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

Avoid	Use Instead
[tool.ty] python-version	[tool.ty.environment] python-version
uv pip install	uv add and uv sync
Editing pyproject.toml manually to add deps	uv add <pkg> / uv remove <pkg>
hatchling build backend	uv_build (simpler, sufficient for most cases)
Poetry	uv (faster, simpler, better ecosystem integration)
requirements.txt	PEP 723 for scripts, pyproject.toml for projects
mypy / pyright	ty (faster, from Astral team)
[project.optional-dependencies] for dev tools	[dependency-groups] (PEP 735)
Manual virtualenv activation (source .venv/bin/activate)	uv run <cmd>
pre-commit	prek (faster, no Python runtime needed)

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]

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

Tool	Purpose	Replaces
uv	Package/dependency management	pip, virtualenv, pip-tools, pipx, pyenv
ruff	Linting AND formatting	flake8, black, isort, pyupgrade, pydocstyle
ty	Type checking	mypy, pyright (faster alternative)
pytest	Testing with coverage	unittest
prek	Pre-commit hooks (setup)	pre-commit (faster, Rust-native)

Security Tools

Tool	Purpose	When It Runs
shellcheck	Shell script linting	pre-commit
detect-secrets	Secret detection	pre-commit
actionlint	Workflow syntax validation	pre-commit, CI
zizmor	Workflow security audit	pre-commit, CI
pip-audit	Dependency vulnerability scanning	CI, manual
Dependabot	Automated dependency updates	scheduled

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

Command	Description
uv init	Create new project
uv init --package	Create distributable package
uv add <pkg>	Add dependency
uv add --group dev <pkg>	Add to dependency group
uv remove <pkg>	Remove dependency
uv sync	Install dependencies
uv sync --all-groups	Install all dependency groups
uv run <cmd>	Run command in venv
uv run --with <pkg> <cmd>	Run with temporary dependency
uv build	Build package
uv publish	Publish to PyPI

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

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