Introducing Jekyll-Scholar

Jekyll-Scholar is formatting references and citations on Jekyll blogs and “formats your bibliographies and reading lists for the web and gives your blog posts citation super-powers.”

Major Lessons

Publication page is necessary for an academic website. Since I’m very lazy, I always wanted to be able to have a single .bib file and a system which generates a webpage from it. Such a pipeline will make it much easier to maintain the website1.

Jekyll-Scholar is a great plugin for this purpose. I spent sometime during the holidays to customize and integrate it to this website. Here, I some challenges that I needed to overcome.

Using a Non-supported Plugin on GitHub

GitHub is very stringent about the plugins that supported on the GitHub-Pages.
Here is the small set of supported plugins which does not include Jekyll-Scholar.

So to use Jekyll-Scholar you need a third party service, which allows other plugins, to serve your website and deploy it to your _site folder on the master/Github-pages branch of your repository.

It seems Netlify is the most popular and user-friendly tool for Continuous Deployment out there and comparing my experience with Wercker, I can confirm that.

It is very easy to link your GitHub repository to Netlify and deploy your website with arbitrary plugins. You can refer to the step-by-step guide on the Netlify website.

Sorting Publication by Year and Topic

After looking around for options, I found that I either should learn and write some Ruby code for this or I can use Jekyll-Scholar ability to work with multiple .bib files and hack through it.

I didn’t want to spend time learning Ruby, so I ended up copy/pasting BibTex entries to separate files, one for each topic, and read them in inside the By Topic page:


<!-- High Dimensional Statistics -->
<h3  class="pubyear">High Dimensional Statistics</h3>
{% bibliography -f hds %}

<!-- Social Network Analysis -->
<h3  class="pubyear">Social Network Analysis</h3>
{% bibliography -f sna %}



Sorting by year is simpler because it needs only a single file. I’m borrowing the code partially from al-folio theme:


{% for y in page.years %}
<h3  id="{{y}}" class="pubyear">{{y}}</h3>
{% bibliography -f papers -q @*[year={{y}}]* %}
{% endfor %}



And you should put years: [2016, 2015, 2013, 2012] in the front matter of the related page.

Adding Abstract, BibTex, PDF Buttons for each Item

Inside the _layouts folder I added the following bibtemplate.html file:


---
---
{{reference}}
{% if entry.abstract %}
<button class="btn btnId btnPub--abstract" id="b_{{key}}-abstract" style="outline:none;">Abstract</button>
{% endif %}

<button class="btn btnId btnPub--BibTex" id="b_{{key}}-bibtex" style="outline:none;">BibTeX</button>

{% endif %}

<a href="{{links['sup.pdf']}}"><button class="btn btnId btnPub--supplement" style="outline:none; position:relative;white-space: normal;">Supplement</button></a>
{% endif %}

<div class="dropDownBibtex" id="{{key}}-bibtex">
<pre>{{entry.bibtex}}</pre>
</div>

<div class="dropDownAbstract" id="{{key}}-abstract">
{{entry.abstract}}
</div>



And set the Jekyll-Scholar configuration in _config.yml file to work with this layout:

  bibliography_template: bibtemplate


I’ll explain different parts of the above file in the following sections.

I wanted to have a drop-down effect for some of the buttons. The mainstream method is to use Twitter’s Bootstrap, but the problem is that I’m using a Jekyll theme which is not supporting the Bootstrap and adding it to the theme just for these two buttons was inefficient.

So I just added the following simple jQuery script in the footer template of the website:


<script>
$(document).ready(function(){ var str =$(this).attr('id');

$(".btnId").click(function(){ var str =$(this).attr('id');
var ret = str.split("_");
var id = ret[1];
\$('#' + id).toggle();
});
});
</script>



Jekyll-Scholar can read PDF files from a specific directly fixed in the _config.yml:

  repository: /publications


The publications directory should be in the root of your repository.
Inside of it, you can add files that have the BibTeX keys as their names.
So pubName.pdf corresponds to a BibTeX entry with the name pubName which is accessible through {{ key }} in the bibtemplate.html.

Supplement Files

If you want to include supplement, presentation, etc. to your publication entry, you can have your extra file in the publications folder as key.sup.pdf which is read into links['sup.pdf'].

1. This is the general philosophy of Jekyll as a static website/blog generator: separating the content from the generation process.

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