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:

• Delete requirements.txt, requirements-dev.txt

• Delete virtual environment (venv/, .venv/)

• Add uv.lock to version control

From setup.py / setup.cfg

• Run uv init --bare to create pyproject.toml

• Use uv add to add each dependency from install_requires

• Use uv add --group dev for dev dependencies

• Copy non-dependency metadata (name, version, description, etc.) to [project]

• Delete setup.py, setup.cfg, MANIFEST.in

From flake8 + black + isort

• Remove flake8, black, isort via uv remove

• Delete .flake8, pyproject.toml [tool.black], [tool.isort] configs

• Add ruff: uv add --group dev ruff

• Add ruff configuration (see ruff-config.md)

• Run uv run ruff check --fix . to apply fixes

• Run uv run ruff format . to format

From mypy / pyright

• Remove mypy/pyright via uv remove

• Delete mypy.ini, pyrightconfig.json, or [tool.mypy]/[tool.pyright] sections

• Add ty: uv add --group dev ty

• 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