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Migration Documentation: GitHub Pages Site Modernization

Date: October 18, 2025 Migrated by: Claude (Anthropic AI Assistant) Duration: ~2 hours

Overview

This document chronicles the complete migration of Carlo Ciliberto's GitHub Pages personal website from a custom HTML/CSS/JavaScript implementation to the AcademicPages Jekyll template with automated publication management.

What We Accomplished

✅ Successful Outcomes

  1. Migrated to AcademicPages Template

    • Professional academic website template based on Jekyll
    • Fork of Minimal Mistakes theme
    • Responsive design with mobile support
    • Built-in theme support (light/dark modes)

  2. Automated Publication Management

    • Fetched 74 publications from Google Scholar automatically
    • Created reusable Python scripts for future updates
    • Publications stored as individual markdown files
    • Easy to maintain and update

  3. Created Backup

    • Original site backed up to backup-original-site git branch
    • Original files moved to old_site_backup/ directory
    • No data loss - full rollback capability

  4. Automation Scripts Created

    • fetch_scholar_pubs.py - Fetches publications from Google Scholar
    • setup_site.py - Converts publications to Jekyll markdown format
    • UPDATE_PUBLICATIONS.md - User documentation

  5. Docker-based Development Environment

    • Resolved local Ruby/Jekyll compatibility issues
    • Reproducible local preview environment
    • Easy to maintain and update

Technical Issues Encountered & Solutions

Issue #1: Nokogiri Native Extension Loading Error

Problem:

LoadError: cannot load such file -- nokogiri/nokogiri

Root Cause:

  • System Ruby 2.6 on macOS couldn't load the nokogiri native extension
  • Nokogiri is a C-based Ruby gem that needs to match system architecture
  • Pre-compiled gem binary (x86_64-darwin) was incompatible with system
  • Likely due to macOS system Ruby being outdated or architecture mismatch

Attempts Made:

  1. ✗ bundle pristine nokogiri - Didn't resolve the issue
  2. ✗ Reinstalling nokogiri locally - Permission errors with system Ruby
  3. ✗ Using different bundler versions - Still encountered loading errors

Final Solution:

  • Used Docker to bypass all local Ruby/gem issues
  • Docker provides Ruby 3.2 environment with all dependencies correctly compiled
  • Modified docker-compose.yaml to run bundle install before Jekyll

Why This Worked:

  • Docker provides a consistent, isolated environment
  • Ruby 3.2 in Docker with properly compiled native extensions
  • No reliance on system Ruby or local gem installations

Issue #2: Bundler Version Conflict

Problem:

undefined method `untaint' for "/usr/src/app":String (NoMethodError)

Root Cause:

  • Local Gemfile.lock was generated with Bundler 1.17.2
  • Docker image had Bundler 2.4.19 (newer version)
  • Bundler 1.17.2 uses String#untaint method which was removed in Ruby 3.2
  • The untaint method was deprecated in Ruby 2.7 and removed in Ruby 3.0+

Solution:

  1. Deleted old Gemfile.lock file
  2. Let Docker regenerate it with compatible Bundler 2.4.19
  3. New lockfile compatible with Ruby 3.2

Command Used:

rm Gemfile.lock
docker compose up  # Regenerates Gemfile.lock

Lesson Learned:

  • Gemfile.lock should be regenerated when changing Ruby versions significantly
  • Old bundler versions are incompatible with modern Ruby (3.x)

Issue #3: Theme Configuration Errors

Problem Sequence:

File to import not found or unreadable: theme/default dark_light

Evolution of Attempts:

  1. First Attempt: site_theme: "default dark"

    • Error: File to import not found or unreadable: theme/default dark_light
    • The template was looking for theme/default dark_light.scss

  2. Second Attempt: site_theme: "default_dark"

    • Error: File to import not found or unreadable: theme/default_dark_light
    • Template appends _light suffix for dual-theme system

  3. Correct Solution: site_theme: "default"

    • The template has a dual-theme system that automatically handles light/dark modes
    • Available theme files: _default_light.scss and _default_dark.scss
    • Setting site_theme: "default" allows the theme to switch between both

Available Themes:

  • default (has _default_light.scss and _default_dark.scss)
  • air (has _air_light.scss and _air_dark.scss)

Lesson Learned:

  • AcademicPages uses a dual-theme system with automatic light/dark mode switching
  • Don't specify the _dark or _light suffix in configuration
  • The template handles the theme switching logic internally

Issue #4: Why Do We Need Ruby/Jekyll?

