Update thesis content and refresh dependencies

.github/workflows/update-search.yml

@@ -2,46 +2,54 @@ name: Update Search Database
 
 on:
   schedule:
-    - cron: '0 4 * * *'  # Run daily at 4:00 UTC
-  workflow_dispatch:  # Allow manual trigger
+    - cron: "0 4 * * *" # Run daily at 4:00 UTC
+  workflow_dispatch: # Allow manual trigger
   push:
-    branches: [ main ]
+    branches: [main]
     paths:
-      - '**/*.md'
-      - '**/*.html'
-      - '.github/workflows/update-search.yml'
+      - "**/*.md"
+      - "**/*.html"
+      - ".github/workflows/update-search.yml"
 
 # Add permissions needed for the workflow
 permissions:
-  contents: write    # This allows the action to commit and push changes
+  contents: write # This allows the action to commit and push changes
 
 jobs:
   update-search:
     runs-on: ubuntu-latest
-    
+
     steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0  # Fetch all history for proper git operations
-
-    - name: Clone comphy-search repository
-      run: |
-        git clone https://github.com/comphy-lab/comphy-search.git
-        mkdir -p assets/js
-
-    - name: Copy search database
-      run: |
-        cp comphy-search/search_db.json assets/js/search_db.json
-
-    - name: Commit and push changes directly (bypassing branch protection)
-      run: |
-        git config --local user.email "action@github.com"
-        git config --local user.name "GitHub Action"
-        git add assets/js/search_db.json
-        if git diff --staged --quiet; then
-          echo "No changes to commit"
-        else
-          git commit -m "Update search database from comphy-search repository"
-          # Use PAT to bypass branch protection
-          git push https://${{ secrets.BYPASS_TOKEN }}@github.com/${GITHUB_REPOSITORY}.git HEAD:main
-        fi
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Fetch all history for proper git operations
+
+      - name: Clone comphy-search repository
+        run: |
+          git clone https://github.com/comphy-lab/comphy-search.git
+          mkdir -p assets/js
+
+      - name: Copy search database
+        run: |
+          cp comphy-search/search_db.json assets/js/search_db.json
+
+      - name: Create GitHub App token
+        id: app-token
+        uses: actions/create-github-app-token@v1
+        with:
+          app-id: ${{ secrets.APP_ID }}
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
+
+      - name: Commit and push changes with app token
+        env:
+          APP_TOKEN: ${{ steps.app-token.outputs.token }}
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "comphy-search-updater"
+          git add assets/js/search_db.json
+          if git diff --staged --quiet; then
+            echo "No changes to commit"
+          else
+            git commit -m "Update search database from comphy-search repository"
+            git push https://x-access-token:${APP_TOKEN}@github.com/${GITHUB_REPOSITORY}.git HEAD:main
+          fi

.gitignore

@@ -6,6 +6,5 @@ _site/
 .bundle/
 vendor/
 # Ignore ai rules
-.windsurfrules
-.cursorrules
 .DS_Store
+CLAUDE.md

