Git intro and resources

Pieter Moris
pmoris@itg.be

Institute of Tropical Medicine Antwerp

June 16, 2026

What is git?

Git is a distributed version control system.

\[ git \ne GitHub \]

CLI tool, but various GUIs exist1

Why use git?

The hope is that it can encourage and facilitate reproducible science, and just make your life easier, by, among other things:

  • Providing a free “backup” of your code on a remote server like GitHub.
  • Allowing you to work “seemlessly” across different computers (or servers like CalcUA).
  • Collaborate at various levels of complexity (from single branch projects up to reviewed pull requests with automated tests)
  • Sharing code for publishing and making it citable, cf. Zenodo https://tutorials.inbo.be/tutorials/git_zenodo/, https://onderzoektips.ugent.be/en/tips/00002267/,
  • Tracking the history of your projects, allowing you to reference specific snapshots in time and see what was changed, why, when and by whom.
  • Enabling you to easily revert mistakes or to jump back in time.
  • Easily deploying a (static) website for a project, host readmes or even R/Python notebooks.
  • Utilising project management tools like issues, wikis or (caveat emptor).
  • Facilitating contributing to open source projects.
  • Making it easier to version packages and dependencies (by combining it with tools like renv, conda/virtualenv environments or containers).

When to use git?

Git is best utilised for plain-text files of any kind.

  • Code: from smaller scripts to packages and software
  • Notes: readme files, personal notes or wiki system, markdown-based articles/presentations/websites/books
  • LaTeX documents (cf. Overleaf)
  • Storing config or dot files (e.g. .bashrc)
  • Smaller datasets

When not to use git?

Avoid git for binary files (Office documents, images, etc.)1 or large files2.

How to use git?

Source: XKCD

General overview

Source: Allison Horst

General overview

Source: https://reproducibility.rocks/materials/day2/02-git/

Learning the basic add -> commit -> push workflow first is crucial

Tip

Read git’s warning and help messages carefully. Once you understand the basic syntax, they can often be very useful to (re)solve basic tasks.

Further reading

My own creations:

General guides:

Complete overviews for beginners

Interactive visualisations and playgrounds

Git internals - for those who like to dive deep

Setup and config

# set username to be associated with commits
$ git config --global user.name 'Sirocco'

$ git config --global user.name
Sirocco

# set email to be associated with commits
$ git config --global user.email 'party.parrot@doc.govt.nz'

# show email
$ git config --global user.email
party.parrot@doc.govt.nz

Remotes

Hosting services like GitHub, Bitbucket, and GitLab.

All very similar. Slight differences in naming conventions (e.g. pull vs merge requests). Offer different higher-level features like issues, pull requests, wikis, project boards, etc.

Source: https://reproducibility.rocks/materials/day2/02-git/

SSH keys

Setup SSH-based authentication so that you can clone/push/pull via the SSH protocol instead of HTTPS (otherwise you have to constantly provide your username).

git@github.com:pmoris/my-repo.git

vs

https://github.com/pmoris/my-repo.git

Public vs private repositories

Remote repositories can (usually) be made public or private.

You can even keep a git repo local only. So there really is no excuse not to use git from a security/privacy standpoint.

Avoid storing git repositories on OneDrive

Ignoring things

List files you do not want to track in .gitignore.

Useful for sensitive data, secrets, temporary files/caches, etc.

Branches

https://pmoris.github.io/git-workshop/chapters/5-branching.html

Diff’ing

Collaboration

Be careful when using --force

git stash

Use meaningful commit messages

Source: XKCD

Split up changes with interactive staging

Makes it easier to chunk changes into sensible commits. Cleaner history + easier to selectively undo/apply changes.

Very easy to do with a dedicated GUI or directly within RStudio/VScode.

Alternative, use git add -i: https://git-scm.com/book/en/v2/Git-Tools-Interactive-Staging

Fixing things or rewriting history

Up-to-date does not mean what you think it means

$ git status
On branch master
Your branch is up-to-date with 'origin/master'.

nothing to commit, working directory clean

Fetch vs pull

git fetch will check the remote and tell you about updates.

git pull will pull them in by running git fetch followed by git merge.

Source: Allison Horst

Reset vs checkout vs restore

Source: Git Pro Book

Checkout and detached head

Source: MarianD - StackOverflow

Terminology

  • Repository (or repo): place where you store your code, your files, and each file’s revision history.
  • Branch: A “branch” is a line of development. The most recent commit on a branch is referred to as the tip of that branch.
    • E.g., main and master. Check with git branch -a.
  • HEAD: A named reference to the commit at the tip of a branch. See https://jvns.ca/blog/2024/03/08/how-head-works-in-git.
  • Remote: A repository stored on a git server like GitHub, instead of it being local to your computer.
    • E.g., Often uses a name like origin. Check with git remote -v.
  • Merging. Take changes from one branch and apply them to another one. Related to pull/merge requests.
  • Fast-forward: a simple merge where one branch is a simple linear extension of another.
  • Cloning: Downloading a (full) copy of a repository from a remote git server.
  • Forking: Creating a new repository that contains a copy of another one (including file history).
  • Upstream: The branch on the original repository that was forked.

Cheatsheet

Source: Setting up git(hub) for a lab

More syntax

Tip

For more advanced terminology, like HEAD~, fast-forwarding, reset vs revert, checkout and detached HEAD, see:

Caret and tilde syntax

Source: https://web.archive.org/web/20190429114424/www.paulboxley.com/blog/2011/06/git-caret-and-tilde