Configure Git and GitHub

Tutorial

Setup

Configure Git and GitHub for course assignments.

Modified

August 30, 2024

Access RStudio

If you plan to use your own computer

Make sure you have completed the software setup instructions.
Open RStudio.

If you plan to use RStudio Workbench

Go to https://rstudio-workbench.infosci.cornell.edu and log in with your Cornell NetID and Password.
Click the “New Session” button on the top of the page. Leave all the settings on their default state and click “Start Session”. You should now see an RStudio session.

Warning

If this is your first time accessing RStudio Workbench for the course, it will take a couple of minutes to prepare your session. Please be patient. When you start a session in the future, your container will already be prepared and it should start within 15 seconds.

Setup your GitHub authentication

If you are using your own computer

Run the following code in the R console to ensure you have the required packages installed:

install.packages(c("usethis", "gitcreds", "gh"))

In order to push changes to GitHub, you need to authenticate yourself. That is, you need to prove you are the owner of your GitHub account. When you log in to GitHub.com from your browser, you provide your username and password to prove your identity. But when you want to push and pull from your computer, you cannot use this method. Instead, you will prove your identity using one of two methods.

Authenticate using a Personal Access Token (PAT)

Note

This method is preferred since it allows for seamless communication between R and Git for all possible applications.

A personal access token (or PAT) is a string of characters that can be used to authenticate a user when accessing a computer system instead of a username and password. Many online services are shifting towards requiring PATs for security reasons.

With this method you will clone repositories using a regular HTTPS url like https://github.com/<OWNER>/<REPO>.git.

If you are using RStudio Workbench

Configure the Git credential helper by running the following R code in the console:

usethis::use_git_config(credential.helper = "store")

Create your personal access token

Run this code from your R console:

usethis::create_github_token(
  scopes = c("repo", "user", "gist", "workflow"),
  description = "RStudio Workbench",
  host = "https://github.coecis.cornell.edu/"
)

This is a helper function that takes you to the web form to create a PAT.

Give the PAT a description (e.g. “PAT for INFO 5001”)
Leave the remaining options on the pre-filled form selected and click “Generate token”. As the page says, you must store this token somewhere, because you’ll never be able to see it again, once you leave that page or close the window. For now, you can copy it to your clipboard (we will save it in the next step).

If you lose or forget your PAT, just generate a new one.

Store your PAT

In order to store your PAT so you don’t have to reenter it every time you interact with Git, we need to run the following code:

gitcreds::gitcreds_set(url = "https://github.coecis.cornell.edu/")

When prompted, paste your PAT into the console and press return. Your credential should now be saved on your computer.

Confirm your PAT is saved

Run the following code:

gh::gh_whoami(.api_url = "https://github.coecis.cornell.edu/")

usethis::git_sitrep()

You should see output that provides information about your GitHub account.

Authenticate using Secure Shell Protocol

Note

You can use this approach to authenticate yourself on GitHub. Note that you may find some limitations communicating with Git outside of standard processes (e.g. cloning/pushing/pulling repos directly), and will still need to create a PAT for some course assignments. However for students using RStudio Workbench, the SSH method will work for the entire semester (i.e. set it up once and never have to worry about it again).

Instructions for authenticating with SSH

The Secure Shell Protocol (SSH) is another method for authenticating your identity when communicating with GitHub. While a password can eventually be cracked with a brute force attack, SSH keys are nearly impossible to decipher by brute force alone. Generating a key pair provides you with two long strings of characters: a public and a private key. You can place the public key on any server (like GitHub), and then unlock it by connecting to it with a client that already has the private key (your computer or RStudio Serve). When the two match up, the system unlocks without the need for a password.

The URL for SSH remotes looks like git@github.com:<OWNER>/<REPO>.git. Make sure you use this URL to clone a repository. If you accidentally use the HTTPS version, the operation will not work.

Set up your SSH key

Note

You only need to do this authentication process one time on a single system.

Type credentials::ssh_keygen() into your console.
R will ask “No SSH key found. Generate one now?” You should click 1 for yes.

You will generate a key. It will begin with “ssh-rsa….” and look something like this:

$key
[1] "/home/bcs88/.ssh/id_rsa"

$pubkey
[1] "ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDJYmJeave083exQwYcIqZJk/Y1mgPxdcTYCTWLL+6mlhN9MM3enjDqb2eZvVJ0JK29NYL1++DTqY/saP08IlswNIMntwaWFDNx42yLsuFrWiPqzm9hWWnRcor/d+4zTrcSIEvfAAnLsYkagNqurrCf2taO62YRepTgxErLvLOG10qn4LKhNfT+PTqdPq2Mr88jXQYYrRxGnOV6oVYf6PurKkiooTsKYxVtJWai8Ek9fhK2y5vaQd5yP0H/3Hbw8Mn+rB+O8Yj6/oQKGBCgxkDB4Aw7T91DkIXlHppneO683Y54WvUftJYvSVsnyt/XuNjvXNAir0+kHETLM32uzH6L"

Copy the entire string of characters (not including the quotation marks) and paste them into the settings page on GitHub. Give the key an informative title such as “INFO 5001 RStudio Workbench”. Click “Add SSH key.”

Configure Git

There is one more thing we need to do before getting started on the assignment. Specifically, we need to configure your git so that RStudio can communicate with GitHub. This requires two pieces of information: your name and email address.

To do so, you will use the use_git_config() function from the usethis package. Type the following lines of code in the console in RStudio filling in your name and the email address associated with your GitHub account.

usethis::use_git_config(
  user.name = "Your name", 
  user.email = "Email associated with your GitHub account"
  )

For example, mine would be

usethis::use_git_config(
  user.name = "Benjamin Soltoff", 
  user.email = "bcs88@cornell.edu"
  )

You are now ready interact with GitHub via RStudio!