Project template

A simple template for research project repos. You can also use data science and reproducible science cookie cutters.

Project structure

This template contains the following folders and files. See README.md in each folder for more details and guidelines.

1. data for raw & derived datasets.
2. libs for libraries for the project.
3. models for trained models.
4. notebooks for (timestamped) experiment notebooks.
5. paper for manuscripts.
6. results for results (figures, tables, etc.)
7. workflow for workflow files and scripts.
8. .gitignore for temporary and binary files to be ignored by git (LaTeX, Python, Jupyter, data files, etc.)

Using Python virtual environment

Use uv to create a virtual environment.

uv venv

.envrc allows automatic activation of virtual environment. See direnv.

Create pyproject.toml file and add necessary packages.

uv init
uv add PACKAGE_NAME

Once pyproject.toml file is created, you can use uv sync to synchronize the virtual environment.

uv sync

If you want to add the local project package and keep it editable, use uv add -e command.

uv add . --editable