python-package-management

name	python-package-management
description	Complete Python package management system. PROACTIVELY activate for: (1) uv package manager (10-100x faster), (2) pyproject.toml configuration, (3) Virtual environment setup, (4) Dependency management with uv.lock, (5) Ruff linting and formatting, (6) src layout project structure, (7) Publishing to PyPI, (8) pip and requirements.txt. Provides: uv commands, pyproject.toml templates, ruff config, pre-commit setup. Ensures modern Python project setup with fast tooling.
auto_load	{"enabled":true,"triggers":{"keywords":["uv","pip","package","dependency","pyproject","venv","virtual","install"],"file_patterns":["pyproject.toml","requirements*.txt","setup.py"]},"priority":"high","load_with":["python-fundamentals"]}

Quick Reference

uv Command	Purpose
uv init my-project	Create new project
uv add <package>	Add dependency
uv add --dev <package>	Add dev dependency
uv sync	Install all dependencies
uv run <command>	Run in virtual env
uv lock --upgrade	Update all deps
uv python install 3.13	Install Python version

Tool	Command	Speed
uv	uv add requests	10-100x faster
pip	pip install requests	Baseline

ruff Command	Purpose
ruff check .	Lint code
ruff check --fix .	Auto-fix issues
ruff format .	Format code

Project Layout	Recommended
src layout	src/my_package/
Tests	tests/
Config	pyproject.toml

When to Use This Skill

Use for project setup and dependencies:

• Starting new Python projects
• Setting up uv for fast package management
• Configuring pyproject.toml
• Setting up linting with ruff
• Publishing packages to PyPI

Related skills:

• For CI/CD: see python-github-actions
• For testing: see python-testing
• For type hints config: see python-type-hints

---

Python Package Management (2025)

Overview

Modern Python package management centers around uv (the fast Rust-based tool), pip, and pyproject.toml. This guide covers best practices for dependency management, virtual environments, and project configuration.

uv - The Modern Package Manager

Why uv?

• 10-100x faster than pip (written in Rust)
• Replaces pip, pip-tools, pipx, poetry, pyenv, virtualenv
• Automatic virtual environment management
• Lockfile support for reproducibility
• ~200x faster venv creation

Installation

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

# Windows (PowerShell)
irm https://astral.sh/uv/install.ps1 | iex

# pip (works everywhere)
pip install uv

# Homebrew
brew install uv

Quick Start

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

# Add dependencies
uv add requests fastapi pydantic

# Add dev dependencies
uv add --dev pytest ruff mypy

# Sync environment (install all dependencies)
uv sync

# Run commands in the environment
uv run python main.py
uv run pytest

Basic Commands

# Package management
uv add <package>              # Add dependency
uv add <package>==1.0.0       # Specific version
uv add --dev <package>        # Dev dependency
uv remove <package>           # Remove dependency
uv sync                       # Sync environment with lockfile

# Virtual environments
uv venv                       # Create .venv
uv venv --python 3.12         # Specific Python version
uv venv my-env                # Named environment

# pip compatibility
uv pip install <package>      # Install (faster pip)
uv pip install -r requirements.txt
uv pip freeze > requirements.txt
uv pip compile pyproject.toml -o requirements.txt

# Python management
uv python install 3.13        # Install Python version
uv python list                # List installed versions
uv python pin 3.12            # Pin project Python version

# Running
uv run <command>              # Run in virtual env
uv run --with httpx python    # Run with temporary package

pyproject.toml with uv

[project]
name = "my-project"
version = "0.1.0"
description = "My Python project"
readme = "README.md"
requires-python = ">=3.11"
license = {text = "MIT"}
authors = [
    {name = "Your Name", email = "[e-mail]"}
]
dependencies = [
    "fastapi>=0.100.0",
    "pydantic>=2.0.0",
    "httpx>=0.25.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=8.0.0",
    "ruff>=0.1.0",
    "mypy>=1.8.0",
]

