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https://github.com/inukshuk/jekyll-scholar

jekyll extensions for the blogging scholar
https://github.com/inukshuk/jekyll-scholar

bibliography bibtex citations csl jekyll jekyll-plugin ruby static-site-generator

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jekyll extensions for the blogging scholar

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Jekyll-Scholar
==============
[![CI](https://github.com/inukshuk/jekyll-scholar/actions/workflows/ci.yml/badge.svg)](https://github.com/inukshuk/jekyll-scholar/actions/workflows/ci.yml)

Jekyll-Scholar is for all the academic bloggers out there. It is a set of
extensions to [Jekyll](http://jekyllrb.com/), 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](https://help.github.com/articles/using-jekyll-with-pages/).
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](http://davidensinger.com/2013/07/automating-jekyll-deployment-to-github-pages-with-rake/)
for details.

Alternatively, you can use a [Github Actions](https://github.com/features/actions) called [jekyll-action](https://github.com/helaili/jekyll-action) to deploy your site to Github Pages

Usage
-----

Install and setup a new [Jekyll](http://jekyllrb.com/) directory (see the
[Jekyll-Wiki](https://github.com/mojombo/jekyll/wiki/Usage) 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`](/lib/jekyll/scholar/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](https://github.com/inukshuk/citeproc-ruby) by name (e.g., apa, chicago-fullnote-bibliography) which is usually the filename as seen [here](https://github.com/citation-style-language/styles) 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](https://github.com/citation-style-language/styles)). |
| `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](https://www.loc.gov/standards/iso639-2/php/code_list.php) 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](https://github.com/inukshuk/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 `` tag, and `superscript` which converts the `\textsuperscript` command into a HTML `` tag. |
| `raw_bibtex_filters` | ` ` | Configures which [BibTeX-Ruby](https://github.com/inukshuk/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:

References

Flanagan, D., & Matsumoto, Y. (2008). The Ruby Programming Language. O’Reilly Media.

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](https://github.com/inukshuk/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](https://github.com/inukshuk/jekyll-scholar/blob/master/features/186.feature)
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: [{{key}}]{{reference}}

This would be processed into something like:


  • [ruby]Matsumoto, Y. (2008). The Ruby Programming Language. O’Reilly Media.
  • 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 %}

    {{ entry.abstract }}


    {% endif %}

    {{ entry.bibtex }}

    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:


    Lorem ipsum dolor sit amet, consectetur adipisicing elit,

    sed do eiusmod tempor.


    Lorem ipsum dolor sit amet, consectetur adipisicing.



    (Derrida, 1975)

    #### 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:

    (Flanagan & Matsumoto 2008; Shaughnessy 2013)

    #### 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:

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

    #### Multiple bibliographies within one document (like [multibib.sty](http://www.ctan.org/pkg/multibib))

    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:

    (Derrida, 1975)

    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 }} [Supporting Materials]

    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:

    ---
    ---



    {{ page.entry.title }}


    {{ page.entry.author }}


    {{ page.entry.abstract }}



    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](http://github.com/inukshuk/jekyll-scholar/).
    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](http://github.com/inukshuk/jekyll-scholar/issues).
    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](http://sylvester.keil.or.at/)

    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.