Version Control with Git

0. Introduction

Before We Start

Create an account at github.com
Open up a terminal

How This Works

I’ll work through on my machine and you follow along
Feel free to ask questions!
Let me know if I’m going too fast

Exercises

You do these on your own. When you finish one:
- Offline put a green post-it on your laptop 🟩
- Online 👍 the exercise message in chat
If you hit a problem:
- Offline put a red post-it note on your laptop 🟥
- Online ✋ raise your hand

1. What is Version Control?

What Does It Do?

Tracks changes to files
Any file can be tracked
Text (.txt, .csv, .py, .c, .R, etc.) works best
- These allow smart diff / merge etc.

Why Use Version Control?

A more efficient backup
Reproducibility

Why Use Version Control?

Sharing
Teamwork

Version Control Tracks Changes

Version Control Tracks Changes

Version Control Tracks Changes

Version Control Alternatives

Git
- Distributed
Subversion (svn)
- Centralised
Mercurial (hg)
- Distributed
Git most widely used in academia
- GitHub
- GitLab

Graphical Version Control

Sourcetree	Git Kraken	Git Desktop

GUIs

PyCharm	RStudio	VS Code

2. Setting Up Git

Key Commands

git config --global user.name "Me"
git config --global user.email "me@email.com"
git config --global core.editor "nano -w"

Check It Worked

git config --list

user.name=Sam Mangham
user.email=mangham@gmail.com
core.editor=nano -w
[plus much more on Windows]

SSH Key Security

Setting Up GitHub

Sign up to GitHub: https://github.com/signup
Open a terminal
ssh-keygen -t ed25519
Accept all the defaults
cat ~/.ssh/id_ed25519.pub
Copy the contents to GitHub: https://github.com/settings/ssh/new
- Or use your own if you have one already

Expected Outputs

Generating public/private ed25519 key pair.
Enter file in which to save the key (/c/Users/Toaster/.ssh/id_ed25519):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /c/Users/Toaster/.ssh/id_ed25519
Your public key has been saved in /c/Users/Toaster/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:<a long string> Toaster@Toast-Nova
The key's randomart image is:
<a square 'picture'>

Checkpoint ☑️

Everyone set their name and email?
Everyone have their SSH key on GitHub?
Common Problems:
- Copying from the terminal - try right-click -> copy
- Changed the save location for ssh-keygen

3. Creating a Repository

GitHub Template

Go to https://github.com/Southampton-RSG-Training/git-novice-template
“Use This Template”
Name it climate-analysis

Key Commands

git clone git@github.com:yourname/climate-analysis
Accept GitHub’s SSH key
cd climate-analysis
ls -a
git status

Expected Outputs

git clone <your repo>

Cloning into 'climate-analysis'...
remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 4 (delta 0), reused 3 (delta 0), pack-reused 0 (from 0)
Receiving objects: 100% (4/4), done.

Expected Outputs

git status

# On branch main
nothing to commit, working tree clean

Checkpoint ☑️

Everyone managed to copy and download the template?
Common Problems:
- Typo in the command (e.g. missing the :)
- SSH key hasn’t been set up
- Not accepting GitHub’s SSH key
- Not used cd to enter climate-analysis

4. Tracking Changes

Key Commands

nano README.md
Ctrl-O then Enter to save, Ctrl-X to quit
git add README.md
git status
git commit -m "Your message"
git status

Expected Outputs

git add README.md

If you’re on Windows, you might see:

warning: in the working copy of 'README.md', LF will be replaced by CRLF the next time Git touches it

git commit -m "Your message"

[main 3347109] Added a basic readme file
1 file changed, 4 insertions(+)
create mode 100644 README.md

Expected Outputs

git status

On branch main
Your branch is ahead of 'origin/main' by 1 commit.
  (use "git push" to publish your local commits)

nothing to commit, working directory clean

Checkpoint ☑️

Everyone created and committed a readme?
Everyone have “nothing to commit” in the status?
Common Problems:
- Stuck in nano (Ctrl-O to save, Ctrl-X to quit)
- Didn’t git add README.md
- Forgot the -m on commit (write your message in nano)

Adding & Committing

Key Commands

git log

Expected Outputs

git log

commit 334710937654821b3a89996c2c6af476548d28e9 (HEAD -> main)
Author: Sam Mangham <mangham@gmail.com>
Date:   Wed Jan 8 18:40:04 2025 +0000

   Added a basic readme file

commit 3f6b071ef0d35af70793954adb00a3fc7fc7b949 (origin/main, origin/HEAD)
Author: Sam Mangham <mangham@gmail.com>
Date:   Wed Jan 8 18:35:45 2025 +0000

   Initial commit

Key Commands

nano climate_analysis.py
git diff
git add climate_analysis.py
git commit -m "Your message"

Expected Outputs

git diff

diff --git a/climate_analysis.py b/climate_analysis.py
index 277d6c7..347c42b 100644
--- a/climate_analysis.py
+++ b/climate_analysis.py
@@ -1,3 +1,5 @@
+"""Tools for analysing climate data files"""
+
 import sys
 import temp_conversion
 import signal

git commit

[main 0010185] Add docstring
 1 file changed, 2 insertions(+)

Challenge ✏️

Use nano to edit climate_analysis.py
Add “# TODO: Add rainfall processing code” to the end
Commit the change to the repository

Solution 👁️

nano climate_analysis.py
git diff
git add climate_analysis.py
git commit -m "Your message"

But What Do We Add?

