Introduction to GitHub and Version Control

👤Ondřej Mottl

November 2025

FZU

🙋Hi! I am Ondřej Mottl

Assistant Professor at Charles University

Head of 🧑‍💻Laboratory of Quantitative Ecology

📧 Ondrej.mottl(at)gmail.com
🦋 ondrejmottl.bsky.social
🐱 Github OndrejMottl
🆔 ORCID 0000-0002-9796-5081
🌐 bit.ly/ondrej_mottl

This presentation

😸Code on GitHub: OndrejMottl/VersionControl_FZU_November2025

🖼️Slides: bit.ly/mottl_prez_fzu_202511

What we’ll cover today

🎯 Main Topics

What is version control?
Technical setup
Make a record of a change (commit)
Sync changes with remote server
Collaboration through branches
Pull Requests workflow

✅ By the end, you’ll be able to:

Understand basic git terminology
Create a GitHub repo
Make commits and push/pull changes
Handle merge conflicts
Work with branches and Pull Requests

Evolution

Open Science

A better view

The Journey

Version control

Ring a bell?

What is Version Control? 🤔

It is all about keeping track of changes 📓✍️

Exercise

03:00

Do you recognize some of these questions?

It broke … hopefully I have a working version somewhere?
Can you please send me the latest version?
Which version are you using?
I am sure it used to work. When did it change?
My laptop is gone. Is my data now gone?

How do you keep track of changes?

project_script.py
project_script1.py
project_script2.py
project_script4.py
project_script4_new.py
project_script_20191212.py
project_script_20200122.py
project_script_final.py
project_script_final_final.py
project_script_final_final_new.py

Fundamentals

Project self-containment

Each “paper” is a single project.

Project file structure

Git

local software
keep track of changes of files

GitHub

host server
store (git) the data
project management, collaboration, publishing

Git/GitHub setup AKA “git hell”

Follow instructions in Version Control - git hell (a separate presentation).

Getting all the necessary software installed, configured, and playing nicely together is honestly half the battle … Brace yourself for some pain

Weapon of choice (GUI)

GUI = Graphical User Interface

I will be showing you how to use:

GH Desktop

VS Code

You still can use the shell.

Basic vocabulary

A script is a record of code.
Project is self contained project/study/paper containg scripts, data, figures, etc.
Every such project is called repository (ie a repo)
Your local repository is called local
Your online repository, is called remote

Note on practical exercises

Git init (project first)

Activate git for a repo

GH Desktop
VS Code
Command line

Create new project with git tracking

Git integration is automatic in Source control panel

For existing project

git init

Create new project with git tracking

git init <DIRECTORY>

Practical Exercise

Make a new project with Git tracking

05:00

A record of a change

a commit

A commit is a record of a change

If you create or edit a file in your repository and save the changes, you need to record your change via a commit

Chess analogy?

Chess move diary:

Bc4 (Bishop to c4)
Nf3 (Knight to f3)
Qc7 (Queen to c7)

a commit

Pawn to d4

Edit line 32 of file A

a commit

3 states of a file

Staging changes

Make a change to a file and save it. Now stage the change:

GH Desktop
VS Code
Command line

The red icon indicates removed files.
The yellow icon indicates modified files.
The green icon indicates added files.

Stage changes:

git add <FILE>

Unstage changes:

git reset <FILE>

Practical Exercise

Make changes to (a) file(s)
Make a new file
Stage and Unstage the changes

05:00

a first commit

Commit (record) staged changes:

GH Desktop
VS Code
Command line

git commit -am "commit message"

Review history

$ git log --stat
commit 085bb3bcb608e1e8451d4b2432f8ecbe6306e7e7
Author: Scott Chacon <schacon@gee-mail.com>
Date:   Sat Mar 15 16:40:33 2008 -0700

    Remove unnecessary test

 lib/simplegit.rb | 5 -----
 1 file changed, 5 deletions(-)

commit a11bef06a3f659402fe7563abf99ad00de2209e6
Author: Scott Chacon <schacon@gee-mail.com>
Date:   Sat Mar 15 10:31:28 2008 -0700

    Initial commit

 README           |  6 ++++++
 Rakefile         | 23 +++++++++++++++++++++++
 lib/simplegit.rb | 25 +++++++++++++++++++++++++
 3 files changed, 54 insertions(+)

Dissecting a commit

SHA - unique identifier

Author - who has done this?

