Overview

This skill implements Trail of Bits' modern Python coding standards for the agent-studio framework. The core philosophy is: use Rust-based tools for faster feedback loops, especially when working with AI agents. Every tool in this stack (uv, ruff, ty) is written in Rust and provides sub-second execution times, enabling tight iteration cycles.

Source repository: https://github.com/trailofbits/skills Template: https://github.com/trailofbits/cookiecutter-python License: CC-BY-SA-4.0

When to Use

When creating new Python projects from scratch
When migrating Python projects from legacy tooling
When setting up CI/CD pipelines for Python projects
When standardizing Python tooling across a team
When writing standalone Python scripts that need proper structure
When an AI agent needs fast feedback from Python tooling

Iron Laws

ALWAYS configure all Python tooling in pyproject.toml -- no separate config files (setup.cfg, .flake8, mypy.ini, black.toml) are permitted.
ALWAYS use uv add/uv remove for dependency management -- never use bare pip install in projects managed by uv.
NEVER commit venv/, .venv/, or pip-generated requirements.txt -- commit uv.lock for reproducible builds.
ALWAYS use uv run to execute tools and scripts -- this ensures the correct virtual environment and dependency resolution.
NEVER use legacy linting/formatting tools (flake8, black, isort, mypy) when ruff and ty are available -- consolidate to the Rust-based stack for speed and consistency.

Anti-Patterns

Anti-Pattern	Why It Fails	Correct Approach
Using `pip install` directly in a uv-managed project	Bypasses lockfile and dependency resolution; creates reproducibility drift	Use `uv add <pkg>` to add dependencies and `uv sync` to install
Maintaining `.flake8`, `mypy.ini`, or `black.toml` config files	Fragments configuration across multiple files; hard to maintain and audit	Consolidate all tool config into `pyproject.toml` under `[tool.ruff]` and `[tool.ty]`
Running `python script.py` instead of `uv run python script.py`	Uses system Python instead of project venv; dependency mismatches	Always use `uv run` to execute within the managed environment
Globally installing CLI tools with `pip install --user`	Pollutes global environment; version conflicts across projects	Use `uv tool run <tool>` or `uvx <tool>` for one-off tool execution
Ignoring ruff security rules (`S` select)	Misses bandit-equivalent security checks like hardcoded passwords and SQL injection	Enable `select = ["S"]` in `[tool.ruff.lint]` for security linting

The Modern Python Stack

Tool	Replaces	Purpose	Speed
uv	pip, Poetry, pipenv, pip-tools	Package & project management	10-100x faster
ruff	flake8, isort, black, pyflakes, pycodestyle, pydocstyle	Linting + formatting	10-100x faster
ty	mypy, pyright, pytype	Type checking	5-10x faster
pytest	unittest	Testing	--
hypothesis	(manual property tests)	Property-based testing	--

Project Setup

New Project

# Create new project with uv
uv init my-project
cd my-project

# Add dependency groups
uv add --group dev ruff ty
uv add --group test pytest pytest-cov hypothesis
uv add --group docs sphinx myst-parser

# Install all dependencies
uv sync --all-groups

pyproject.toml Configuration

[project]
name = "my-project"
version = "0.1.0"
requires-python = ">=3.12"
dependencies = []

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

# === Ruff Configuration ===
[tool.ruff]
target-version = "py312"
line-length = 100

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # pyflakes
    "I",      # isort
    "N",      # pep8-naming
    "UP",     # pyupgrade
    "B",      # flake8-bugbear
    "A",      # flake8-builtins
    "C4",     # flake8-comprehensions
    "SIM",    # flake8-simplify
    "S",      # flake8-bandit (security)
    "TCH",    # flake8-type-checking
    "RUF",    # ruff-specific rules
]

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S101"]  # Allow assert in tests

[tool.ruff.format]
quote-style = "double"
indent-style = "space"

# === Pytest Configuration ===
[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = [
    "--strict-markers",
    "--strict-config",
    "-ra",
]

[tool.coverage.run]
source = ["src"]
branch = true

[tool.coverage.report]
fail_under = 80
show_missing = true
exclude_lines = [
    "if TYPE_CHECKING:",
    "if __name__ == .__main__.:",
]

Daily Workflow Commands

Package Management (uv)

# Add a dependency
uv add requests

# Add a dev dependency
uv add --group dev ipdb

# Remove a dependency
uv remove requests

# Update all dependencies
uv lock --upgrade

# Update a specific dependency
uv lock --upgrade-package requests

# Run a script in the project environment
uv run python script.py

# Run a tool (without installing globally)
uv run --with httpie http GET https://api.example.com

Linting and Formatting (ruff)

# Check for lint errors
uv run ruff check .

# Auto-fix lint errors
uv run ruff check --fix .

# Format code
uv run ruff format .

# Check formatting (dry run)
uv run ruff format --check .

# Check specific rules
uv run ruff check --select S .  # Security rules only

Type Checking (ty)

