Lab #0.5: Git & Chisubmit¶

You must be logged into a CS server using vDesk, NoMachine (the vDesk app), or ssh to do this lab.

Objectives¶

Learn the basics of git
Learn how to use chisubmit, our submission software

Git¶

Git is a system used for developing software in a group. This system maintains files and all changes that are applied to them. You will each have a personal Git repository that is hosted on a central server. The server stores the project files and stores all changes to those files that have been uploaded to the repository.

We have created accounts and repositories for each of you on a CS department Git server. We will seed your repositories with templates and files that you need for your class work. Also, we will be able to see any changes you upload to your repository, which allows us to provide help remotely and to grade your programming assignments.

Git tracks every version of a file or directory using commits. When you have made changes to one or more files, you can logically group those changes into a “commit” that gets added to your repository. You can think of commits as “checkpoints” in your work, representing the work you’ve done since the previous checkpoint. This mechanism makes it possible to look at and even revert to older versions of a file by going back to your code as it was when you “checkpointed” it with a commit.

Git is a complex system that you will learn about over time. In this course, we will stick to the basics. Your workflow will be as follows:

Log into a CS machine using vDesk, NoMachine, or ssh.
Change to your cmsc12100-aut-20-username directory, which you created in Lab #0
Download updates from the Git server (we will add files to your repository throughout the quarter). In Git, this operation is called pulling from the server.
Work on your files
Create a commit with any changes you have made
Upload the commit to the Git server. In Git, this operation is called pushing to the server.

The course staff does not have access to any files stored in your home directory or files on your laptop. All we can access are files that have been pushed to the Git server, so remember to always push your latest commits when you’re done or when you ask a question on Piazza that will require us to look at your code.

Please note that for this lab, indeed, for the rest of the quarter, username should always be replaced with your CNetID.

Setting up your repository¶

If you have not already done so, make sure to follow the instructions under “Setting Up Your CMSC 12100 Directory” in Lab #0. This will result in the creation of a cmsc12100-aut-20-username directory which will contain your Git repository.

Exercises¶

The rest of the lab requires you to have some modified some files. If you have worked through all of Lab #0, you have already modified the files we need you to modify. If not, make sure to do the following with the files contained in the lab0 directory:

Replace Firstname Lastname in the file test.txt with your name
Replace "Hello World!" in hello_world.py with "Hello NAME!" (where NAME should be replaced with your name)

Recall that you can use the Linux cat or less commands to look at the contents of a file to check whether you made these changes in Lab #0.

Creating a commit¶

Creating a commit is a two-step process. First, you have to indicate what files you want to include in your commit. Let’s say we want to create a commit that only includes the hello_world.py file that you just modified. We can specify this operation explicitly using the git add command from the Linux command-line:

$ git add hello_world.py

(Recall that we use $ to indicate the Linux command-line prompt. It is not part of the command.)

There are various shortcuts that will allow you to add all of the files in a directory, such as git add . or git add --all. Using these commands is poor practice, because you can easily end up adding files that you did not intend. Instead, it is better to add files explicitly (as shown above) when you create them and then use the following command:

$ git add -u

when you want to add any previously-added file that has changed since your last commit.

To create the commit, use the git commit command. This command will take all the files you added with git add and will bundle them into a commit:

$ git commit -m"Made some changes to hello_world.py"

The text after the -m is a short message that describes the changes you have made since your last commit. Common examples of commit messages might be “Finished part 1 of the programming assignment” or “Finished lab 1”.

Note

If you forget the -m"Comment" at the end then Git will think that you forgot to specify a commit message. It will graciously open up a default editor so that you can enter such a message. You may be taken to either a Vim editor or a nano editor. If you are not comfortable using these text-based editors, please see I didn’t specify a commit message, and now I’m in a screen I don’t know how to get out of in our FAQ for instructions on how to exit the editor, and then re-run git commit with the -m"Comment" option.