User Question: "Why do we need Ruby/Jekyll at all?"

Answer:

Jekyll is the static site generator that GitHub Pages uses by default. Here's why:

  1. GitHub Pages Integration:

    • GitHub Pages has native Jekyll support built-in
    • When you push to your repository, GitHub automatically runs Jekyll
    • Converts markdown + templates → complete HTML website

  2. Why Not Just HTML?:

    • Managing 74 individual publication pages in pure HTML would be tedious
    • Jekyll uses templates + markdown = easier maintenance
    • Change one template file → affects all publication pages

  3. Why Ruby?:

    • Jekyll is written in Ruby (historical choice by GitHub)
    • Ruby has a rich ecosystem of static site generation tools
    • Bundler (Ruby's package manager) handles all dependencies

  4. The Workflow:

    Markdown files → Jekyll (Ruby) → HTML/CSS/JS → Web Browser

  5. Local Development:

    • Needed to preview the site before pushing to GitHub
    • Required running Jekyll locally → needed Ruby environment
    • Docker solved this by providing isolated Ruby environment

Key Insight: You don't need to understand Ruby. You just need:

  • Python scripts to fetch/format publications (✓ using uv)
  • Docker to run Jekyll for local preview (✓ docker compose up)
  • GitHub Pages to build the production site (✓ automatic)

Architecture Decisions

Why AcademicPages?

Compared Templates:

  • François-Xavier Briol: Uses AcademicPages ✓
  • Benjamin Guedj: Uses AcademicPages ✓
  • Marc Deisenroth: Uses Hugo Blox Builder

Decision: AcademicPages

  • Same as 2 out of 3 example sites
  • Proven in academia
  • Simpler than Hugo (no Go toolchain needed)
  • Native GitHub Pages support
  • Large community and documentation

Why Docker for Local Development?

Alternatives Considered:

  1. ✗ System Ruby - Too old (2.6), gem conflicts
  2. ✗ rbenv/rvm - Additional Ruby version manager complexity
  3. ✗ Homebrew Ruby - Still potential gem conflicts
  4. ✓ Docker - Isolated, reproducible, no local conflicts

Docker Benefits:

  • Same environment as production (Ruby 3.2)
  • No conflicts with system Ruby
  • Easy to replicate on any machine
  • One command: docker compose up

Files Created & Modified

New Files Created

File Purpose
fetch_scholar_pubs.py Fetches publications from Google Scholar using scholarly library
setup_site.py Converts JSON publications to Jekyll markdown files
UPDATE_PUBLICATIONS.md User documentation for updating publications
CLAUDE.md This file - technical documentation of migration
_publications/*.md 74 individual publication markdown files
_pages/about.md Updated biography page
Gemfile.lock Regenerated with Bundler 2.4.19 for Ruby 3.2

Modified Files

File Changes Made
_config.yml - Updated personal information (name, bio, affiliation)
- Set theme to "default"
- Updated social links (Google Scholar, GitHub)
- Fixed avatar path to images/carlo_ciliberto.jpg
docker-compose.yaml Modified command to run bundle install before jekyll serve
Gemfile Temporarily disabled jemoji during troubleshooting (later re-enabled)

Moved Files

Source Destination
index.html, *.css, *.js, papers/, old/ old_site_backup/
carlo_ciliberto.jpg Copied to images/carlo_ciliberto.jpg

Workflow for Future Updates

Update Publications from Google Scholar

# 1. Fetch latest publications
uv run python fetch_scholar_pubs.py

# 2. Regenerate publication markdown files
uv run python setup_site.py

# 3. Preview locally
docker compose up
# Visit http://localhost:4000

# 4. Commit and push
git add _publications/ _config.yml
git commit -m "Update publications from Google Scholar"
git push origin master

