jekyll-theme-petridish 3.0

data/_includes/toc.html

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+{% capture tocWorkspace %}
+    {% comment %}
+        Copyright (c) 2017 Vladimir "allejo" Jimenez
+
+        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.
+    {% endcomment %}
+    {% comment %}
+        Version 1.2.0
+          https://github.com/allejo/jekyll-toc
+
+        "...like all things liquid - where there's a will, and ~36 hours to spare, there's usually a/some way" ~jaybe
+
+        Usage:
+            {% include toc.html html=content sanitize=true class="inline_toc" id="my_toc" h_min=2 h_max=3 %}
+
+        Parameters:
+            * html         (string) - the HTML of compiled markdown generated by kramdown in Jekyll
+
+        Optional Parameters:
+            * sanitize      (bool)   : false  - when set to true, the headers will be stripped of any HTML in the TOC
+            * class         (string) :   ''   - a CSS class assigned to the TOC
+            * id            (string) :   ''   - an ID to assigned to the TOC
+            * h_min         (int)    :   1    - the minimum TOC header level to use; any header lower than this value will be ignored
+            * h_max         (int)    :   6    - the maximum TOC header level to use; any header greater than this value will be ignored
+            * ordered       (bool)   : false  - when set to true, an ordered list will be outputted instead of an unordered list
+            * item_class    (string) :   ''   - add custom class(es) for each list item; has support for '%level%' placeholder, which is the current heading level
+            * submenu_class (string) :   ''   - add custom class(es) for each child group of headings; has support for '%level%' placeholder which is the current "submenu" heading level
+            * base_url      (string) :   ''   - add a base url to the TOC links for when your TOC is on another page than the actual content
+            * anchor_class  (string) :   ''   - add custom class(es) for each anchor element
+            * skip_no_ids   (bool)   : false  - skip headers that do not have an `id` attribute
+
+        Output:
+            An ordered or unordered list representing the table of contents of a markdown block. This snippet will only
+            generate the table of contents and will NOT output the markdown given to it
+    {% endcomment %}
+
+    {% capture newline %}
+    {% endcapture %}
+    {% assign newline = newline | rstrip %} <!-- Remove the extra spacing but preserve the newline -->
+
+    {% capture deprecation_warnings %}{% endcapture %}
+
+    {% if include.baseurl %}
+        {% capture deprecation_warnings %}{{ deprecation_warnings }}<!-- jekyll-toc :: "baseurl" has been deprecated, use "base_url" instead -->{{ newline }}{% endcapture %}
+    {% endif %}
+
+    {% if include.skipNoIDs %}
+        {% capture deprecation_warnings %}{{ deprecation_warnings }}<!-- jekyll-toc :: "skipNoIDs" has been deprecated, use "skip_no_ids" instead -->{{ newline }}{% endcapture %}
+    {% endif %}
+
+    {% capture jekyll_toc %}{% endcapture %}
+    {% assign orderedList = include.ordered | default: false %}
+    {% assign baseURL = include.base_url | default: include.baseurl | default: '' %}
+    {% assign skipNoIDs = include.skip_no_ids | default: include.skipNoIDs | default: false %}
+    {% assign minHeader = include.h_min | default: 1 %}
+    {% assign maxHeader = include.h_max | default: 6 %}
+    {% assign nodes = include.html | strip | split: '<h' %}
+
+    {% assign firstHeader = true %}
+    {% assign currLevel = 0 %}
+    {% assign lastLevel = 0 %}
+
+    {% capture listModifier %}{% if orderedList %}ol{% else %}ul{% endif %}{% endcapture %}
+
+    {% for node in nodes %}
+        {% if node == "" %}
+            {% continue %}
+        {% endif %}
+
+        {% assign currLevel = node | replace: '"', '' | slice: 0, 1 | times: 1 %}
+
+        {% if currLevel < minHeader or currLevel > maxHeader %}
+            {% continue %}
