Cookiecutter Scientific Paper

A cookiecutter template for scientific papers that embraces open science principles and collaborative GitHub-based workflows.

This template creates a comprehensive project structure with:

• Paper manuscript in Markdown with LaTeX math support
• Reproducible analysis code
• Python package for reusable methods
• Data management structure
• GitHub integration for collaboration
• Automatic DOI generation via Zenodo

Features

• Open Science Ready: Built with transparency and reproducibility as core principles
• GitHub Integrated: Issue templates, GitHub Actions workflows, and web rendering
• Comprehensive: Covers paper writing, code development, and data management
• Citable: Includes proper citation metadata and DOI integration
• Collaborative: Designed for easy contributions and peer review through GitHub
• Automated Distribution: Built-in system for distributing papers without traditional journals

Requirements

• Python 3.7+
• Cookiecutter (pip install cookiecutter)
• Git

Usage

# Create a new scientific paper project
cookiecutter gh:yourusername/cookiecutter-science-paper

# Answer the prompts to customize your project

Project Structure

The generated project will have the following structure:

your-project-name/
├── .github/                      # GitHub integration
├── paper/                        # Manuscript and supporting files
├── src/                          # Source code for reusable package
├── code/                         # Analysis and experiment code
└── data/                         # Data management

Example

For a complete example of a paper using this template, see example-paper.

License

This template is licensed under the MIT License - see the LICENSE file for details.