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Intro to Git
## Git intro
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follow along!

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Why use version control?

collaboration
reproducibility
backups

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Version control in academia

software
writing
citations

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Types of version control

Centralized

Decentralized

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clicks: 3

git building blocks

  • commits: a snapshot of your files*
  • commit graph: commits are organized into a directed acyclic graph

history

*if git is tracking the files

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Create a repository

https://github.com/new

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Clone the repository

git clone

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The basics

  • git add
  • git commit
  • git push
  • git pull
  • git status
  • git log

committing changes

interact with GitHub

view what you've done

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The three trees

File states

modified

staged

committed

The index / staging area

  • staging changes: git add <files>
  • viewing the index: git status

Committing changes

git commit

  • only changes in the staging area are added to the commit
  • commits need a commit message

Viewing changes

  • working tree staging area: git diff
  • staging area HEAD (the parent commit): git diff --staged

Exercise

  1. modify the contents of your README.md file
  2. stage those changes (git add)
  3. commit the changes (git commit)

Viewing history

git log

Exercise

  1. create a new file: test.md
  2. write stuff in test.md
  3. add test.md to the staging area
  4. commit your changes

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Commit philosophy

When to commit?

  • you complete a logical, atomic unit of work
  • you might want to undo those changes

What to commit?

do commit

  • source code
  • documentation

don't commit

  • build artifacts
  • large data files

Commit messages

philosophy

  • tell a story of your project's history
  • capture why

content

  • short summary
  • extended description

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oops!

Reverting changes

git revert

Exercise

  1. revert your first commit

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Interacting with GitHub

local vs. remote repositories

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Exercise

pushing to GitHub (the "remote" repository)

  1. verify that your local branch is ahead of the remote
             git status
  2. push your local changes to the GitHub repository (remote)

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Exercise

pulling from GitHub

  1. edit a file and make a commit using your repo's GitHub webpage
  2. pull those changes into your local repo

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Tags and branches

a commit by any other name...

Tags

git tag -a v0.1

Exercise

  1. tag your most recent commit as v1.0

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Branches

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Branching commands

  • create branch: git branch <branch-name>
  • change current branch: git switch <branch-name>

Exercise

  1. create a branch called cool-feature and switch to it
  2. add hello from cool-feature branch to your README.md

Merging branches

Merging branches

git merge <branch-to-merge>

  • need to be in the branch you want to merge into

Exercise

  1. switch to your main branch
  2. merge cool-feature into main

Typical feature branch workflow

gitGraph:
  commit
  commit
  commit
  branch feature1
  checkout feature1
  commit
  commit
  checkout main
  merge feature1
  commit tag: "v1.0.0"
  branch feature2
  commit
  commit
  checkout feature2
  commit
  commit
  commit
  checkout main
  commit "v.1.1.0"
  branch feature3
  checkout feature3
  commit
  commit
  checkout main
  merge feature3 tag: "v1.2.0"
  checkout feature2
  commit
  checkout main
  merge feature2
  commit tag: "v2.0.0"

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Bonus slides

routeAlias: zenodo

Archiving code with Zenodo

assign DOIs to your code

Resources

Playground: https://git-school.github.io/visualizing-git

<iframe src="https://git-school.github.io/visualizing-git" title="https://git-school.github.io/visualizing-git"></iframe>