+        {% endif %}
+
+        {% assign _workspace = node | split: '</h' %}
+
+        {% assign _idWorkspace = _workspace[0] | split: 'id="' %}
+        {% assign _idWorkspace = _idWorkspace[1] | split: '"' %}
+        {% assign htmlID = _idWorkspace[0] %}
+
+        {% assign _classWorkspace = _workspace[0] | split: 'class="' %}
+        {% assign _classWorkspace = _classWorkspace[1] | split: '"' %}
+        {% assign htmlClass = _classWorkspace[0] %}
+
+        {% if htmlClass contains "no_toc" %}
+            {% continue %}
+        {% endif %}
+
+        {% if firstHeader %}
+            {% assign minHeader = currLevel %}
+        {% endif %}
+
+        {% capture _hAttrToStrip %}{{ _workspace[0] | split: '>' | first }}>{% endcapture %}
+        {% assign header = _workspace[0] | replace: _hAttrToStrip, '' %}
+
+        {% if include.item_class and include.item_class != blank %}
+            {% capture listItemClass %} class="{{ include.item_class | replace: '%level%', currLevel | split: '.' | join: ' ' }}"{% endcapture %}
+        {% endif %}
+
+        {% if include.submenu_class and include.submenu_class != blank %}
+            {% assign subMenuLevel = currLevel | minus: 1 %}
+            {% capture subMenuClass %} class="{{ include.submenu_class | replace: '%level%', subMenuLevel | split: '.' | join: ' ' }}"{% endcapture %}
+        {% endif %}
+
+        {% capture anchorBody %}{% if include.sanitize %}{{ header | strip_html }}{% else %}{{ header }}{% endif %}{% endcapture %}
+
+        {% if htmlID %}
+            {% capture anchorAttributes %} href="{% if baseURL %}{{ baseURL }}{% endif %}#{{ htmlID }}"{% endcapture %}
+
+            {% if include.anchor_class %}
+                {% capture anchorAttributes %}{{ anchorAttributes }} class="{{ include.anchor_class | split: '.' | join: ' ' }}"{% endcapture %}
+            {% endif %}
+
+            {% capture listItem %}<a{{ anchorAttributes }}>{{ anchorBody }}</a>{% endcapture %}
+        {% elsif skipNoIDs == true %}
+            {% continue %}
+        {% else %}
+            {% capture listItem %}{{ anchorBody }}{% endcapture %}
+        {% endif %}
+
+        {% if currLevel > lastLevel %}
+            {% capture jekyll_toc %}{{ jekyll_toc }}<{{ listModifier }}{{ subMenuClass }}>{% endcapture %}
+        {% elsif currLevel < lastLevel %}
+            {% assign repeatCount = lastLevel | minus: currLevel %}
+
+            {% for i in (1..repeatCount) %}
+                {% capture jekyll_toc %}{{ jekyll_toc }}</li></{{ listModifier }}>{% endcapture %}
+            {% endfor %}
+
+            {% capture jekyll_toc %}{{ jekyll_toc }}</li>{% endcapture %}
+        {% else %}
+            {% capture jekyll_toc %}{{ jekyll_toc }}</li>{% endcapture %}
+        {% endif %}
+
+        {% capture jekyll_toc %}{{ jekyll_toc }}<li{{ listItemClass }}>{{ listItem }}{% endcapture %}
+
+        {% assign lastLevel = currLevel %}
+        {% assign firstHeader = false %}
+    {% endfor %}
+
+    {% assign repeatCount = minHeader | minus: 1 %}
+    {% assign repeatCount = lastLevel | minus: repeatCount %}
+    {% for i in (1..repeatCount) %}
+        {% capture jekyll_toc %}{{ jekyll_toc }}</li></{{ listModifier }}>{% endcapture %}
+    {% endfor %}
+
+    {% if jekyll_toc != '' %}
+        {% assign rootAttributes = '' %}
+        {% if include.class and include.class != blank %}
+            {% capture rootAttributes %} class="{{ include.class | split: '.' | join: ' ' }}"{% endcapture %}
+        {% endif %}
+
+        {% if include.id and include.id != blank %}
+            {% capture rootAttributes %}{{ rootAttributes }} id="{{ include.id }}"{% endcapture %}
+        {% endif %}
+
+        {% if rootAttributes %}
+            {% assign nodes = jekyll_toc | split: '>' %}
+            {% capture jekyll_toc %}<{{ listModifier }}{{ rootAttributes }}>{{ nodes | shift | join: '>' }}>{% endcapture %}
+        {% endif %}
+    {% endif %}
+{% endcapture %}{% assign tocWorkspace = '' %}{{ deprecation_warnings }}{{ jekyll_toc -}}