AGENTS.md

@@ -0,0 +1,111 @@
+# Agent Instructions
+
+This file provides guidance to Claude Code and OpenCode/Codex when working
+with code in this repository.
+
+## Overview
+
+This is Vatsal Sanjay's personal website built with Jekyll and hosted on
+GitHub Pages at <https://comphy-lab.org/vatsalsy>. The site serves as a
+redirect hub to the [CoMPhy Lab website](https://comphy-lab.org) for research
+content, team information, and contact details.
+
+## Development Commands
+
+### Local Development
+
+```bash
+# Install dependencies (first time setup)
+bundle install
+
+# Run local development server
+bundle exec jekyll serve
+# Site will be available at <http://localhost:4000>
+
+# Build the site without serving
+bundle exec jekyll build
+```
+
+### Ruby Version
+
+This project uses Ruby ~> 3.2.0. Ensure you have the correct version
+installed.
+
+## Architecture
+
+### Key Files and Their Purpose
+
+1. **index.html**: Main homepage that displays intro section and loads about
+   content dynamically
+2. **aboutVatsal.md**: Contains the about section content that gets loaded via
+   JavaScript into the homepage
+3. **\_includes/theme-init.html**: Theme initialization script that handles
+   dark/light mode persistence across page loads
+4. **assets/js/main.js**: Core JavaScript handling:
+   - Dynamic loading of aboutVatsal.md content using marked.js
+   - Mobile menu functionality
+   - Smooth scrolling
+   - Email copy functionality
+   - Back to top button
+5. **assets/js/command-palette.js**: Command palette functionality for
+   keyboard navigation and quick actions
+6. **assets/js/command-data.js**: Command definitions and data for the command
+   palette system
+7. **assets/js/platform-utils.js**: Platform detection utilities for
+   OS-specific keyboard shortcuts and behaviors
+
+### Content Pages
+
+- **phd-thesis.md**: Full content page for PhD thesis "Viscous Free-Surface
+  Flows" with:
+  - Hero section with thesis title and download badges
+  - Part I: Drop Impact section
+  - Part II: Retraction & Bursting section
+  - Thesis information with DOI, ISBN, and LaTeX source link
+  - Note: This page is included in the main navigation menu and is also
+    accessible via direct URL
+
+### Redirect Pages
+
+The following pages redirect to the CoMPhy Lab website:
+
+- about.md → /#about (homepage section)
+- contact.md → <https://comphy-lab.org/join>
+- research-interests.md, research-interest.md →
+  <https://comphy-lab.org/research>
+- talks.md → <https://comphy-lab.org/research>
+
+### Jekyll Configuration
+
+- **\_config.yml**: Site configuration including title, URL, plugins, and
+  collections
+- **\_layouts/default.html**: Base template for all pages
+- **Gemfile**: Ruby dependencies including Jekyll 4.3.2 and various
+  plugins
+
+### Content Management
+
+- Team information and research papers are managed at the CoMPhy Lab
+  organization repository
+- This site primarily serves as a personal landing page with redirects
+- About content is loaded dynamically from aboutVatsal.md
+
+**IMPORTANT**: When updating `aboutVatsal.md`, also update the fallback content
+in `about.md` (lines 15-37) to keep them synchronized. The fallback is used
+when JavaScript is disabled.
+
+### Assets Structure
+
+- CSS files including academicons, fontello icons, and custom styles
+- Favicon files in multiple formats
+- Logo files for CoMPhy Lab and personal branding
+- Team member images (though team management happens at CoMPhy Lab site)
+
+## Important Notes
+
+- This is a redirect-focused site - most content lives at
+  <https://comphy-lab.org>
+- Changes to team or research content should be made in the CoMPhy Lab
+  organization repository
+- The site uses GitHub Pages for automatic deployment on push to main branch
+- Local testing is recommended before committing changes

_layouts/default.html

@@ -25,6 +25,18 @@
   <link rel="stylesheet" href="{{ site.baseurl }}/assets/css/styles.css">
   <link rel="stylesheet" href="{{ site.baseurl }}/assets/css/command-palette.css">
 
+  <script>
+    window.MathJax = {
+      tex: {
+        inlineMath: [['\\(', '\\)'], ['$', '$']]
+      },
+      svg: {
+        fontCache: 'global'
+      }
+    };
+  </script>
+  <script defer src="{{ site.baseurl }}/assets/js/mathjax/tex-svg.js"></script>
+
   <script>
     document.documentElement.classList.remove('no-js');
     document.documentElement.classList.add('js');
@@ -179,6 +191,7 @@
           <li style="background: none;"><a href="https://github.com/VatsalSy" style="background: none; padding: 0;" aria-label="GitHub Profile"><i class="fa-brands fa-github" style="font-size: 1.75em"></i></a></li>
           <li><a href="{{ site.baseurl }}/#about" class="smoothscroll">About</a></li>
           <li><a href="https://comphy-lab.org/research">Research</a></li>
+          <li><a href="{{ site.baseurl }}/phd-thesis/">PhD Thesis</a></li>
           <li><a href="https://raw.githubusercontent.com/VatsalSy/Vatsal_CV/master/Vatsal_CV.pdf" target="_blank" download>CV <i class="fa-solid fa-download nav-external-icon"></i></a></li>
           <li><a href="https://blogs-comphy-lab.org/" target="_blank">Blog</a></li>
           <li style="background: none;"><a href="https://bsky.app/profile/comphy-lab.org" style="background: none; padding: 0;" aria-label="Bluesky Profile"><i class="fa-brands fa-bluesky" style="font-size: 1.75em;"></i></a></li>