AGENTS.md

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

Commands

• Build/Preview locally: bundle exec jekyll serve (serves at http://localhost:4000)
• Build with dev config: bundle exec jekyll serve --config _config.dev.yml
• Build for production: bundle exec jekyll build
• Install dependencies: bundle install
• JS minification: npm run build:js (uglifies JS assets)
• Update GitHub Pages gem: bundle update github-pages
• Talk map generation: Run python talkmap.py from the _talks/ directory (requires getorg and geopy)
• Publication markdown generator: Jupyter notebooks in markdown_generator/ (e.g., publications.ipynb, talks.ipynb)

Project Structure

Jekyll-based academic personal website using the Minimal Mistakes theme, deployed via GitHub Pages.

Key Directories

• _pages/ — Core site pages (about, cv, full-publications, standards, teaching, talks, portfolio, etc.). The homepage is _pages/about.md (permalink: /).
• _publications/ — Full publication list page (Full publications.md).
• _talks/ — Talk markdown files with YAML front matter including location fields (used by talkmap).
• _teaching/ — Teaching experience entries.
• _posts/ — Blog posts (dated markdown files).
• _data/ — Site data:
  • navigation.yml — Main navigation bar links (currently: Full Publications, Standards)
  • authors.yml — Author definitions (theme feature, not actively used here)
  • ui-text.yml — UI string translations
• _layouts/ — Layout templates (single, archive, talk, splash, compress, default, archive-taxonomy).
• _includes/ — Reusable HTML snippets (masthead, footer, analytics, comments, etc.).
• _sass/ — SCSS partials for styling.
• assets/ — Compiled CSS, fonts, JS, and publication PDFs (assets/papers/).
• images/ — Site images and author portrait (zhengfangyu_potrait.jpg).
• talkmap/ — Generated talk location map (Leaflet-based, output of talkmap.py).
• markdown_generator/ — Jupyter notebooks and Python scripts to generate publication/talk markdown from TSV/BibTeX.
• files/ — Miscellaneous downloadable files.

Theme & Configuration

• Uses Minimal Mistakes Jekyll theme (v3.4.2), configured via _config.yml.
• GitHub Pages–compatible: Gemfile uses the github-pages gem with plugins (jekyll-feed, jekyll-sitemap, jemoji, jekyll-paginate, etc.).
• Markdown: kramdown with GFM input. Highlighter: rouge.
• Collections: teaching, publications, portfolio, talks (each with their own permalink pattern).
• Author info defined in _config.yml under author: (name, avatar, bio, social links).

Content Updates

• Publications: Edit _pages/about.md for selected publications, or _pages/full-publications.md for the complete list. Publication PDFs go in assets/papers/.
• Standards: Edit _pages/standards.md.
• Navigation: Edit _data/navigation.yml to add/remove menu links.
• Profile: Edit the author: block in _config.yml.
• New posts: Add dated .md file to _posts/ with proper YAML front matter.