Scientific Paper Template

A modular, Git-tracked scientific writing workflow using Markdown, Pandoc, and automated Makefile compilation.

Suggestions

• Maintain AUTHORS.md from day 1 of your project.
• If you are an author, for the changes obtained through extensive use of AI, start the commit message with AI, optionally including the chat history doi as well.

🛠️ Features

• Write the manuscript in lightweight Markdown (paper.md)
• Use a modular AUTHORS.md for author contributions
• Format control via metadata.yaml
• Output to multiple formats: PDF, DOCX, and LaTeX
• Automatic injection of author metadata using a preprocessing script
• Easy build automation with Makefile

🗂️ Project Structure

text your-paper/ ├── manuscript/ │ ├── paper.md # Main manuscript in Markdown │ ├── AUTHORS.md # Author list and contributions │ ├── refs.bib # BibTeX bibliography ├── presentation/ │ ├── slides.md # Markdown-based presentation │ ├── slides.qmd # Quarto format (optional) │ ├── Makefile # Build slides into HTML/PDF │ └── build/ # Compiled outputs ├── shared/ │ ├── figures/ # Reusable diagrams and plots │ └── data/ # Reusable data (raw/processed) ├── metadata.yaml # Document styling and layout ├── inject-authors.py # Preprocessor script ├── Makefile # Build automation ├── build/ # Compiled outputs (ignored by Git) ├── scripts/ # Code used for analysis or figure generation │ ├── generate_figures.py │ ├── stats.R ├── .gitignore # Clean up your repo ├── LICENSE # Usage rights ├── CITATION.cff # Citation metadata └── README.md # Project overview and instructions

🔧 Requirements

• Pandoc

• pandoc-include

  pip install pandoc-include

🚀 Build Instructions

Run the following from the repository root:

bash make # Compiles PDF, DOCX, and LaTeX make pdf # Compiles PDF only make docx # Compiles DOCX only make tex # Generates LaTeX file only make clean # Cleans build artifacts

🧑‍🤝‍🧑 Contributions

See manuscript/AUTHORS.md for author roles and ORCID IDs.

📜 Citation

Please cite this work using the details in CITATION.cff.

Inspired by

• Scientific Markdown
• Scientific Writing with Markdown
• Copilot

🔓 License

Licensed under Creative Commons Attribution 4.0.