data/_layouts/archive.html

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+---
+layout: base
+description: Template for a list of posts as cards, with full width.
+---
+
+<div class="row">
+  <div class="col">
+
+    {{ content }}
+  
+  </div>
+</div>
+
+<div class="row cards">
+  {% for item in site.posts %}
+    <div class="col-md-6 col-lg-4">
+      {% include card.html %}
+    </div>
+  {% endfor %}
+</div>
+
+<script>
+  // Filter cards on ?tag=value
+  $(document).ready(function() {
+    const urlParams = new URLSearchParams(window.location.search);
+    
+    if (urlParams.has("tag") && urlParams.get("tag") != "") {
+      const tag = urlParams.get("tag"); // Will return 1st tag value + decode URI
+      const cleanTag = $.trim(tag.toLowerCase()); // Create tag as written in .card data-tags
+      
+      $(".card").each(function() {
+        const cardTags = $(this).data("tags").split("|");
+        // Hide card if it does not contain the selected tag
+        if (!cardTags.includes(cleanTag)) {
+          $(this).parent().addClass("d-none");
+        }
+      });
+
+      $(".header .tags").append(
+        '<a class="badge{% if site.rounded_corners != false %} rounded-pill{% endif %}" href="{{ site.archive_permalink | relative_url }}">' + 
+        tag + '<span class="btn-close btn-close-white"></span>' + 
+        '</a>'
+      );
+    }
+  });
+</script>

data/_layouts/base.html

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+<!DOCTYPE html>
+<html>
+
+  {% include head.html %}
+
+  <body>
+    {% include navbar.html %}
+
+    <main>
+      {% include header.html %}
+
+      <div class="container content">
+          
+        {{ content
+          | replace: '<table', '<div class="table-responsive"><table'
+          | replace: '</table>', '</table></div>'
+          | replace: '<table>', '<table class="table">'
+        }}
+
+      </div>
+    </main>
+
+    {% include footer.html %}
+
+  </body>
+</html>

data/_layouts/default.html

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+---
+layout: base
+description: Default template for pages and posts, with contained width.
+---
+
+<div class="row">
+  {% if page.toc %}
+  <div class="col-md-10 col-lg-3 mx-auto">
+    <div class="toc">
+      <h6>On this page</h6>
+      {% include toc.html
+        html=content
+        sanitize=true
+        h_min=2
+        h_max=3
+      %}
+    </div>
+  </div>
+  {% endif %}
+  <div class="col-md-10 col-lg-8 order-lg-first mx-auto">
+
+    {{ content }}
+
+    {% if page.comments %}
+      <div id="disqus_thread"></div>
+      <script>
+        // Configuration variables: https://disqus.com/admin/universalcode/#configuration-variables
+        var disqus_config = function () {
+          this.page.url = "{{ page.url | absolute_url }}";
+        };
+        (function() { // Don't edit below this line
+          var d = document, s = d.createElement("script");
+          s.src = "https://{{ site.social.disqus }}.disqus.com/embed.js";
+          s.setAttribute("data-timestamp", +new Date());
+          (d.head || d.body).appendChild(s);
+        })();
+      </script>
+      <noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript" rel="nofollow">comments powered by Disqus.</a></noscript>
+    {% endif %}
+  </div>
+</div>

data/_layouts/home.html

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+---
+layout: base
+description: Template for homepage.
+remark: See also page.layout == 'home' in head.html and header.html.
+---
+
+{% if site.tweets_on_home and site.social.twitter %}
+  {% assign two_col = true %}
+{% endif %}
+
+<div class="row">
+  <div class="{% if two_col %}col{% else %}col-md-10 col-lg-8 mx-auto{% endif %}">
+    <div class="row">
+      <div class="col">
+
+        {{ content }}
+
+      </div>
+
+      {% if two_col %}
+        <div class="col-lg-4">
+          <a class="twitter-timeline" data-height="500" data-link-color="{{ site.colors.links }}" href="https://twitter.com/{{ site.social.twitter }}?ref_src=twsrc%5Etfw">
+            Tweets by {{ site.social.twitter }}
+          </a>
+          <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
+        </div>
+      {% endif %}
+    </div>
+    
+    {% if site.posts_on_home > 0 %}
+      <div class="row cards mt-4">
+        {% for item in site.posts limit:site.posts_on_home %}
+          <div class="col-md-6{% if two_col %} col-lg-4{% endif %}">
+            {% include card.html %}
+          </div>
+        {% endfor %}
+      </div>
+    {% endif %}
+</div>

