Repository Template for Reproducible Research

Click "Use this template" at the top of the webpage on GitHub to create a new repository with the same folder structure. You can then add your own files and edit this README for your particular project.

• This simple project structure template repository is adapted from https://github.com/UtrechtUniversity/simple-python-template.
• You can find a guide to getting set up with Git, and slides from a workshop on reproducible research, in the doc/ folder.
• See here for a useful guide to installing a minimal Python environment and setting up in VS Code and conda.
• For more detail on Git, see this great free tutorial
• If you plan to develop a package, check out the template repository for a Python package.

How to run this code

Update for your specific project

You will need

• Git (configured: check with git config --list )

  • git config --global user.name "Your Name"

  • git config --global user.email "you@example.com"

  • For complete instructions, see doc/git_setup_guide.md

• Python (latest stable version, e.g., 3.10+)

• An active GitHub account

• A terminal or IDE of your choice (VS Code recommended)

Clone this repository

git clone https://github.com/YOUR-USERNAME/YOUR-REPO-NAME.git

Change directory to this folder

cd YOUR-REPO-NAME

Set up virtual environment

1. Create a virtual environment: python -m venv venv
2. Activate the environment:
   • Windows: source venv/Scripts/activate
   • Linux/macOS: source venv/bin/activate
3. Install required packages: pip install -r requirements.txt
   • If you haven't yet set up this file, you can first install the required packages, then use pip freeze > requirements.txt to write all the dependencies (and their versions) to this file. Note that this can be a bit overkill with the number of dependencies listed: see here for an improved method.

Execute code

For example: change these based on your specific files, and add detail about what each step involves

python scripts/01_get_data.py
python scripts/02_clean_data.py
python scripts/03_analysis.py

Project Structure

Recommended: change based on your specific files. For example, you may also want a src/, models/ or notebooks/ folder. (If you are inside notebooks/ you will likely want to put sys.path.append(os.path.abspath("..")) at the start of your notebook, so that you can import funcs from scripts/

.
├── README.md          <- Overview of the project, how to install and use 
├── LICENSE            <- License for open-source projects
│── CITATION.cff       <- Citation file for academic use
├── .gitignore         <- Files to ignore (e.g., __pycache__, logs, data)
├── requirements.txt   <- Dependencies (if using pip: use environment.yml if using conda)
├── venv               <- Virtual environment (git ignored)
├── data/              <- Data directory (typically ignored in version control)
│   ├── raw/           <- Raw input data (DO NOT MODIFY!)
│   └── processed/     <- Processed datasets
├── doc/               <- Written reports, papers, and documentation
│   ├── project_overview.md
│   ├── final_paper.pdf
├── outputs/           <- Outputs like figures, results, model
│   └── figs/          <- Plots and figures
└── scripts/           <- Your codes
    ├── utils.py       <- Functions used by multiple scripts
    ├── 01_get_data.py
    ├── 02_clean_data.py
    └── 03_analysis.py

Share your software

1. Link Zenodo to your GitHub account
2. Use Zenodo to create a DOI for the current version of this repo
3. Use this DOI when creating a citation file for your repository using cffinit

License

This project is licensed under the terms of the MIT License.