Adam Y. He

Adam Y. He

Genomics, gene regulation, and machine learning

CLAUDE.md

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+). Ruby version is pinned via .ruby-version (rbenv).

If a conda/miniforge environment is active, its CC/CXX/LDFLAGS/CPPFLAGS (pointing at miniforge3) get picked up by native gem extension builds (bigdecimal, nokogiri, etc.) and break them with duplicate-LC_RPATH or “compiler cannot create executables” errors. Run bundle install / rbenv install with those variables unset (or conda deactivate first) if this happens.

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
  • _portfolio/ — Software/package entries (Markdown), rendered as a collection and listed on the /portfolio/ page (_pages/portfolio.html); front matter’s link points to the project’s GitHub repo
  • _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 a row to markdown_generator/publications.tsv / talks.tsv and run the corresponding .ipynb (documented) or .py (plain) script to auto-generate Markdown files. markdown_generator/PubsFromBib.ipynb / pubsFromBib.py instead generate publication Markdown directly from a BibTeX file.

talkmap.py (or talkmap.ipynb) scrapes the location field from every file in _talks/, geocodes it, and regenerates the Leaflet cluster map assets in talkmap/; run it from inside _talks/.

Pages in pages_not_included/ and _drafts/ are excluded from the published site.