Introduction to version control with Git

Scientific workflows: Tools and Tips 🛠️

2025-07-17

Scientific workflows: Tools and Tips 🛠️

📅 Every 3rd Thursday 🕓 4-5 p.m. 📍 Webex

Why version control?

Why version control?

Git is like a Lab Notebook for your scripts

  • Tracks every change in your scripts
  • Helps you recover older versions
  • Enables safe and easy collaboration
  • Makes it easy to share your work with others

Today

  • Introduction to Git
  • Simple Git workflow in theory and practice
  • Publish your work on GitHub
  • Find detailed how-to guides on the website

What is Git?

  • Open source and free to use version control software

  • Quasi standard for software development

  • Complete and long-term history of every file in your project

  • A whole universe of other software and services around it

What is Git?

  • For projects with mainly text files (e.g. code, markdown files, …)

  • Basic idea: Take snapshots (commits) of your project over time

  • A project version controlled with Git is a Git repository (repo)

Version control with Git

Git is a distributed version control system

Idea: many local repositories synced via one remote repo


How to use Git

After you installed it there are different ways to interact with the software.

How to use Git - Terminal

Using Git from the terminal

➕ Most control

➕ A lot of help/answers online

➖ You need to use terminal 😱

How to use Git - Integrated GUIs

A Git GUI is integrated in most (all?) IDEs, e.g. R Studio, VS Code

➕ Easy and intuitive

➕ Stay inside IDE

➖ Different for every program

How to use Git - Standalone GUIs

Standalone Git GUI software, e.g. GitHub Desktop, Source Tree, …

➕ Easy and intuitive

➕ Use for all projects

➖ Switch programs to use Git

How to use Git

Which one to choose?

  • Depends on experience and taste
  • You can mix methods because they are all interfaces to the same Git
  • We will use GitHub Desktop
    • Beginner-friendly, intuitive and convenient
    • Nice integration with GitHub

Tip

Have a look here to find How-To guides for the other methods as well.

The basic Git workflow

git init, git add, git commit, git push

Example

A cook book project to collect all my favorite recipes.

In real life this would be e.g. a data analysis project, your thesis in LaTex, a software project, …

Step 1: Initialize a Git repository

Step 1: Initialize a Git repository

Step 1: Initialize a Git repository

Step 2: Add and modify files

Git detects any changes in the working directory

Step 2: Stage changes

Staging a file means to list it for the next commit.

Step 2: Stage changes

Staging a file means to list it for the next commit.

Step 3: Commit changes

Commits are the snapshots of your project state

Step 3: Commit changes

Commits are the snapshots of your project state

Step 3: Commit changes

Changes are part of Git history and staging area is clear again

The commit history

 

Good commit messages

xkcd on commit messages

Good commit messages

Good commit messages are descriptive and helpful.

✔️

Add pie recipe

This is my favorite pie in the world. 
The recipe comes from my grandfather and 
he learned it from his neighbor.

❌

added a file.

This is really good.

See here for more details on good commit messages.

Step 4: Share changes with the remote repo

Use remote repos (on a server) to backup, synchronize, share and collaborate

  • can be private (you + collaborators) or public (visible to anyone)

Step 4: Share changes with the remote repo

Use remote repos (on a server) to backup, synchronize, share and collaborate

  • can be private (you + collaborators) or public (visible to anyone)

Recap

Basic Git workflow:

  1. Initialize a Git repository
  2. Work on the project
  3. Stage and commit changes to the local repository
  4. Push to the remote repository

Recap

Basic Git workflow:

  1. Initialize a Git repository
  2. Work on the project
  3. Stage and commit changes to the local repository
  4. Push to the remote repository

Recap

Git is a distributed version control system

  • Idea: many local repositories synced via one remote repo
  • Collaborate with
    • yourself on different machines
    • your colleagues and friends
    • strangers on open source projects

Get a repo from a remote

In Git language, this is called cloning


You can clone all public repositories and private repositories if you are a owner/collaborator

Get a repo from a remote

In Git language, this is called cloning


You can clone all public repositories and private repositories if you are a owner/collaborator

Get changes from the remote

  • Local changes, publish to remote: git push
  • Remote changes, pull to local: git pull

A simple collaboration workflow


  • One remote repo on GitHub, multiple local repos
  • Idea: Everyone works on the same branch
    • Pull before you start working
    • Push after you finished working

A branching-merging workflow


  • One remote repo on GitHub, multiple local repos
  • Idea: Everyone works on the their separate branch
    • Merge branch with the main when work is done
  • Check out the How-To guide for details

Publishing your work

Remote repositories

  • There are commercial and self-hosted options for your remote repositories
    • Commercial: GitHub, Gitlab, Bitbucket, …
    • Self-hosted: Gitlab (maybe at your institution?)
  • Please be aware of your institutional guidelines
    • Servers outside EU
    • Privacy rules might apply depending on type of data

Public repositories

  • Making a repository public is a good way to publish and share your work
  • Always add a README.md file
  • Always add a LICENSE file
    • This is important to clarify how others can use your work
  • Connect your repo with Zenodo to get a DOI

If you are interested, browse some nice GitHub repositories for inspiration (e.g. Git training repository, Computational notebooks, Repo to publish code from a manuscript)

Outlook

  • Git can do much more than we covered today
    • Complex collaboration workflows with code review steps
    • Rolling back to previous versions
    • Ignoring files from the repository
    • …
  • GitHub et al. offer many more features
    • Issues, pull requests, code review, project management, …
    • Host websites, wikis, …
  • Start with the basic workflow and build on that

Next lecture

Summer/Conference break in August and September!

Topic of next lecture t.b.a.

📅 16th October 🕓 4-5 p.m. 📍 Webex

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Thanks for your attention

Questions?

Summary of the basic steps

  • git init: Initialize a git repository
    • Adds a .git folder to your working directory
  • git add: Add files to the staging area
    • This marks the files as being part of the next commit
  • git commit: Take a snapshot of your current project version
    • Includes time stamp, commit message and information on the person who did the commit
  • git push: Push new commits to the remote repository
    • Sync your local project version with the remote e.g. on GitHub

Undo things

git revert

Revert changes

  • Use git revert to revert specific commits
  • This does not delete the commit, it creates a new commit that undoes a previous commit
    • It’s a safe way to undo commited changes

Go back in time

git checkout

Checkout a previous commit

Take your work space back in time temporarily with git checkout

Ignoring files with .gitignore

Ignore files with .gitignore

  • Useful to ignore e.g.
    • Compiled code and build directories
    • Log files
    • Hidden system files
    • Personal IDE config files
    • …

Ignore files with .gitignore

  • Create a file with the name .gitignore in working directory

  • Add all files and directories you want to ignore to the .gitignore file

Example

*.html    # ignore all .html files
*.pdf     # ignore all .pdf files

debug.log # ignore the file debug.log

build/    # ignore all files in subdirectory build

See here for more ignore patterns that you can use.