Version Control with `Git`

Agentic Programming

Florian Oswald and The Software Carpentry

13 October, 2026

Version What?

Question

What is Version Control and Why Should I Care?

Objectives

Understand the benefits of an automated version control system.
Understand the basics of how automated version control systems work.

Final.doc

“Piled Higher and Deeper” by Jorge Cham, http://www.phdcomics.com

Undo

The latest version is often best for text documents.
However, sometimes our view of best evolves. Then, we want to undo.
Undo means going back in history.

MS Word etc have track changes features.
Once you accepted the proposed changes of a collaborator, can you go back?
What about Dropbox-like solutions? (What is dropbox actually?)

Which Version: 20210611_draft.tex

Research team 👇 orders files by YYYYMMDD.

Hey, fixed that thing last week.
In 20220629-paper.tex?
Erm. Yes. No. I think 20211203-paper.tex - messed up the file name.
Ok, can you copy it into the latest version?
Sure. Damn, can’t find it anymore. I’ll just write it again. All in my head. 🤯

Which Version 2: Why is the sample size so small suddenly?

We had 800 observations, now 733. Why?
Erm…😱 No clue!
Well you must have changed the code.
Yes, I improved the code in several parts.
Well you have to find out what happened.
But that was weeks ago - I don’t remember! 😢

Hard Bugs

The hard bugs 🐛 are the ones you see only after a while.
See result today, error was introduced long ago.
You can rewind dropbox 30 days. What if… ?
Also, throw away 30 days of work?
😱 😱 😱 😱

Setting Up Git

We all installed git.
Let’s setup our name

$ git config --global user.name "Your Name"
$ git config --global user.email "your@mail.com"

Line Endings on Windows:

git config --global core.autocrlf false

Creating a Git Repository

Question

Where does Git store information?

Objectives

Create a local repository
Describe purpose of .git directory

House Prices Project

Let’s create a project folder in our home to look at the house prices from last week.

$ cd    # going to home dir 
$ mkdir houseprices  # create directory
$ cd houseprices 
$ git init

Now the directory ~/houseprices is endowed with git version control.
What does that look like?

Where is Git?

Remember hidden files and folders?

$ ls -a 
./    ../   .git/

Git for this repository resides in .git

Danger Zone

If you delete that folder, the entire version control is GONE.
Be very careful that you really want to do that.

Tracking Changes with Git

Question

How do I record changes in Git?
How do I check the status of my version control repository?
How do I record notes about what changes I made and why?

Objectives

Understand the benefits of an automated version control system.
Understand the basics of how automated version control systems work.

Adding Code and Text

Note

Notice: The code we produce is text.
Remember what we learned about file endings.

Let’s add a shell script where we add our pipeline from last week.

run to get the raw data again:

wget https://static.data.gouv.fr/resources/demandes-de-valeurs-foncieres/20240408-125738/valeursfoncieres-2023.txt

Adding Code and Text

create a script

nano maketable.sh  # open nano
# type this:
cd ~/houseprices   # make sure we are in the right place
cut -d '|' -f 18 valeursfoncieres-2023.txt | sort | uniq -c | sort -r | head -n 10
# save and exit

(Does it work?)

ls .  # check the new file is there
./maketable.sh   # run it!

No, it doesn’t. 😖

chmod +x ./maketable.sh  # add executable mode
ls -a
./maketable.sh

Viewing Changes

Ok, now let’s see what git makes of our additions to this directory.

floswald@PTL11077 ~/houseprices (main)> git status
On branch main

No commits yet

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        valeursfoncieres-2023.txt
        maketable.sh

It is actually helpful not to use bash as a shell…
Customizing your shell is an extremely effective procrastination device.
You must know what shaving a Yak means before you walk out of my class.

Seeing the Difference

the command git diff shows you what changed between versions.
lets see what it shows now:

$ git diff

It shows nothing, i.e. an empty diff, because there are no commits yet to compare with.
Ok, let’s change that.

Modify-Add-Commit 1

git reports about untracked files. We need to decide what to track.

Move files to staging area:

git add maketable.sh 
git status

Notice that I did not want to track the csv file.

On branch main

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)
        new file:   maketable.sh

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        valeursfoncieres-2023.txt

Modify-Add-Commit 2

Now, let’s record what is in the staging area.

$ git commit -m 'added the maketable script'

[main (root-commit) 9956506] added the maketable script
 1 file changed, 2 insertions(+)
 create mode 100644 maketable.sh

check status:

$ git status

On branch main
Untracked files:
  (use "git add <file>..." to include in what will be committed)
        valeursfoncieres-2023.txt

nothing added to commit but untracked files present (use "git add" to track)
➜  gasprices git:(main) ✗

Modify-Add-Commit 3

Let’s check what’s in the log.

$ git log 

commit 9956506dc3159403b87aea3b04654c293e82c680 (HEAD -> main)
Author: Florian Oswald <florian.oswald@gmail.com>
Date:   Tue Feb 7 10:50:51 2023 +0100

    added the maketable script

Modify-Add-Commit 4

Now let’s modify the script finally.

$ nano maketable.sh

# add this line on top 
echo hello user, will make a contigency table now.
# save and exit

now - what’s the difference in the repo?

Diffing

there are still the same files here:

$ ls 
valeursfoncieres-2023.txt  maketable.sh

But we can now compare versions:

$ git diff 

diff --git a/maketable.sh b/maketable.sh
index 7e01058..3b7007e 100644
--- a/maketable.sh
+++ b/maketable.sh
@@ -1,2 +1,3 @@
+echo hello user, will make a contigency table now.
 cd ~/valeursfoncieres-2023.txt   # make sure we are in the right place
 cut -d ';' -f 5 valeursfoncieres-2023.txt | tr [:lower:] [:upper:] | sort | uniq -c | sort

Commiting Changes Again

let’s first check everything runs

$ ./maketable.sh

good. commit!

