GitHub + Thetapad: Version Control for LaTeX Projects

# Create project directory
mkdir my-paper
cd my-paper
 
# Initialize Git
git init
 
# Create .gitignore for LaTeX
cat > .gitignore << 'EOF'
# LaTeX auxiliary files
*.aux
*.bbl
*.blg
*.fdb_latexmk
*.fls
*.log
*.out
*.toc
*.synctex.gz
*.synctex(busy)
 
# Generated files
*.pdf
 
# Editor files
*.swp
*~
.DS_Store
 
# Backup files
*.bak
*.backup
EOF
 
# Create initial structure
touch main.tex
mkdir figures
mkdir sections
 
# Initial commit
git add .
git commit -m "Initial project structure"

# Create repo on GitHub first, then:
git remote add origin https://github.com/yourusername/my-paper.git
git branch -M main
git push -u origin main

gh repo create my-paper --private --source=. --push

# Start of session: get latest changes
git pull
 
# Write your content in Thetapad...
 
# End of session: commit and push
git add .
git commit -m "Draft introduction section"
git push

"updates"
"fixed stuff"
"asdfasdf"

"Add literature review for ML section"
"Fix citation format in methodology"
"Revise abstract based on advisor feedback"
"Add Figure 3: experimental results comparison"

# View commit history
git log --oneline
 
# See what changed in a specific commit
git show abc1234
 
# See changes between versions
git diff HEAD~5 HEAD -- chapter2.tex
 
# See who changed what line (useful for collaboration)
git blame chapter2.tex

# All work on main
git checkout main
# write...
git commit -m "Progress on results section"
git push

# Create branch for a specific task
git checkout -b add-methodology-section
 
# Work on the branch
# ... write methodology ...
git commit -m "Draft methodology section"
 
# When done, merge back
git checkout main
git merge add-methodology-section
git branch -d add-methodology-section
git push

# Create branch for journal submission
git checkout -b journal-nature
# Modify format, length, etc.
git commit -m "Format for Nature submission"
 
# Create another for conference
git checkout main
git checkout -b conference-neurips
# Different modifications
git commit -m "Format for NeurIPS submission"

# Split document into sections
main.tex          # Just includes
sections/
├── intro.tex     # Alice works here
├── methods.tex   # Bob works here
├── results.tex   # Carol works here

git pull  # Always do this first!

# Small, frequent commits > large, rare commits
git commit -m "Add paragraph on data preprocessing"
# Not: one commit with 3 days of work

git pull
# CONFLICT in chapter2.tex
 
# Open the file, find conflict markers:
<<<<<<< HEAD
Your version of the text
=======
Their version of the text
>>>>>>> abc1234
 
# Edit to resolve, then:
git add chapter2.tex
git commit -m "Resolve conflict in chapter2"
git push

Thetapad ←→ Local Files ←→ Git ←→ GitHub

# After editing in Thetapad
git add .
git commit -m "Your message"
git push

# Using a file watcher (example with fswatch on Mac)
fswatch -o *.tex | xargs -n1 -I{} git commit -am "Auto-save"

# .latexmkrc in your project
$pdf_mode = 1;
$pdflatex = 'pdflatex -interaction=nonstopmode';
$bibtex_use = 2;

# Pre-commit hook to ensure document compiles
# .git/hooks/pre-commit
#!/bin/bash
latexmk -pdf main.tex
if [ $? -ne 0 ]; then
    echo "LaTeX compilation failed!"
    exit 1
fi

# Install Git LFS
git lfs install
 
# Track large files
git lfs track "*.pdf"
git lfs track "figures/*.png"
git lfs track "figures/*.jpg"
 
# Commit the tracking config
git add .gitattributes
git commit -m "Configure Git LFS for large files"

# .github/workflows/compile.yml
name: Compile LaTeX
 
on:
  push:
    branches: [ main ]
 
jobs:
  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
 
      - name: Compile LaTeX
        uses: xu-cheng/latex-action@v2
        with:
          root_file: main.tex
 
      - name: Upload PDF
        uses: actions/upload-artifact@v3
        with:
          name: paper
          path: main.pdf

# Tag submission versions
git tag -a v1.0-submitted -m "Initial journal submission"
git push --tags
 
# Later, after revisions
git tag -a v2.0-revised -m "Revised submission with reviewer comments"
git push --tags
 
# View tags
git tag -l
 
# Checkout a tagged version
git checkout v1.0-submitted

This is the first sentence. This is the second sentence. This is the third sentence that goes on for quite a while and makes it hard to see what changed.

This is the first sentence.
This is the second sentence.
This is the third sentence that goes on for quite a while.

my-paper/
├── main.tex           # Document root
├── preamble.tex       # Packages and config
├── references.bib     # Bibliography
├── sections/
│   ├── 01-intro.tex
│   ├── 02-methods.tex
│   ├── 03-results.tex
│   └── 04-conclusion.tex
├── figures/
│   ├── fig1-overview.pdf
│   └── fig2-results.pdf
└── appendices/
    └── supplementary.tex

# Good: separate commits for separate changes
git commit -m "Add Figure 2: experimental setup"
git commit -m "Write results for experiment A"
git commit -m "Fix typo in abstract"
 
# Bad: everything in one commit
git commit -m "Various updates"

git checkout -b experimental-restructure
# Try major changes
# If it works: merge back
# If it fails: git checkout main (abandon branch)

# End of every session
git push
 
# Your work is now:
# - On your machine
# - On GitHub's servers
# - (Optionally) synced to collaborators

# Check status
git status
 
# If untracked files, add them
git add .
 
# If changes not staged, add them
git add -A

# Undo commit but keep changes
git reset --soft HEAD~1
 
# Undo commit and changes (careful!)
git reset --hard HEAD~1

# See what files have conflicts
git status
 
# Edit files to resolve (remove <<< === >>> markers)
# Then mark as resolved
git add <resolved-file>
git commit -m "Resolve merge conflict"

# Remove from history (dangerous, coordinate with team)
git filter-branch --force --index-filter \
  'git rm --cached --ignore-unmatch large-file.pdf' HEAD
 
# Better: set up .gitignore first
echo "*.pdf" >> .gitignore
git add .gitignore
git commit -m "Ignore PDF files"