Python Project Setup

Python Project Setup

Instructions

Step 1: Gather Requirements

Ask:

1. What type of project? (library/package, web app, CLI tool, data pipeline)
2. Minimum Python version? (default: 3.11+)
3. Package manager preference? (pip, uv, poetry, pdm)
4. Layout preference? (src-layout or flat-layout)
5. What frameworks? (FastAPI, Django, Flask, Click, Typer)
6. CI platform? (GitHub Actions, GitLab CI)

Step 2: Project Structure

src-layout (recommended for libraries):

my-project/
  src/
    my_package/
      __init__.py
      main.py
      models.py
  tests/
    __init__.py
    conftest.py
    test_main.py
  pyproject.toml
  README.md
  .pre-commit-config.yaml
  .github/
    workflows/
      ci.yml

flat-layout (simpler, for apps):

my-project/
  my_package/
    __init__.py
    main.py
  tests/
    conftest.py
    test_main.py
  pyproject.toml
  README.md

Use src-layout by default. It prevents accidental imports of the source during testing.

Step 3: Generate pyproject.toml

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

[project]
name = "my-package"
version = "0.1.0"
description = "A brief description of the project"
readme = "README.md"
license = "MIT"
requires-python = ">=3.11"
authors = [
    { name = "Your Name", email = "you@example.com" },
]
dependencies = []

[project.optional-dependencies]
dev = [
    "pytest>=8.0",
    "pytest-cov>=5.0",
    "ruff>=0.4",
    "mypy>=1.10",
    "pre-commit>=3.7",
]

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

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

[tool.ruff]
target-version = "py311"
line-length = 88

[tool.ruff.lint]
select = [
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings
    "F",    # pyflakes
    "I",    # isort
    "B",    # flake8-bugbear
    "C4",   # flake8-comprehensions
    "UP",   # pyupgrade
    "SIM",  # flake8-simplify
]

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

[tool.mypy]
python_version = "3.11"
strict = true
warn_return_any = true
warn_unused_configs = true

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

[tool.coverage.report]
fail_under = 80
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "if TYPE_CHECKING:",
]

Step 4: Configure Linting and Formatting

Ruff (recommended - replaces flake8, isort, black):

Add to pyproject.toml (shown above). Ruff handles both linting and formatting:

# Lint
ruff check .

# Format
ruff format .

# Fix auto-fixable issues
ruff check --fix .

Type checking with mypy:

mypy src/

For strict mode, address these common issues:

• Add return type annotations to all functions
• Use from __future__ import annotations for modern syntax
• Add py.typed marker file for library packages

Step 5: Testing Setup

conftest.py with common fixtures:

import pytest

@pytest.fixture
def sample_data():
    """Provide sample test data."""
    return {"name": "test", "value": 42}

@pytest.fixture
def tmp_config(tmp_path):
    """Create a temporary config file."""
    config_file = tmp_path / "config.toml"
    config_file.write_text('[app]\ndebug = true\n')
    return config_file

Run tests with coverage:

pytest --cov --cov-report=term-missing --cov-report=html

Step 6: Pre-commit Hooks

.pre-commit-config.yaml:

repos:
  - repo: https://github.com/astral-sh/ruff-pre-commit
    rev: v0.4.4
    hooks:
      - id: ruff
        args: [--fix]
      - id: ruff-format

  - repo: https://github.com/pre-commit/mirrors-mypy
    rev: v1.10.0
    hooks:
      - id: mypy
        additional_dependencies: []

  - repo: https://github.com/pre-commit/pre-commit-hooks
    rev: v4.6.0
    hooks:
      - id: trailing-whitespace
      - id: end-of-file-fixer
      - id: check-yaml
      - id: check-toml
      - id: check-added-large-files

Install: pre-commit install

Step 7: Development Workflow Commands

Provide a Makefile or document these commands:

.PHONY: install lint format test typecheck all

install:
	pip install -e ".[dev]"
	pre-commit install

lint:
	ruff check .

format:
	ruff format .

test:
	pytest --cov --cov-report=term-missing

typecheck:
	mypy src/

all: lint typecheck test

Example

User says: "Set up a new Python CLI tool project"

Response:

• src-layout with Click/Typer for CLI framework
• pyproject.toml with CLI entry point in [project.scripts]
• Ruff for linting and formatting
• pytest with fixtures for CLI testing (CliRunner)
• Pre-commit config
• GitHub Actions CI workflow

Guidelines

• Default to src-layout for libraries, flat-layout for single-purpose apps
• Always use pyproject.toml over setup.py or setup.cfg (PEP 621)
• Recommend ruff over separate flake8+isort+black installations
• Pin minimum versions in dependencies, not exact versions
• Use optional dependency groups: dev, test, docs
• Include py.typed marker for typed libraries
• Set coverage threshold at 80% minimum
• Configure strict mypy mode from the start (easier than adding later)
• Use uv for faster dependency resolution when available

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: timwukp
• Source: timwukp/agent-skills-best-practice
• License: MIT

Install and usage instructions live in the source repository linked above.