Git and GitHub for Ag Data Science 🌱

A beginner-friendly introduction to version control and collaboration in R projects using GitHub and GitHub Desktop.

1 Common Problems Without Git & GitHub ❌

Have you ever struggled with:

• Messy file versions? 📂 Naming files like code.R, code_final.R, code_final_final.R, codefinal3.R, or code_seethis.R? 🤯
• Lost in email threads? 📧 Collaborating with colleagues by sending multiple file versions via email, leading to confusion and mistakes?
• Untracked changes? 🔄 Making edits but forgetting what changed and why?

If so, you’re not alone! These are common challenges in agriculture data science and research projects. Fortunately, Git and GitHub provide an efficient way to manage and collaborate on code without the chaos.

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2 🚀 Why use version control? 🔄

Version control is essential for reproducible research 📑 and collaborative work 🤝. Git and GitHub help:

• Track changes 📝 in your code over time.
• Collaborate with others without overwriting files.
• Manage projects efficiently with branches and pull requests.
• Store backups in the cloud ☁️.

If you work in agriculture data science, keeping track of scripts, models, and datasets is crucial for transparency and efficiency. Let’s explore how to get started!

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3 What are Git and GitHub?

• Git
  • A version control system that tracks changes in files on your local computer, allowing you to manage versions and revert to previous work.
• GitHub
  • An online platform for hosting Git repositories, enabling easy collaboration, project sharing, and cloud storage.

4 What is GitHub?

GitHub is an internet hosting service designed for software development and version control using Git. Basically, GitHub facilitates to work in a collaborative manner through multiple features designed to efficiently control changes made by users during a working session.

5 🛠 Setting Up Git and GitHub

5.1 1️⃣ Install Git

Git is a version control system that runs locally on your computer. To install it:

• 📥 Download Git from git-scm.com
• Follow the installation instructions for your OS (Windows, macOS, Linux)
• Open RStudio, go to the “Terminal” tab,
• Verify the installation by running this line:

git --version

5.2 2️⃣ Create a GitHub Account

GitHub is a cloud-based platform that stores your Git repositories online.

• 🌍 Go to GitHub and sign up.
• Set up your GitHub profile and SSH key (optional but recommended for authentication).

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6 🔄 Basic Git Workflow

Once Git is installed, you can start managing projects with a simple workflow:

1. Initialize a repository 🏗

   git init

2. Check repository status 🔍

   git status

3. Add files to staging 📂

   git add filename.R

4. Commit changes 💾

   git commit -m "Added data processing script"

5. Push changes to Remote 🚀

   git push origin main

7 Key Git VERBS

• git commit -m "message": Save current version of files to the .git directory
• git push: Upload your latest commits to the remote repo. First time = publish
• git pull: Download the latest commits from the remote repo

8 📖 GitHub Vocabulary:

#	Concept	Description
1	version control	is the practice of tracking and managing changes to software code
2	repository	is a code hosting platform for version control and collaboration.
3	branch	is a unique set of code changes with a unique name.
5	clone	is to copy a remote repository into your local
4	remote/local	they are Git repositories hosting code at different locations. “Remote” means located on the internet or another network. “Local” means located in your machine.
5	origin	is the remote version of a given repository.
6	main/master	is the name of the default branch. In the past “master” was the default. Since 2020, “main” is the default name of all new source code.
7	commit	is a “revision” or individual set of changes to a file or group of files within a branch.
8	pull / fetch	is the action to fetch and download content from a remote repository to update your local repository.
9	push	is the action to upload content from a local repository to update its remote version (all within a given branch).
10	pull request	is to let the repository owner to know about changes you’ve made to his code pushing to a new named branch. It allows to discuss, review, accept/reject the changes, and eventually accept and merge your branch to update the old version (normally, the “main” branch). Note: This action allows users to appear into the “contributors” list of a repository.
11	merge	is the action of combining two branches into one, and putting a combined “forked history”.
12	rebase	is moving or combining a sequence of commits to a new base commit.
13	fast-forward	is merging when there is a direct linear path from the source branch (updating from) to the target branch (the one updating to).
14	stash*	it temporarily shelves changes you’ve made to your copy so you can work on something else, and then come back and re-apply them later. *very useful when you need to pull and update from the remote but you have been working on your local file.
15	revert	is the “undo” action to safely undoing changes. It creates a new commit that inverses changes.
16	fork	is to copy others’ repository into your account. Your forked repo will act as an independent branch, so you can commit changes and put pull request from the forked repo.
17	Issues	is a section of any GitHub repository that allows to track issues experienced by users. Particularly useful for packages. Issues can be quoted and linked to pull requests.
18	PATs	stands for Personal Access Tokens, which are an alternative authentication method to passwords and SSH
19	lfs	the lfs stands for Large File Storage. It allows you to track heavy files that are not allowed by default.
20	GitHub Actions	is the way to automate continuous integration and delivery (CI/CD). Particularly, CI is a very important a software practice for package development, since it allows to detect errors on different operative systems via multiple automated tests.

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9 🖥 Using GitHub Desktop (GUI Approach)

For those who prefer a graphical user interface (GUI), GitHub Desktop 🖥 simplifies Git operations. GitHub Desktop is beginner-friendly and helps visualize your repository history 🔄.

🎯 Steps: 1. Download and install GitHub Desktop 2. Sign in with your GitHub account

9.1 ✅ Creating a GitHub Repository

1. Open GitHub and click New Repository ➕.
2. Name the repository (e.g., my-first-repo) and choose Public or Private.
3. Click Create Repository 🚀.

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9.2 📂 Creating an R Script and Committing Changes

1. Open GitHub Desktop and click Clone a Repository.

2. Select your repository and choose a local directory.

3. Create a new Quarto file:

   • Go to File → New File → Quarto Document…
   • Title: Hello Quarto
   • Format: HTML
   • Click Create

4. Save the file inside your repository folder as hello.qmd.

5. Add the following content to hello.qmd:

---
title: "Hello Quarto"
format: html
---

# My first Quarto file
This document includes text and an R code chunk.

7. Create your first code chunk

## My first chunk:
    print("Hello Quarto world!")

[1] "Hello Quarto world!"

7. Render the document in RStudio:

   • Click Render
   • This should create an output file like hello.html in the same folder.

8. Return to GitHub Desktop.

9. You should see changes listed (often hello.qmd and hello.html).

10. Write a commit message (e.g., “Added hello.qmd”) and click Commit to main.

11. Click Push origin to upload the changes to GitHub.

9.3 🔄 Cloning or Pulling Changes

1. If you want to work on an existing repository, click Clone Repository in GitHub Desktop.

2. Select a repository and choose a local directory.

3. If changes have been made remotely, click Fetch Origin and then Pull Origin to update your local version.

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10 📚 Further Learning

• 📘 Pro Git Book (Free)
• 🎥 GitHub Docs & Tutorials
• 🏆 Awesome GitHub Repositories