Git Notes

Setup

Source Files

Repo: github.com/DaraMac/git-masterclass

Downloading Git

Instructions: git-scm.com/install
Linux: Use package manager
Mac: Package manager (brew.sh) or Xcode
Windows: Git Bash

Setting Up A Forge

GitHub: github.com
GitLab: gitlab.com
Codeberg: codeberg.org
Forgejo: forgejo.org
SourceHut: sourcehut.org
cgit: git.zx2c4.com/cgit/about

Connecting GitHub

Follow this guide, line-by-line, no skipping!
docs.github.com/en/authentication/connecting-to-github-with-ssh

Getting a GUI

Official list: git-scm.com/tools/guis
GitHub Desktop: github.com/apps/desktop
Windows: GitHub desktop (download from link)
Mac: GitHub desktop (Brew formula available)
Linux: codeberg.org/ckruse/Gitte

Editor Integration

RStudio: happygitwithr.com/rstudio-git-github.html
VSCode: code.visualstudio.com/docs/sourcecontrol/quickstart

Nicer Command Line

Motivation

Goals

All your code will be backed up, and be done easily and continually from now on

Version Control

A way of backing up, and also versioning any text
A free and fairly easy and quick way to ensure you don’t ever lose your code
Also keeps track of versions, no more FINAL, FINAL (2), LAST EDIT, COPYv2
Share and collaborate more easily
Reproducibility
Keep everything organised in one place

What to Version Control

Everything text
- Code
- Papers (if not already on Overleaf)
- Notes
- Configuration files (dotfiles)

Datasets?

A small to mid size csv maybe
Possibly not pure text, so not a good fit for version control systems
Maybe too big
But some will be appropriate
Should be backed up somewhere!

Reproducibility

Personal
- Ask yourself, how long would it take to restore your work and working environment on a brand new machine,
- No need for hypothetical, test right now!
For other researchers / users
Licences!

Other Useful Things in Forges

Testing and CI/CD
Releases

Git

Most popular and thus well supported and resourced version control system
xkcd.com/1597

GitHub

Most popular and thus well supported and resourced git forge
Not official!

Fun Things

GitHub Pages site
Social network features
- Stars
- Following
Cinema!

Introduction

Resources

wizardzines.com/git-cheat-sheet.pdf, save this!
ohshitgit.com, some common problems
git-scm.com/book/en/v2, the official book on git
wizardzines.com/zines/git, educational comics
happygitwithr.com, specifically for R users
book.the-turing-way.org/reproducible-research/vcs, general guide for open data science

Model

Distributed version control system (VCS)
It’s just files in .git/
Graphs!
Hashs

Configuring

git config --global user.name "Your Name"
git config --global user.email yourEmail@example.com
git config --global push.autoSetupRemote true
git config --global init.defaultBranch main
git config --list shows current settings
See book chapter on setting up and chapter on configuration for more information

Initialising a Repo

git init

Ignoring

Create a .gitignore file and add names
.DS_Store
__pycache__
.Renviron
Other language or development tool specific files

Cloning

git clone url
Make sure to clone over SSH for repos you work on

Status

git status

Remotes

git remote
Add --verbose or -v for more information

Adding

git add

Committing

git commit
git commit --amend

Pushing

git push

Seeing History

git log
There’s lots of options to change what you see

Branching

git branch name
git switch name
- Create with -c flag

Diffing

git diff
git diff --staged

Pulling

git pull
Not to be confused with a pull request

Merging

git merge name
This is the stage where conflicts might occur on multi-user repos

Tagging

git tag name
git push --tags

Throwing Away Changes

git restore name

Undoing Change

git revert hash
git checkout hash -- path/to/file

The Nuclear Option

rm -rf
Then clone the repo again

Next Steps

Collaborating!

Add other people to private repos
Or just leave it public
Find a project that’s interesting to contribute to
Pull Requests

Hooks

Located in a project’s .git/hooks/ folder
pre-commit.com
Book chapter on hooks

Actions

docs.github.com/en/actions