Date - when was this done?

Message - description of what has been done

Stats - what has changed?

Practical Exercise

commit some changes
review history

05:00

Commit message

Commits are quick and cheap. Therefore:

commit often (!)
provide useful commit messages.

Commit history

Remote

remote

Update remote - PUSH

Now we need to sync changes with the remote using PUSH

GH Desktop
VS Code
Command line

Add a remote to existing local repo (only once):

Push local to remote (GitHub):

Add a remote to existing local repo (only once):

Push local to remote (GitHub):

Add a remote to existing local repo (only once):

git remote add origin https://github.com/<OWNER>/<REPO>

Push local to remote (GitHub):

git push

Practical Exercise

Publish repo to GitHub
make new commit(s)
Push changes to remote

05:00

update local- PULL

Now we need to sync changes from the remote to local using PULL

GH Desktop
VS Code
Command line

Pull from remote (GitHub) to local

Pull from remote (GitHub) to local

Pull from remote (GitHub) to local:

git pull

GitHub intermezzo

A GitHub repo

GitHub creating a repo (repo first)

README - description of the project

.gitignore - list of files ignored by GitHub (more about it later)

license - tell other what they can do with your code

GitHub creating a repo (repo first)

Practical Exercise

Create a new repo on GitHub
Delete a repo on GitHub

05:00

Roles (permissions)

Practical Exercise

Add someone as a collaborator to your repo
Change the role of the collaborator
Remove the collaborator

05:00

Git Clone (repo first)

Git clone (repo first)

Copy (download) from remote repo to local machine

Example of online repo: OndrejMottl/VersionControl-playground

GH Desktop
VS Code
Command line

Open Command Palette (Ctrl+Shift+p)

Paste in URL: "https://github.com/<OWNER>/<REPO>.git"

git clone https://github.com/<OWNER>/<REPO>.git <DIRECTORY>

Practical Exercise

clone a repo (e.g. any repo from OndrejMottl)

05:00

Merge conflict

Merge conflict 💩💩💩

A merge conflict can occur when you are changing the same line in one file differently.

Merge conflict 💩💩💩

To https://github.com/picardis/myrepo.git
 ! [rejected]        master -> master (fetch first)
error: failed to push some refs to 'https://github.com/picardis/myrepo.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

a good strategy to avoid such conflicts:

Commit often
Work in small steps
Push and pull regularly
Organize your code in small modules (scripts)

Merge conflicts cannot always be avoided (but can be mitigated by branches; later).

Merge conflict 💩💩💩

If you have questions, please
<<<<< HEAD
open an issue
=======
ask your question in IRC.
>>>>> branch-a

Delete the unwanted text (including the decorations)

If you have questions, please
ask your question in IRC.

Then save the file, stage, and commit again

Ups! I have made a mistake 😮

How to undo last commit?

Variant A: I commited but NOT pushed yet.

GH Desktop
VS Code
Command line

Open Command Palette (Ctrl+Shift+p)

Write Git: Undo Last Commit

git reset --soft HEAD@{1}

Ups! I have made a mistake 😮

How to undo last commit?

Variant B: I commited AND pushed already.

GH Desktop
VS Code
Command line

Right-click on the commit you would like to undo to and select Revert a commit.

In the Source control panel -> COMMITS section -> Right-click on the commit you want to revert to -> Select the Reset Current Branch to Previous Commit