C/C++ files before each commit.

Python Linting: Ruff¶

Ruff is used for Python linting and formatting. It replaces several traditional tools (flake8, isort, pyupgrade) with a single fast linter. Configuration is in bindings/python/pyproject.toml under [tool.ruff].

Enabled rule sets¶

Rule set	Description
`E`, `W`	pycodestyle errors and warnings
`F`	pyflakes (unused imports, undefined names)
`I`	isort (import sorting)
`UP`	pyupgrade (Python version upgrades)
`B`	flake8-bugbear (common bug patterns)
`SIM`	flake8-simplify (code simplification)
`RUF`	Ruff-specific rules

Running locally¶

cd bindings/python

# Check for lint errors
ruff check genalyzer/

# Auto-fix safe issues
ruff check --fix genalyzer/

# Check formatting
ruff format --check genalyzer/

# Apply formatting
ruff format genalyzer/

Python Type Checking: ty¶

ty is used for Python type checking. It is an extremely fast type checker from the same team that builds Ruff. Configuration is in bindings/python/pyproject.toml under [tool.ty].

The type checker is configured to ignore unresolved imports (third-party dependencies may not be installed in all environments) and relaxes rules for legacy modules (simplified_beta, helpers, pytest).

Running locally¶

cd bindings/python

# Run type checks
ty check genalyzer/

CI Integration¶

All three tools run automatically in CI through the GitHub Actions workflow defined in .github/workflows/lint.yml. The workflow runs on every push and pull request with three parallel jobs:

clang-format - Verifies C/C++ formatting
ruff - Checks Python linting and formatting
ty - Runs Python type checking

Additionally, the main test workflow (.github/workflows/test.yml) includes a combined lint job that runs pre-commit hooks, Ruff, and ty together.

Adding new rules¶

To enable additional Ruff rules, add the rule code to the select list in bindings/python/pyproject.toml. See the Ruff rule reference for available rules.

To adjust ty strictness, modify the [tool.ty.rules] section. See the ty rule reference for available rules.