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ORMIR community template for readme.md file in a GitHub repository

by Serena Bonaretti, Donnie Cameron, Michelle Alejandra Espinosa Hernandez, Gianluca Iori, 2023
Version 1.0

  • In the following, you will find suggestions on how to structure the readme.md file of your GitHub repository
  • Instructions are in italics, and you can delete them when using this template
  • Feel free to add figures and videos illustrating your package in any section

  • See some README.md file examples here:

  • Delete the lines above when releasing your own README.md

Package_name

Installation

  • Specify how to install your package, such as:

    Install [package_name] by pasting the following line in a terminal:
    pip install package_name

  • If you install from Anaconda:

    Install [package_name] by pasting the following line in a terminal:
    conda install package_name

Development installation

  • If you want to contribute, start by cloning the repository:

    !git clone https://github.com/[account_name]/[package_name].git

  • Navigate to repo folder:

    %cd [package_name]

  • Install using pip:

    !pip install .

Usage

  • A Python package can usually be imported in Python code and/or run from a command line as a script.

  • If you package is imported in Python code, add something like:

    To use [package_name] in your code, import it as:
    import package_name

  • If you package can be run from command line, add something like:

    To run [package_name] from terminal, type:
    package_name parameter1 parameter2

User guide / Tutorials

  • Please, take particular care of documentation and examples, so that other researchers can easily use your code

  • Use cases

    • Directly here in the readme file (see example here)
    • As links to notebooks (see example here_tbd). In this case, add links to binder whenever possible (learn how to link your GitHub repository to Binder, by reading this documentation or watching this video)
    • As a link to a separate website (see example here_tbd)
    • As a combination of the above

How to contribute

  • Install as a developer [add link]
  • Make your changes. If you want to coordinate the development with the main mainteners, write to [email protected]
  • Commit your changes
  • Send a pull request

API documentation

  • Guidelines on how to create API documentation in Sphynx here

Citation

  • We definitely want our code to be cited! Specify here how. Example:

When using pyKNEEr, please cite code and paper:

  • To know how to make your code citable by getting a Zenodo DOI, read this blog post or watch this video

License

Legal aspects

  • You can specify the legal aspects of your project. Here is an example:

This code is freely available only for research purposes. The software has not been certified as a medical device and, therefore, must not be used for diagnostic purposes. Commercial use of the provided code and the pre-trained models is strictly prohibited, since they were developed using the medical datasets under restrictive licenses.

Acknowledgments

  • Acknowledgments to collaborators and funding agencies

  • Footnote