Modern Python

Modern Python

Guide for modern Python tooling and best practices, based on trailofbits/cookiecutter-python.

When to Use This Skill

• Creating a new Python project or package
• Setting up pyproject.toml configuration
• Configuring development tools (linting, formatting, testing)
• Writing Python scripts with external dependencies
• Migrating from legacy tools (when user requests it)

When NOT to Use This Skill

• User wants to keep legacy tooling: Respect existing workflows if explicitly requested
• Python < 3.11 required: These tools target modern Python
• Non-Python projects: Mixed codebases where Python isn't primary

Anti-Patterns to Avoid

Key principles:

• Always use uv add and uv remove to manage dependencies
• Never manually activate or manage virtual environments—use uv run for all commands
• Use [dependency-groups] for dev/test/docs dependencies, not [project.optional-dependencies]
• Never use inline imports — all imports must be at the top of the file, per PEP 8

Decision Tree

What are you doing?
│
├─ Single-file script with dependencies?
│   └─ Use PEP 723 inline metadata (./references/pep723-scripts.md)
│
├─ New multi-file project (not distributed)?
│   └─ Minimal uv setup (see Quick Start below)
│
├─ New reusable package/library?
│   └─ Full project setup (see Full Setup below)
│
└─ Migrating existing project?
    └─ See Migration Guide below

Tool Overview

Security Tools

See security-setup.md for configuration and usage.

Quick Start: Minimal Project

For simple multi-file projects not intended for distribution:

# Create project with uv
uv init myproject
cd myproject

# Add dependencies
uv add requests rich

# Add dev dependencies
uv add --group dev pytest ruff ty

# Run code
uv run python src/myproject/main.py

# Run tools
uv run pytest
uv run ruff check .

Full Project Setup

If starting from scratch, ask the user if they prefer to use the Trail of Bits cookiecutter template to bootstrap a complete project with already preconfigured tooling.

uvx cookiecutter gh:trailofbits/cookiecutter-python

1. Create Project Structure

uv init --package myproject
cd myproject

This creates:

myproject/
├── pyproject.toml
├── README.md
├── src/
│   └── myproject/
│       └── __init__.py
└── .python-version

2. Configure pyproject.toml

See pyproject.md for complete configuration reference.

Key sections:

[project]
name = "myproject"
version = "0.1.0"
requires-python = ">=3.11"
dependencies = []

[dependency-groups]
dev = [{include-group = "lint"}, {include-group = "test"}, {include-group = "audit"}]
lint = ["ruff", "ty"]
test = ["pytest", "pytest-cov"]
audit = ["pip-audit"]

[tool.ruff]
line-length = 100
target-version = "py311"

[tool.ruff.lint]
select = ["ALL"]
ignore = ["D", "COM812", "ISC001"]

[tool.pytest]
addopts = ["--cov=myproject", "--cov-fail-under=80"]

[tool.ty.terminal]
error-on-warning = true

[tool.ty.environment]
python-version = "3.11"

[tool.ty.rules]
# Strict from day 1 for new projects
possibly-unresolved-reference = "error"
unused-ignore-comment = "warn"

3. Install Dependencies

# Install all dependency groups
uv sync --all-groups

# Or install specific groups
uv sync --group dev

4. Add Makefile

.PHONY: dev lint format test build

dev:
	uv sync --all-groups

lint:
	uv run ruff format --check && uv run ruff check && uv run ty check src/

format:
	uv run ruff format .

test:
	uv run pytest

build:
	uv build

Migration Guide

When a user requests migration from legacy tooling:

From requirements.txt + pip

First, determine the nature of the code:

For standalone scripts: Convert to PEP 723 inline metadata (see pep723-scripts.md)

For projects:

# Initialize uv in existing project
uv init --bare

# Add dependencies using uv (not by editing pyproject.toml)
uv add requests rich  # add each package

# Or import from requirements.txt (review each package before adding)
# Note: Complex version specifiers may need manual handling
grep -v '^#' requirements.txt | grep -v '^-' | grep -v '^\s*$' | while read -r pkg; do
    uv add "$pkg" || echo "Failed to add: $pkg"
done

uv sync

Then:

1. Delete requirements.txt, requirements-dev.txt
2. Delete virtual environment (venv/, .venv/)
3. Add uv.lock to version control

From setup.py / setup.cfg

1. Run uv init --bare to create pyproject.toml
2. Use uv add to add each dependency from install_requires
3. Use uv add --group dev for dev dependencies
4. Copy non-dependency metadata (name, version, description, etc.) to [project]
5. Delete setup.py, setup.cfg, MANIFEST.in

From flake8 + black + isort

1. Remove flake8, black, isort via uv remove
2. Delete .flake8, pyproject.toml [tool.black], [tool.isort] configs
3. Add ruff: uv add --group dev ruff
4. Add ruff configuration (see ruff-config.md)
5. Run uv run ruff check --fix . to apply fixes
6. Run uv run ruff format . to format

From mypy / pyright

1. Remove mypy/pyright via uv remove
2. Delete mypy.ini, pyrightconfig.json, or [tool.mypy]/[tool.pyright] sections
3. Add ty: uv add --group dev ty
4. Run uv run ty check src/

Quick Reference: uv Commands

Ad-hoc Dependencies with --with

Use uv run --with for one-off commands that need packages not in your project:

# Run Python with a temporary package
uv run --with requests python -c "import requests; print(requests.get('https://httpbin.org/ip').json())"

# Run a module with temporary deps
uv run --with rich python -m rich.progress

# Multiple packages
uv run --with requests --with rich python script.py

# Combine with project deps (adds to existing venv)
uv run --with httpx pytest  # project deps + httpx

When to use --with vs uv add:

• uv add: Package is a project dependency (goes in pyproject.toml/uv.lock)
• --with: One-off usage, testing, or scripts outside a project context

See uv-commands.md for complete reference.

Quick Reference: Dependency Groups

[dependency-groups]
dev = ["ruff", "ty"]
test = ["pytest", "pytest-cov", "hypothesis"]
docs = ["sphinx", "myst-parser"]

Install with: uv sync --group dev --group test

Pre-commit Workflow

Always install and run pre-commit hooks before making any commits. This is the most common cause of "lint failed on CI but passed locally". No commits should be made before hooks are active.

Setup (once per clone)

# Install the git hooks so they run automatically on every commit
uv run pre-commit install
# — or, if the project uses prek instead —
prek install

Before every commit

# Run all hooks against every tracked file and fix auto-fixable issues
uv run pre-commit run --all-files
# Re-stage any files that were auto-fixed, then commit

Agent checklist

When making code changes in this repository:

• pre-commit install has been run in this clone (git hooks are active)
• pre-commit run --all-files passes with no failures before using report_progress

Best Practices Checklist

• Use src/ layout for packages
• Set requires-python = ">=3.11"
• Configure ruff with select = ["ALL"] and explicit ignores
• Use ty for type checking
• Enforce test coverage minimum (80%+)
• Use dependency groups instead of extras for dev tools
• Add uv.lock to version control
• Use PEP 723 for standalone scripts

Read Next

• migration-checklist.md - Step-by-step migration cleanup
• pyproject.md - Complete pyproject.toml reference
• uv-commands.md - uv command reference
• ruff-config.md - Ruff linting/formatting configuration
• testing.md - pytest and coverage setup
• pep723-scripts.md - PEP 723 inline script metadata
• prek.md - Fast pre-commit hooks with prek
• security-setup.md - Security hooks and dependency scanning
• dependabot.md - Automated dependency updates