Overview of Github

Note

This page was created for the 2021 University of Michigan fMRI Course. More material will be added to it as time goes on.

Introduction

Github is a website for hosting code: Python, C++, Matlab, and any other computer language. Code is hosted in repositories created by a user, and this code can be copied to a local machine (in Github terminology, cloned).

Glossary

The following is a list of terms that you will come across with Github. Example code has been provided for certain terms to build your intuition about what these words mean.

Repository: A webpage that contains folders and sub-folders to help organize a project. For example, Andy’s github (found here <https://github.com/andrewjahn?tab=repositories>__) contains repositories such as AFNI_Scripts, SPM_Scripts, and FSL_Scripts. Each of these folders in turn contains code that is relevant for analyzing data using AFNI, SPM, or FSL, respectively.

OpenScience/OS/Github_Repositories.png — Example of repositories on a Github page.

Clone: Copying a repository to your local machine. For example, if I want to clone the repository SPM_Scripts from Andy’s Github page, I would need to know the link to the page (i.e., https://github.com/andrewjahn/SPM_Scripts), and then use it with the git command:

git clone https://github.com/andrewjahn/SPM_Scripts

This will clone the SPM_Scripts repository to my local machine, from where I ran the git command.

Branching: Each repository has a main branch, which contains all of the final edits that are seen by the public. A new branch is created to make edits, and can be called anything you like; when the edits are approved by whoever owns the repository, they are merged into the main branch.

Commit: An edit that is made, which can be either accepted or rejected by the owner of the repository. Commits can be labeled with notes describing what the change is.
Fork: Create a copy of a repository. Edits made to this copy will not be seen by the public until the changes are merged.