Website for the Cenik Lab at the University of Texas at Austin, built using the Chirpy Jekyll Theme.

To develop locally you'll need to:

• Install Jekyll (which includes Ruby and bundler, Ruby's package manager)
• Install Node.js version 18.x. (Try earlier versions at your own risk, I had to update from 16.x to get it working.)
• Install Ruby dependencies with bundle install
• Install Node.js dependencies with npm install

Alternatively, you can develop the site in a Docker devcontainer with VS Code. The associated configuration details are in this repo under .devcontainer, and essentially go through the above steps but inside a container. However, you might find performance suffers when developing under this approach. The build when running on a Windows laptop takes 10-20 seconds, while inside a devcontainer takes 150-180 seconds.

bundle exec jekyll serve

If you update the JS files for some reason to customize the theme, you might have to run an npm run build for your changes to propagate.

npm run build
bundle exec jekyll build

If you want to simulate a production build, make sure to set the production flag when building the Jekyll site. This will apply minifcation to the site files.

JEKYLL_ENV=production jekyll build

The Windows way of setting environment variables before running a command works differently than it does on nix machines. npm run build-win will run a production Node build command in a Windows compatible way. To do a Jekyll production build, run set JEKYLL_ENV=production && jekyll build.

_posts includes markdown files representing small pieces of news. These are currently displayed on the Updates page.

_alumni, _collaborators, _team, _research, and _publication are site collections that keep track of data in markdown files similar to _posts

_posts2 is a list of example posts that came with the theme. They are not deployed, but are simply in the repo for reference.

_layouts control the actual templates that match up to each page. Here's an example of a newly added layout

---
# when adding a new layout, you probably want to extend upon the page layout
layout: page 

# The theme does some weird refactoring to images. If it causes you problems, you can turn it off.
refactor: false

# By default, the content of the page sits in the middle, with a list of recently updated posts displayed on the right. If you set fullwidth to true, the content of the page will fill up the whole width.
fullwidth: true
---

Tabs are controlled using the _tabs collection. The Chirpy theme did not originally support have nested subtabs, so this feature was implemented. Here's an example of a tab definition.

---
# this represents the layout in _layouts to show for this page
layout: publications 

# this is the font awesome icon that shows in the sidebar
icon: fas fa-book-open 

# this is the ordering in the sidebar
order: 2 

# If a tab has subtabs define them here
# You must use the exact title of the subtab
sub_pages:
    - Selected Publications
    - Pubmed 
    - Google Scholar
---

Define each subtab in a seperate md file. In the subtab, you'll want to do some additional configuration. Let's look at the Pubmed subtab.

---
# this ensures that the theme doesn't render this as a top level tab
hidden: true 

# order here doesn't really mean anything, but jekyll will complain if we don't specify an order here
order: -1 

# Title to display for the subtab. This must match with the listing in the sub_pages of the tab this is under.
title: Pubmed 

# Optionally, if you want the tab to link to an external site, add a link property
link: https://pubmed.ncbi.nlm.nih.gov/?term=cenik+c&sort=date
---

_sass contains styling for the site. If you want to modify or add CSS rules, look here. There are global color variables you can modify to quickly change the look and feel of the site. Try to modify these instead of adding new styling rules when possible. For example, an excerpt from the light theme color scheme that was customized:

/* Sidebar */
--sidebar-bg: radial-gradient(circle, #1b65b0 0%, #1f59cc 100%);
--sidebar-muted-color: whitesmoke;
--sidebar-active-color: white;
--sidebar-hover-bg: rgba(227, 227, 227, 0.208);

_javascript contains some small bits of JS that initialize parts of the site. For example, I added a masonry grid plugin that needed to be initialized here. If you update these in development you'll need to run an npm run build to see your changes.

This theme originally displayed the posts collection, along with pagination, on the homepage. We wanted to move displaying this collection, along with pagination, to another tab. To get this to work with Jekyll's built in pagination, a lot of things had to be changed.

• Changing some settings in config.yml:

paginate: 10
paginate_path: "/lab_updates/page:num/"
paginate_root: "/lab_updates" # this is not used by the paginate plugin but custom defined for use in this project

• Creating a dummy "Updates" tab that actually links to "/lab_updates"
• Creating a simple lab_updates/index.html page so Jekyll recognizes it as a valid place to inject pagination information.

In addition to these changes, hardcoded parts of the theme templates that make checks to do something if the page.layout == 'home' also had to be modified. Not all of these were changed, and depending on how the site is updated, more of these hardcoded values might need changing. Of special note is the _includes/js-selector.html file, which decides to load certain pieces of important initialization code depending on which page the user is on.

Previously, new images were added by adding markup to the lab_life.md file. Now, the images are displayed in a carousel. To add images to this carousel, prepend them to the list of objects in the front matter of lab_life.md. For example:

images:
  - src: "/img/lab_life/2023/ian_paper.jpg" # path to image
    caption: "We celebrated Ian's Genome Biology paper playing Secret Hitler!" # caption corresponding to image
  - src: "/img/lab_life/2022/ceniklab_hike_oct_18_2022.jpg"
    caption: "We opened the hiking season with the San Gabriel Trail."
...

The actual markdown contents of the file do not do anything anymore, and are kept for reference only.

The site is built and deployed automatically to Github Pages upon a push to the master branch using Github Actions. The build script essentially runs the JS and Jekyll build commands, with production flags, and deploys the site.

To explore usage, development, and upgrade guide of the project, please refer to the Wiki.