Jekyll-Scholar

Jekyll-Scholar is for all the academic bloggers out there. It is a set of extensions to Jekyll, the awesome, blog aware, static site generator; it formats your bibliographies and reading lists for the web and gives your blog posts citation super-powers.

Already using Jekyll-Scholar and interested to help out? Please get in touch with us if you would like to become a maintainer!

Installation

$ [sudo] gem install jekyll-scholar

Or add it to your Gemfile:

gem 'jekyll-scholar', group: :jekyll_plugins

Github Pages

Note that it is not possible to use this plugin with the default Github pages workflow. Github does not allow any but a few select plugins to run for security reasons, and Jekyll-Scholar is not among them. You will have to generate your site locally and push the results to the master resp. gh-pages branch of your site repository. You can keep sources, configuration and plugins in a separate branch; see e.g. here for details.

Alternatively, you can use a Github Actions called jekyll-action to deploy your site to Github Pages

Usage

Install and setup a new Jekyll directory (see the Jekyll-Wiki for detailed instructions). To enable the Jekyll-Scholar add the following statement to a file in your plugin directory (e.g., to _plugins/ext.rb):

require 'jekyll/scholar'

Alternatively, add jekyll-scholar to your gem list in your Jekyll configuration:

plugins: ['jekyll/scholar']

Configuration

In your Jekyll configuration file you can adjust the Jekyll-Scholar settings using the scholar key. For example, the following sets the bibliography style to modern-language-association.

scholar:
  style: modern-language-association

The table below describes some commonly used configuration options. For a description of all options and their defaults, see defaults.rb.

Option	Default	Description
style	apa	Indicates the style used for the bibliography and citations. You can use any style that ships with CiteProc-Ruby by name (e.g., apa, chicago-fullnote-bibliography) which is usually the filename as seen here without the .csl ending; note that you have to use dependent/style if you want to use one from that directory. Alternatively you can add a link to any CSL style (e.g., you could link to any of the styles available at the official CSL style repository).
locale	en	Defines what language to use when formatting your references (this typically applies to localized terms, e.g., 'Eds.' for editors in English).
source	./_bibliography	Indicates where your bibliographies are stored.
bibliography	references.bib	Indicates the name of your default bibliography. For best results, please ensure that your bibliography is encoded as ASCII or UTF-8. A string that contains a * will be passed to Dir::glob, so **/*.bib{,tex} will find all files named *.bib and *.bibtex under source.
allow_locale_overrides	false	When true, allows the language entry in the BibTex to override the locale setting for individual entries. When the language is missing it will revert back to locale. The language value should be encoded using the two-letter ISO 639-1 standard. Ex. English = 'en', Spanish = 'es'.
sort_by	none	Specifies if and how bibliography entries are sorted. Entries can be sorted on multiple fields, by using a list of keys, e.g. year,month. Ordering can be specified per sort level, e.g. order: descending,ascending will sort the years descending, but per year the months are ascending. If there are more sort keys than order directives, the last order entry is used for the remaining keys.
order	ascending	Specifies order bibliography entries are sorted in. Can be ascending or descending. Ordering can be specified per sort level, e.g. descending,ascending will sort in descending on the first key then ascending order on the second key. If there are more sort keys than order directives, the last order entry is used for the remaining keys.
group_by	none	Specifies how bibliography items are grouped. Grouping can be multi-level, e.g. type, year groups entries per publication type, and within those groups per year.
group_order	ascending	Ordering for groups is specified in the same way as the sort order. Publication types -- specified with group key type, can be ordered by adding type_order to the configuration. For example, type_order: [article,techreport] lists journal articles before technical reports. Types not mentioned in type_order are considered smaller than types that are mentioned. Types can be merge in one group using the type_aliases setting. By default phdthesis and mastersthesis are grouped as thesis. By using, for example, type_aliases: { inproceedings: article}, journal and conference articles appear in a single group. The display names for entry types are specified with type_names. Names for common types are provided, but they can be extended or overridden. For example, the default name for article is Journal Articles, but it can be changed to Papers using type_names: { article: Papers }.
bibtex_filters	latex,smallcaps,superscript	Configures which BibTeX-Ruby formatting filters values of entries should be passed through. The default latex filter converts LaTeX character escapes into unicode, smallcaps converts the \textsc command into a HTML <font style=\"font-variant: small-caps\"> tag, and superscript which converts the \textsuperscript command into a HTML <sup> tag.
raw_bibtex_filters		Configures which BibTeX-Ruby formatting filters the raw BiBTeX entry (i.e. that available through {{ entry.bibtex }}) should be passed through. This can be used to e.g. strip excess newlines by using the linebreaks filter.

