Week 1: Git, GitHub, and the Command Line¶

Overview¶

This session does double duty: it teaches the foundational tools (git, terminal, GitHub) and sets the stage for the entire course. The core argument is simple: AI coding agents like Claude Code are extraordinarily powerful, and that power is exactly why you need version control, quality assurance (QA), and structured workflows.

Slides¶

Use arrow keys to navigate. Press F for fullscreen, ? for shortcuts.

Setup Guide¶

A step-by-step walkthrough for getting your research computing environment ready. No prior coding experience is assumed.

1. Open Your Terminal¶

Every operating system has a built-in terminal. This is where you type commands instead of clicking buttons.

wsl --install

Once your terminal is open, verify it works:

pwd    # Where am I?
ls     # What files are here?
ls -la # List with details

2. Install a Package Manager¶

Package managers let you install software from the command line. Think of them as an app store for developer tools.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

brew --version

sudo apt update

3. Install Git and the GitHub CLI¶

You need two command-line tools: git for version control and gh (the GitHub CLI) for interacting with GitHub.

brew install git gh

sudo apt install git gh

Verify both:

git --version
gh --version

Configure your git identity (use the same email you will use for GitHub):

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

4. Understanding git vs gh¶

These two tools work together but handle different things:

git commands you will use daily:

git init           # Start tracking a folder
git add file.md    # Stage a file
git commit -m ""   # Save a snapshot
git push           # Send to remote
git pull           # Get updates
git log --oneline  # View history
git diff           # See what changed
git clone <url>    # Copy a remote repo locally

gh commands for GitHub operations:

gh repo create     # Create a new GitHub repo
gh repo clone      # Clone a GitHub repo (shorthand)
gh issue create    # Open an issue
gh issue develop   # Create a branch from an issue
gh pr create       # Open a pull request
gh pr view         # View PR details

5. Create a GitHub Account¶

If you do not already have one:

1. Go to github.com
2. Click Sign up
3. Choose a username, enter your email, create a password
4. Verify your email address

GitHub Education (free upgrades for researchers)¶

GitHub offers free benefits for students, faculty, and research labs. These are worth setting up before you go further.

Set up SSH keys (recommended)¶

SSH keys let you push to GitHub without typing your password every time.

# Generate a new SSH key
ssh-keygen -t ed25519 -C "your.email@example.com"

Press Enter to accept the default file location. You can set a passphrase or press Enter for none.

# Start the SSH agent
eval "$(ssh-agent -s)"

# Add your key
ssh-add ~/.ssh/id_ed25519

cat ~/.ssh/id_ed25519.pub | pbcopy

cat ~/.ssh/id_ed25519.pub
# Select and copy the output manually

Then add it to GitHub:

1. Go to github.com/settings/keys
2. Click New SSH key
3. Paste your key and give it a title (e.g., "My Laptop")
4. Click Add SSH key

Test the connection:

ssh -T git@github.com

You should see: Hi username! You've successfully authenticated...

Authenticate the GitHub CLI¶

gh auth login

Follow the prompts: select GitHub.com, choose SSH, and authenticate through your browser.

6. Terminal Navigation Basics¶

pwd              # Print working directory (where you are)
ls               # List files and folders
cd Documents     # Change directory
cd ..            # Go back up one level
mkdir my-project # Create a new folder
cd my-project    # Move into it

7. Create Your First Repository¶

# Create a project folder and move into it
mkdir my-research-project
cd my-research-project

# Initialize git tracking
git init

Create a file and make your first commit:

# Create a README
echo "# My Research Project" > README.md
echo "" >> README.md
echo "This is my first git repository." >> README.md

# Stage and commit
git add README.md
git commit -m "Add README with project description"

Make a few more commits to practice:

# Add a notes file
echo "## Research Notes" > notes.md
echo "" >> notes.md
echo "- Started project setup" >> notes.md
git add notes.md
git commit -m "Add initial research notes"

# Update the README
echo "" >> README.md
echo "## Goals" >> README.md
echo "- Learn git and GitHub" >> README.md
echo "- Set up a reproducible workflow" >> README.md
git add README.md
git commit -m "Add project goals to README"

View your history:

git log --oneline

8. Push to GitHub¶

Create a remote repository:

1. Go to github.com/new
2. Name it my-research-project
3. Leave it public (or private, your choice)
4. Do not check "Add a README" (you already have one)
5. Click Create repository

Connect and push:

git remote add origin git@github.com:YOUR-USERNAME/my-research-project.git
git branch -M main
git push -u origin main

Refresh the GitHub page. Your files and commits are now online.

9. Verify Everything Works¶

git --version       # Git is installed
gh --version        # GitHub CLI is installed
pwd                 # You are in your project
git status          # Git is tracking the project
git log --oneline   # You have commits
git remote -v       # Your remote is set

If all of these work, you are ready for Week 2.

Before Next Session¶

brew install claude-code

curl -fsSL https://claude.ai/install-cli | sh

claude --version

Quick Reference¶

Terminal¶

Git (version control)¶

GitHub CLI (gh)¶

Resources¶

• Git documentation
• GitHub Skills (free interactive courses)
• Course repository
• Open Science Collective Discord
• research-skills plugin