Once you run the above command, you will see something like the following output:

[master 99232df] Made some changes to hello_world.py
1 file changed, 1 insertion(+), 1 deletion(-)

You’ve created a commit, but you’re not done yet: you haven’t uploaded it to the server. Forgetting this step is a very common mistake, so don’t forget to upload your changes. You must use the git push command for your changes to actually be uploaded to the Git server. If you don’t push your commit, the instructors and graders will not be able to see your code. Simply run the following command from the Linux command-line:

$ git push

You should see something like this output:

Counting objects: 7, done.
Delta compression using up to 16 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (4/4), 452 bytes, done.
Total 4 (delta 1), reused 0 (delta 0)
To git@git-dev.cs.uchicago.edu:cmsc12100-aut-20/username.git
   c8432e4..99232df  master -> master

You can ignore most of those messages. The important thing is to not see any warnings or error messages.

You can verify that our Git server correctly received your commit by visiting the following page:

https://mit.cs.uchicago.edu/cmsc12100-aut-20/username

Where username should be replaced by your CNetID.

This URL takes you to the web frontend of our Git server (please note that you will have to log in using your CNetID and password). More specifically, the above URL will show you the contents of your repository, exactly as it appears on the Git server. You can click on “Files” to see your repository’s files, and on “Commits” to see the latest commits uploaded to the server. If you see a commit titled “Made some changes to hello_world.py”, then your commit was successfully uploaded.

In general, if you’re concerned about whether the graders are seeing the right version of your code, you can just go to the above URL. Whatever is shown on that page is what the graders will see. If you wrote some code, and it doesn’t show up in the above URL, make sure you didn’t forget to add your files, create a commit, and push the most recent commit to the server.

Pulling changes from “upstream”¶

When we distribute new course materials, we will do so through Git. These files are located in a separate repository on our Git server, which we call the “upstream” repository. The setup script you ran earlier already configured your Git repository so you can easily download any new files we upload to the upstream repository). To download these changes, run this command from inside the cmsc12100-aut-20-username directory:

$ git pull upstream master

Run this command now. You’ll likely see something like this output:

From git-dev.cs.uchicago.edu:cmsc12100-aut-20/cmsc12100-aut-20
 * branch            master     -> FETCH_HEAD
Already up-to-date.

If we had changed a file between when you ran the setup script and when you ran this command, you might have seen something like this output:

Updating e73ccd2..5cc9de1
Fast-forward
grader.py => common/grader.py | 0
1 file changed, 0 insertions(+), 0 deletions(-)
rename grader.py => common/grader.py (100%)

When you pull from “upstream”, Git automatically downloads any new files or changes that have been committed to “upstream” and updates the files in your repository. If you have made local changes to files that have changed upstream, Git will attempt to merge these changes.

After you’ve pulled from upstream, any new files or changes will only be downloaded to your local copy of cmsc12100-aut-20-username. As with any other changes to your code, you need to run git push to upload them to the Git server (you don’t need to do a git commit to prepare a commit, though; git pull already takes care of this task).

Note

Every time you work on your code, you should run git pull upstream master in your cmsc12100-aut-20-username directory before you do anything else. Sometimes, the instructors notice typos or errors in the code provided for an exercise or programming assignment, and they’ll commit fixes to upstream. By running git pull upstream master, you can make sure that those fixes propagate to your code too.

Pulling changes from the server¶

Your instructor and the teaching assistants have access to your repository. Imagine that one of us made a change to your repository and pushed it to the server. How would you integrate those changes into your local copy of the repository? You will pull them, Specifically, you will run:

$ git pull

from inside your cmsc12100-aut-20-username directory.

It is important that you commit your changes after every session and run git pull and git pull upstream master before you start to do any work. These steps will be particularly important when or if you start working in pairs.

`git add` revisited and `git status`¶

So far, we’ve created a single commit with a single file that we had already supplied in the lab0 directory. If you create new files, Git will not consider them a part of the repository. You need to add them to your repository explicitly. For example, let’s create a copy of hello_world.py:

$ cp hello_world.py hello_universe.py

Is hello_universe.py part of your repository? You can use the following command to ask Git for a summary of the files it is tracking:

$ git status

This command should output something like this:

On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   test.txt

Untracked files:
   (use "git add <file>..." to include in what will be committed)

    hello_universe.py

no changes added to commit (use "git add" to track).

