LaTeX and git - ProHealth REU Summer 2022

Abstract

A crash course in using git for document version control. We'll motivate this as a method for keeping track of changes in a $\LaTeX$ document over time, and use git repositories to store research code.

Introduction

Slides are online:

• https://hayesall.com/talks/managing-research/

git : GitHub :: LaTeX : Overleaf

git is to GitHub as LaTeX is to Overleaf

Terminology:

• git: a tool that assists with version control—or tracking changes in files
• GitHub: a website for hosting, sharing, and collaborating on git repositories
• LaTeX: a collection of tools for editing and typesetting documents, built on the TeX language
• Overleaf: a website for hosting and collaborating on LaTeX projects

When you see a block like this:

git status
python -m dosomething

… it usually represents running a command in a terminal emulator.

Click here for more notes on terminals

• MacOS: ⌘ + spacebar to open Spotlight, then search for "Terminal"
• GNU/Linux: ⊞ usually opens a search mode, look for "Terminal"
• Chromebook: A terminal is available after you Set up Linux on your Chromebook
• Windows: There are several options
  • Windows Terminal
  • PowerShell
  • Windows Subsystem for Linux (WSL)
  • Git Bash
  • Alexander's recommendation: Start with "Git Bash," but eventually switch to the Windows Terminal.

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Activity

We'll explore the following flow chart:

  flowchart TD
    A[0 - Check that git is installed] --> B[1 - Clone the repository];
    B --> C[2 - Edit main.tex or main.bib];
    C --> E[Optional: pdflatex]
    C --> D[3 - What does git status say?]
    D --> F[4 - What's the diff?]
    F --> G[5 - Add all changes to the staging area]
    G --> I[Optional: Incremental staging / git add main.bib]
    G --> H[6 - Commit the changes to the local history]
    H --> J[7 - Read the log]
    J --> K[Optional: Time travel]
    J --> L[Optional: Modify the figure in the results directory]
    J --> M[Optional: Fork the repository, push changes]
    M --> N[Optional: Import your repository to Overleaf]

(0) Check that git is installed

git --version

Click here if something unexpected happens

• MacOS: Should know about git. It might say something like "You need to install Xcode," follow those prompts.
• GNU/Linux: Should ship with git. If it isn't available, use your system dependency manager (apt/yum/gulp, etc.)
• Chromebook: Should ship with git. If not, apt install git
• Windows:
  • Git Bash is the quickest option to get started, the default settings should be fine.
  • If you have the "Windows Terminal," install git with your preferred package manager
    • Chocolately
    • Windows Package Manager (winget)

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(1) Clone the repository

git clone https://github.com/iuprohealth/reu-latex-git-tutorial.git

Then change your working directory:

cd reu-latex-git-tutorial

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(2) Edit the main.tex file or the main.bib file with a text editor.

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(Optional): Build a copy of the PDF

If you have texlive or a TeX distribution installed, you can build a copy of the PDF:

pdflatex main
bibtex main
pdflatex main
pdflatex main

Overleaf is doing something comparable to this process in the background.

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(3) What does the following command return?

git status

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(4) View the changes (or the diff) from the previous state:

git diff

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(5) Add all changes to the staging area

git add .

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(Optional): Incremental Staging, add files in logical groups

You can add files to the staging area separately. git reset will remove all changes from the staging area, but will not alter file contents.

git add main.tex

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(6) Commit the changes to the local history

git commit

By default: this will probably open a "Vi" prompt.

• Type (i) to enter "insert" mode to write your message
• Type (:wq) to save and exit

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(7) Read the history in the log

The "git log" contains a complete copy of the history for a project. Running this:

git log

… should now show your contribution at the top, with all the previous contributions below.

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(Optional): Time Travel

Using git for time travel is controversial, but it's an intriguing feature to know about.

• Skim the documentation for the git branch subcommand: https://git-scm.com/docs/git-branch
• Skim the documentation for the git checkout subcommand: https://git-scm.com/docs/git-checkout
• Read about "Branching Workflows": https://git-scm.com/book/en/v2/Git-Branching-Branching-Workflows
• Read about "Rewriting History": https://git-scm.com/book/en/v2/Git-Tools-Rewriting-History

Copy the first seven characters from a commit hash:

commit 01ec7e5304d51df30195f2b07dee2117ff145307           <----- This part
Author: hayesall <alexander@batflyer.net>
Date:   Mon May 23 18:03:46 2022 -0400

    📄 Add CC-BY-SA 4.0 LICENSE

What does checking out a hash do?

git checkout 01ec7e

If you're in a "detatched HEAD" mode, what happens to the log when you start down a new branch?

git checkout -b my-version-of-history

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(Optional): Try to reproduce the figure, or modify it

The results/chicken_wing_plots.png file is produced by the chicken_wings.csv and the plot_data.py script.

pip install -r requirements.txt
python plot_data.py

Try something like:

1. Make a copy of the chicken_wing_plots.png. e.g.: mv chicken_wing_plots.png chicken_wing_plots_backup.png
2. Run the script
3. Are the two figures the same?
   • Do they look the same?
   • Do the figures contain exactly the same data? (see also: https://en.wikipedia.org/wiki/Md5sum)

Now try modifying the code or the data (chicken_wings.csv):

1. Add an additional line to the data
2. Remove some lines from the data

Improve the figure:

1. matplotlib can output PDF figures
2. Edit the Python script to produce a PDF image instead of a PNG image
3. Edit the main.tex document to use the new figure

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(Optional): Fork the repo and share your changes

So far we've recorded changes to our local history. We can share our local changes by pushing them to a remote server.

• Read about "Forking repositories" in the GitHub documentation
• Fork this repository
• Change the "remote," swapping the hayesall with your GitHub username

git remote remove origin
git remote add origin https://github.com/hayesall/reu-latex-git-tutorial.git

Now push your local changes to your modified remote:

git push -u origin main

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(Optional): Import your repository into Overleaf

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Homework

1. Write a reflection about the "Saving Data and Code" section
   • Did you learn something new? Do you have some prior knowledge about the topics?
   • Did you explore one of the [Optional] paths? If so, what did you learn? If not, what might be interesting to explore further?
   • Do you foresee incorporating this into your workflow? What barriers, advantages, or disadvantages might occur?
2. Read the NeurIPS / PapersWithCode guide on "Publishing Research Code." Summarize its main topics, AND pick one of the following topics to read further about:
   • How would you define the terms "reproducibility" and "replicability?" What does the phrase "the replicability crisis" mean? (You might find it helpful to express this in terms of the entire inquiry process from data collection, to analysis, to publication). Cite the sources you read.
   • There exist "Open Access Journals" where paper writing, reviewing, and publishing all occur in public. Find a paper that has already been reviewed and published and read the discussion between the authors, reviewers, and editors.(https://github.com/openjournals/joss-reviews/issues?q=is%3Aissue+is%3Aclosed+label%3Areview+). As an example, Alexander was a reviewer on this paper: openjournals/joss-reviews#3465
     • (You don't have to share the exact paper you read if you do not want to). What requirements did the submission process require up-front? What did reviewers request?
     • What do you think about this process? Can you think of any advantages or disadvantages?
3. Fork this reu-latex-git-tutorial repository to your GitHub profile, and use Overleaf's "Import from GitHub." Include a link to your "fork" in your blog post.

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Cheat Sheets

git Cheatsheet

First-time setup:

git config --global user.name "Your Name"
git config --global user.email "youremail@example.com"

Commands:

git clone [url]     # clone a repository from a remote destination
git add [file]      # add a file
git status          # what files are changed / staged / unstaged?
git diff            # what unstaged changes exist?
git commit          # tell (local) git about your changes
git push            # send your changes upstream
git remote -v       # what remote repository does git know about?

Modify remote and push to a different upstream

git remote remove origin
git remote add origin https://github.com/your-user/your-repo.git
git push -u origin main

Bash/Terminal Cheatsheet

Moving around:

cd [directory]      # Change Directory: ``cd ~/Downloads/`
cd ..               # go "down" one directory

Listing files:

ls                  # List files in current directory
ls [directory]      # List files in another directory

Other helpful tricks

pwd                 # Present Working Directory: where am I?
exit                # Exit current session / close tab
(CTRL-l)            # Clear terminal screen
(CTRL-t)            # New tab
(up arrow)          # Last command

Further Reading

git

If you read only one thing, read the blog post by Rachel M. Carmena

• "Pro Git," Scott Chacon and Ben Straub (2nd Edition) (CC BY-NC-SA 3.0)
• "How to teach Git," Rachel M. Carmena
• "Learn Git Branching," (Interactive Tutorial)
• Tim Holy (video lecture), "Open Source, Julia Packages, git, and GitHub"
• What is a commit message?
  • Message templates: https://github.com/joelparkerhenderson/git-commit-message
  • "gitmoji": An emoji guide for your commit messages: https://gitmoji.dev/
• GitKraken GUI + Git CLI: https://www.gitkraken.com/
• Visualizing GitHub Repositories: https://mango-dune-07a8b7110.1.azurestaticapps.net/?repo=iuprohealth%2Fhmc-dashboard

LaTeX

• "The TeXbook," by Donald E. Knuth. http://visualmatheditor.equatheque.net/doc/texbook.pdf
• LaTeX + VSCode
  • LaTeX Workshop Extension: https://marketplace.visualstudio.com/items?itemName=James-Yu.latex-workshop
• "LaTeX/Bibliography Management," WikiBooks. https://en.wikibooks.org/wiki/LaTeX/Bibliography_Management
• KaTeX: LaTeX typesetting for the web
  • https://katex.org/
  • Typesetting equations: https://katex.org/docs/supported.html
• GitHub supports LaTeX math notation in Markdown (as of 2022-05-19):
  • https://github.blog/2022-05-19-math-support-in-markdown/

License

This work is licensed under a Creative Commons Attribution 4.0 International License.