Code, documentation, configuration files
For one project or paper
Usually, not data
- Small common files e.g. tables of atomic weights are OK!
- Anything 10MB+… not really
Files you can meaningfully compare
See the Library for data storage

5. Exploring History

Key Commands

git log
git diff HEAD~1 climate_analysis.py
git diff HEAD~2 climate_analysis.py

Expected Outputs

git log

commit ed664c6d480f93829608791f3d8158f2dcab4107 (HEAD -> main)
Author: Sam Mangham <mangham@gmail.com>
Date:   Thu Jan 9 10:11:27 2025 +0000

    Added rainfall processing placeholder

[3 more commits]

Expected Outputs

git diff HEAD~1 climate_analysis.py

diff --git a/climate_analysis.py b/climate_analysis.py
index 347c42b..ce8ef32 100644
--- a/climate_analysis.py
+++ b/climate_analysis.py
@@ -27,3 +27,6 @@ for line in climate_data:
             kelvin = temp_conversion.fahr_to_kelvin(fahr)

             print(str(celsius)+", "+str(kelvin))
+
+# TODO: Add rainfall processing code
+

Challenge ✏️

Get the ID of your first commit
Get a summary of the changes to climate_analysis.py since then

Solution 👁️

git log
Take the first 7 characters of the last commit
git diff <COMMIT ID> climate_analysis.py

More Differences

Key Commands

rm climate_analysis.py
git status
git restore climate_analysis.py
If restore doesn’t work, try checkout

Expected Outputs

git status

On branch main
Your branch is ahead of 'origin/main' by 3 commits.
  (use "git push" to publish your local commits)

Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        deleted:    climate_analysis.py

no changes added to commit (use "git add" and/or "git commit -a")

Advanced Use

git checkout <COMMIT ID> climate_analysis.py

Restoring Files

6. Remote Repositories

Local Repo

Remote Backups

Collaboration

Key Commands

git push
Accept GitHub’s SSH key if asked

Expected Output

git push

Counting objects: 11, done.
Delta compression using up to 32 threads.
Compressing objects: 100% (9/9), done.
Writing objects: 100% (9/9), 1.11 KiB | 0 bytes/s, done.
Total 9 (delta 2), reused 0 (delta 0)
remote: Resolving deltas: 100% (2/2), completed with 1 local object.
To git@github.com:smangham/climate-analysis
   70bf8f3..501e88f  main -> main

Checkpoint ☑️

Everyone successfully pushed to GitHub?
Common Problems:
- Cloned with https rather than ssh

Conflict Creation

Local:

nano README.md
Add your email to the end
git commit -am "Your message"

Remote:

Go to your repo on GitHub
Edit README.md to add install info to the end
Commit directly to main

Conflict Creation

git push

Expected Outputs

git push

To git@github.com:smangham/climate-analysis
 ! [rejected]        main -> main (fetch first)
error: failed to push some refs to 'git@github.com:smangham/climate-analysis'
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 merge the remote changes (e.g.,
hint: 'git pull') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

Checkpoint ☑️

Everyone managed to edit both the local and remote main branches?

Conflict Resolution

git pull
git config pull.rebase false if it fails
nano README.md and remove the <<</===/>>>
git add README.md
git commit -am "Your message"
git push

Expected Outputs

git pull

remote: Enumerating objects: 5, done.
remote: Counting objects: 100% (5/5), done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 3 (delta 0), reused 0 (delta 0), pack-reused 0
Unpacking objects: 100% (3/3), done.
From github.com:smangham/climate-analysis
   501e88f..023f8f6  main       -> origin/main
Auto-merging README.md
CONFLICT (content): Merge conflict in README.md
Automatic merge failed; fix conflicts and then commit the result.

Checkpoint ☑️

Everyone managed to create a conflict, then fix it?
Common Problems:
- Not committing the changes to your local repo before pulling
- Committing your remote changes to a different branch

Remote Commands

7. Branches

Branching Workflows

Feature Branch

Creating branches

git branch
git branch dev
git switch dev
If switch doesn’t work, try checkout

Expected Outputs

git switch dev

Switched to branch `dev`

If git switch dev doesn’t work, try git checkout dev

Branch files

nano rainfall_conversion.py
git add rainfall_conversion.py
git commit -m "Your message"
ls
git log

Switching Branches

git switch main
ls
git log

Pushing Branches

git switch dev
git push origin dev
git config --global push.autoSetupRemote true

Expected Outputs

git push origin dev

Enumerating objects: 25, done.
Counting objects: 100% (25/25), done.
Delta compression using up to 20 threads
Compressing objects: 100% (25/25), done.
Writing objects: 100% (25/25), 4.40 KiB | 2.20 MiB/s, done.
Total 25 (delta 6), reused 3 (delta 0), pack-reused 0
remote: Resolving deltas: 100% (6/6), done.
remote:
remote: Create a pull request for 'dev' on GitHub by visiting:
remote:      https://github.com/smangham/climate-analysis/pull/new/dev
remote:
To github.com:smangham/climate-analysis
 * [new branch]      dev -> dev

Checkpoint ☑️

Everyone managed to create and push a branch?
Common Problems:
- Not pushing to origin dev
- Committing to main not dev

Merging Branches

git switch main
git merge dev

8. Ignoring Things

Create Temporary Files

git switch dev
mkdir results
touch example.csv results/example.txt
git status

Expected Outputs

git status

On branch dev
Your branch is up to date with 'origin/dev'.

Untracked files:
  (use "git add <file>..." to include in what will be committed)
        example.csv
        results/example.txt

nothing added to commit but untracked files present (use "git add" to track)

Create Git Ignore

nano .gitignore
Lines for *.csv and results/
git status
git add .gitignore
git commit -m "Your message"

Expected Outputs

git status

On branch dev
Your branch is up to date with 'origin/dev'.

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

nothing added to commit but untracked files present (use "git add" to track)