armbrustlab.github.io

This repository holds Jekyll site source for the Armbrust Lab at the University of Washington. It uses a modified version of the al-folio Jekyll theme.

Local development installation

These instructions assume MacOS or Linux.

Clone the repository

git clone https://github.com/armbrustlab/armbrustlab.github.io.git

To bring up a Docker container to host a development version of the website run

cd armbrustlab.github.io
docker-compose -f docker-local.yml up

Now access the site at http://localhost:8080.

Notes on source organization

Top-level pages, those listed in the primary menu, are located in _pages. Other pages are organized as Jekyll collections and can be found in folders _people, _research, and _tools. Images are located in assets/img.

All pages should be written in Markdown text format. See here for a quick summary of major syntax.

Theme customizations

This site has modified the base al-folio theme, forked around March 2023, in the following places:

`_includes/footer.html`

Removed Jekyll / theme, modified copyright to reference _config.yml copyright_holder site variable.

`_includes/bio_row.html`

Created a new include definition for the profile entry for each lab member to be included in _pages/people.md.

`_layouts/bib_bio.html`

Modified default bibliography layout originally found in _layouts/bib.html. The jekyll-scholar section of _config.yml has been modified to make this the default bibliography template.

Common tasks

Create internal links

Links to places within the site should be created using the the Liquid template tag {% link %}. See https://jekyllrb.com/docs/templates/#link. Using a link tag ensures that internal links on the site will be valid for each build. If a link is invalid and can't be generated the build will fail. As an example, to create a link to https://armbrustlab.ocean.washington.edu/tools/seaflow, you would use {% link _tools/seaflow.md %}. This could be wrapped into a Markdown link as [SeaFlow]({% link _tools/seaflow.md %}).

Add a new lab member page

To add a new lab member simply create a new Markdown file at _people and name it lastname.md. It's easiest to copy an existing lab members profile file, then edit the YAML Front Matter header at the top of the file and the actual Markdown content below. To add a profile picture add the image file to /assets/img, sized appropriately, then update the bio page frontmatter section. Here's an example of the front matter section for a lab member profile page.

---
first_name: FirstName
last_name: LastName
profile:
  align: right
  image: LastName_profile.jpg  # this image should exist in /assets/img
  image_circular: false # crops the image to make it circular
---

Add a new research or tools section page

Create a new markdown file, or copy an existing one, at _research or _tools. The Front Matter should follow this pattern

title: ecology
description: Phytoplankton ecology and physiology along environmental gradients
order: 1
img: assets/img/CTD_at_sunrise_preview.jpg

where the title, description, and img are used to create an entry in the /research/ or /tools page tiself. And the order controls the sort order of research sections listed on the /research/ or /tools page.

Add an image to a page

See above for adding profile images to lab member pages.

The general method to add an image in the contents of a page would follow this template using a Liquid Template include snippet

{% include figure.html path="assets/img/SeaFlowAnalysis-logo.png" alt="SeaFlow Logo" class="img-fluid rounded z-depth-1" %}

where the optional class parameters rounded rounds out the image box corners, and z-depth-1 adds depth and creates a subtle drop shadow. figure.html is the include to use, defined at _includes/figure.html.

For more control over image presentation and alignment you could embed HTMl in your Markdown file.

<figure class="figure w-100 text-center">
  <img src="{% link assets/img/metagenome-small.gif %}" title="metagenome" class="figure-img img-fluid"/>
  <figcaption class="figure-caption text-center">Within each liter of seawater, how do a billion individual microbial cells compete for available resources, interact with one another, shape and respond to environmental change, and ultimately reproduce or perish?</figcaption>
</figure>

You could even have the image function as a link

<figure class="figure w-100 text-center">
  <a href="{% link assets/img/metagenome-large.gif %}">
    <img src="{% link assets/img/metagenome-small.gif %}" title="metagenome" class="figure-img img-fluid"/>
  </a>
  <figcaption class="figure-caption text-center">Within each liter of seawater, how do a billion individual microbial cells compete for available resources, interact with one another, shape and respond to environmental change, and ultimately reproduce or perish?</figcaption>
</figure>

You can control image and caption alignment by altering the CSS class text-center to one of text-left, text-center, or text-right.

Add a publications section to your profile page

As an alternative to maintaining a list of your publications as Markdown text, you can upload a bibtex file with your publications to _bibliography and have a publications automatically generated based on the contents of that file.

To do this you should add a section like this to your profile page, assuming you've already uploaded a bibtext file named _bibliography/bibtex_file_name.bib.

#### Publications

<div class="publications">
{%- assign years = (site.min_pub_year..site.max_pub_year) | reverse %}
{%- for y in years %}
  {%- capture bib_count %}
    {%- bibliography_count -f bibtex_file_name -q @*[year={{y}}]* %}
  {%- endcapture %}
  {%- assign bib_count = bib_count | to_integer %}
  {%- if bib_count > 0 %}
    <h3 class="year">{{y}}</h3>
    {% bibliography -f bibtex_file_name -q @*[year={{y}}]* %}
  {%- endif %}
{% endfor %}
</div>

This will group your publications by year, most recent first.

To produce an reverse chronological list of publications with no grouping by year you could simply use this

#### Publications

<div class="publications">
  {% bibliography -f bibtex_file_name %}
</div>

Remember to change bibtext_file_name to match the bibtex file placed in _bibliography, without the .bib extension.

armbrustlab / armbrustlab.github.io