Using Git with RStudio

Git allows groups of people to work on the same documents (often code) at the same time, and without stepping on each other's toes. It's a distributed version control system.

(cribbed from tryGit)

Intro to practical version control for scientists

These slides are courtesy of Bernhard Konrad.

Installation and configuration of git

If you've already installed and configured git, skip ahead to Learn to use git with RStudio.

Install git

Mac OS 10.9 Mavericks comes with git installed. To check that git is installed, open a Terminal and run…

which git
git --version

These commands should display something similar to this:

➜  which git
/usr/bin/git
➜  git --version
git version 1.9.3

For all other operating systems, go to the Git downloads web site, and click on the appropriate icon for your operating system.

If on a Mac the official Git package gives you any trouble, use the following instructions to install Git using Homebrew.

Install git using Homebrew

Homebrew is the missing package manager for Mac OS X. To install Homebrew and use brew to install Git, run…

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
brew install git

Test that git is installed and working by running…

which git
git --version

Configure git

Git associates your name and e-mail address with each commit, which helps when multiple people collaborate on a project. To configure your name and e-mail address in git, open the Terminal and run…

git config --global user.name 'Your Name'
git config --global user.email 'your@email.com'

On a Mac, configure git to remember your password.

git config --global credential.helper osxkeychain

For more help configuring git, see…

• GitHub
• UBC STAT 540

• Open RStudio
• Click Tools -> Global Options -> Git/SVN
• If Git executable shows (none), click Browse and select the git executable installed on your system
  • On a Mac, this will likely be one of
  • /usr/bin/git
  • /usr/local/bin/git
  • /usr/local/git/bin/git
  • On Windows, git.exe will likely be somewhere in Program Files
• Click OK

Create a new project

Or if you prefer, see below for instructions to open an existing project.

• Open RStudio
• Create a new project
  • Click File -> New Project -> New Directory -> Empty Project
  • Check Create a git repository for this project

Open an existing project

• Open an existing project
  • Click File -> Open Project

If you already have a tab labeled Git next to the tabs Environment and History, skip these instructions.

• Enable git for this project
  • Click Tools -> Version Control -> Project Setup
  • Click the dropdown box Version control system and select Git
  • If you don't have a Git option go back to Configure RStudio. Do not pass Go. Do not collect $200

Create and commit a file

• Make your first commit
  • Click the Git tab
  • Check Staged next to .gitignore and hello.Rproj
  • Click Commit
  • Type a message in Commit message
  • Click Commit
• Create a new Rmd file
  • Click File -> New File -> R Markdown
  • Edit the file and change the title
  • Save the file
• Commit the new Rmd file
  • Check Staged and click Commit

Knit the HTML report

• Knit the Rmd file to generate an HTML report
  • Click Knit HTML
• Commit the generated report
  • Check Staged for the md and html files and the figures directory
  • Click Commit

Change the plot

• Replace the plot with ggplot or qplot and save your changes
• Commit the change
• Knit the report
• Commit all the modified files

Make a change and revert it

• Make an erroneous change to the file and save it
• Click Diff and then Revert
• The erroneous change has been undone and the previous version restored

Delete a file

• Create a new file named doomed.md
• Enter some text and save it
• Delete this doomed file
  • Under the Files tab check the box next to doomed.md
  • Click Delete
• Under the Git tab, a red D appears next to the deleted file
• Stage the change by clicking the checkbox and commit it

Inspect your work

• Make a few more changes and commits
• Click History under the Git tab to review your day's work
• Git has recorded a complete history of your work
• In the event of impish gnomes introducing errors into your work, you can browse through your history, find the gnome to blame, and restore your previous good work. Gnomes be damned.

Use the git command line

There are many graphical interfaces for git—RStudio is one—but there is only one git command line interface, which is the common engine being used behind the scenes. If your graphical interface ever lets you down, it's useful to peak under the hood.

• Click File -> New File -> Text File
• Describe your project in this new file
• Save this file and name it README.md
  • Case matters! Name the file README.md and not readme.md or any other variation
  • Don't be imaginative. Get used to being pedantic. Foster your inner OCD
  • md is the extension of a Markdown file
  • Note the yellow question marks indicating the new file that's not being tracked by git
• Open a shell (also known as a Terminal)
  • Under the Git tab, click More -> Shell
• Stage README.md using the git command line
  • Run git add README.md
  • The yellow question mark changes to a green A
  • Checking the Staged check box in fact runs git add
• Unstage README.md
  • Run git reset README.md
  • The green A changes back to a yellow question mark
  • Unchecking the Staged check box in fact runs git reset

• Stage and commit README.md

  • Run…

  git add README.md
  git commit -m 'Add README.md'
  

  • The -m option of git commit specifies the git log message

• Browse the git history in RStudio, and inspect this commit

Learn more about the git command line

Go to tryGit and learn more about the git command line!