data/_layouts/team.html

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+---
+layout: default
+description: Template for team page.
+---
+
+{% if page.team and site.data[page.team] %}
+  {% assign team = site.data[page.team] %}
+{% elsif site.data.team %}
+  {% assign team = site.data.team %}
+{% endif %}
+
+{{ content }}
+
+{% for member in team %}
+  <div class="d-flex team-member">
+    <div class="flex-shrink-0 me-3">
+      {% if member.image %}
+        <img src="{{ member.image | relative_url }}" alt="{{ member.name }}">
+      {% endif %}
+    </div>
+    <div>
+      <h5 id="{{ member.name | strip | url_encode }}">
+        {{ member.name }}
+        {% if member.role %}
+          <small class="text-muted">| {{ member.role }}</small>
+        {% endif %}
+      </h5>
+
+      {{ member.description | markdownify }}
+
+      <ul class="list-inline">
+        {% if member.orcid %}
+          <li class="list-inline-item">
+            <a href="https://orcid.org/{{ member.orcid }}"><i class="ai ai-orcid"></i></a>
+          </li>
+        {% endif %}
+
+        {% if member.researchgate %}
+          <li class="list-inline-item">
+            <a href="https://researchgate.net/profile/{{ member.researchgate }}"><i class="ai ai-researchgate"></i></a>
+          </li>
+        {% endif %}
+        
+        {% if member.googlescholar %}
+          <li class="list-inline-item">
+            <a href="https://scholar.google.com/citations?user={{ member.googlescholar }}"><i class="ai ai-google-scholar"></i></a>
+          </li>
+        {% endif %}
+
+        {% if member.twitter %}
+          <li class="list-inline-item">
+            <a href="https://twitter.com/{{ member.twitter }}"><i class="fab fa-twitter"></i></a>
+          </li>
+        {% endif %}
+
+        {% if member.mastodon %}
+          <li class="list-inline-item">
+            <a href="{{ member.mastodon }}"><i class="fab fa-mastodon"></i></a>
+          </li>
+        {% endif %}
+
+        {% if member.github %}
+          <li class="list-inline-item">
+            <a href="https://github.com/{{ member.github }}"><i class="fab fa-github"></i></a>
+          </li>
+        {% endif %}
+
+        {% if member.email %}
+          <li class="list-inline-item">
+            <a href="mailto:{{ member.email }}"><i class="far fa-envelope"></i></a>
+          </li>
+        {% endif %}
+      </ul>
+    </div>
+  </div>
+{% endfor %}

data/_sass/_base.scss

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+// General styling
+// 
+// For content styling, see _content.scss
+
+body {
+  word-wrap: break-word; // Allow long words (e.g. URLs) to wrap, so they don't break out of container
+  position: relative; // Required for scrollspy
+}
+
+.btn {
+  white-space: normal; // Wrap button within container
+}
+
+// Add padding to code blocks
+pre.highlight {
+  padding: 0.25rem;
+  margin-bottom: $grid-gutter-width / 2;
+}

data/_sass/_card.scss

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+// Blog post card
+
+.cards {
+  // Mimics Bootstrap v4 .card-deck, stretching cards to equal height, but without
+  // stretching width when there are fewer cards on one row (cards remain equal width)
+  div[class*="col"] {
+    display: flex;
+    align-items: stretch;
+  }
+}
+
+.card {
+  margin-bottom: $grid-gutter-width;
+  min-width: 100%; // Use allowed width even if content is smaller
+
+  .card-title {
+    a {
+      text-decoration: none;
+    }
+  }
+
+  .card-img-top {
+    height: 150px;
+    object-fit: cover;
+  }
+
+  .card-subtitle {
+    color: $gray-600;
+    margin-bottom: 0.5rem;
+  }
+
+  .card-footer {
+    background: inherit;
+    border-top: none;
+
+    // Smaller badge then the one defined in _header.scss
+    .badge {
+      border: 1px solid $link-color;
+      color: $link-color;
+      font-family: $font-family-base;
+      text-decoration: none;
+      text-transform: uppercase;
+
+      &:hover,
+      &:focus {
+        border: 1px solid $link-hover-color;
+        color: $link-hover-color;
+      }
+    }
+  }
+}

