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2. Git and GitHub

By the end of this guide, you will have your own account at GitHub, where you can conveniently access and share code with the community.

Why?

When working with code, you need to:

  • Access code others have shared — download projects, examples, and libraries
  • Share your own code — let others use, review, or collaborate on your work
  • Keep your code safe — store it somewhere that won't disappear if your laptop breaks

GitHub is a website for sharing code. Git is a tool for downloading and uploading code to GitHub.

What is GitHub?

GitHub is a website for hosting and sharing code. Think of it as Google Drive for code, but with features designed specifically for programmers.

Key concepts:

  • Repository (repo): A project folder containing code and files, hosted on GitHub. Each repo belongs to a user account or an organization.
  • Fork: A copy of a repository on Github. If you fork a repository, you get your own copy of a repository on Github. You can modify it without affecting the original repository.

Getting Started with GitHub

Creating an Account

If you don't already have a GitHub account:

  1. Go to github.com
  2. Click "Sign up"
  3. Follow the registration steps
  4. Verify your email address

If you already have an account, just sign in.

Browsing a Repository

You can explore any public repository without logging in:

  1. Go to a repository URL, for example: github.com/dhis2-chap/chap-workshop-python
  2. You'll see:
  3. File list: All the files and folders in the project
  4. README: A description of the project (displayed at the bottom)
  5. Code button: For downloading or cloning the code
  6. Fork button: For creating your own copy (top right)

Click on any file to view its contents. Click on folders to navigate into them.

Forking a Repository

Forking creates your own copy of a repository that you can modify:

  1. Navigate to the repository you want to fork
  2. Click the "Fork" button in the top right
  3. Select your account as the destination
  4. You now have your own copy at github.com/YOUR-USERNAME/repo-name

Your fork is completely independent — changes you make won't affect the original.

What is Git?

Git is a command-line tool that works with GitHub. While GitHub is the website where code is stored, Git is the tool you use to:

  • Download code from GitHub to your computer
  • Upload your changes back to GitHub
  • Track changes to your code over time (so you can see what changed and undo mistakes)

Using Git

Installation

macOS:

Show command 
brew install git

Linux (Ubuntu/Debian) / WSL:

Show command 
sudo apt update
sudo apt install git

Initial Setup

Configure your identity (this labels your changes):

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

GitHub CLI (Authentication)

To push and pull code without entering passwords, install the GitHub CLI and authenticate:

Installation:

macOS:

Show command 
brew install gh

Linux (Ubuntu/Debian) / WSL:

Show command 
(type -p wget >/dev/null || (sudo apt update && sudo apt-get install wget -y)) \
&& sudo mkdir -p -m 755 /etc/apt/keyrings \
&& out=$(mktemp) && wget -nv -O$out https://cli.github.com/packages/githubcli-archive-keyring.gpg \
&& cat $out | sudo tee /etc/apt/keyrings/githubcli-archive-keyring.gpg > /dev/null \
&& sudo chmod go+r /etc/apt/keyrings/githubcli-archive-keyring.gpg \
&& echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
&& sudo apt update \
&& sudo apt install gh -y

Authenticate:

gh auth login

When prompted:

  1. Select GitHub.com
  2. Select HTTPS
  3. Select Yes to authenticate with GitHub credentials
  4. Select Login with a web browser and follow the prompts

Once authenticated, Git will use your GitHub credentials automatically.

Cloning a Repository

"Cloning" means downloading a repository to your computer. You download a repo by running git clone followed by the repository link. For example, to clone the Chap Core repo:

git clone https://github.com/dhis2-chap/chap-core

This command creates a folder named chap-core in your current directory with all the repository files.

To enter the folder:

cd chap-core

Making Changes

After cloning, you can edit files normally with any text editor. When you're ready to save your changes, you'll use a two-step process: staging and committing.

1. Check what's changed:

git status

This shows which files you've modified, added, or deleted.

2. Stage your changes:

git add .

Staging selects which changes you want to include in your next save. The . means "all changes", but you can also stage specific files with git add filename.py. Think of it as putting items in a box before shipping.

3. Commit your changes:

git commit -m "Describe what you changed"

Committing saves a snapshot of your staged changes with a message describing what you did. This creates a checkpoint you can return to later. The message helps you (and others) understand what changed and why.

Pushing to GitHub

After committing, your changes are saved locally on your computer. To share them on GitHub, you need to push:

git push

This uploads your commits to GitHub, making them visible to others and backing them up online.

Pulling Updates

If the repository has changed on GitHub (e.g., you made changes on another computer, or a collaborator pushed updates), you need to pull those changes to your local copy:

git pull

This downloads any new commits from GitHub and updates your local files.

Exercise

Part 1: GitHub (Web Interface)

1. Create a GitHub account

Go to github.com and sign up (if you haven't already).

Verify: You can log in to github.com

2. Browse a repository

Go to github.com/dhis2-chap/chap-workshop-python

R users: You can also use github.com/dhis2-chap/chap-workshop-r instead.

Verify: You can see the list of files and the README at the bottom

3. Fork the repository

  1. Click "Fork" in the top right
  2. Select your account

Verify: You now have a copy at github.com/YOUR-USERNAME/chap-workshop-python

Part 2: Git (Command Line)

4. Check Git is installed

git --version

Verify: You should see a version number like git version 2.x.x

5. Configure your identity

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

Verify: Run git config --list and confirm your name and email appear

6. Install GitHub CLI and authenticate

Install GitHub CLI:

macOS:

Show command 
brew install gh

Linux (Ubuntu/Debian) / WSL:

Show command 
(type -p wget >/dev/null || (sudo apt update && sudo apt-get install wget -y)) \
&& sudo mkdir -p -m 755 /etc/apt/keyrings \
&& out=$(mktemp) && wget -nv -O$out https://cli.github.com/packages/githubcli-archive-keyring.gpg \
&& cat $out | sudo tee /etc/apt/keyrings/githubcli-archive-keyring.gpg > /dev/null \
&& sudo chmod go+r /etc/apt/keyrings/githubcli-archive-keyring.gpg \
&& echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | sudo tee /etc/apt/sources.list.d/github-cli.list > /dev/null \
&& sudo apt update \
&& sudo apt install gh -y

Then authenticate:

gh auth login

Select: GitHub.com → HTTPS → Yes → Login with a web browser

Verify: Run gh auth status and confirm you're logged in

7. Clone your fork

First, navigate to where you want the repository folder to be created. For example, to put it in your home directory:

cd ~

Now clone your fork. This creates a new folder named chap-workshop-python in your current location:

git clone https://github.com/YOUR-USERNAME/chap-workshop-python.git
cd chap-workshop-python

Verify: Run ls and you should see the repository files

8. Check the remote

git remote -v

Verify: You should see origin pointing to your GitHub fork

9. Make a change

To find where the repository is on your computer, run:

pwd

This shows the full path (e.g., /home/username/chap-workshop-python). Open this folder in your code editor (like VS Code), or navigate to it in your file explorer.

Open the README.md file in your editor, add a line (e.g., your name or a note), and save the file.

10. Check the status

git status

Verify: You should see README.md listed as modified (in red)

11. Stage, commit, and push

git add README.md
git status

Verify: README.md should now be listed as staged (in green)

git commit -m "Add my name to README"
git push

Verify: Visit your fork on GitHub and you should see your change in the README

If all verifications passed, you're ready for the next guide: Virtual Environments

Learn More

Want to dive deeper? Here are some helpful resources:

GitHub:

Git: