ETC5513: Reproducible and Collaborative Practices

Undoing, exporing and cleaning with git

Lecturer: Michael Lydeamore

Department of Econometrics and Business Statistics

michael.lydeamore@monash.edu
Week 7
rcp.numbat.space

Open Frame

Fixing your commit messages

Last week most of us got stuck in Vi mode

To fix this, run the following:

Windows

git config --global core.editor notepad

MacOS

git config --global core.editor "open -e -W -n"

This will set either notepad or TextEdit to be your commit editor (much nicer).

On Mac, note you must quit (not just close the window) for the commit message to be complete.

🧠 Today’s Goals

Learn how to safely undo and explore commits
Understand how to recover lost work
Get more comfortable with the Git timeline and history
Clean up messy projects

🧠 Git Mental Model

Git works across three layers:

Working Directory: your actual files
Index (Staging Area): what will be in your next commit
HEAD (Repository): your last committed snapshot

Some examples: - git add moves changes → index - git commit moves index → HEAD - git reset moves HEAD pointer (soft/mixed/hard)

🔁 Reverting and Resetting – Recap

`git revert`

Creates a new commit that undoes a previous one
Safe on shared branches (e.g. main)

git revert <commit-hash>

`git reset`

Moves your branch pointer backward
Can rewrite history (dangerous on shared branches!)
Options:
- --soft: Keep changes staged
- --mixed: Keep changes unstaged
- --hard: Deletes changes

git reset --soft HEAD~1

🧵 Detached HEAD

Happens when you check out a specific commit, not a branch
Useful for exploring history
If you make changes in this state, they can be lost unless you make a branch

🧪 Demo: Detached HEAD + Branch

In the terminal or Git pane:

git log --oneline

Copy a commit hash from earlier and run:

git checkout <commit-hash>

You’re now in detached HEAD!

🛟 Rescue Your Work

If you want to keep changes made in detached HEAD:

git switch -c recovered-work

✅ This creates a new branch from that point!

✍️ `git commit --amend`

Use this when you:

Made a typo in the last commit message
Forgot to include a file
Want to slightly edit the last commit

🧪 Demo: Amending a Commit

Make a small commit
Realize you forgot something
Stage the missing file, then run:

git commit --amend

🎯 You can edit the message or leave it the same

⚠️ Avoid --amend if you’ve already pushed the commit

🔍 `git reflog`

Shows every move of HEAD (including things Git log forgets)
Useful to recover commits after a reset or checkout

git reflog

🧪 Activity: Oops, I reset too far!

Make a commit
Reset to a previous state:

git reset --hard HEAD~1

Run git reflog to find the lost commit
Use:

git checkout <hash>

Then:

git switch -c recovered-branch

🎉 You’ve recovered “lost” work!

🗑️ `git rm`: Remove Files from the Repository

Use git rm to delete a tracked file from both your working directory and Git’s index.
Git will stage the deletion automatically.

git rm filename.txt
git commit -m "Remove filename.txt"

✅ After this commit, the file will no longer exist in your working directory or the repository.

❗ Why Not Just Delete the File?

If you delete a file in RStudio or your file browser:
- Git will show it as “deleted: filename.txt”
- But you still need to git add the deletion

# After deleting manually:
git status         # Shows deletion
git add filename.txt
git commit -m "Remove file"

✅ git rm does both steps at once — it’s safer and cleaner

💡 Recovering a Deleted File

If you haven’t committed the deletion yet:

git restore filename.txt

If you already committed the deletion:

git checkout HEAD~1 -- filename.txt

✅ Or use git reflog to find the commit where the file still existed

🧾 `git rm --cached`: Keep the File, Remove It from Git

Use this when you’ve added a file to Git by mistake, but you don’t want to delete it from your computer
Git stops tracking it — but the file stays in your working directory

git rm --cached data.csv
git commit -m "Stop tracking data.csv"

✅ The file will still be on disk, but not in the next commit

🧠 Common Use Case

You committed a large data file by accident

Add the filename to .gitignore
Run:

git rm --cached data.csv
git commit -m "Remove data.csv from tracking"

Push your changes
The file is now ignored and won’t be re-added

✅ Useful for cleaning up mistakes without losing the file

🧹 `git clean`

Deletes untracked files (not in Git yet)
Helpful when switching branches or cleaning clutter

git clean -n   # dry run
git clean -f   # permanently delete

⚠️ Warning

git clean is permanent
You can’t undo it with reflog or reset
Always use -n first to preview

🧪 Activity: Cleaning Up

In RStudio, create a few new files but don’t add them to Git
Run:

git status
git clean -n

If it looks right:

git clean -f

✅ Now those untracked files are gone!

🧠 When to Use What

Situation	Use This
Undo safely on shared branches	`git revert`
Clean up your last commit	`git commit --amend`
Rewind local commit history	`git reset`
Accidentally reset or lost work	`git reflog`
Delete untracked junk	`git clean`

Questions?

When would you not use reset?
What does reflog help you find that log doesn’t?
Have you ever thought you lost work but actually didn’t?

🍥 What Is Squashing?

Squashing means combining multiple commits into a single one.

It’s useful for:

Cleaning up messy history
Preparing code before pushing or merging
Grouping small fixes into one meaningful commit

Squashing doesn’t change your code — just your history!