# Run type checker
uv run ty check

# Check specific file
uv run ty check src/main.py

Testing (pytest)

# Run all tests
uv run pytest

# Run with coverage
uv run pytest --cov

# Run specific test file
uv run pytest tests/test_auth.py

# Run with verbose output
uv run pytest -v

# Run and stop at first failure
uv run pytest -x

Migration Guide

From pip/requirements.txt

# Install uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# Initialize project from existing requirements
uv init
uv add $(cat requirements.txt | grep -v '^#' | grep -v '^$')

# Remove old files
rm requirements.txt requirements-dev.txt

From Poetry

# uv can read pyproject.toml with Poetry sections
uv init

# Move Poetry dependencies to [project.dependencies]
# Move [tool.poetry.group.dev.dependencies] to [dependency-groups]
# Remove [tool.poetry] section

uv sync

From flake8/black/isort to ruff

# Remove old tools
uv remove flake8 black isort pyflakes pycodestyle

# Add ruff
uv add --group dev ruff

# Convert .flake8 config to ruff (manual)
# ruff supports most flake8 rules with same codes

# Remove old config files
rm .flake8 .isort.cfg pyproject.toml.bak

From mypy to ty

# Remove mypy
uv remove mypy

# Add ty
uv add --group dev ty

# ty uses the same type annotation syntax as mypy
# Most code requires no changes

CI/CD Configuration

GitHub Actions

name: CI

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]

jobs:
  check:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: astral-sh/setup-uv@v4
        with:
          enable-cache: true

      - name: Install dependencies
        run: uv sync --all-groups

      - name: Lint
        run: uv run ruff check .

      - name: Format check
        run: uv run ruff format --check .

      - name: Type check
        run: uv run ty check

      - name: Test
        run: uv run pytest --cov --cov-report=xml

      - name: Upload coverage
        uses: codecov/codecov-action@v4
        with:
          file: coverage.xml

Dependabot Configuration

# .github/dependabot.yml
version: 2
updates:
  - package-ecosystem: 'uv'
    directory: '/'
    schedule:
      interval: 'weekly'
    groups:
      all:
        patterns:
          - '*'

Pre-commit Hooks

# .pre-commit-config.yaml
repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.9.0
    hooks:
      - id: ruff
        args: [--fix]
      - id: ruff-format

Code Patterns

Type Annotations

from __future__ import annotations

from collections.abc import Sequence
from typing import TypeAlias

# Use modern syntax (Python 3.12+)
type Vector = list[float]  # Type alias (PEP 695)

def process_items(items: Sequence[str], *, limit: int = 10) -> list[str]:
    """Process items with a limit."""
    return [item.strip() for item in items[:limit]]

# Use | instead of Union
def maybe_int(value: str) -> int | None:
    try:
        return int(value)
    except ValueError:
        return None

Project Structure

my-project/
  pyproject.toml          # Single config file for all tools
  uv.lock                 # Locked dependencies (commit this)
  src/
    my_project/
      __init__.py
      main.py
      models.py
      utils.py
  tests/
    __init__.py
    test_main.py
    test_models.py
    conftest.py           # Shared fixtures
  .github/
    workflows/
      ci.yml
    dependabot.yml
  .pre-commit-config.yaml

Common Pitfalls

Using pip directly: Always use uv add / uv remove / uv run. Never pip install.
Separate config files: All configuration goes in pyproject.toml. Delete .flake8, mypy.ini, black.toml.
Global installs: Use uv run or uv tool run instead of globally installing CLI tools.
Missing lock file: Always commit uv.lock for reproducible builds.
Old Python syntax: Use ruff --select UP to auto-upgrade to modern syntax (match statements, | unions, etc.).
Ignoring security rules: Enable S (bandit) rules in ruff to catch security issues.

Integration with Agent-Studio

Recommended Workflow

Use modern-python to set up or migrate Python projects
Use python-backend-expert for framework-specific patterns (Django, FastAPI)
Use tdd skill for test-driven development workflow
Use comprehensive-unit-testing-with-pytest for test strategy

Complementary Skills

Skill	Relationship
`python-backend-expert`	Framework-specific patterns (Django, FastAPI, Flask)
`comprehensive-unit-testing-with-pytest`	Testing strategies and patterns
`comprehensive-type-annotations`	Type annotation best practices
`prioritize-python-3-10-features`	Modern Python language features
`tdd`	Test-driven development methodology
`property-based-testing`	Hypothesis-based testing patterns

Memory Protocol

Before starting: Check if the project already has Python tooling configured. Identify which legacy tools need migration.

During setup: Write configuration incrementally, verifying each tool works before moving to the next. Run ruff check, ruff format --check, and uv run pytest at each step.

After completion: Record the toolchain versions and any migration issues to .claude/context/memory/learnings.md for future reference.

modern-python

Modern Python Skill