CLAUDE.md — Codebase Guide for AI Assistants

This is the personal academic portfolio website for Amutheezan Sivagnanam, a Postdoctoral Fellow at the University of Houston researching AI for Transportation Optimization and Reinforcement Learning. The site is deployed at https://amutheezan.com.

Technology Stacks

Static site generator: Jekyll (via the github-pages gem)
Theme: Minimal Mistakes (v3.4.2, vendored in-repo)
Templating: Liquid
Stylesheets: SCSS (compiled by Jekyll)
JavaScript: jQuery + plugins, minified via uglify-js
Hosting: GitHub Pages with custom domain (amutheezan.com, see CNAME)
Comments: Staticman (configured but inactive)

Directory Structure

.
├── _config.yml            # Main Jekyll configuration
├── _config.dev.yml        # Development overrides (local URL, no analytics)
├── Gemfile                # Ruby gem dependencies (Jekyll, hawkins)
├── package.json           # Node.js build scripts (JS minification)
├── CNAME                  # Custom domain: amutheezan.com
│
├── _data/
│   ├── navigation.yml     # Top-nav menu items
│   ├── authors.yml        # Author metadata (bio, links, avatar)
│   └── ui-text.yml        # Localized UI strings for the theme
│
├── _layouts/              # Liquid HTML layout templates
│   ├── default.html       # Base layout (includes head, masthead, footer)
│   ├── single.html        # General page/post layout
│   ├── talk.html          # Talk-specific layout
│   ├── splash.html        # Hero/splash page layout
│   ├── archive.html       # Archive/listing page layout
│   └── compress.html      # HTML minification layout (wraps default)
│
├── _includes/             # Reusable Liquid partials (~36 files)
│   ├── head/              # <head> section includes
│   ├── footer/            # Footer includes
│   ├── masthead.html      # Top navigation bar
│   ├── author-profile.html# Sidebar author bio
│   ├── archive-single.html# Single entry in archive/listing views
│   └── ...
│
├── _sass/                 # SCSS source modules
│   ├── _variables.scss    # Colors, typography, breakpoints
│   ├── _base.scss         # Base element styles
│   ├── _page.scss         # Page/post layout styles
│   ├── _archive.scss      # Archive/listing styles
│   ├── _sidebar.scss      # Sidebar styles
│   ├── _navigation.scss   # Nav/masthead styles
│   ├── _syntax.scss       # Code block syntax highlighting
│   └── vendor/            # Third-party SCSS (Breakpoint, Susy, Font Awesome, Magnific Popup)
│
├── assets/
│   ├── css/
│   │   ├── main.scss      # CSS entry point (imports all _sass modules)
│   │   └── academicons.css# Academic icon set
│   └── js/
│       ├── _main.js       # Custom jQuery initialization (source)
│       ├── main.min.js    # Minified bundle (DO NOT edit directly)
│       ├── plugins/       # jQuery plugins (source)
│       └── vendor/        # Vendor JS (jQuery 1.12.4)
│
├── _pages/                # Static site pages
│   ├── about.md           # Home page (permalink: /)
│   ├── cv.md              # Full curriculum vitae
│   ├── publications.html  # Publications archive page
│   ├── talks.html         # Talks archive page
│   ├── workshops.html     # Workshops archive page
│   ├── projects.html      # Projects archive page
│   └── 404.md             # 404 error page
│
├── _publications/         # Research publication entries (6 items)
├── _talks/                # Conference talk entries (3 items)
├── _workshops/            # Workshop entries (1 item)
├── _projects/             # Portfolio project entries (6 items)
├── _posts/                # Blog posts (~40 entries, 2012–2016)
├── _drafts/               # Unpublished draft posts
│
├── files/                 # Downloadable assets
│   ├── CurriculumVitae.pdf
│   ├── MLE_Resume.pdf
│   ├── DS_Resume.pdf
│   ├── SE_Resume.pdf
│   ├── Presentations/     # PDF slides from talks
│   └── Posters/           # Conference poster PDFs
│
└── images/                # Image assets (~50+ files)

Collections and Content Conventions

Jekyll collections are defined in _config.yml. Each collection item is a Markdown file with YAML frontmatter.

Publications (`_publications/`)

File naming: YYYY-MM-DD-short-slug.md

Required frontmatter:

---
title: "Full paper title"
collection: publications
permalink: /publications/slug/
date: YYYY-MM-DD
venue: "Venue name (e.g., ICML 2024)"
citation: "Full citation string"
---

Body: Markdown with links to paper (OpenReview/PMLR/ACM), source code, videos, posters, slides. Use standard Markdown links — no custom shortcodes.

Talks (`_talks/`)

File naming: YYYY-MM-DD-short-slug.md

Required frontmatter:

---
title: "Talk title"
collection: talks
type: "Talk"                # or "Poster", "Workshop"
permalink: /talks/slug/
date: YYYY-MM-DD
venue: "Conference Name"
location: "City, Country"
---

Body: Links to slides (PDF in files/Presentations/), posters (PDF in files/Posters/), paper, code.