$ git add maketable.sh 
$ git commit -m 'added message to user'

Adding a README

Good. Now let’s add a README file.
It’s customary to write this in markdown

$ nano README.md

write this in nano and save when done.

# Gas Prices

This repo contains code to analyse gas prices at French gas stations.

add to staging area, so we can take a snapshot

$ git add README.md 
$ git commit -m 'added readme'

What is this Staging Area?

git is like a fotographic camera.
before you take a picture of your friends, you need to arrange them somehow, so that all fit, and so that all 😁.
You put them on stage. Same for files in your repo.

figure from software carpentry

What is this Staging Area?

I took that picture at CDG airport

Looking at History

Question

How can I identify old versions of files?
How do I review my changes?
How can I recover old versions of files?

Objectives

Explain what the HEAD of a repository is and how to use it.
Identify and use Git commit numbers.
Compare various versions of tracked files.
Restore old versions of files.

The most recent version: HEAD

Let’s change the maketable.sh script again:

$ nano maketable.sh
echo program run successfully
# save exit

$ git add maketable.sh

The most recent version of our repo is called HEAD.

$ git diff # compares entire repo to HEAD 
$ git diff HEAD maketable.sh

Whoops, typo

Oh no, we wrote program run successfully. That should be ran not run.
What now?

we have not committed this yet!
we can just get back the version in HEAD, and edit again:

$ git restore maketable.sh
$ git checkout maketable.sh # also works

edit the script, add and commit.

How to get a specific version

What if you want something else than HEAD?
like, the first version of maketable.sh?
look at history:

$ git log --oneline --graph

* a6f023b (HEAD -> main) added readme
* 9956506 added the maketable script

The 9956506 is the unique identifier of that version.
We can go back to that version:

$ git checkout 9956506 maketable.sh

Key Points

git diff displays differences between commits.
git checkout recovers old versions of files.

So, how does this thing work?

software carpentry image.

Version Control with VScode

Download Visual Studio Code
Start
Open folder ~/gasprices
check version control tab on the left.

Version Control with RStudio

top right click on new project
Select existing directory
Select ~/gasprices
checkout out the git tab in Rstudio!

Collaborating with Git on GitHub

Create repo
copy ssh remote URL
connect local to remote repo

SSH connections

Secure Shell Protocol
Private-Public key pair. It’s like a lock, and you have the only key.
Let’s check if you have one already!

ls -la ~/.ssh

if error, create one:

ssh-keygen -t ed25519 -C "your@email.com"

press enter (no passphrase)

check

ls -la ~/.ssh

Communicate with GitHub Remote

Let’s ping the remote server at GitHub now.

ssh -T git@github.com

right, of course Github doesn’t have our public key yet (the lock for our key!)
copy from your terminal

cat ~/.ssh/id_ed25519.pub  # or your *.pub

Go to github.com, click top right corner, settings, SSH keys.

Adding a Remote to your local Repo

Now that we can talk to Github.com, let’s add the remote to our local repo.
We add a remote by getting the SSH url from the repository (green button) online.

$ git remote add origin git@github.com:YOUR_USER/YOUR_REPO.git

origin is the name of the remote server. your choice, but origin is common.
this should set that remote both for sending and retrieving stuff from the repo. pull and push, in git language:

$ git remote --v

Pushing It

Now we can push our local repository to the remote repo.
There will be a full copy of what is in .git (i.e., the entire history of the repo) on that remote machine.
You will be able to use it like a central backup location for your work.

$ git push -u origin main

the -u flag sets the main branch as default upstream branch to track.

Branching It

Next to different versions of a file/directory over time, we can have versions evolving in parallel.
Imagine development history branching off into 2 separate directions at one point.
They may converge at some point again, but maybe one of them will turn out a failure and we drop it.
Branches are hugely useful to organize team work.

$ git checkout -b testing # checkout repo on new branch `testing`
Switched to a new branch 'testing'

Now can develop stuff on the testing branch.
Later on, we can merge it back into main if we like it.

The Full Picture(s)

picture from @MarkLodato - click for more!

Pushing Branches to GitHub

Once you created a local branch you can of course copy (push) it to your remote to share with others.
you would amend the push command:

# make sure you are on the desired branch 
$ git branch 
  main
* testing

$ git push origin testing

Version Control with Git

Version What?

Final.doc

Undo

Which Version: 20210611_draft.tex

Which Version 2: Why is the sample size so small suddenly?

Hard Bugs

Setting Up Git

Creating a Git Repository

House Prices Project

Where is Git?

Tracking Changes with Git

Adding Code and Text

Adding Code and Text

Viewing Changes

Seeing the Difference

Modify-Add-Commit 1

Modify-Add-Commit 2

Modify-Add-Commit 3

Modify-Add-Commit 4

Diffing

Commiting Changes Again

Adding a README

What is this Staging Area?

What is this Staging Area?

Looking at History

The most recent version: HEAD

Whoops, typo

How to get a specific version

So, how does this thing work?

Version Control with VScode

Version Control with RStudio

Collaborating with Git on GitHub

SSH connections

Communicate with GitHub Remote

Adding a Remote to your local Repo

Pushing It

Branching It

The Full Picture(s)

Pushing Branches to GitHub

Version Control with `Git`