git and GitHub

Installing git

If you have already installed git, you don’t need to worry about this section. If you haven’t, download the appropriate version for your operating system.

In both cases, VS Code’s built-in terminal (Ctrl + `) will also work once git is on your system PATH. If git is not in your system PATH, check the troubleshooting section below for instructions on how to fix this.

Windows

Use Git for Windows, which installs Git Bash — a terminal that understands git and standard Unix commands. The installer includes Git Credential Manager, which handles authentication for you.

MacOS

You have three options:

  1. Standalone installer (recommended): Download and run the macOS Git installer. This installs Git and Git Credential Manager, which handles GitHub authentication automatically.
  2. Homebrew: If you already use Homebrew, run brew install git from Terminal.
  3. Xcode Command Line Tools: git is bundled with these tools. If you haven’t installed them yet, running git from Terminal will prompt you to install them.

Verify that git is installed by opening a terminal and running:

git --version

You should see something like git version 2.49.0 (or newer).

Once git is installed, you need to tell it who you are. Run these two commands, replacing the name and email with your own:

git config --global user.name "Your Name"
git config --global user.email "your-github-email@example.com"

Git attaches this information to every commit you make. The email should match the one you use for your GitHub account.

Setting Up a GitHub Account

If you already have a GitHub account, you can use that for this course and do not need to create a new account.

Create a GitHub account. It doesn’t have to be linked to your Cornell email or use your Cornell NetID.

For homework assignments and mini-projects, you should use the GitHub Classroom link to “accept” the assignment provided on Ed Discussion, which will give you your own GitHub repository for that assignment1. The first time you click one of these links, you will need to link your name on the course roster with your GitHub account. After this, you will not need to do so again.

1 Even if you don’t want to use the provided Jupyter Notebook, you will be given starting environment files with packages we think will be necessary or useful, and we will expect that you use GitHub for sharing files if you need help with your code.

Basic Git Workflow

After accepting an assignment, you’ll have a repository on GitHub. To work on it from your computer, you’ll use four commands: clone, commit, pull, and push.

Clone (get the repo onto your computer)

“Cloning” downloads a copy of your repository. Open a terminal, navigate to where you want the repository to live, and run:

git clone <link to your repository>

Replace the URL with the link from your GitHub Classroom assignment or any other repository you’re trying to clone (click the green Code button on your repository page to copy it).

Pull (get the latest version)

If you’re working across multiple computers, or collaborating, always pull before you start:

git pull

This downloads any changes that were pushed by your other machine (or teammates) and merges them into your local copy. Failing to do this ahead of making changes can lead to merge conflicts and rejected pushes, which are not always easy to resolve.

Make changes and commit

After making changes to files (editing code, writing answers, etc.), you “commit” a snapshot of those changes:

git status                 # see which files you've changed
git add .                  # stage all changes for the commit
git commit -m "describe what you changed"

You can alternatively pick specific files to add instead of using the ., e.g. git add file1.jl file2.jl if you created or modified some files you do not want to commit. Good commit messages are short but descriptive (e.g., "Answer problem 2", not "stuff").

Push (send your commits to GitHub)

Once you’ve committed, push your changes so they’re saved on GitHub:

git push

Typical Workflow

  1. git clone — once, to get the repo
  2. git pull — before you start working, to get the latest version
  3. Make edits to your files
  4. git add . and git commit -m "message" — whenever you finish a chunk of work
  5. git push — to save your work on GitHub
  6. Repeat steps 3–5 as you work through the assignment

Authentication

When you git push for the first time, GitHub will ask for credentials to ensure that you are actually the owner of your account. The simplest approach for this course is HTTPS with a personal access token:

  1. On GitHub, go to Settings → Developer settings → Personal access tokens → Tokens (classic) (or go to https://github.com/settings/tokens).
  2. Generate a new token (make sure to select a Classic Token), choose a date after the end of the semester or with no expiration date, select the repo, user, and workflow scope, and copy the token.
  3. When prompted for a password during git push, paste the token instead of your GitHub password.

If you installed Git for Windows or the standalone Git for macOS installer, Git Credential Manager should handle this for you — you’ll log in through your browser once and won’t need to re-enter credentials.

Troubleshooting

git: command not found

If your terminal says command not found: git (macOS) or 'git' is not recognized... (Windows), git may not be installed or not added to your system PATH.

Windows:

  1. Re-run the Git for Windows installer.
  2. On the Select Components screen, make sure Git Bash Here and Git GUI Here are checked.
  3. On the Adjusting your PATH environment screen, select Git from the command line and also from 3rd-party software (the recommended option).
  4. Complete the installer, then restart any open terminals (or VS Code).

macOS:

  • If you used the standalone installer, git should be in your PATH automatically. If not, restart your terminal or run:

    export PATH="/usr/local/git/bin:$PATH"

    To make it permanent, add that line to ~/.zshrc (or ~/.bash_profile if using bash).

  • If you used Homebrew, git is symlinked into /usr/local/bin (Intel Macs) or /opt/homebrew/bin (Apple Silicon). Verify with brew list git and restart your terminal if needed.

  • If you used Xcode Command Line Tools, run xcode-select --install to reinstall if git is missing.

After adjusting your PATH, run git --version again to confirm it works.

fatal: not a git repository

You ran a git command outside of a cloned repository. Make sure you cd into the repository folder first (the one created by git clone). You can check you’re in the right place by looking for a hidden .git folder with:

ls -a  # macOS / Git Bash
# or
dir /a  # Command Prompt on Windows

failed to push some refs (push rejected)

This usually means the remote repository has commits you don’t have locally. Run git pull first to sync, then git push again.

Authentication errors on git push

  • Make sure you’re using a personal access token (not your GitHub password). See the Authentication section above.
  • If you’re prompted repeatedly despite using Git Credential Manager, open Credential Manager on Windows (search from Start) or Keychain Access on macOS and remove any stale github.com entries, then try git push again — you’ll be re-prompted to log in.

Further Resources

For a deeper dive into git, see the GitHub Resources page, which includes interactive tutorials and video walkthroughs.