Bibliographies

Once you have loaded Jekyll-Scholar, all files with the extension .bib or .bibtex will be converted when you run Jekyll (don't forget to add a YAML header to the files); the file can contain regular HTML or Markdown and BibTeX entries; the latter will be formatted by Jekyll-Scholar according to the citation style and language defined in your configuration file.

For example, if you had a file bibliography.bib in your root directory:

---
---
References
==========

@book{ruby,
  title     = {The Ruby Programming Language},
  author    = {Flanagan, David and Matsumoto, Yukihiro},
  year      = {2008},
  publisher = {O'Reilly Media}
}

It would be converted to bibliography.html with the following content:

<h1 id='references'>References</h1>

<p>Flanagan, D., &#38; Matsumoto, Y. (2008). <i>The Ruby Programming Language</i>. O&#8217;Reilly Media.</p>

This makes it very easy for you to add your bibliography to your Jekyll-powered blog or website.

If you are using other converters to generate your site, don't worry, you can still generate bibliographies using the bibliography tag. In your site or blog post, simply call:

{% bibliography %}

This will generate your default bibliography; if you use multiple, you can also pass in a name to tell Jekyll-Scholar which bibliography it should render.

Let's say you have two bibliographies stored in _bibliography/books.bib and _bibliography/papers.bib; you can include the bibliographies on your site by respectively calling {% bibliography --file books %} and {% bibliography --file papers %}. For example, you could have a file references.md with several reference lists:

---
title: My References
---

{{ page.title }}
================

The default Bibliography
------------------------

{% bibliography %}

Secondary References
--------------------

{% bibliography --file secondary %}

Finally, the bibliography tag supports an optional filter parameter. This filter takes precedence over the global filter defined in your configuration.

{% bibliography --query @*[year=2013] %}

The example above would print a bibliography of all entires published in the year 2013. Of course you can also combine the file and filter parameters like this:

{% bibliography -f secondary -q @*[year=2013] %}

This would print the publications from 2013 of the bibliography at _bibliography/secondary.bib.

For more details about filters, see the corresponding section below or consult the BibTeX-Ruby documentation.

If you need to limit the number of entries in your bibliography, you can use the --max option:

{% bibliography --max 5 %}

This would generate a bibliography containing only the first 5 entries of your bibliography (after query filters and sort options have been applied). Limiting entries is disabled if grouping is active.

Return number of publications in bibliography

The bibliography_count returns the number of items that would be rendered in a bibliography. This tag accepts the same parameters as the bibliography tag.

{% bibliography_count -f references --query @book[year <=2000] %}

See #186 for further examples.

Bibliography Template

Your bibliography is always rendered as an ordered list. Additionally, each reference is wrapped in an HTML tag (span by default but you can change this using the reference_tagname setting) with the cite key as id. The reference string itself is governed by the rules in your CSL style but you can also customize the main template a little bit. By default, the template is {{reference}} – this renders only the reference tag. The template uses Liquid to render and, in addition to the reference, exposes the cite-key (as key), the entry's type, the index in the bibliography, and the link to file repository as link. Thus, you could customize the template in your configuration as follows:

scholar:
  bibliography_template: <abbr>[{{key}}]</abbr>{{reference}}

This would be processed into something like:

