code-quality-tools

# Code Quality Tools for Scientific Python

Master the essential code quality tools that keep scientific Python projects maintainable, consistent, and error-free. Learn how to configure **ruff** for lightning-fast linting and formatting, **mypy** for static type checking, and **pre-commit** hooks for automated quality gates. These tools help catch bugs early, enforce consistent style across teams, and make code reviews focus on logic rather than formatting.

**Key Tools:**
- **Ruff**: Ultra-fast Python linter and formatter (replaces flake8, black, isort, and more)
- **MyPy**: Static type checker for Python
- **Pre-commit**: Git hook framework for automated checks

## Quick Reference Card

### Installation & Setup
```bash
# Using pixi (recommended for scientific projects)
pixi add --feature dev ruff mypy pre-commit

# Using pip
pip install ruff mypy pre-commit

# Initialize pre-commit
pre-commit install
```

### Essential Ruff Commands
```bash
# Check code (linting)
ruff check .

# Fix auto-fixable issues
ruff check --fix .

# Format code
ruff format .

# Check and format together
ruff check --fix . && ruff format .
```

### Essential MyPy Commands
```bash
# Type check entire project
mypy src/

# Type check with strict mode
mypy --strict src/

# Type check specific file
mypy src/mymodule/analysis.py

# Generate type coverage report
mypy --html-report mypy-report src/
```

### Essential Pre-commit Commands
```bash
# Run all hooks on all files
pre-commit run --all-files

# Run hooks on staged files only
pre-commit run

# Update hook versions
pre-commit autoupdate

# Skip hooks temporarily (not recommended)
git commit --no-verify
```

### Quick Decision Tree

```
Need to enforce code style and catch common errors?
  YES → Use Ruff (linting + formatting)
  NO → Skip to type checking

Want to catch type-related bugs before runtime?
  YES → Add MyPy
  NO → Ruff alone is sufficient

Need to ensure checks run automatically?
  YES → Set up pre-commit hooks
  NO → Run tools ma