data/_sass/_content.scss

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+// Content
+
+.content {
+  font-family: $custom_font, $font-family-sans-serif;
+  
+  // Use base font for headings
+  h1,
+  h2,
+  h3,
+  h4,
+  h5,
+  h6 {
+    font-family: $font-family-base;
+  }
+
+  // Hide h1 headings in content, its use is reserved for header
+  // If the markdown file has no frontmatter (e.g. README.md), Jekyll will use the first heading
+  // as page title, which would then appear in header and content. This avoids that.
+  h1 {
+    display: none;
+  }
+
+  // Add some space before h2, which are the main headings in content
+  h2 {
+    margin-top: 2rem;
+
+    // Don't add space if h2 is first element in content
+    &:first-child {
+      margin-top: 0;
+    }
+  }
+
+  .anchorjs-link:hover {
+    text-decoration: none;
+  }
+
+  // Add extra padding between checkbox and item
+  .task-list-item-checkbox {
+    margin-right: 0.5rem;
+  }
+
+  // Style blockquotes
+  blockquote {
+    border-left: 0.25rem solid $gray-200;
+    color: $gray-600;
+    padding: 0 1rem;
+  }
+
+  // Add aliases for float-left / float-right
+  .float-left {
+    @extend .float-start;
+  }
+  .float-right {
+    @extend .float-end;
+  }
+
+  // Style images (excluding inline images not wrapped in p)
+  p {
+    img {
+      display: block;
+      height: auto;
+      margin-left: auto; // Mimick .mx-auto
+      margin-right: auto; // Mimick .mx-auto
+      max-width: 100%; // Mimick .img-fluid
+
+      // Add margin between floated img and text
+      &.float-start {
+        margin-right: 0.5rem;
+        margin-bottom: 0.5rem;
+      }
+      &.float-end {
+        margin-left: 0.5rem;
+        margin-bottom: 0.5rem;
+      }
+    }
+
+    // Style captions
+    img + em {
+      display: block;
+      margin-top: 0.5rem;
+      margin-bottom: 0.5rem;
+      text-align: center;
+    }
+
+    // Add margin between floated paragraphs (often containing img) and text
+    &.float-left {
+      margin-right: 0.5rem;
+      margin-bottom: 0.5rem;
+    }
+    &.float-right {
+      margin-left: 0.5rem;
+      margin-bottom: 0.5rem;
+    }
+  }
+
+  // Style embedded content (video, Twitter feed)
+  iframe {
+    margin-bottom: $headings-margin-bottom;
+  }
+
+  // Force Twitter timeline to remain in container
+  .twitter-timeline {
+    width: 100vw !important;
+  }
+
+  // Style tables
+  // This is done by replacing '<table' with '<table class="table"' in {{ content }}
+}

data/_sass/_custom.scss

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+// Custom styling
+// 
+// Include the file _sass/_custom.scss to your site to add custom styling

data/_sass/_footer.scss

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+// Footer
+
+body > footer {
+  background-color: $footer;
+  border-top: 5px solid lighten($footer, 50);
+  color: lighten($footer, 50);
+  font-size: 0.9rem;
+  padding: $grid-gutter-width / 2 0;
+
+  .container {
+    margin-top: 1rem;
+  }
+
+  a,
+  a:hover,
+  a:visited {
+    color: $white;
+  }
+
+  // Font Awesome icons
+  .fa-inverse {
+    color: $footer;
+  }
+  .fa-ul {
+    margin-left: 1.5rem;
+  }
+
+  // License notice
+  .small.mt-2 {
+    p {
+      display: inline;
+
+      & + p:before {
+        content: " — ";
+      }
+    }
+  } 
+}