Modern Python

Trail of BitsOfficialPublished by Trail of Bits

Skill
Tool integration
Security
CC-BY-SA-4.0
Medium risk

From the author

Configures Python projects with modern tooling (uv, ruff, ty). Use when creating projects, writing standalone scripts, or migrating from pip/Poetry/mypy/black.

— the description by Trail of Bits

AutoGineer summary

Written by AutoGineer from the skill’s own files, not by the author

This skill provides a structured approach to setting up and maintaining Python projects using contemporary tooling. It focuses on replacing legacy workflows with tools such as uv for dependency management, ruff for linting and formatting, and ty for type checking. The guide includes instructions for new project bootstrapping, migration strategies for existing codebases, and best practices for dependency management and security.

What it does

Provides configuration patterns for pyproject.toml
Outlines migration steps from legacy tools like pip, Poetry, and mypy
Defines best practices for dependency management using uv
Offers guidance on setting up linting, formatting, and type checking
Includes security-focused setup instructions for dependency auditing
Provides templates for project structure and CI integration

When to use it

When starting a new Python project or package
When migrating an existing project from legacy tools
When configuring development environments for linting and testing
When writing standalone Python scripts with external dependencies

Advantages

Centralizes project configuration in pyproject.toml
Standardizes development workflows across projects
Provides clear paths for migrating away from legacy tooling
Integrates security auditing into the development lifecycle

Usage examples

“How do I start a new Python project with modern tools?”: The agent will guide you through using uv init to create a project structure and configure your pyproject.toml with recommended dependency groups.
“Migrate my existing project from pip and flake8.”: The agent will provide a step-by-step plan to remove legacy files, initialize uv, and configure ruff for linting and formatting.
“How should I manage dev dependencies?”: The agent will explain how to use dependency groups in pyproject.toml and the uv sync command to manage your development environment.
“How do I run a script with temporary dependencies?”: The agent will demonstrate the use of uv run --with to execute scripts without adding dependencies to your project configuration.

Install

Download the skill as a ZIP:
https://autogineer.com/agent-skills/trailofbits/modern-python/download

Unzip it into the cross-client skills folder of your project:

mkdir -p .agents/skills && unzip modern-python.zip -d .agents/skills

Documentation by Trail of Bits

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

Files

ATTRIBUTION.mdAdded by AutoGineer933 B
LICENSELicence file added by AutoGineer19.7 KiB
SKILL.md9.8 KiB
agents/openai.yaml226 B
assets/trail-of-bits-mark.svg3.0 KiB
references/dependabot.md1.8 KiB
references/migration-checklist.md3.0 KiB
references/pep723-scripts.md5.0 KiB
references/prek.md5.8 KiB
references/pyproject.md5.6 KiB
references/ruff-config.md5.3 KiB
references/security-setup.md6.4 KiB
references/testing.md5.1 KiB
references/uv-commands.md4.5 KiB
templates/dependabot.yml958 B
templates/pre-commit-config.yaml2.2 KiB

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Requirements and compatibility

Works with: Claude Code, Claude apps, OpenAI Codex, GitHub Copilot, Cursor, Gemini CLI, Kiro, OpenCode, Goose, Amp, Roo Code, JetBrains Junie, Factory Droid, Devin (ex-Windsurf), Mistral Vibe, OpenHands, Letta

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Needs: Needs Python

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Instructions that use the network
Downloads piped into a shell

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Attribution and licence

Published by

Trail of Bits

Publisher

Trail of Bits (Official)

Source

trailofbits/skills · plugins/modern-python/skills/modern-python · commit e4dd0bb

Licence

Creative Commons Attribution-ShareAlike 4.0 International (redistribution allowed)

LICENSE (added by AutoGineer from LICENSE)
ATTRIBUTION.md (written by AutoGineer)

Synced

2026-11-09

AutoGineer is not affiliated with or endorsed by Trail of Bits or Trail of Bits.

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The ZIP holds the skill’s files, its licence files and an ATTRIBUTION.md. Download modern-python.zip

From the author

AutoGineer summary

What it does

When to use it

Advantages

Usage examples

Install

Documentation by Trail of Bits

Modern Python

When to Use This Skill

When NOT to Use This Skill

Anti-Patterns to Avoid

Decision Tree

Tool Overview

Security Tools

Quick Start: Minimal Project

Full Project Setup

1. Create Project Structure

2. Configure pyproject.toml

3. Install Dependencies

4. Add Makefile

Migration Guide

From requirements.txt + pip

From setup.py / setup.cfg

From flake8 + black + isort

From mypy / pyright

Quick Reference: uv Commands

Ad-hoc Dependencies with --with

Quick Reference: Dependency Groups

Best Practices Checklist

Read Next

Files

LICENSE

Requirements and compatibility

Security

Attribution and licence

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Download ZIP

Ad-hoc Dependencies with `--with`