Lab Research Project Template

This repository is a template for setting up research projects in our lab. It supports Python (via Miniforge3), Jupyter, Quarto, and Wolfram Language (Mathematica), and is optimized for use in VSCode with GitHub integration.

🧱 Directory Structure

project-template/ ├── .vscode/ # VSCode settings and extension recommendations ├── .github/ # GitHub Actions workflows and issue templates ├── .gitattributes # Git LFS configuration ├── data/ # Raw input data (or references to external datasets) ├── docs/ # Documentation, paper drafts, Quarto site ├── notebooks/ # Wolfram, Jupyter, Quarto notebooks and packages ├── results/ # Outputs, plots, processed data ├── scripts/ # Python/Wolfram scripts for analysis and workflows ├── CITATION.cff # Citation metadata ├── environment.yml # Conda environment definition (via Miniforge3) ├── LICENSE # Project license ├── Makefile # Setup and cleanup utilities ├── README.md # This file ├── references.bib # BibTeX references for citations └── version.json # Project versioning

🚀 Getting Started

1. Clone the repository

bash git clone https://github.com/YOUR-LAB-NAME/project-template.git your-project-name cd your-project-name

⚠️ If using this as a GitHub template, click "Use this template" on GitHub and create your own copy.

2. Set up the Python environment

We recommend using Miniforge3:

bash conda env create -f environment.yml conda activate lab-env

Or use make:

bash make setup

3. Open in VSCode

This repo includes recommended extensions and settings in the .vscode/ folder. Just launch VSCode in the root folder:

bash code .

4. Enable Git LFS (if needed)

If you're working with large binary files like .png, .exr, .mov, enable Git LFS:

bash git lfs install

Git LFS is pre-configured for common binary types in .gitattributes.

📝 Notes

• You can write documentation in Quarto (.qmd) in the docs/ folder.
• If publishing a Quarto site, the default output goes to docs/, which is GitHub Pages–ready.
• GitHub Actions are included for:
  • Linting Python code (black, flake8)
  • Rendering Quarto documents on push

📄 Citation

If you use this template in a publication, please cite the associated metadata in CITATION.cff.