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Git and GitHub for Public Health

2 Workshop Setup

This pre-workshop guide is designed to walk you through the initial setup of Git on your computer.

If you have any issues, please reach out to us at and .

2.1 Introduction

Git is a version control system that allows you to track changes in your code.

In order to get setup, you need to install Git on your computer, make a GitHub account, and then configure Git on your computer.

If you are attending a live workshop, we will cover the details of how to use Git during the workshop. To ensure the workshop runs smoothly and efficiently, we request you to complete the following steps before the workshop – this enables us to spend all of the workshop time on using Git rather than on setup. Thank you!

2.2 Install R and RStudio

If you don’t already have R and RStudio please install them. While the workshop will also give options using SAS, everyone needs R and RStudio for some pieces of the workshop – it should only take a few minutes to download and install each of these.

Link to both downloads: https://posit.co/download/rstudio-desktop/

If you downloads each of these a while ago, we recommend that you update the versions so everthing runs smoothly.

2.3 Open RStudio and install the following packages

  • tidyverse
  • usethis
  • gitcreds
  • broom

To do this, run the following code in the RStudio console (lower left-hand side panel, of the four panel pane):

install.packages('tidyverse')
install.packages('usethis')
install.packages('gitcreds')
install.packages('broom')

If any of these packages fail to install, please let us know.

If this is your first time using R/RStudio, this video shows how to type the commands into the console and R looks like when the installs runs smoothly. Please view this video in full screen and at high quality to see it properly.

2.4 Create a GitHub account

https://github.com/

2.5 Install Git

Installing Git is different depending on whether you are using a Windows or Mac. Follow the relevant instructions.

2.5.1 Windows Instructions

  1. Download Git for Windows: https://git-scm.com/download/win. Once the download begins, there are many menu items to click through. As recommended on the fantastic website HappyGitWithR, accept the default selections except for the item “Adjusting your PATH environment”. There, make sure to select “Git from the command line and also from 3rd-party software”. HappyGitWithR also notes that “RStudio for Windows prefers for Git to be installed below C:/Program Files and this appears to be the default. This implies, for example, that the Git executable on my Windows system is found at C:/Program Files/Git/bin/git.exe. Unless you have specific reasons to otherwise, follow this convention.

The following video shows how to download and install Git for Windows. View it on full screen and in high quality if you want to follow along:

  1. Once you have Git downloads, confirm you have access to Git Bash. To do so, it should appear in your Start menu: Start menu > Git > Git Bash.

  2. RStudio should automatically detect the presence of Git Bash. You can inspect and influence this directly via Tools > Global Options > Terminal. Unless you have good reason to do otherwise, you want to see “Git Bash” in the “New terminals open with …” dropdown menu.

  3. The next set of tasks are done in RStudio and outlined below in the section “Configure Git using an HTTPS token” below the Mac instructions.

2.5.2 Mac Instructions

  1. Open up the Terminal application, and type git --version to check if Git is already installed. If it is, you will see a version number. If it is not, type: git config and then press return. You will be prompted to install Git and follow the prompts!

2.6 Configure Git using an HTTPS token

In RStudio, load the libraries usethis & gitcreds:

Use the function use_git_config() to configure Git using an HTTPS token. To do so, type the following in the RStudio Console (lower left panel), filling in a user name, and email. The user name is up to you – it doesn’t need to be your GitHub user name. user.email is the email address linked to your GitHub account.

use_git_config(user.name = "Your user name",
               user.email = "your.email.adress@gmail.com")

Next up, you will need to create a personal access token. This is a way to authenticate yourself with GitHub. You will need to do this in order to push and pull from your GitHub repository. To do so, run the following in the R console:

This will bring you to a browser page. Put in a description for your token and then select an expiration date from the drop down - please select No expiration. Scroll down and click the Generate token button. Copy the token that is generated and paste it somewhere where you will be able to access it.

Go back to R/RStudio and run the following:

gitcreds::gitcreds_set()

When prompted, paste in the GitHub token you copied from the website. This will add your credentials to your cache. The following will print out to the RStudio console:

? Enter password or token: ghp_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  
-> Adding new credentials...
-> Removing credentials from cache...
-> Done.

2.7 Resources

You are now set up to use Git and GitHub! If you had any issues, here are a few links you can look at for help. If you are still having trouble, please reach out to us before the workshop.

If you are attending the live workshop, we will cover the rest of this website live. See you there!