🧠 How Squash Works

Before squashing:

A -- B -- C -- D  (main)
         ↑
       Fix typo

If B, C, and D are all part of one logical change, we can squash:

A -- [B+C+D]  (main)

✅ One clean commit — easier to read, review, and share.

🛠️ How to Squash Commits

Use interactive rebase to squash:

git rebase -i HEAD~3

You’ll see:

pick abc123 Add feature
pick def456 Fix typo
pick ghi789 Update docs

Change to:

pick abc123 Add feature
squash def456
squash ghi789

Then save + edit the commit message.

⚠️ When (and When Not) to Squash

✅ Good times to squash:

Before pushing a feature branch
To combine tiny commits (“fix typo”, “rename var”, “oops”)

❌ Avoid squashing:

After you’ve pushed to a shared branch (rewrites history!)

LaTeX

LaTeX more info

LaTeX template


\begin{document}
% Packages to be used
1\usepackage{amsmath}

2% Creating title
\title{This is an example}
\author{ETC5513, Monash University}

1: List all the packages
2: % = comments

LaTeX template


1\begin{document}
\maketitle

2\section{Introduction}

% Introduction content

3\end{document}

1: Open the document
2: Sections each get a ‘section’ header
3: Close the document at the end.

We are going to use LaTeX via Quarto files

In order to be able to use LaTeX within our Quarto documents, we need to install tinytex:

quarto install tinytex

quarto install tinytex --update-path

You don’t need the full LaTex installation for this unit, just this package.

Integrate a LaTeX template into a quarto file

There are different ways:

If the file features are not too complicated. We can simply add some of the necessary LaTeX packages into our YAML preamble. You will be working with this example in the tutorial:

title: "Reproducible and Collaborative Practices"
subtitle: "Tutorial 7"
author: "Your Name"
institute: "Department of Econometrics and Business Statistics"
output: 
 pdf:
   toc: true
   toc_depth: 2
   number_sections: true
   highlight: tango
header-includes: 
  - \usepackage{titling}
  - \pretitle{\begin{center} \includegraphics[width=5in,height=13in]{figs/front.jpg}\LARGE\\}
  - \posttitle{\end{center}}
  - \usepackage{fontawesome}
  - \usepackage[most]{tcolorbox}
  - \usepackage{xcolor}
  - \usepackage{sectsty}
  - \sectionfont{\color{olive}}
  - \usepackage{verbatim}

Integrate a LaTeX template into a quarto file

There are different ways:

Another possibility is to use a preamble.tex
And incorporate that into our Quarto file (we will look into this in Week 8):

Reference

LaTeX in 24 Hours A Practical Guide for Scientific Writing

Quarto PDF themes

Another way to include styling is to use a Quarto PDF extension. For example:

…and more here

Quarto PDF themes

These themes have the advantage of having done a lot of the LateX formatting for you. Looking inside the Quarto Monash memo, we have:

\pretitle{%
$if(branding)$%
\begin{textblock}{4}(1.9,0.85)\includegraphics[height=1.5cm]{monash2}\end{textblock}%
\begin{textblock}{4}(17.25,0.8)\includegraphics[height=1.5cm]{MBSPortrait}\end{textblock}%
\begin{textblock}{6}(13,28)\includegraphics[height=0.7cm]{AACSB}~~~
        \includegraphics[height=0.7cm]{EQUIS}~~~
        \includegraphics[height=0.7cm]{AMBA}
\end{textblock}

Which is doing a lot of positioning of pictures for the template.

Week 6 Lesson

Recap

Undoing mistakes with amend, revert, and rm
Cleaning repos
An introduction to latex

ETC5513: Reproducible and Collaborative Practices

Undoing, exporing and cleaning with git

Open Frame

Fixing your commit messages

Windows

MacOS

🧠 Today’s Goals

🧠 Git Mental Model

🔁 Reverting and Resetting – Recap

git revert

git reset

🧵 Detached HEAD

🧪 Demo: Detached HEAD + Branch

🛟 Rescue Your Work

✍️ git commit --amend

🧪 Demo: Amending a Commit

🔍 git reflog

🧪 Activity: Oops, I reset too far!

🗑️ git rm: Remove Files from the Repository

❗ Why Not Just Delete the File?

💡 Recovering a Deleted File

🧾 git rm --cached: Keep the File, Remove It from Git

🧠 Common Use Case

🧹 git clean

⚠️ Warning

🧪 Activity: Cleaning Up

🧠 When to Use What

Questions?

🍥 What Is Squashing?

🧠 How Squash Works

🛠️ How to Squash Commits

⚠️ When (and When Not) to Squash

LaTeX

LaTeX template

LaTeX template

LaTeX template

We are going to use LaTeX via Quarto files

Integrate a LaTeX template into a quarto file

Integrate a LaTeX template into a quarto file

Reference

Quarto PDF themes

Quarto PDF themes

Week 6 Lesson

`git revert`

`git reset`

✍️ `git commit --amend`

🔍 `git reflog`

🗑️ `git rm`: Remove Files from the Repository

🧾 `git rm --cached`: Keep the File, Remove It from Git

🧹 `git clean`