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GitHub Classroom Guide for Students

This is a guide for students to setup Git and GitHub for use with GitHub Classroom. We use RStudio in our class, so we will give instructions on how to use RStudio to setup Git locally. However, this is not necessary.

Steps for getting setup with GitHub

  1. Register for account on GitHub ( We recommend using a username that incorporates your name (jfiksel, mtaub, lrjager)

  2. Download RStudio ( and R (

  3. Install Git. Directions for both Windows & Mac here: Windows users should follow Option 1 in 7.2. Mac users can follow Option 1 in 7.3 if comfortable, otherwise follow Option 2. Below, I show how you would access the terminal on a Mac, as well as how to enter the commands given in the link. Windows users should consult the video posted under Resources

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  1. Setup options in Git. In you have a Mac, open up the shell in R Studio by clicking Tools -> Shell. If you don't want to enter RStudio, you can go to the terminal if you have a Mac (Applications -> Utilities -> Terminal) as shown above. If you have a Windows, open Git BASH, which you should have downloaded in step 3. Enter the three lines of code here:, changing the first two lines to your own name and email (this should be the email associated with your GitHub account). Note that Windows users should read section 8.1 in the above link carefully. Below is an example of what this process looks like on a Mac:

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  1. Generate a SSH key so you don’t need to enter your password every time you interact with GitHub. First check to see if you have a SSH key. Go into the shell (again, either through RStudio, Terminal for Mac, or Git Bash for Windows) and complete on this page, which is Chapter 12 in Happy Git with R. The instructions are quite thorough, so if you want to follow along with a visualization, I recommend watching the Git setup videos under resources. This is covered starting at 9:32 in the Mac video and 9:18 in the Windows video.

  2. Follow the instructions here ( to ensure you can connect to GitHub from your computer. Here are step-by-step GIFs from a Mac that help visualize this process.

Make a repo on GitHub

Below we make a repository and copy the link so that we can get the repository onto our own computer.

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Clone the repo to your local computer

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Make a local change, commit, and push and confirm the local change propogated to the GitHub Remote

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Steps for downloading and editing assignments from GitHub Classroom

  1. Have a folder specifically for your class (call it something like classroom-fall-2017). Within this folder, I would recommend a folder titled lectures (this can be pulled from the organization--we will show you how to do this), as well a folder title homework.

Note you can do this as you normally would with pointing and clicking, but you can also use the shell! This is good practice if you want to use Git outside of the class, as you normally have to use the Shell to interact with Git. Sean Kross has a great guide for using the shell here-- However, I'll show you the basic steps you need.

One thing that the shell does is allow you to navigate through all of your files by typing commands, rather than using your mouse. When you open up the shell, you can type PWD. This tells you the directory (folder) that you are in. You can also type ls. This lists the directories available to you. For example when I type PWD, the result is /Users/jfiksel. This tells me that I am in my own directory inside of my computer. When I type ls, I see directories such as Applications, Documents, etc... I can also enter into a directory using the cd command. If I type cd Documents, then I am now inside of the Documents directory. When I type PWD, the result is now /Users/jfiksel/Documents. I can go back to /Users/jfiksel by typing cd ...

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Now I want to make a directory (note I'm using directory and folder interchangeably here). I can use the mkdir command. To make a directory called class-directory (it's good practice to not have spaces in your folder names), I can type mkdir class-directory. If you type ls, you'll now see class-directory appear. You can then enter cd class-directory to go into the class-directory. Finally, to make the two directories that I talked about, we type mkdir lectures and mkdir homeworks. Here is a basic illustration of how my directory structure looks for a class titled Advanced Biostatistics Lab taken in Fall 2017 at Johns Hopkins.


And here is what the process of creating these directories looks like from the terminal on a Mac:

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  1. We will give you a link to an assignment, either through email or the class page. This will happen for each new assignment Then follow the instructions for getting the homework repository set up. You should now have a repository for this homework. Note that after you accept an assignment for the first time, we will send you an invite to join the classroom organization as a member. Please accept this. You will probably get an email with the invitation, but you should also see a link at the top of your main GitHub page. Here is an image of what you should see after clicking the link:

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  1. Enter the homework repository on GitHub (this is online--GitHub is different from Git!). Click “Clone or Download”, and make sure it says “Clone with SSH” in bold in the top left of the pop-up box. If not, click on the blue “Use SSH” button on the top right of the pop-up box. Now copy the link in the box to your clipboard.

