Getting Started with Git and GitHub

• Section 1: Version Control

  • define a clear history by taking “snapshots” as you work

  • track only certain files with .gitignore files

  • bonus: set Visual Studio Code as your Git editor

• Section 2: GitHub, Merging, and Branching

  • share code with collaborators

  • resolve conflicts

  • review code with pull requests

• Section 3: Setting up Git and GitHub

  • set up Git on your computer

  • clone a repo from GitHub and make your first commit!

  • additional useful links

Section 1: Version Control with Git

• Git tracks your changes, allowing you to define a clear history

• Whenever you’d like to add to your history, take a snapshot, called a “commit”, and add a message.

• To look at a previous version of a project and its commit message, check out the previous commit, then come back to the newest version.

• Git helps you take care of your future self, so you’ll know exactly which version of your code created that design report!

Let’s create a new project directory and see how Git can help us track our changes.

note: The code command I use below only works if you’ve set Visual Studio Code as your Git editor. To do so, follow Bonus: Set Up Visual Studio Code instructions at the bottom of this page. Otherwise, you can skip lines starting with code, replacing them by creating and editing your readme.md file in another text editor.

mkdir example-repo # create a new folder
cd example-repo
git init # create a Git repository
git status
code readme.md # create and make changes to the readme in VSCode
git add readme.md # stages file
git commit -m"starting a readme for docs" # create a new commit with a log message
git log # to see our repos commit history. each commit has a unique ID, called a SHA
git show SHA # use SHA to see only its changes
code readme.md # make new changes to the readme
git diff # see only new differences
git add readme.md # add these changes
git reset # oops! didn't mean to add those

Now, you have a Git repo!

Control what you track with a Gitignore File

We want to track:

• scripts: any kind of code in R, Rmd, Python, Julia, Fortran…

• text documentation:

  • readme files

  • data dictionaries

  • data analysis pipelines (instructions for reproducing results)

We do not want to track:

• large or sensitive data files. (Unauthorized users cannot access private repos, but its still not best practice to track data files.)

• pdfs, images, figures: instead, document how they can be reproduced

• MS Word/Powerpoint documents

To avoid accidentally adding these files, we can use a gitignore file.

note: To use the code command used below, follow the Bonus: Set Up Visual Studio Code at bottom of this page. Otherwise, you can skip lines starting with code, instead creating and editing your data.csv, words.docx, words2.docx files in another text editor.

code data.csv # add a data file to the repository. We dont want to track this!
code words.docx # create a word document. We dont want to track this either
git status
code . # VSCode bolds all file names
code .gitignore # create a .gitignore file, add *.csv, *.docx, any other file extensions you dont want to track
git status
git add .gitignore
git commit -m"adding a gitignore file to ignore csv and docx files"
code words2.docx # create another word file
git status # git automatically ignores this new docx file
code . # ignored files are now lighter in VSCode

Version Control with Git: Summary

• tracks your changes as you work, allowing you to define a clear history

• .gitignore files help us control what is tracked

• useful commands
  git status: summarizes changes that are staged/not staged for next commit
  git add: stages changes
  git reset: unstages changes
  git diff: shows differences in files since last commit
  git commit -m”commit message”: commits stages changes with a message
  git log: shows Git history, with each commit’s SHA (id)
  git show SHA: shows commit’s changes and log message

Bonus: Set Up Visual Studio Code

To use the code command and set Visual Studio Code as your Git editor, follow these instructions (from the VSCode docs).

Step 1: Download Visual Studio Code here.
Step 2: Add code command to path.

• macOS: From the View menu, select Command Palette. Within the Command Palette, type: Shell Command: Install ‘Code’ command in path
• Windows: Make sure you selected Add to PATH during the installation.
• Linux: Make sure you installed Code via our new .deb or .rpm packages.

Step 3: In the terminal, type:

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

You’re all set!

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Section 2: GitHub, Merging, and Branching

Section 3: Setting up Git and GitHub, Useful Links