Git tips and tricks

Basic Git & GitHub Guide for Scientific Projects

About

This guide is for beginners who are new to Git and GitHub. It walks you through the process of setting up Git on your computer, creating a GitHub account, learning basic commands, and joining a GitHub organization (e.g., rlaplaza-lab). In the near future, it will probably be helpful to do the same in the supercomputers you use as well.

Step 1: Create a GitHub Account

1. Go to https://github.com
2. Click Sign up
3. Choose a username, enter your email, and create a secure password
4. Verify your email and follow the on-screen instructions

Step 2: Install Git

On macOS

Use Homebrew:

brew install git

On Ubuntu/Debian

sudo apt update
sudo apt install git

On Windows

Download from the official site: https://git-scm.com/download/win

Follow the installer with default settings.

Step 3: Set Up Git

Open your terminal or Git Bash and configure Git with your name and email:

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

You can check the configuration with:

git config --list

Step 4: Generate an SSH Key (Optional but Recommended)

This allows you to securely connect to GitHub.

ssh-keygen -t ed25519 -C "your@email.com"

Then add your key to the SSH agent:

eval "$(ssh-agent -s)"
ssh-add ~/.ssh/id_ed25519

Copy your SSH public key:

cat ~/.ssh/id_ed25519.pub

Go to GitHub SSH settings, click “New SSH key”, and paste the key there.

Step 5: Request Access to rlaplaza-lab

1. Contact Ruben and share your GitHub username
2. You will be invited to the rlaplaza-lab GitHub organization
3. Accept the invitation via email or at https://github.com/orgs/rlaplaza-lab

Step 6: Clone a Repository

Once you have access to a repository, you can clone it to your computer:

git clone git@github.com:rlaplaza-lab/project-name.git

Or with HTTPS:

git clone https://github.com/rlaplaza-lab/project-name.git

Step 7: Basic Git Commands

Check project status

git status

Add changes to staging

Staging is a temporary area that holds the changes you plan to make to the repository. Adding changes to staging is how you tell Git which of your edits should go into the next commit.

git add filename.py

Or add everything:

git add .

Commit changes with a message

A commit is a snapshot of the repository. Once all the changes you want are staged, you save them together in a single commit.

git commit -m "Describe your changes clearly"

Push changes to GitHub

Now we can upload our commit to the remote repository on GitHub.

git push

Pull latest changes from GitHub

We can also download the latest commits from the remote repository. It is possible to push and pull from different branches, but we do not cover that here.

git pull

Step 8: Best Practices

• Commit often with clear messages
• Use branches for new features or experiments:

  git checkout -b new-feature
  

• Keep your main or master branch clean
• Pull often to avoid conflicts
• Document your code and changes in a README.md or CHANGELOG.md

Resources

• Introduction to Github by the excellent Prof. Ayers
• Git Book (free)
• GitHub Docs
• Git Cheat Sheet
• Oh My Git! Game – Learn Git by playing
• GitHub Student Developer Pack – Free tools for students