Projects (`_projects/`)

File naming: YYYY-MM-DD-short-slug.md

Frontmatter fields: title, collection: projects, permalink, date. Body describes the project.

Blog Posts (`_posts/`)

File naming: YYYY-MM-DD-slug.md

Frontmatter:

---
type: post
title: "Post Title"
author: amutheezan
category: [category1]
date: YYYY-MM-DD HH:MM:SS
last_modified_at: YYYY-MM-DD HH:MM:SS
tags: [tag1, tag2]
---

Existing posts cover technical tutorials from 2012–2016 (HL7, WSO2, Arduino, RFID, healthcare IT).

Key Configuration: `_config.yml`

Important settings to be aware of:

url: https://amutheezan.com — production URL
baseurl: "" — no subdirectory; all paths are root-relative
Collections: publications, talks, workshops, projects (all with output: true)
Default layouts: posts → single, talks → talk, all with author_profile: true
Plugins: jekyll-paginate, jekyll-sitemap, jekyll-gist, jekyll-feed, jekyll-redirect-from
SASS: compressed style in production; _config.dev.yml overrides to expanded

Navigation is controlled by _data/navigation.yml. Author info (bio, avatar, social links) is in _data/authors.yml.

Local Development

Prerequisites

Ruby + Bundler
Node.js + npm

Setup

bundle install    # Install Jekyll and Ruby gems
npm install       # Install JS build tools (uglify-js, onchange)

Running the dev server

# Standard (uses production config)
bundle exec jekyll serve

# With development overrides (local URL, no analytics, expanded SASS)
bundle exec jekyll serve --config _config.yml,_config.dev.yml

# With live reload (hawkins gem)
bundle exec hawkins --config _config.yml,_config.dev.yml

Site is available at http://localhost:4000.

JavaScript build

Only needed when editing JS source files in assets/js/plugins/ or assets/js/_main.js:

npm run build:js    # Minify all JS into assets/js/main.min.js
npm run watch:js    # Auto-rebuild on changes

Important: Never edit assets/js/main.min.js directly — it is generated by the build script.

Styling Conventions

SCSS variables (colors, fonts, breakpoints) are defined in _sass/_variables.scss. Modify there for theme-wide changes.
The CSS entry point is assets/css/main.scss which imports all modules via @import.
Vendor SCSS lives in _sass/vendor/ — do not modify vendor files.
The site uses Font Awesome (via SCSS) and Academicons (via assets/css/academicons.css) for icons.
HTML is compressed via the compress layout wrapping default — avoid inline <script> blocks with // JS comments (compression strips newlines and breaks them).

Deployment

Automatic: Push to master → GitHub Pages rebuilds and publishes.
Custom domain: Controlled by CNAME file (amutheezan.com). Do not delete or modify this file.
No CI pipeline — GitHub Pages handles the build.

Common Tasks

Add a new publication

Create _publications/YYYY-MM-DD-slug.md with required frontmatter (see above).
Optionally add PDF/slides to files/Presentations/ or files/Posters/.
Update _pages/cv.md to include the publication in the CV section.

Add a new talk

Create _talks/YYYY-MM-DD-slug.md with required frontmatter.
Add slides PDF to files/Presentations/ and poster PDF to files/Posters/ if applicable.

Update the CV

Edit _pages/cv.md directly. It is a plain Markdown file — no special data source. Keep the existing formatting conventions (section headers, bullet lists).

Edit _data/authors.yml. The sidebar profile pulls data from this file. Fields include name, bio, location, email, uri, and social links (github, linkedin, twitter, google_scholar, orcid, researchgate).

Edit _data/navigation.yml. The main key controls the top navigation bar.

Update downloadable files (CV PDF, resumes)

Replace files directly in the files/ directory. The _pages/cv.md links to these paths.

What NOT to do

Do not edit assets/js/main.min.js directly — it is auto-generated.
Do not delete CNAME — it controls the custom domain.
Do not modify files in _sass/vendor/ — these are vendored third-party libraries.
Do not add --- YAML frontmatter to files in assets/ — Jekyll will try to process them.
Avoid inline JS // line comments inside <script> tags in layouts/includes (HTML compression removes newlines and will break the JS).

Amutheezan

CLAUDE.md — Codebase Guide for AI Assistants

Technology Stacks

Directory Structure

Collections and Content Conventions

Publications (_publications/)

Talks (_talks/)

Projects (_projects/)

Blog Posts (_posts/)

Key Configuration: _config.yml

Local Development

Prerequisites

Setup

Running the dev server

JavaScript build

Styling Conventions

Deployment

Common Tasks

Add a new publication

Add a new talk

Update the CV

Update author bio or social links

Add/remove navigation items

Update downloadable files (CV PDF, resumes)

What NOT to do

Publications (`_publications/`)

Talks (`_talks/`)

Projects (`_projects/`)

Blog Posts (`_posts/`)

Key Configuration: `_config.yml`