[project.scripts]
my-cli = "my_project.cli:main"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.uv]
dev-dependencies = [
    "pytest>=8.0.0",
    "ruff>=0.1.0",
    "mypy>=1.8.0",
]

uv.lock

# Lockfile is auto-generated and should be committed
# Contains exact versions for reproducibility

# Update all dependencies
uv lock --upgrade

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

# Install from lockfile only
uv sync --frozen

Project Structure

Recommended: src Layout

my-project/
├── src/
│   └── my_package/
│       ├── __init__.py
│       ├── main.py
│       ├── models.py
│       └── utils/
│           ├── __init__.py
│           └── helpers.py
├── tests/
│   ├── __init__.py
│   ├── conftest.py
│   ├── test_main.py
│   └── test_models.py
├── docs/
│   └── index.md
├── pyproject.toml
├── uv.lock
├── README.md
├── LICENSE
└── .gitignore

Why src Layout?

1. Prevents import confusion - Can't accidentally import from project root
2. Forces installation - Must install package to test
3. Cleaner distributions - Only package code in wheels
4. Semantic clarity - Clear separation of code, tests, docs

Flat Layout (for simpler projects)

my-project/
├── my_package/
│   ├── __init__.py
│   └── main.py
├── tests/
│   └── test_main.py
├── pyproject.toml
└── README.md

pyproject.toml Complete Reference

[project]
name = "my-project"
version = "1.0.0"
description = "A comprehensive Python project"
readme = "README.md"
requires-python = ">=3.11"
license = {text = "MIT"}
keywords = ["python", "example", "package"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
]
authors = [
    {name = "Your Name", email = "[e-mail]"}
]
maintainers = [
    {name = "Maintainer", email = "[e-mail]"}
]

dependencies = [
    "fastapi>=0.100.0",
    "pydantic>=2.0.0",
    "sqlalchemy>=2.0.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=8.0.0",
    "pytest-cov>=4.0.0",
    "ruff>=0.1.0",
    "mypy>=1.8.0",
    "pre-commit>=3.0.0",
]
docs = [
    "mkdocs>=1.5.0",
    "mkdocs-material>=9.0.0",
]
all = ["my-project[dev,docs]"]

[project.scripts]
my-cli = "my_package.cli:main"

[project.entry-points."my_package.plugins"]
plugin1 = "my_package.plugins:Plugin1"

[project.urls]
Homepage = "https://github.com/user/my-project"
Documentation = "https://my-project.readthedocs.io"
Repository = "https://github.com/user/my-project"
Changelog = "https://github.com/user/my-project/blob/main/CHANGELOG.md"

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/my_package"]

# Ruff configuration
[tool.ruff]
target-version = "py311"
line-length = 88
src = ["src", "tests"]

[tool.ruff.lint]
select = [
    "E",     # pycodestyle errors
    "W",     # pycodestyle warnings
    "F",     # Pyflakes
    "I",     # isort
    "B",     # flake8-bugbear
    "C4",    # flake8-comprehensions
    "UP",    # pyupgrade
    "ARG",   # flake8-unused-arguments
    "SIM",   # flake8-simplify
]
ignore = [
    "E501",  # line too long (handled by formatter)
]

[tool.ruff.lint.isort]
known-first-party = ["my_package"]

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

# Mypy configuration
[tool.mypy]
python_version = "3.12"
strict = true
warn_return_any = true
warn_unused_ignores = true
disallow_untyped_defs = true
plugins = ["pydantic.mypy"]

[[tool.mypy.overrides]]
module = "tests.*"
disallow_untyped_defs = false

# Pytest configuration
[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = [
    "-ra",
    "-q",
    "--strict-markers",
    "--cov=src/my_package",
    "--cov-report=term-missing",
]

# Coverage configuration
[tool.coverage.run]
branch = true
source = ["src/my_package"]
omit = ["*/tests/*", "*/__init__.py"]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise NotImplementedError",
    "if TYPE_CHECKING:",
]

Ruff - Linting and Formatting

Why Ruff?

