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 / uv remove 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 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

1. 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.ini_options ] 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"

1. Install Dependencies

Install all dependency groups

uv sync --all-groups

Or install specific groups

uv sync --group dev

1. 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 Add dependency uv add --group dev Add to dependency group uv remove Remove dependency uv sync Install dependencies uv sync --all-groups Install all dependency groups uv run Run command in venv uv run --with 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