Project Organization

Use this skill when creating new projects, scaffolding packages, or reviewing project structure to ensure consistency with established patterns.

Quick Reference

R packages: See R project patterns Julia packages: See Julia project patterns

Core Principles

Project Root Structure

Every project should have:

project/ ├── .claude/ # Claude Code project config (optional) │ └── CLAUDE.md # Or in project root ├── .github/ # GitHub Actions and templates │ └── workflows/ ├── .pre-commit-config.yaml ├── .gitignore ├── CLAUDE.md # Project-specific instructions ├── LICENSE.md ├── NEWS.md # Changelog ├── README.md # Or README.Rmd for R └── CITATION.cff # Citation metadata

CLAUDE.md Structure

Every project CLAUDE.md should include:

• Package/Project Overview - What it does, core purpose

• Development Commands - How to test, build, document

• Architecture - Key components and their relationships

• Testing Patterns - Framework, conventions, special considerations

• Code Style - Language-specific guidelines beyond global rules

Template:

CLAUDE.md

This file provides guidance to Claude Code when working with this repository.

Package Overview

[Brief description of purpose and core functionality]

Development Commands

# Key commands with comments

Architecture

Core Components

- Component: Description

- Component: Description

Testing Patterns

[Framework, conventions, file naming]

Code Style

[Project-specific rules beyond global CLAUDE.md]

### Pre-commit Hooks

All projects use pre-commit for automated quality checks:

```bash
# Install
pip install pre-commit
pre-commit install

# Run manually
pre-commit run --all-files

Common hooks:

- Trailing whitespace removal

- End of file fixing

- Large file checks

- YAML validation

- Language-specific linting and formatting

When to Use This Skill

Activate when:

- Creating a new R or Julia package

- Setting up a research project repository

- Reviewing project structure for consistency

- Adding configuration files to existing projects

- Scaffolding CI/CD workflows

For language-specific patterns, see the reference files.