Cookiecutter Research Project Template

A flexible Cookiecutter template for creating well-structured research project directories in Python. Designed to promote organization and reproducibility across various research domains, including:

• Data Science & Machine Learning (Classification, Regression)
• Neuroimaging (BIDS structure awareness, fMRI GLM analyses)
• Computational Modeling (e.g., Reinforcement Learning)
• Behavioral Analyses
• Web-based experiment deployment (optional structure for JS/FastAPI)

Features

This template provides a standardized layout:

• config/: Store configuration files (parameters, settings).
• data/: Organized data storage (raw, processed, external), compatible with BIDS in raw.
• docs/: Project documentation (methods, reports).
• notebooks/: Jupyter notebooks for exploration and prototyping.
• reports/: Final notebooks/scripts generating figures/reports from results/.
• src/: Reusable source code (Python modules/packages).
• scripts/: Runnable analysis scripts orchestrating the workflow.
• tests/: Unit/integration tests for your source code.
• results/: Organized storage for outputs (figures, tables, trained models, statistical maps) grouped by analysis.
• experiment_code/: (Optional) Separate directory for data collection code (e.g., PsychoPy, web tasks).
• Standard files like README.md, requirements.txt, environment.yml (optional).

Requirements

You need to have Cookiecutter installed:

pip install cookiecutter

Usage

To use this template to start a new project:

1. Navigate to the directory where you want to create your project folder.

2. Run the cookiecutter command, pointing it to this repository:

   cookiecutter gh:krkulkarni/cookiecutter-research-project

3. Cookiecutter will prompt you for the following information:

   • project_name: The human-readable name of your project (e.g., "My Awesome Research").
   • project_slug: The directory and Python package name (auto-generated from project_name, e.g., "my_awesome_research").
   • author_name: Your name.
   • author_email: Your email address.
   • description: A short description of the project.
   • version: Initial project version (e.g., "0.1.0").
   • project_url: URL for the project's repository (defaults based on GitHub username and project_slug).
   • open_source_license: Choose a license for the generated project.
   • python_interpreter: Preferred Python command (python3 or python).

4. A new directory named according to project_slug will be created, containing the populated project structure.

License

The Cookiecutter template itself is licensed under the MIT License. The license chosen during the setup (open_source_license variable) applies to the project generated by this template.

Contributing

Suggestions and improvements to this template are welcome! Please feel free to open an Issue or Pull Request.