Sharing your code

Overview

Teaching: 10 min
Exercises: 10 min
Questions
  • How can I share my code with others?

  • What should I take into account when sharing my code?

Objectives
  • Differentiate the use case for public and private repositories.

  • Describe the key information that should be present in a software repository.

  • Configure git with your GitHub credentials.

  • Setup a repository in GitHub.

Collaborating: what you need to know?

Often, you will need to share your code with others, either with just another person in the same office or anyone, anywhere in the world. Repository hosting services let you do precisely that, keeping all the advantages of VCS and adding on top tools to ease the collaborative development of the code:

GitHub: Why GitHub?

There are several widely used repository hosting services using Git, such as GitLab or Bitbucket. In this course we will use GitHub because:

Private vs public repositories

Depending of who you want to give access to your repository, there are two broad types of repositories: private and public. This choice, the first one you will need to make, is not written in stone and you can set a repo private initially and making it public later on.

When you are part of an organization account, there are more options to control the visibility of a repository.

Private repositories

Public repositories

Open Source Projects

There is a growing recognition that reproducibility and open source practices in scientific software development are closely interrelated. It is increasingly expected that publications are accompanied by the analysis code and raw data used to create them. As a budding researcher one of the best ways to improve the impact of your work is to make it as easy to reproduce as possible.

Read more:

Things to include in your project

There are a few files that should get used to always include in the root directory of your repository:

README.md

Licence

See GitHub Help: Adding a license to a repository

Licence for Imperial College London software

Imperial College’s preferred licence is the permissive BSD 2- or 3-clause. You can check the details at Imperial website: Open Source Software Licences. The guidance on this site is primarily intended for members of staff however it is correct for graduate students with the exception that (subject to certain conditions) you are entitled to hold the copyright. This site also tells you who you should contact in case you want a different licence model for your work e.g. commercial.

Open Source software licences

There is a huge range of different licences, ranging from fully permissive to very restrictive. A couple of websites with more information on the topic (including how to licence things that are not software) are:

Installation process/instructions

CITATION.txt

Digital Object Identifiers (DOI)

If you are serious about what you are doing and want people to really cite your work properly - and get recognition for it - consider providing your repo with a digital object identifier (DOI). You can get one from:

CONTRIBUTING.md

See GitHub Help: Setting guidelines for repository contributors.

Creating a repository

Now you have all the information you need to create a new repository in GitHub. Just follow this steps:

  • Once logged in to GitHub, press the + symbol in the top right, and choose new repository from the dropdown menu.
  • Give your repository the name example.
  • Add a short description for your project.
  • You are going to create a Public repository, so select that option.
  • Click on Initialize this repository with a README. This will create an empty README file in the root directly that you can edit later on.
  • Select a licence for your repository. Which one is up to you, but make sure you have read what they entail before (Tip: there is a little “i” next to the dropdown list with some help on this. In case of doubt, choose BSD 3 -clause.

Solution

Your repository is now ready and you should see something similar to this: New Repository It tells you there is only 1 commit, 1 branch and 1 contributor, the type of licence you have chosen and also that there are two files: LICENSE and README.md, which is also rendered immediately below.

To make this complete, let’s add some contributing guidelines:

  • Go to Insights in the upper right corner of the repository.
  • And then click on Community on the left hand side.
  • The screen now shows how the project compares with the recommended community standards. Is not bad, but could be better.
  • Click on Add in the Contributing line. In the new screen you can write your contributing guidelines. Tip: No one writes this from scratch.

Have a look at some Examples of contributing guidelines and copy/paste those parts relevant for your project.

  • Once you are done, click on Commit new file and the changes will be confirmed. Now you should see a CONTRIBUTING.md file in the root directory.

Key Points

  • Public repositories are open to anyone to use and contribute.

  • Private repositories are just for yourself or a reduced set of contributors.

  • README contains a description of the software and, often, some simplified installation instructions.

  • The LICENSE describes how the software must be distributed and used.

  • Using one of the OSI (open source initiative) licenses is recommended if the repository is public.

  • CONTRIBUTING describes how other users can help developing the software.

  • CITATION helps others to cite your software in their own papers.

  • GitHub can be used to setup a software repository, share your code and manage who and how can access it.