The exact output may vary slightly (in particular, if you created more files in Lab #0, they will show up under Untracked files). However, the important thing is that there are two types of files listed here:

Changes not staged for commit: This is a list of files that Git knows about and have been modified since your last commit, but which have not been added (with git add).
Untracked files: This is a list of files that Git has found in the same directory as your repository, but which Git isn’t tracking.

You may see some automatically generated files in your Untracked files section. Files that start with a pound sign (#) or end with a tilde (~) should not be added to your repository. Files that end with a tilde are backup files created by some editors that are intended to help you restore your files if your computer crashes. In general, files that are automatically generated should not be committed to your repository. Other people should be able to generate their own versions, if necessary.

To add a previously untracked file to your repository, you can just use git add (IMPORTANT: unlike the previous commands, don’t actually run this just yet; you will be doing a similar exercise later on):

$ git add hello_universe.py

If you re-ran git status you would see something like this:

On branch master
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

    new file:   hello_universe.py

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   test.txt

Notice how there is now a new category of files: Changes to be committed. Adding hello_universe.py not only added the file to your repository, it also staged it into the next commit (which, remember, won’t happen until you actually run git commit).

The git status command reports the status on the local copy of the full repository. If you wish to look at the status of a smaller part of the repository (the directory you are working in for example), you can add a path name to the status command. For example:

$ git status .

reports the status of the current directory (a single dot is the path used to refer to the current directory).

Unstaging, discarding changes, and removing files¶

Take a closer look at the git status output above. Git is providing you hints in case you want to undo some of your work.

For example, you can use git reset hello_universe.py to unstage the file. Doing so reverses git add hello_universe.py so you can create a commit only of changes to other files. This is good practice if you think the changes you made to hello_universe.py don’t logically go in the commit you are about to make.

Another useful git command is git checkout. This command will undo modifications to files. If you again look at the above git status output, you will see in the last line that test.txt was modified. To undo any changes to the file, type git checkout test.txt. This command will revert the file content to match the last commit you made in your repository’s history.

Finally, if you would like to remove a file from your repository, using git rm test.txt combines the result of doing rm test.txt and git add test.txt.

Looking at the commits log¶

Once you have made multiple commits, you can see these commits, their dates, commit messages, author, and an SHA-1 hash (a value used by git to uniquely identify the commit) by typing git log. This command will open a scrollable interface (using the up/down arrow keys) that you can get out of by hitting q.

Exercises¶

You have already changed the test.txt file in your lab0 directory. Verify this by using the command git status. You should see it under Changes not staged for commit.
Use git add and git commit to create a commit that includes only the test.txt file. A good commit message would be “Added my name as Author in test.txt”.
Upload your work to the server using git push.
Verify that this file was sent by again using the command git status. You should see that the file test.txt is no longer listed.
If you have not already done so, use cp to make a copy of hello_world.py named hello_universe.py.
If you run git status, hello_universe.py should show up under Untracked files. Add it to the repository using git add.
Run git status again. Is hello_universe.py in a different category of files now?
Although we have added this file, we have not yet created a commit. Create a commit and push it to the server.
Run git status a final time to verify that hello_universe.py was committed (if so, you should not see it in any category of files)
Run git push to upload your changes to the server.

We strongly recommend you to add, commit and push changed files as often as possible, especially if you finished some work and are about to log off a computer. (We often refer to the process of adding/committing/pushing as *checking-in* your code or *syncing* your repository.) This way the latest files are accessible from any other computer where your repository is set up.

chisubmit¶

You will be using a locally-developed system named chisubmit to submit your programming assignments. (You’ll upload files directly to Gradescope for the short exercises and timed assessments.) The set-up script that you ran earlier set you up to use chisubmit in addition to initializing your Git repository.

