Preparation 2 - Connecting RStudio and GitHub

All of your work for STA 418/518 will be stored in GitHub. This activity will walk you through practicing some of the GitHub steps to get more comfortable with this workflow.

Estimated Time

☑️ Six Tasks: 45–60 minutes

How to Set up Git

As I said in the syllabus, Happy Git with R is by far the most complete resource for setting up Git and GitHub. If you would like to set up R, RStudio, Git, and GitHub on your own machine, I would recommend you use this text. Luckily for us, Git is already installed on GVSU’s RStudio Workspace (and of course R and RStudio are available here too) so we will only need to focus on having our RStudio sessions communicate with GitHub.

☑️ Task 1: Fork this repo

To begin, we need to make your own copy of this GitHub repo.

Click on the Fork icon in the upper-right-hand corner of this repo.

After a few seconds, you should be taken to a new repo at <username>/preparation02, where <username> is your GitHub username.

☑️ Task 2: Configure Git

Login to the RStudio Workspace using your GVSU username and password,
Verify that you are in an RStudio session (i.e., not the RStudio Workbench Sessions/Project screen).

There are a couple of ways to configure Git in RStudio. For STA 418/518, we will use {usethis}.

Note that when you see something like {name} in my documents, I mean the R package called name.

Specifically, we will use the edit_git_config function from {usethis}. Throughout the semester, I will shorten this to be usethis::edit_git_config or, “from the R package usethis, use the function edit_git_config” (in general, package::function).
In your Console pane (left-hand pane), type the following pressing Enter/Return after each line:
```
library(usethis)
edit_git_config()
```
A file should open in the pane above your Console that is called .gitconfig. In this file, copy the information provided below, then update it with your preferred name (or pseudonym) and email (can be any email, but it would probably be helpful to use the same one you signed up for GitHub to avoid confusion). Remember that this information will be publicly available.
```
[user]
  name = "name"
  email = "user@subdomain.domain"
[credential]
  helper = cache --timeout=10000000
```
Note that in the information above, we are also instructing RStudio to remember your GitHub credentials for 10,000,000 seconds (or roughly 16 weeks) - the [credential] portion. RStudio is not remembering your credentials yet, but we will resolve this shortly.
Click on the icon and you can close this .gitconfig file.

☑️ Tasks 3: Connect RStudio and GitHub

Now that you have Git set up within RStudio, we can enable RStudio and GitHub to communicate. To do this, we will need your GitHub username and a Personal Access Token (PAT). PATs are designed to be more secure than your password when communicating between your computer session and GitHub. Conveniently, {usethis} has a function for this!

To create a PAT, type the following in your Console and press Enter/Return:
```
create_github_token()
```
Note that you previously loaded {usethis} (using library(usethis)) so I did not ask you to do this again. Once you load a package in your current RStudio session, you do not need to load it again.
You will be directed to a “New personal access token” page on GitHub in your browser. Since I work on multiple machines (i.e., my personal laptop, my work laptop, my personal desktop, and the RStudio Workspace), I like to name each PAT. For example, in the Note text field, I called this token “GVSU RStudio Workspace”.

Most of the other options you will accept the default selections. However, you might want to change the Expiration date. A couple of suggestions: have this PAT expire at the end of this semester (e.g., Dec. 18, 2021) or (risky) choose “No expiration”. After choosing a PAT expiration, scroll down and click on the green Generate Token button.
After clicking on Generate Token, you will be taken to a “Personal access tokens” page that has a seemingly random string presented to you beginning with ghp_. Keep this page open for a little bit (I will tell you when it is safe to close it), as once you close this page, you will never be able to view this PAT again! I highly recommend that you store this code somewhere safe (e.g., a password manager tool). However, if you do lose it, you can go through this process again to create a new one.
Now we need to associate this PAT in RStudio so that RStudio can connect to your GitHub account. Back in your RStudio Console, type the following and press Enter/Return after each line:
```
library(gitcreds)
gitcreds_set()
```
In your Console you will be asked to ? Enter password or token: Paste your PAT here (NOT your GitHub password) and press Enter/Return. You should see a message similar to:
```
-> Adding new credentials...
-> Removing credentials from cache...
-> Done.
```

☑️ Tasks 4: Clone GitHub repo

Now that RStudio and GitHub are connected, we can clone this repo (i.e., copy the repo to our RStudio session)!

In RStudio, click on the icon (the icon below the Edit drop-down menu);
Click on Version Control on the New Project Wizard pop-up;
Click on Git and you should be on a “Clone Git Repository” page;
Back to your preparation02 GitHub repo, click on the green Code button near the top of the page;
Verify that HTTPS is underlined in red on the pop-down, then copy the URL provided;
Back in RStudio, paste the URL in the “Repository URL” text field;
The “Project directory name” text field should have automatically populated with preparation02. If yours did not, click into this box and press Ctrl/Cmd (usually this is a Mac issue);
In the “Create project as subdirectory of” field, click on Browse…. Create a New Folder called “STA 418” of “STA 518” (depending on your course), then within this folder, create a New Folder called “Preparations”, think click Choose. Note that I am forcing you to use my file system management style.
Click on Create Project.

Your screen should refresh and the Files pane should say that you are currently in your preparation02 folder that currently has three files (.gitignore, preparation02.Rproj, and README.md) and a folder (README-img/). If you are asked for your GitHub credentials, provide your GitHub username and your PAT.

☑️ Tasks 5: Create, Edit, Commit, and Push

Before we wrap-up, we will create a new file and see how to commit these changes and view the commit history.

In RStudio, click on the and select an R Script,
Click on the icon to save this file. Name it preparation02-file.R (notice the capital “R” for the file type).
Type the following code within in your R script:

# Here are some simple calculations
2 + 2
(2 * 3)^2

Run each line to verify that you get the results you would expect, then save your file,
In the Git pane (upper-right pane), check the box next to all items listed (under the “Staged” column) and click on Commit,
In the pop-up, provide a commit message of Adding some calculations, then click on Commit, and
In this same pop-up, switch from Changes to History (upper-left corner).

Reflect on how this way of looking through your commit history compares to GitHub. Feel free to add more to your R script, save, and commit.
To update GitHub with these changes, in the Git pane of RStudio click on Push. When asked for your GitHub credentials, provide your GitHub username and GitHub PAT (as your password). This should be the last time you need your GitHub PAT, but I would encourage you to keep this in a secure place.

☑️ Tasks 6: Wrapping Up

Go back to your preparation02 GitHub repo and verify that your preparation02-file.R file is here. You can now close the PAT page tab.

There is nothing to submit for this Preparation. However, find the item that your instructor created in Slack. In this item, reply with what was the muddiest from the Preparation. If someone else already mentioned what you thought was muddy, give them a “+ 1” 👍.

Attribution

This document is based on David Keyes’ tutorial at R for the Rest of Us and Happy Git with R by Jenny Bryan et al.

dikshashrestha/preparation02