CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Overview

Academic personal website for Adam Y. He (computational biologist), built with Jekyll using the Academic Pages theme. Hosted on GitHub Pages at https://adamyhe.github.io.

Common Commands

# Install dependencies
bundle install

# Serve locally with live reload (accessible at localhost:4000)
jekyll serve -l -H localhost

# JavaScript build
npm run build:js       # Build minified JS
npm run watch:js       # Watch for JS changes

Requires Ruby, Bundler, Node.js, and webrick gem (for Ruby 3.0+).

Architecture

Static site generator pipeline:

_config.yml — Main site configuration (author info, social links, collections, plugins)
_pages/ — Site pages (about, cv, publications, etc.) written in Markdown with YAML front matter
_publications/ — Individual publication entries (Markdown), rendered as a collection
_talks/ — Talk entries (Markdown), rendered as a collection
_layouts/ — Jekyll HTML layout templates (single, talk, archive)
_includes/ — Reusable Liquid template partials (header, footer, sidebar, SEO, scripts)
_sass/ — SCSS stylesheets
_data/ — YAML data files driving navigation (navigation.yml) and author metadata
images/ — Project/research images
files/ — Downloadable PDFs

Content generation: markdown_generator/ contains Python/Jupyter notebooks that convert TSV data into Markdown files for publications and talks.

Key configuration in _config.yml: Collections (publications, talks, teaching, portfolio), author profile, social links, permalink structure, and plugin list. The site uses kramdown with GFM for Markdown rendering.

Content Workflow

To add a publication or talk: either create a new Markdown file in the appropriate collection directory with proper YAML front matter, or add data to the TSV files in markdown_generator/ and run the corresponding notebook to auto-generate Markdown files.

Pages in pages_not_included/ are archived and not published.