The purpose of this template is to be a foundation for creating a new research project, specifically for data/network science research in the NERDS research group - but feel free to use it in any way. The template comes with a basic folder structure and a workflow adapted for programming using Python.

⚠️ Read TEMPLATE.md to know how to use the template ⚠️

This is the source code for the scientific paper/project PROJECTNAME by AUTHOR1, AUTHOR2, and AUTHOR3. The code SHORTEXPLANATION.

Preprint: arXiv:XXXX.XXXXX
Data repository: zenodo.XXXXXXX

To install and use the code, you need to have installed JupyterLab.

First clone the repository:

git clone https://github.com/USER/REPO.git

Go to the cloned folder and create a new virtual environment.

Installation with pixi is fastest and most stable. Setup a new virtual environment using the environment.yml file:

pixi init --import environment.yml

Now build the environment and run it:

pixi run jupyter lab

An instance of Jupyter lab is automatically going to open in your browser after the environment is built.

You can either create a new virtual environment then install the necessary dependencies with pip using the requirements.txt file:

pip install -r requirements.txt

Or create a new environment with the dependencies with conda or mamba using the environment.yml file:

mamba env create -f environment.yml

Then, install the virtual environment's kernel in Jupyter:

mamba activate ENVNAME
ipython kernel install --user --name=ENVNAME
mamba deactivate

You can now run jupyter lab with kernel ENVNAME (Kernel > Change Kernel > ENVNAME).

├── data
│   ├── processed           <- Modified data
│   └── raw                 <- Original, immutable data
├── notebooks               <- Jupyter notebooks
├── plots                   <- Generated figures
├── scripts                 <- Scripts to execute
├── .gitignore              <- Files and folders ignored by git
├── .pre-commit-config.yaml <- Pre-commit hooks used
├── CITATION.cff            <- Citation file (template)
├── README.md
├── TEMPLATE.md             <- Explanation for the template, delete it after use
├── environment.yml         <- Environment file to set up the environment using conda/mamba
└── requirements.txt        <- Requirements file to set up the environment using pip

Please cite as:

AUTHOR1, AUTHOR2, and AUTHOR3, PROJECTNAME, JOURNAL (YYYY), DOIURL

Development of PROJECTNAME was supported by FUNDER.