20 Git & GitHub

There are two common challenges when working on data analysis projects:

  1. Versioning
    • How best should you keep track of each iteration of your analysis?
  2. Collaboration
    • How can multiple people work on the same project together efficiently?

Git and GitHub are two tools to help with both of these issues. Git takes care of the versioning and tracking changes, and GitHub helps you share and collaborate on your code. Let’s look at them both.

20.1 Git

Git is an open-source versioning system, designed to promote collaboration and efficiency. Git tracks repositories - folders containing files, often code - and any changes that are made. For now we’re going to go through the basics of Git but we really will just scratch the surface of the power of Git.

20.1.1 Repositories

A Git repository is a collection of files and folders that are tracked for changes. The files don’t necessarily need to contain code, but they often do. You work on a local copy of the repository, with a master version of the repo help somewhere somewhere else (like a server). Git will then integrate the changes that you’ve made to your version of the repo with the central version. This allows multiple people to work on the same repository at once - they each have their own version.

20.1.2 Commits

Once you’ve made a change to your local repository, you need to commit that change. Commits should be accompanied with a useful message that describes the changes that were made.

Commits should be made regularly and for each distinct set of changes you make - you can always revert back to a previous version.

20.1.3 Pushing & Pulling

When working on a local version of a repository, you will need to send your changes to the remote version of the repo once you’ve committed them. We call this ‘pushing’ the changes. When you push your changes, Git will check the commits you’ve made, and then integrate your changes into the remote version of the repo if there aren’t any conflicts.

Pulling is the process of updating your local version of the repository to match the server version changes. For example, you and a colleague from a different timezone may be working on the same project. When you start for the day you might want to pull all the changes from the remote version of the repo to make sure that you’ve got all the changes that your colleague has pushed while you were asleep. Conflicts

If you try and push a change to the remote version of the repository, but that change can’t be integrated (say someone has already edited that file before you pushed your changes), then Git will mark a conflict. Conflicts need to be resolved before the push can complete, either by accepting the current or incoming version of the file or by integrating the changes yourself.

20.1.4 Branches

Each repo will have at least 1 branch. Historically this was called the ‘master’ branch but it’s increasingly common to see it called the ‘main’ branch. When you create a new branch, the new branch is split from the original branch, meaning that any changes you make are now specific to the new branch. You can then choose to merge branches which will integrate all of the changes you’ve made to one branch into the other.

You may want to use branches for a number of reasons. For example, say you want to try developing a new implementation of one of your functions. You don’t know whether it’s going to be any better than the original implementation though, and you don’t want to have to revert back 20-odd commits if you find out that it wasn’t worth the change. Instead, you can split into a new branch and make the changes there. Then, if you want to integrate the implementation into the main repository, you can just merge the branches.

Alternatively, you might want to have a ‘development’ and a ‘main’ branch. You do work on the ‘development’ branch and then when you’re sure things have been tested are stable, you can then merge the changes into the ‘main’ branch.

20.2 GitHub

GitHub is a repository hosting service. You can use GitHub to store the remote versions of your repositories and perform things like Continuous Integration. GitHub is free for open-source projects, and you can have as many repositories as you like. I host all of my projects (including this book series) on my GitHub account.

When working on R projects with Git, I would highly recommend using GitHub. It helps promote open-source development and some R tools have been specifically designed to install packages directly from GitHub (e.g. remotes::install_github()). Also, you can use GitHub to do things like track issues, host your documentation, and testing.

There are a couple of extra terms that you’ll need to be aware of when using GitHub.

20.2.1 Forking

When you fork a repository, you make your own copy of the repo (a bit like a branch). You can then make changes independent of the original repository but then merge them later on.

20.2.2 Pull Requests

When you do try and merge changes into a branch, you’ll create a pull request. This request will outline the changes that have been made since the branches split, and if there are any conflicts that mean they can’t be merged. Most often, someone will manually check that pull request and then accept or decline it.

20.3 Git, GitHub & RStudio

Getting Git and GitHub working with RStudio is relatively straightforward, but there are lots of edge cases that make things tricky. I’ll outline the general workflow here but the Happy Git with R book outlines how to install and set up Git and Git repositories in much greater detail.

To use Git in RStudio, make sure you have Git installed. Once you do, when you create a new project, RStudio will have a checkbox to ‘Initialise a Git repository’. Make sure that’s ticked. This will create a local repository, but you’ll still need to create the origin (the master version) on GitHub.

Go to GitHub and create a new project. The name doesn’t have to be the same as your project, but it makes things easier. Once you’ve created the GitHub repo, add that url as the origin for your local repository. Now when you push any changes, they’ll be pushed to the GitHub origin.