  2. In RStudio, go to File -> New Project. Click Version Control, then Git. Paste the link you just copied into the Repository URL box. Leave the Project directory name blank. Create this as a subdirectory of your homeworks folder. An RStudio project should now open up, which will allow you to start working on your homework assignment. You will probably see a blank console screen. However, in RStudio you should also see a list of all of the files available. Click on whatever file you want to edit (probably the .Rmd file) and edit away. If you save and close R Studio and want to go back to editing your project, open up R Studio, then go to File -> Open Project. Navigate to the project directory and double click on the .Rproj file.

If you're not working with RStudio, you can do this in the shell. Navigate inside of your homeworks directory and then type git clone repository-link where repository link should be replaced with the link you copied to your clipboard in step 3. You now have the files, but note that this is not an R project, which means you will have to do all of your committing and pushing via the command line. This is fine, but only if you feel comfortable with it.

Note that if you received an error in the above steps, you may have to clone with HTTPS instead of SSH. You can do this by again clicking on the "Clone or Download" button in the repository page, then clicking "Use HTTPS" in the top right of the pop-up box. Now copy the link and repeat this step.

Here is a visualization of cloning an assignment onto your computer through R Studio on a Mac:

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  1. After you make changes to the homework assignment, commit them. What are commits you ask? Commits are essentially taking a snapshot of your projects. For example, if I make changes to a code so that it prints "Hello world", and then commit them with an informative message, I can look at the history of my commits and view the code that I wrote at that time. If I made some more changes to the function that resulted in an error, I could go back to the commit where the code was originally working. This prevents you from creating several versions of your homework (homework-v1, homework-v2, ...) or from trying to remember what your code originally looked like.

You can make commits using the GIT toolbar in RStudio (in RStudio make sure the toolbar is visible by doing View -> Show Toolbar). I have made a video on how to do this here (available under resources--How to clone, edit, and push homework assignments with GitHub Classroom), and you can read how to do this in RStudio in more detail here: Click the Commit button in the GIT toolbar dropdown menu. Check the files that you want to commit, enter your commit message, then hit Commit. Here is also a short GIF showing how to do this:

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You can also do this through the shell. Navigate to the homework directory. If I am are working on homework-1, when I type PWD I will see /users/jfiksel/hopkins-documents/advanced-biostatistics-lab/homework/homework-1. Now type git add -A, and then git commit -m "My commit message". git add is a command that tells git which files you want to record the changes to when you make your commit. For example, if I made changes to file1 and file2 since my last commit, I can choose to only commit (take a snapshot of) the changes I made to file1. git add -A says to add all of the files that have changed since the last commit. If I just want to add file1, I would instead type git add file1.

Two things about committing. One, you should commit somewhat frequently. At minimum, if you're doing a homework assignment, you should make a commit each time that you've finished a question. Two, leave informative commit messages. "Added stuff" will not help you if you're looking at your commit history in a year. A message like "Added initial version of hello-world function" will be more useful.

  1. At some point you'll want to get the updated version of the assignment back onto GitHub, either so that teachers/TAs can help you with your code, or so that it can be graded. You can do this by using a command called git push. If you are ready to push, you can again click on the GIT toolbar dropdown menu in RStudio, and then click Push branch. You can also do this after you commit in RStudio by clicking Push in the top right corner of the Commit pop-up box. Here is a visualization of both options:

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Again, you can also do this in the shell. Simply navigate inside of your homework directory and then enter git push. Easy!

Obtaining and pulling a shared repository

Your classroom may have a repository where everyone in the class has access to it, such as a class materials repository (if you're in my class, we will have this). This repository will probably be updated throughout the class, and it will be useful to constantly have the most updated materials on your local computer. You can do this by first cloning the repository, and then pulling in changes. Here are the steps.

  1. Clone the repository via command line. Read through step 1 in the previous section if you want a refresher about navigating with the command line. Remember, Mac users should use Terminal, and Windows users should use Git Bash. Go into your class directory--in step 1, this would be the advanced-biostatistics-lab-fall-2017 directory.

    In GitHub, navigate to the shared directory. Repeat step 3 from above, where we copy the link that we will use to clone this repository. If you get an error using SSH, you should instead use HTTPS. Go back to the command line and type git clone repo-url where the repo-url is replaced with the URL you just copied. If you type ls, the directory should now appear.

  2. To pull in changes, navigate inside of this shared directory. For example, let's say the repo we just copied is called class-materials if you are in the advanced-biostatistics-lab-fall-2017 directory, and you type ls, you should see a directory called class-materials. Now type cd class-materials. You should now be inside of this directory. To get the most recent version of this directory, you simply have to type git pull. If you get an error about merge conflict, don't freak out! This can happen if you edit locations in files that are also changed by a professor. Professors should be doing their best to ensure this doesn't happen, but if it does, simply contact your professor or TA to get it worked out. Or even better, try to google the error message and try to fix it yourself!



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