• 10-100x faster than Flake8, Black combined
• Single tool for linting AND formatting
• 800+ built-in rules
• Auto-fix capabilities
• Written in Rust (by Astral, same as uv)

Basic Usage

# Linting
ruff check .                   # Check for issues
ruff check --fix .             # Auto-fix issues
ruff check --watch .           # Watch mode

# Formatting
ruff format .                  # Format all files
ruff format --check .          # Check formatting

# Both
ruff check --fix . && ruff format .

Configuration

# pyproject.toml
[tool.ruff]
target-version = "py311"
line-length = 88
src = ["src", "tests"]

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # Pyflakes
    "I",      # isort
    "B",      # flake8-bugbear
    "C4",     # flake8-comprehensions
    "UP",     # pyupgrade
    "ARG",    # flake8-unused-arguments
    "SIM",    # flake8-simplify
    "TCH",    # flake8-type-checking
    "PTH",    # flake8-use-pathlib
    "ERA",    # eradicate (commented code)
    "PL",     # Pylint
    "PERF",   # Perflint
    "RUF",    # Ruff-specific rules
]
ignore = [
    "E501",   # line too long (handled by formatter)
    "PLR0913", # too many arguments
]

# Per-file ignores
[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S101"]  # Allow assert in tests
"__init__.py" = ["F401"]    # Allow unused imports

[tool.ruff.lint.isort]
known-first-party = ["my_package"]
force-single-line = true

[tool.ruff.format]
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"

Pre-commit Integration

# .pre-commit-config.yaml
repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.4.0
    hooks:
      - id: ruff
        args: [--fix]
      - id: ruff-format

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.9.0
    hooks:
      - id: mypy
        additional_dependencies:
          - pydantic
          - types-requests

pip and requirements.txt

When to Use pip

• Production environments requiring stability
• Legacy projects
• Simple scripts without complex dependencies

requirements.txt Best Practices

# requirements.txt - Pinned versions for production
fastapi==0.109.0
pydantic==2.5.3
sqlalchemy==2.0.25
httpx==0.26.0

# requirements-dev.txt
-r requirements.txt
pytest==8.0.0
ruff==0.1.14
mypy==1.8.0

Generating requirements.txt

# From uv
uv pip compile pyproject.toml -o requirements.txt
uv pip compile pyproject.toml --extra dev -o requirements-dev.txt

# From pip-tools
pip-compile pyproject.toml -o requirements.txt
pip-compile pyproject.toml --extra dev -o requirements-dev.txt

# Freeze current environment (not recommended for reproducibility)
pip freeze > requirements.txt

Virtual Environment Best Practices

Location

# Recommended: Project-local .venv
project/
├── .venv/        # Virtual environment here
├── src/
├── tests/
└── pyproject.toml

# uv creates .venv by default
uv venv

# Explicit location
uv venv .venv
python -m venv .venv

.gitignore

# Virtual environments
.venv/
venv/
ENV/
env/

# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python

# Distribution
build/
dist/
*.egg-info/

# IDE
.idea/
.vscode/
*.swp
*.swo

# Testing
.pytest_cache/
.coverage
htmlcov/
.mypy_cache/

# Ruff
.ruff_cache/

Activation (when needed)

# Usually not needed with uv - just use `uv run`

# Linux/macOS
source .venv/bin/activate

# Windows (PowerShell)
.venv\Scripts\Activate.ps1

# Windows (cmd)
.venv\Scripts\activate.bat

# Deactivate
deactivate

Publishing Packages

Build and Publish

# Build with uv
uv build

# Publish to PyPI
uv publish

# Or with twine
pip install twine
twine upload dist/*

# Test PyPI first
twine upload --repository testpypi dist/*

Version Management

# pyproject.toml - dynamic version from __init__.py
[project]
dynamic = ["version"]

[tool.hatch.version]
path = "src/my_package/__init__.py"

# src/my_package/__init__.py
__version__ = "1.0.0"