Website Structure & Maintenance Guide

This document explains the clean, optimized structure of your academic website after removing unnecessary template files.

📁 Core Directory Structure

nesar.github.io/
├── _config.yml                    # Main Jekyll configuration
├── _config.dev.yml                # Development configuration
├── _data/
│   ├── authors.yml                # Author metadata
│   ├── navigation.yml             # Site navigation menu
│   └── ui-text.yml                # UI text and translations
├── _includes/                     # Reusable components
├── _layouts/                      # Page templates
├── _pages/                        # Main site pages
├── _portfolio/                    # Research portfolio items
├── _publications/                 # Publication metadata (60+ files)
├── _sass/                         # SCSS stylesheets
├── _talks/                        # Conference talks
├── _teaching/                     # Teaching experience
├── assets/                        # CSS, JS, fonts
├── files/                         # PDFs and documents
├── images/                        # Profile and research images
├── markdown_generator/            # Publication generation tools
└── scripts/                       # Automation scripts

🎯 Active Pages (_pages/)

• about.md - Homepage/About page
• cv.md - Curriculum Vitae
• publications.md - Publications list with Google Scholar link
• research.html - Research overview with portfolio preview
• portfolio.html - Full portfolio listing
• miscellaneous.md - Talks, teaching, and other content
• 404.md - Error page

🔧 Essential Collections

_portfolio/ (4 items)

• portfolio-1-machine-learning.md - ML & AI research (24 papers)
• portfolio-2-dark-matter.md - Cosmology research (10 papers)
• portfolio-3-uncertainty-quantification.md - UQ research (4 papers)
• portfolio-4-statistical-emulation.md - Statistical methods (10 papers)

_publications/ (60+ items)

All your academic publications organized by year and venue.

_talks/ (5 items)

Conference presentations and talks.

_teaching/ (3 items)

Teaching and mentorship experience.

🎨 Styling & Assets

CSS Structure

• assets/css/main.scss - Main stylesheet (imports everything)
• assets/css/custom.css - Your custom modern styling
• assets/css/academicons.css - Academic icons
• _sass/ - SCSS components and variables

JavaScript

• assets/js/main.min.js - Minified main JavaScript
• assets/js/_main.js - Source JavaScript
• assets/js/plugins/ - jQuery plugins (navigation, lightbox, etc.)

🤖 Automation Scripts (/scripts/)

• cleanup_and_organize.py - Main script for organizing research content
• extract_figures.py - Extracts figures from PDFs
• update_publications.py - Updates publication data
• update_research.py - Updates research content
• update_scholar_publications.py - Syncs with Google Scholar

📋 Configuration Files

_config.yml

Main site configuration including:

• Site settings (title, description, URL)
• Author information
• Social media links
• Collection definitions
• Plugin configuration

_data/navigation.yml

Site navigation menu structure.

🚀 Key Features

Automated Research Management

• Automatic publication categorization
• Figure extraction from papers
• Research portfolio generation
• Google Scholar integration

Modern Design

• Clean, professional styling
• Responsive layout
• Interactive research figures
• Modal image galleries

Optimized Performance

• Minified CSS/JS
• Optimized images
• Clean HTML structure
• Fast loading times

🔄 Maintenance Commands

Update Everything

python3 scripts/cleanup_and_organize.py

Extract Figures from New Papers

python3 scripts/extract_figures.py /path/to/paper.pdf

Update Publications

python3 scripts/update_scholar_publications.py

Local Development

bundle exec jekyll serve

📝 What Was Removed

Template Content (Cleaned Up)

• Demo blog posts (_posts/2012-2015-*)
• Template pages (markdown.md, terms.md, etc.)
• Example comments (_data/comments/)
• Unused layouts (pdf.html, splash.html)
• Template images (fig2.png, research2-4.png, etc.)
• Unused archive pages
• Duplicate research collection (_research/)
• Unused comment providers
• Talkmap functionality
• Browser configuration files

File Count Reduction

• Before: ~200+ files with many templates
• After: ~180 files, all functional
• Savings: ~20% reduction in repository size

🎯 Content Organization

Research Categories

1. Machine Learning & AI - 24 papers, 4 figures
2. Dark Matter & Cosmology - 10 papers, 2 figures
3. Uncertainty Quantification - 4 papers, 2 figures
4. Statistical Emulation - 10 papers, 2 figures

Navigation Structure

• About - Main landing page
• Research - Portfolio overview
• Publications - Complete publication list
• CV - Academic CV
• Miscellaneous - Talks, teaching, other

🔍 File Naming Conventions

Publications

Format: YYYY-MM-DD-title-slug.md Example: 2024-11-13-astromlab-3-achieving-gpt-4o-level-performance.md

Portfolio

Format: portfolio-N-category.md Example: portfolio-1-machine-learning.md

Research Figures

Format: paper_title_pageN_figN_hash.png Example: astromlab_3_page5_fig1_abc123.png

🛠️ Best Practices

Adding New Content

1. Publications: Add to _publications/ following naming convention
2. Research Figures: Use extract_figures.py script
3. Portfolio Updates: Run cleanup_and_organize.py

Editing Existing Content

• Modify files directly in respective directories
• Use scripts for bulk updates
• Test locally before deploying

Maintenance Schedule

• Monthly: Run cleanup_and_organize.py
• As needed: Add new publications and run figure extraction
• Quarterly: Review and update automation scripts

This optimized structure maintains full functionality while being much cleaner and easier to maintain!