<li><abbr>[ruby]</abbr><span id="ruby">Matsumoto, Y. (2008). <i>The Ruby Programming Language</i>. O&#8217;Reilly Media.</span></li>

If you have more complex requirements, it quickly becomes tedious to have the template inside the configuration; for this reason, you can also put the bibliography template into your layouts directory. Jekyll-Scholar will load this template if the option set in your configuration matches an existing layout (without the file extension). That is to say, if you set:

scholar:
  bibliography_template: bib

And there is a file _layouts/bib.html (or with another extension) the contents of this file will be used as the template. Please note that it is important for this file to contain the YAML front matter! For example, this would be a more complex template file:

---
---
{{ reference }}

{% if entry.abstract %}
<p>{{ entry.abstract }}</p>
{% endif %}

<pre>{{ entry.bibtex }}</pre>

You can also override the default bibliography template, by passing the --template or -T option parameter to the bibliography tag.

Citations

If you want to reference books or papers from your bibliography in your blog posts, Jekyll-Scholar can help you, too. Simply use the cite tag with the appropriate key of the item you want to cite and Jekyll-Scholar will create a formatted citation reference for you. For a quick example, take following blog post:

---
layout: default
title: A Blogging Scholar
---

{{ page.title }}
================

Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
Duis 'aute irure dolor in reprehenderit in voluptate' {% cite derrida:purveyor %}
velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat
cupidatat non proident, 'sunt in culpa qui officia deserunt mollit anim id est
laborum' {% cite rabinowitz %}.

Duis 'aute irure dolor in reprehenderit in voluptate' {% cite breton:surrealism %}
velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat
cupidatat non proident, 'sunt in culpa qui officia deserunt mollit anim id est
laborum' {% cite rainey %}.

References
----------

{% bibliography %}

Note that this will print your entire bibliography in the Reference section. If you would like to include only those entries you cited on the page, pass the cited option to the bibliography tag:

{% bibliography --cited %}

By default, the --cited option will still sort your bibliography if you set the sort option. Especially for styles using citation numbers, this is usually not the desired behaviour. In such cases you can use --cited_in_order instead of --cited and your bibliography will contain all cited items in the order they were cited on the page.

For longer quotes, Jekyll-Scholar provides a quote tag:

{% quote derrida:purveyor %}
Lorem ipsum dolor sit amet, consectetur adipisicing elit,
sed do eiusmod tempor.

Lorem ipsum dolor sit amet, consectetur adipisicing.
{% endquote %}

For example, this could be rendered as:

<blockquote>
  <p>Lorem ipsum dolor sit amet, consectetur adipisicing elit,<br/>
  sed do eiusmod tempor.</p>
  <p>Lorem ipsum dolor sit amet, consectetur adipisicing.</p>
  <cite>
    <a href="#derrida:purveyor">(Derrida, 1975)</a>
  </cite>
</blockquote>

Multiple citation

You can cite multiple items in a single citation by referencing all ids of the items you wish to quote separated by spaces. For example, {% cite ruby microscope %} would produce a cite tag like:

<a href="#ruby">(Flanagan &amp; Matsumoto 2008; Shaughnessy 2013)</a>

Citations when there's more than one bibliography

Let's return to the example above where you have two bibliographies stored in _bibliography/books.bib and _bibliography/papers.bib. We also must have the main bibliography, e.g., _bibliography/references.bib. As we know from above, it's possible to use bibliographies other than the main bibliography by calling {% bibliography --file books %} or {% bibliography --file papers %}.

Though what if we want to cite an article that's not in the main bibliography? We use the same approach as above; to cite an article in the books.bib bibliography, we simply call {% cite ruby --file books %}

Suppressing author names

Sometimes you want to suppress author names in a citation, because the name has already been mentioned in your text; for such cases Jekyll-Scholar provides the --suppress_author option (short form: -A): ...as Matz explains {% cite ruby -A -l 42 %} would produce something like: ...as Matz explains (2008, p. 42).

Page numbers and locators

If you would like to add page numbers or similar locators to your citation, use the -l or --locator option. For example, {% cite ruby --locator 23-5 %} would produce a citation like (Matsumoto, 2008, pp. 23-5).

When quoting multiple items (see above) you can add multiple locators after the list of ids. For example, {% cite ruby microscope -l 2 -l 24 & 32 %}.

Page is the default locator, however, you can indicate the type of locator by adding a -L or --label option (one for each locator) for instance, {% cite ruby microscope --label chapter --locator 3 -L figure -l 24 & 32 %} produces something like: (Matsumoto, 2008, chap. 3; Shaughnessy, 2013, figs. 24 & 32).

Displaying formatted references

If you want to display the full formatted reference entry, you can use the reference tag. For example, given the following Bibtex entry,

@book{ruby,
  title     = {The Ruby Programming Language},
  author    = {Flanagan, David and Matsumoto, Yukihiro},
  year      = {2008},
  publisher = {O'Reilly Media}
}

using {% reference ruby %} anywhere in your page, it will print "Flanagan, D., & Matsumoto, Y. (2008). The Ruby Programming Language.. O'Reilly Media" (the exact result depends on your formatting style).

The reference tag accepts the same --file/-f parameter as the bibliography tag. This can be handy if you want to use a special BibTeX file as input for a specific page. As an example, the tag

{% reference ruby --file /home/foo/bar.bib %}

will attempt to read the key ruby from file /home/foo/bar.bib. It will not fallback to the default BibTeX file.

Citation pointing to another page in your site

In some cases, you might want your citation to link to another page on your cite (ex. a separate works cited page). As a solution, add a relative path to your scholar configurations:

    scholar:
      relative: "/relative/path/file.html"

Multiple bibliographies within one document (like multibib.sty)

When you have multiple {% bibliography %} sections in one file, Jekyll-Scholar will generate several lists containing the same publications that have the same id attributes. As a result, when you cite a reference the link to an id attribute cannot be resolved uniquely. Your browser will always take you take you to the first occurrence of the id. Moreover, valid HTML requires unique id attributes. This scenario may happen, for example, if you cite the same reference in different blog posts, and all of these posts are shown in one html document.

As a solution, Jekyll-Scholar provides the --prefix tag. In your first post you might cite as

---
title: Post 1
---
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor
incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
Duis 'aute irure dolor in reprehenderit in voluptate'
{% cite derrida:purveyor --prefix post1 %} velit esse cillum
dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat
non proident, 'sunt in culpa qui officia deserunt mollit anim id
est laborum' {% cite rabinowitz --prefix post1 %}.

References
----------

{% bibliography --cited --prefix post1 %}

For the second blog post you would cite as follows:

---
title: Post 2
---
Duis 'aute irure dolor in reprehenderit in voluptate'
{% cite rabinowitz --prefix post2 %} velit esse cillum
dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat
non proident, 'sunt in culpa qui officia deserunt mollit anim id
est laborum' {% cite rainey --prefix post2  %}.

References
----------

{% bibliography --cited --prefix post2 %}

Even though both posts cite 'rabinowitz', both citations will be assigned unique identifiers linking to the respective references section, although both posts will be rendered into a single HTML document.

Add a custom class for the citation reference

By default Jekyll Scholar generate a link with a class:

<a href="#ruby" class="citation">(Derrida, 1975)</a>

You can custom this class in your configuration:

scholar:
  cite_class: citation

File Repositories

File repository support was added to Jekyll-Scholar starting at version 2.0. Currently, if you have a folder in your site that contains PDF or Postscript files of your papers, you can use the configuration option repository to indicate this directory. When generating bibliographies, Jekyll-Scholar will look in that folder to see if it contains a filename matching each entry's BibTeX key: if it does, the path to that file will be exposed to the bibliography template as the link property.

