Abhigyan Chakraborty

Git and GitHub for Reproducible Research

Phase 2: The Research Infrastructure — Part 2

(Part 6 of series Blueprint for a Modern Research Computing Environment)

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Quick Summary

This article installs and configures Git, connects your machine to GitHub over SSH, and pushes project_1 as your first repository. It closes with the everyday four-command Git workflow you’ll use from here on, plus a map of what else Git and GitHub offer — branching, pull requests, forking, Issues, and Actions.

Objective

You’ve been writing code. It works. You change something — now it doesn’t. You don’t remember what you changed. Sound familiar? Now imagine two people editing the same script. Who has the latest version? What did the other person change? How do you combine your work without overwriting each other?

These are not hypothetical problems. Every researcher who writes code eventually faces them. Git is the solution, tracking every change you make to your code. GitHub is where you store that history online — making your code accessible from anywhere, shareable with collaborators, and safe from your hard drive failing.

By the end of this part, you’ll have:

Content

💡 Getting Unstuck (Expand for AI Troubleshooting Prompts)

AI tools (like Claude, Grok, Gemini, or ChatGPT) give the best troubleshooting advice when they have the exact text of the tutorial. To ensure the AI understands what you are trying to build, we will give it the actual file.

1. Download the tutorial file

2. Upload it to your AI

3. Ask for Help Copy and paste this exact prompt into the chat along with your file:

I have attached the markdown file for the tutorial I am following. Please read it so you understand the specific environment I am trying to build.

I need help with the following:

Step [X]: [paste exact step text from the blog]

Command I ran: [paste exact command]

What happened: [paste full output/error — if the terminal was truly blank, say so explicitly]

Please help me troubleshoot and fix this error. You can use your general knowledge to solve the problem, but your solution MUST align with the architecture and tools taught in the attached file. Do not suggest alternative setups that contradict the tutorial. Once fixed, tell me what to do next in the article.

To go deeper on a step before you run a command:

I have attached the Part6.md file. Look at Step [X] and explain exactly what the command does and why we are doing it before I run it.

Think of this series as the roadmap and your AI assistant as your learning companion.

Prerequisites

Step 1 — Create a GitHub Account

Go to https://github.com and sign up for a free account. Choose your username carefully — it will be visible on every repository you create.

Step 2 — Install Git

Open your terminal and type:

sudo apt update
sudo apt install git

Verify:

git --version

Step 3 — Configure Git

Tell Git who you are:

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

Set VS Code as your default Git editor:

git config --global core.editor "code --wait"

Step 4 — Generate an SSH Key for GitHub

Generate a key specifically for GitHub:

ssh-keygen -t ed25519 -C "your_email@example.com"

When asked where to save it, type ~/.ssh/id_ed25519_github to avoid overwriting existing keys. Set correct permissions:

chmod 600 ~/.ssh/id_ed25519_github

Step 5 — Add the SSH Key to GitHub

Copy your public key:

cat ~/.ssh/id_ed25519_github.pub

Add it to GitHub:

  1. Go to https://github.com/settings/keys
  2. Click New SSH key
  3. Paste the key and save

Step 6 — Configure SSH to Use Your GitHub Key

Tell SSH which key to use:

nano ~/.ssh/config

Add these lines:

Host github.com
  HostName github.com
  User git
  IdentityFile ~/.ssh/id_ed25519_github

Test the connection:

ssh -T git@github.com

Step 7 — Create a Repository on GitHub

  1. Go to https://github.com/new
  2. Name it project_1
  3. Click Create repository

Step 8 — Push project_1 to GitHub

Navigate to your project folder:

cd ~/project_1
git init

Create a .gitignore file to exclude temporary files:

nano .gitignore

Add these lines:

__pycache__/
*.pyc
.ipynb_checkpoints/

Stage and commit:

git add .
git commit -m "Initial commit: project_1 setup"

Connect to GitHub and push:

git remote add origin git@github.com:yourusername/project_1.git
git branch -M main
git push -u origin main

Step 9 — The Everyday Git Workflow

Every time you make changes, follow this workflow:

  1. Check status: git status
  2. Stage: git add .
  3. Commit: git commit -m "Describe what you changed"
  4. Push: git push

Step 10 — Cloning a Repository

To download an existing project:

git clone git@github.com:yourusername/project_1.git

Step 11 — What Else Exists in Git and GitHub

Beyond basic pushes, explore these features:

What’s Next

What You’ve Done:

Next: Part 7 — Project Organization and Managing Scientific Data | Previous: Part 5 — Linux Essentials

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