Architecture

Current as of 2026-06-03.

Overview

Static Jekyll site for MethylGrammarLab, deployed as GitHub Pages for methylgrammarlab.org via CNAME.

Runtime And Dependencies

• Ruby/Jekyll via Gemfile; .ruby-version pins local development to Ruby 3.3.4, matching the current GitHub Pages runtime.
• The primary dependency is the github-pages gem; local bundle install currently resolves github-pages 232 and Jekyll 3.10.0.
• Local Ruby is provided by rbenv under /Users/benbfly/.rbenv; ~/.zshrc initializes rbenv so fresh zsh shells use .ruby-version automatically.
• The local Ruby was compiled with ruby-build, local OpenSSL, and local libyaml so native gems build for arm64 macOS instead of relying on Apple system Ruby.
• These local Ruby/rbenv changes do not affect GitHub Pages hosting. GitHub Pages builds with GitHub’s own runtime; .ruby-version is a local development hint.
• _config.yml enables jekyll-feed and jekyll-sitemap; templates also use `

, so the GitHub Pages stack is expected to provide jekyll-seo-tag`.

• CSS is compiled from assets/main.scss, which imports vendored Bootstrap 4 Sass, Bootstrap-4-Jekyll helpers, syntax highlighting, and local customization.
• Bootstrap and jQuery browser assets are vendored under _sass/bootstrap/ and assets/javascript/bootstrap/; update_bootstrap.sh refreshes them with npm.
• External browser scripts are loaded from _includes/head.html: Altmetric/CloudFront embed, Citation.js, and Dimensions badges.

Layout And Rendering

• _layouts/default.html composes _includes/head.html, _includes/header.html, page content, and _includes/footer.html.
• _layouts/page.html, _layouts/post.html, and _layouts/home.html are thin wrappers around default.
• Header navigation comes from _config.yml header_pages; the Join us! link is hard-coded in _includes/header.html.
• index.md uses default and includes _includes/desc.html for the homepage text.

Content Model

• Top-level Markdown/HTML files define public pages such as index.md, people.md, research.md, pubs.md, openings.md, and contact.md.
• Jekyll collections in _config.yml: members, jobs, projects, tools, and teaching. They are consumed by listing pages and are not configured for standalone output.
• people.md reads _members/current and _members/past; member front matter supports optional website, orcid, current_address, and current_address_url fields in addition to the existing name/position/contact/photo fields. research.md reads _projects; openings.md reads _jobs; tools.md and teaching.md read their matching collections.
• Publications are CSL-style JSON records under _data/pubs rendered by pubs.md; _bibliography/toprefs.bib is a BibTeX source/reference file.

Assets And Styling

• Images, PDFs, RMarkdown/html workshop material, and a bigWig data file live under assets/ and datafiles/.
• assets/css/cards.css provides shared card styles for people, research, publications, and openings pages.
• Theme variables are Sandstone/Bootswatch-derived in _sass/_variables.scss; _sass/_bootstrap_customization.scss currently offsets the fixed-top navbar.

Build And Deployment

• Local build/serve: open a fresh shell with rbenv initialized, cd /Users/benbfly/Documents/benbfly.github.io, then run bundle exec jekyll build or bundle exec jekyll serve.
• The normal preview URL is http://127.0.0.1:4000; the in-app browser can be used to inspect it before commits.
• .travis.yml runs Ruby 2.2 and bundle exec jekyll build.
• .gitignore excludes generated build/dependency outputs including _site, .sass-cache, .jekyll-metadata, node_modules, package-lock.json, and Gemfile.lock.