Template for Reproducible Research Papers

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This repository provides a template for Python code that is accompanying a research paper. Most likely, this will be an implementation of an algorithm and/or simulation results.

The code should be made publicly accessible in order to allow everybody to reproduce the results presented in the paper.

You can use this template/fork it and use it as a starting point. You find a basic structure in main.py, where only need to add your custom code. This README also already contains all important information and you only need to adjust the parts specific to your project. The run.sh script should contain the exact commands that you used to generate the results/plots in your paper. In particular, you should make sure to specify all of the parameters.

The proposed structure of the README is

1. Information about the paper (title, authors, journal/conference, DOI, arXiv)
2. File list of all files that are provided in the repository (with short description)
3. Usage description. If you provide Jupyter notebooks this can also include a link to Binder.
4. Acknowledgements (funding information, ...)
5. License and Referencing (description of license and how to cite your work, e.g., the bibtex entry of your paper)

You can find some general ideas on the structure and required aspects of the repository in this blog post (independent of the used programming language).

File List

The following files are provided in this repository:

• run.sh: Bash script that reproduces the figures presented in the paper.
• util.py: Python module that contains utility functions, e.g., for saving results.

- `main.py`: Python script that...
- ...

Usage

Running it online

The easiest way is to use services like Binder to run the notebook online. Simply navigate to

! Add binder link.

to run the notebooks in your browser without setting everything up locally.

Local Installation

If you want to run it locally on your machine, Python3 and Jupyter are needed. The present code was developed and tested with the following versions:

- Python 3.8
- Jupyter 1.0
- numpy 1.18
- scipy 1.4

Make sure you have Python3 installed on your computer. You can then install the required packages (including Jupyter) by running

pip3 install -r requirements.txt
jupyter nbextension enable --py widgetsnbextension

This will install all the needed packages which are listed in the requirements file. The second line enables the interactive controls in the Jupyter notebooks.

Finally, you can run the Jupyter notebooks with

jupyter notebook

You can also recreate the figures from the paper by running

bash run.sh

Acknowledgements

This research was supported by

! Add funding information

License and Referencing

This program is licensed under the GPLv3 license. If you in any way use this code for research that results in publications, please cite our original article listed above.

You can use the following BibTeX entry

@article{...,
  author = {...},
  title = {...},
  ...
}

! Add bibtex entry of the published paper