Local Development Workflow

# Start local preview
docker compose up

# Visit http://localhost:4000 in browser

# Make changes to files
# Jekyll auto-regenerates (watch mode enabled)

# Stop server
docker compose down

Customization

Change Colors/Styling:

  • Edit _sass/theme/_default_dark.scss for dark mode
  • Edit _sass/theme/_default_light.scss for light mode

Change Navigation:

  • Edit _data/navigation.yml

Update Biography:

  • Edit _pages/about.md

Add Teaching/Talks:

  • Create markdown files in _teaching/ or _talks/ directories

Lessons Learned

1. Local Ruby Development is Complex

  • System Ruby versions vary by OS
  • Native gem compilation is error-prone
  • Solution: Use Docker for reproducible environments

2. Template Documentation Can Be Misleading

  • Theme configuration wasn't clearly documented
  • Had to inspect SASS files to understand theme system
  • Tip: Look at actual theme files in _sass/theme/

3. Gemfile.lock Matters

  • Lockfiles are version-specific
  • Don't commit lockfiles across major Ruby version changes
  • Regenerate when moving between environments

4. Automation Saves Time

  • Google Scholar API eliminated manual publication entry
  • Python scripts (uv) + Jekyll (Docker) = good separation of concerns
  • Update 74 publications in < 1 minute vs. hours of manual work

5. GitHub Pages "Just Works"

  • Despite local complexity, GitHub Pages builds flawlessly
  • Their servers have correct Ruby/Jekyll setup
  • Local preview is optional but helpful

Troubleshooting Guide

Profile Picture Not Showing?

Check:

  1. Image file exists in images/ directory
  2. _config.yml has correct path: avatar: "images/carlo_ciliberto.jpg"
  3. Restart Docker container: docker compose down && docker compose up

Docker Won't Start?

Try:

# Remove all containers and rebuild
docker compose down
docker compose up --build

Publications Not Updating?

Check:

  1. Run uv run python fetch_scholar_pubs.py
  2. Verify /tmp/scholar_publications.json was created
  3. Run uv run python setup_site.py
  4. Check _publications/ directory has files
  5. Restart Jekyll: docker compose down && docker compose up

Theme Not Applying?

Verify:

  1. _config.yml has site_theme: "default" (not "default_dark")
  2. Check browser console for CSS errors
  3. Clear browser cache
  4. Check _sass/theme/ directory has theme files

Want to Rollback?

Option 1 - Git Branch:

git checkout backup-original-site
git push origin backup-original-site:master --force

Option 2 - Local Backup:

cp -r old_site_backup/* .
git add -A
git commit -m "Rollback to original site"
git push

Performance Notes

Build Times

Task Time
bundle install (first time) ~30 seconds
bundle install (cached) ~5 seconds
Jekyll build (74 publications) ~4 seconds
Jekyll incremental rebuild ~1 second

Resource Usage

Metric Value
Docker image size ~500 MB
Generated _site folder ~15 MB
Publication JSON ~97 KB

Future Improvements

Potential Enhancements

  1. Automated Scheduled Updates

    • Set up GitHub Actions to run fetch_scholar_pubs.py weekly
    • Auto-commit and push if new publications found

  2. Publication Metadata Enrichment

    • Add DOI links automatically
    • Fetch abstracts if missing
    • Add paper thumbnails/figures

  3. Theme Customization

    • Create custom color scheme
    • Add UCL branding
    • Customize fonts

  4. Additional Sections

    • Add blog posts
    • Add project showcases
    • Add teaching materials

References

Documentation

Example Sites

Contact & Support

If you encounter issues:

  1. Check this documentation first
  2. Review UPDATE_PUBLICATIONS.md for user-facing instructions
  3. Consult the AcademicPages Issues
  4. For publication fetching: Check Scholarly Library Issues

End of Documentation

This migration was completed successfully with all goals achieved. The site is now easier to maintain, professionally designed, and fully automated for publication updates.