GitHub in GEN242

  • Note, this class will make heavy use of GitHub
  • Homework assignments will be submitted to private GitHub repositories: one repository for each student
  • Course projects will also use private GitHub repositories: one repository for each course project (shared among students of each project)
  • Each student will need a personal GitHub account. They can be created here.
  • GitHub provides an unlimited number of free public repositories to each user. Via GitHub Education students can sign up for free private GitHub accounts (see here).
  • All private GitHub accounts required for this class will be provided by the instructor via GitHub Classroom
  • For beginners this quick guide may be useful

What are Git and GitHub?

  • Git is a distributed version control system similar to SVN
  • GitHub is an online social coding service based on Git
  • Combined Git/GitHub: environment for version control and social coding

Installing Git

  • Install on Windows, OS X and Linux
  • When using it from RStudio, it needs to find the Git executable

Git Basics from Command-Line

Also try interactive git tutorial.

  • Finding help from command-line

      git <command> --help
  • Initialize a directory as a Git repository

      git init
  • Add specific files to Git repository (staging area)

     git add myfile
  • Add all files recursively

    To ignore specific files (e.g. temp files), list them in a .gitignore file in your repository’s root directory. Regular expressions are supported. See here for more details.

     git add -A :/
  • After editing file(s) in your repos, record a snapshot of the staging area

     git commit -am "some edits"

GitHub Basics from Command-Line

  1. Generate a new remote repository on GitHub online or use hub command-line wrapper for this. To avoid errors with the online method, do not initialize the new repository with README, license, or .gitignore files. You can add these files after your project has been pushed to GitHub.

    git remote add origin<user_name>/<repos_name>.git
  2. Push updates to remote. Next time one can just use git push

     git push -u origin master
  3. Clone existing remote repository

     git clone<user_name>/<repos_name>.git
  4. Before working on project, update local git repos

     git pull 
  5. Make changes and recommit local to remote

     git commit -am "some edits"; git push -u origin master


Run the following git/github excercise from the command-line.

git clone<user or org>/<repo name> 
cd <repo name>
git pull
touch test # Creates empty file for testing
git add -A
git commit -am "some edits"
git push -u origin master
##-> Edit test file online and then run `git pull` to inspect changes

Online file upload

This could be useful for new users who want to upload their homework assignments to GitHub but are not familiar enough with the command-line yet.

  1. Press Create new file button on your repository.
  2. Under the file path window add required subdirectory structure and a dummy file name (e.g. Homework/HW1/dummy.txt)
  3. After this press Upload files and upload any file (e.g. homework) to the newly create directory. After this the initial dummy file can be deleted. The latter is necessary since empty directories are not visible on GitHub.

Using GitHub from RStudio

  • After installing Git (see here), set path to Git executable in Rstudio:
    • Tools > Global Options > Git/SVN
  • If needed, log in to GitHub account and create repository. Use option Initialize this repository with a README.

  • Clone repository by copying & pasting URL from repository into RStudio’s ‘Clone Git Repository’ window:
    • File > New Project > Version Control > Git > Provide URL
  • Now do some work (e.g. add an R script), commit and push changes as follows:
    • Tools > Version Control > Commit
  • Check files in staging area and press Commit Button

  • To commit changes to GitHub, press Push Button

  • Shortcuts to automate above routines are here

  • To resolve password issues, follow instructions here.