All chisubmit commands should be run from within your cmsc12100-aut-20-username directory.

chisubmit has commands for managing assignments. Here are descriptions and sample runs of some of the more useful commands. You can run these commands as you read through this section.

chisubmit student assignment list: lists upcoming programming assignments and their deadlines.

$ chisubmit student assignment list

pa0 2020-10-09 23:59:00-05:00       Programming Assignment #0

“Programming Assignment #0” is a mock programming assignment that we have created just so you can familiarize yourself with chisubmit. It will not be graded.

chisubmit student assignment show-deadline <assignment name>: lists deadline information for the specified programming assignment.

$ chisubmit student assignment show-deadline pa0

Programming Assignment #0

      Now: 2020-09-26 13:33:23-05:00
 Deadline: 2020-10-09 23:59:00-05:00

The deadline has not yet passed
You have 13 days, 10 hours, 25 minutes, 37 seconds left

chisubmit student assignment register <assignment name>: registers a student for a specific assignment. You will do this step once per assignment.

$ chisubmit student assignment register pa0
Your registration for pa0 (Programming Assignment 0) is complete.

chisubmit student assignment submit pa0: submits your current commit

$ chisubmit student assignment submit pa0

SUBMISSION FOR ASSIGNMENT pa0 (Programming Assignment 0)
--------------------------------------------------------

This is an INDIVIDUAL submission for Gustav Martin Larsson

The latest commit in your repository is the following:

     Commit: eeed8efa66a13c0b04c587acdda43fbe75c9b99b
       Date: 2020-09-25 14:48:16-05:00
    Message: Added log for testing purposes
     Author: Gustav Martin Larsson <larsson@cs.uchicago.edu>

PLEASE VERIFY THIS IS THE EXACT COMMIT YOU WANT TO SUBMIT

You currently have 2 extensions

You are going to use 0 extensions on this submission.

You will have 2 extensions left after this submission.

Are you sure you want to continue? (y/n):  y

Your submission has been completed.

chisubmit has many other commands, including commands for canceling registrations, canceling submissions etc. You can find detailed instructions on these and other commands here.

Exercises¶

Navigate to pa0 and add your name to the test.txt file in the pa0 directory (if you don’t see a pa0 directory in your repository, run git pull upstream master to fetch it).
Sync your code with the git server using add, commit, and push.
Register for pa0 using the chisubmit registration command.
Submit your “solution” for pa0 using the chisubmit submit command.

Note

VERY IMPORTANT If you work on this lab after October 9th, do not make a submission for PA #0 with chisubmit. This will require using your extensions, which are intended for the real programming assignment (we will revert any extensions you mistakenly use on PA #0, but this is a cumbersome manual process, and we prefer that you simply not make any submissions for PA #0 that involve consuming an extension).

Cleaning Up¶

Use git status to check that you have left the local copy of repository on the CS file server in a clean state. In particular, make sure you have added (or removed) any extra files that you might have created. (As always, be careful when you remove a file to make sure you are in the appropriate directory and are removing the right files.) And then, if necessary, add/commit/push your files to the server.

Summary¶

You should always run git pull and git pull upstream master before you start working. When you are done working, you should always add, commit, and push your code to the git server. Also, remove any extra files that you might have created along the way. (As always, when you remove files make sure you are in the appropriate directory and that you use the correct file names!).

Keeping your local copy of your repository (that is, the one in your home directory on the CS file server) clean and keeping the git server and your home copy of the repository in sync will save you a lot of grief over the course of the term.

Lab #0.5: Git & Chisubmit¶

Objectives¶

Git¶

Setting up your repository¶

Exercises¶

Creating a commit¶

Pulling changes from “upstream”¶

Pulling changes from the server¶

git add revisited and git status¶

Unstaging, discarding changes, and removing files¶

Looking at the commits log¶

Exercises¶

chisubmit¶

Exercises¶

Cleaning Up¶

Summary¶

`git add` revisited and `git status`¶