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Setting up a Git-RStudio-GitHub workflow

Here we focus on getting set up with a workflow that has three components:

  1. Git
  2. Rstudio
  3. GitHub

We will address rationale and usage later.
Prerequisite: RStudio installed and up to date.

Register a GitHub account

https://github.com/
Use your colorado.edu email.
Email me your GitHub username so I can add you to the class's GitHub organization.

Install Git

There are lots of options for Git clients (including GitHub desktop) but the official Git version is recommended:
https://git-scm.com.
Go to downloads and choose your operating system. The current version is 2.33.0. On Windows, this official version installs both a CLI (command line interface) and a GUI (graphical user interface). On MacOS, it's best to install via homebrew and you need to separately install both git and git-gui.

On this website there is also a section for third-party GUI clients. You can ignore this section but feel to try some out.

Windows
When installing, there will be a bunch of questions. For most, the defaults are good. These two are important:

  1. Override the default branch name for new repositories: main
  2. Choose default editor - I suggest nano, or notepad++.
  3. Adjust your path environment if necessary: Git from the command line and also from 3rd-party software (this is the default choice). This is important to allow Rstudio to find Git. Depending on your Windows version and installation this may or may not work with RStudio automatically. If not, in RStudio -> Tools -> Global Options -> Git/SVN -> enter the path to git.exe (and restart Rstudio).

Mac
If asked, install Xcode command line developer tools also.

Linux
Instructions for different distributions here: https://git-scm.com/download/linux.

Set up Git

Open a CLI shell. A shell can be opened through R studio > Tools > Shell.
Otherwise, you can do this:
Windows: start the "Git bash" program/app (which you installed above)
Mac: start the terminal app.
Linux: fire up a terminal.

Set up Git with your name and email. These will label your commits to document who made changes - important when you are collaborating. You will enter this line by line into the CLI shell.

git config --global user.name "Your_full_name"
git config --global user.email "your.email@address"
git config --global --list

The email address should be the same one you used to register on GitHub. That's all you should need to set up. For more options, see https://swcarpentry.github.io/git-novice/02-setup.

Set up a test Git repository (or two)

First test that everything works. Do this directly from your personal GitHub account (i.e. not from the class organization at this stage), setting up public repos each time. Follow the directions in Happy Git with R Can you hear me now? working through Chapters 9-11. Don't worry about understanding what is going on too much at this stage. Just follow the directions and type carefully (or copy and paste). I suggest using a personal access token with HTTPS, in which case you'll follow the directions in Chapter 9 to do this then skip Chapter 10. You can alternatively set up SSH keys if you prefer, in which case you'll follow Chapter 10 instead of Chapter 9. In Chapter 11 you'll make the basic connection between Git and Github. Finish by cleaning up as directed.

Now we're going to do that all again but this time with RStudio. Follow the directions in Happy Git with R Chapter 12. Finish by cleaning up as directed.

If you run into trouble with any of this, there are lots of resources at Happy Git with R, especially Chapter 14.