Since version 4.1.0 repositories are not limited to PDF and PS files. These files are mapped to the links property in your bibliography template. Here is an example of template that utilizes this feature to link to supporting material in a ZIP archive:

{{ reference }} [<a href="{{links.zip}}">Supporting Materials</a>]

Since version 5.9.0, Jekyll-Scholar matches files which begin with a BibTeX key and are immediately followed by a delimiter (default: "."). All text proceeding the delimiter is treated as the file extension. For example, if two files named key.pdf and key.slides.pdf are found, {{links.pdf}} and {{links['slides.pdf']}} will both be populated. You can use the configuration option repository_file_delimiter to change the default delimiter.

Detail Pages

If your layouts directory contains a layout file for bibliography details (the details_layout configuration options), Jekyll-Scholar will generate a details page for each entry in you main bibliography. That is to say, if your bibliography contains the following entry:

@book{ruby,
  title     = {The Ruby Programming Language},
  author    = {Flanagan, David and Matsumoto, Yukihiro},
  year      = {2008},
  publisher = {O'Reilly Media}
}

Then a page 'bibliography/ruby.html' will be generated according to your details page layout. In the layout file, you have access to all fields of your BibTeX entry. Here is an example of a details page layout:

---
---
<html>
<head></head>
<body>
  <h1>{{ page.entry.title }}</h1>
  <h2>{{ page.entry.author }}</h2>
  <p>{{ page.entry.abstract }}</p>
</body>
</html>

When Jekyll-Scholar generates detail pages, it also adds links to each entry's detail page to the generated bibliography. You can alter the name of the link via the 'details_link' configuration option.

Jekyll-Scholar also provides a Liquid tag for conveniently adding links to individual detail pages. For example, if you would like to add a simple link to one of the items in your bibliography on a page or in a blog post you can use the cite_details tag to generate the link. For this to work, you need to pass the BibTeX key of the element you want to reference to the tag and, optionally, provide a text for the link (the default text can be set via the 'details_link' configuration option).

Duis 'aute irure dolor in reprehenderit in voluptate' velit esse cillum
dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non
proident {% cite_details key --text Click Here For More Details %}.

Alternatively, you can use the details_link tag to get just the URL to a details page. This can be used to link to details pages in markdown the same way you would link to a blog post with Jekyll's link tag.

[See our blog post]({% link _posts/2020-01-01-research-post.md %}) 
or [find more details]({% details_link key %}).

Bibliography Filters

By default, Jekyll-Scholar includes all entries in you main BibTeX file when generating bibliographies. If you want to include only those entries matching certain criteria, you can do so by adjusting the 'query' configuration option. For example:

query: "@book" #=> includes only books
query: "@article[year>=2003]" #=> includes only articles published 2003 or later
query: "@*[url]" #=> includes all entries with a url field
query: "@*[status!=review]" #=> includes all entries whose status field is not set to 'review'
query: "@book[year <= 1900 && author ^= Poe]" #=> Books published before 1900 where the author matches /Poe/
query: "!@book" #=> includes all entries with a type other than book

Please note that some of these queries require BibTeX-Ruby 2.3.0 or later versions. You can also overwrite the configuration's query parameter in each bibliography tag individually as described above.

Contributing

The Jekyll-Scholar source code is hosted on GitHub. You can check out a copy of the latest code using Git:

$ git clone https://github.com/inukshuk/jekyll-scholar.git

To use this lasted version instead of the one provide by RubyGems, just add the line

$:.unshift '/full/path/to/the/repository/lib'

to your _plugins/ext.rb before requiring 'jekyll/scholar', where /full/path/to/the/repository is the path to your local version of Jekyll-Scholar.

When contributing to Jekyll-Scholar, please make sure to install all dependencies and run the cucumber features:

$ bundle install
$ rake

If you've found a bug or have a question, please open an issue on the Jekyll-Scholar issue tracker. Or, for extra credit, clone the Jekyll-Scholar repository, write a failing example, fix the bug and submit a pull request.

Additionally, if we merged at least one of your pull request you will get write permissions to the repository if you want them.

License

Jekyll-Scholar is distributed under the same license as Jekyll.

Copyright (c) 2011-2015 Sylvester Keil

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the 'Software'), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.