Chevrette Lab @ UF

This is the online home of the Chevrette Lab at the University of Florida. This site and repository is currently under construction.

Some helpful resources for interacting with github pages and jekyll:

Main GH pages site: https://pages.github.com/

GH with jekyll main page: https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll

Windows:

• Set up Ruby:
  • NOTE: jekyll will break with ruby versions 3.x and above on windows (not sure why). Use version 2.7.x. (issue here https://github.com/jekyll-one-org/j1-template/issues/1)
  • Install RubyInstaller https://rubyinstaller.org/downloads/
• Install dependencies: gem install jekyll bundler
• Install yarn & nodejs
  • https://github.com/yarnpkg/yarn/releases/download/v1.22.4/yarn-1.22.4.msi
  • https://github.com/coreybutler/nvm/releases
  • https://nodejs.org/en/download/
• add J1: gem install j1-template

Ubuntu quick setup: NOTE: still in dev. does not quite work yet on chevrette-lab workstation under ubuntu 22.04 (all installs, but yarn breaks in subsequent steps)

• sudo apt-get install build-essential dh-autoreconf ubuntu-dev-tools nodejs npm
• conda create -n myenv ruby gcc gxx_linux-64 yarn
• conda activate myenv
• gem update && gem install jekyll bundler && gem install j1-template

Downgrade npm npm install -g npm@^8

• NOTE: in ubuntu, conda sometimes screws up the ruby path so for the bundle commands to work, adding a sym link to ruby in the rubygems might be needed... ln -s $(conda info --base)/envs/$CONDA_DEFAULT_ENV/bin/ruby $(conda info --base)/envs/$CONDA_DEFAULT_ENV/share/rubygems/bin/ruby

bundle update && bundle install

• If on windows, fix eventmachine issues (see https://stackoverflow.com/questions/30682575/unable-to-load-the-eventmachine-c-extension-to-use-the-pure-ruby-reactor):

  • Make sure git is installed
    • update global email: git config --global user.email [email protected]
    • as administrator, add git config --system core.longpaths true
  • If exists, uninstall eventmachine: gem uninstall eventmachine
  • Edit gemfile in project folder to include: gem install 'eventmachine', '1.2.7', git: 'https://github.com/eventmachine/eventmachine.git', tag: 'v1.2.7'
  • bundle update
  • bundle install

• Set up new project: j1 generate ./ --force

• Setup site: yarn setup

  • Note: yarn reset will reset to factory if need be

Build and locally host site: yarn site (off a fresh clone, run yarn setup first)

https://jekyll.one/pages/public/learn/kickstart/web_in_a_day/create_content/

Almost everything worth editing lives in the _data or pages dirs. If you can't find what you're looking for below, odds are it's somewhere in _data.

Note: *.adoc markup is a little strange, so see https://docs.asciidoctor.org/asciidoc/latest/ for a cheat sheet

• _config.yml for the main site components
• pages/public/*/*.adoc for static (non-news) pages
• _data/modules/navigator_menu.yml for nav bar menu
• _data/modules/navigator.yml for nav bar buttons and layout
• _data/modules/defaults/navigator.yml for nav bar buttons
  • Note: Icon gallery https://jekyll.one/pages/public/previewer/mdi_font/
  • Note: turning icons on/off in the nav bar requires proper mdi icon names (default j1 messed up github)
• _data/blocks/banner.yml for the banner content on the homepage
• _data/blocks/panel.yml for the middle content panels on the homepage (and elsewhere)
• _data/blocks/footer.yml for the bottom content panels on the homepage (and elsewhere)
• collections/posts/public/*/* for news (blog) items
• pages/public/blog/navigator/index.html (actually a yml/markdown) for blog landing page
• index.html for the home page

• yarn add gh-pages
• add "predeploy": "yarn run build", "deploy": "gh-pages -b master -d _site" to the scripts block of package.json (on source branch)
• add "homepage": "https://chevrettelab.github.io/", to package.json (just above "dependencies")

(off a fresh clone, run yarn setup first)

• from the source branch, run yarn predeploy
  • this will build the site
• push changes to the source branch (not sure if this is necessary before yarn deploy, but it works reliably)
• from the source branch, run yarn deploy
  • this will rebuild the site, push to the master branch (which only includes the static _site dir), and trigger a build/deploy on github pages