jekyll-theme-petridish 3.0

checksums.yaml

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+---
+SHA256:
+  metadata.gz: 267d6da8663223b23d3b86d562a47d4b3f92c20a3601ec1114a02c06d2b29939
+  data.tar.gz: f1ae8acb9a10cf6c1baac0b7138ae8d3e246d8388c2740e43fbd001c4b8dff50
+SHA512:
+  metadata.gz: 1c131505d5dd161858910c7e18b7cdee1bf23294226a1c3f3a19db4598739223d948adace2145124a21c648acd87ec12811a85ced6a974cfb444358c7eec0536
+  data.tar.gz: c87726cdc714bd6045f15d97d1e315f4d69c176e5f6cfb7c97648e7da7f0179aee8e38d5bcadecedc52d9085989736fdc44ecc2d66f093f0de375b34a77012b2

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2019 Peter Desmet
+
+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.

data/README.md

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+# petridish 🧫
+
+Petridish is a Jekyll theme for research project websites. Or your personal blog or lab website. 👩‍🔬 It's mobile-friendly (thanks to [Bootstrap 5](https://getbootstrap.com/docs/5.1/)), free, easy to customize, and designed to work well with [GitHub Pages](https://pages.github.com/).
+
+## Installation
+
+See the demo website for instructions:
+
+- [Installation](https://peterdesmet.github.io/petridish/docs/installation)
+- [Configuration](https://peterdesmet.github.io/petridish/docs/configuration)
+- [Markdown](https://peterdesmet.github.io/petridish/docs/markdown)
+
+## Preview
+
+[Demo website](https://peterdesmet.github.io/petridish)
+
+[![screenshot](screenshot.png)](https://peterdesmet.github.io/petridish)
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/peterdesmet/petridish. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## License
+
+[MIT License](LICENSE)
+
+---
+
+<!-- All the above is about the Petridish theme, so you might want to remove that. -->
+
+_The instructions below can be adapted/included in the README of your site repository._
+
+## Usage
+
+This website makes use of the static website generator [Jekyll](https://jekyllrb.com/) and the [Petridish](https://github.com/peterdesmet/petridish) theme. **Each commit to `main` will automatically trigger a new build on GitHub Pages.** There is no need to build the site locally, but you can by installing Jekyll and running `bundle exec jekyll serve`.
+
+Minor changes can be committed directly to `main`.
+
+Changes requiring review (e.g. new blog posts) should be created in a separate branch and submitted as a pull request. Some guidelines:
+
+- Use `72dpi` as image resolution
+- Place background images in `assets/backgrounds/`, name them after their corresponding page/post and ideally crop them to `2100 x 700px`
+- Place content images in `assets/images/`, name them after their corresponding page/post + a suffix, e.g. `-figure-1`
+- Add tags to posts to create relevant groups (e.g. same topic, project).
+- Create internal links as `[previous post]({{ '/permalink/to/post/' | relative_url }})`
+
+## Repo structure
+
+The repository structure follows that of Jekyll websites.
+
+- General site settings: [_config.yml](_config.yml)
+- Pages: [pages/](pages/)
+- Posts: [_posts/](_posts/)
+- Images & static files: [assets/](assets/)
+- Top navigation: [_data/navigation.yml](_data/navigation.yml)
+- Footer content: [_data/footer.yml](_data/footer.yml)
+- Team members: [_data/team.yml](_data/team.yml)

data/_config.yml

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+# SITE SETTINGS
+title: Petridish                        # Title in top navigation bar (navbar) and <head>
+author: Peter Desmet                    # Used for copyright statement in footer
+baseurl: "/petridish"                   # Only required if your site is in a directory e.g. https://username.github.io/sitename
+                                        # which has url: "https://username.github.io" (no slash) and baseurl: "/sitename" (leading slash)
+                                        # A baseurl affects internal links, see http://peterdesmet.github.io/petridish/markdown/#links
+
+# SOCIAL PROFILES
+social:
+  email: name@example.com
+  twitter: peterdesmet
+  github: github_username               # Can also be a github_username/repository
+  mastodon: https://mastodon.social/@mastodon_username
+  facebook:                             # A URL
+  disqus: disqus_sitename               # Enable Disqus comments from disqus_sitename.disqus.com
+
+# THEME SETTINGS (ALL OPTIONAL)
+posts_on_home: 3                        # Show x number of latest posts on homepage, can be 0
+tweets_on_home: true                    # Show Twitter feed of social.twitter on homepage
+archive_permalink: /blog/               # Permalink of page using the archive.html layout, required when using post tags
+github_edit: true                       # Show an "edit this page" link in the footer, can also be name of branch (default: main)
+colors:
+  links: "#007bff"                      # Color for links: use a readable color that contrasts well with dark text
+  banner: "#007bff"                     # Background color for page banners: use color that contrasts well with white
+  footer: "#6c757d"                     # Background color for footer: use color that contrasts well with white
+font_serif: true                        # Font type for page content: serif (default) or slightly smaller sans-serif
+rounded_corners: true                   # Enable (default) rounded corners on boxes and buttons
+logo: /assets/theme/images/petri-dish_1f9eb.png # Logo in navbar, will be displayed with 30px height
+
+# BUILD SETTINGS
+markdown: kramdown
+plugins:                                # If you build your site on gh-pages, only use these plugins: https://pages.github.com/versions/
+  - jekyll-feed
+  - jekyll-sitemap
+exclude:
+  - README.md
+  - Gemfile
+  - Gemfile.lock
+  - node_modules
+  - LICENSE
+  - package-lock.json
+  - package.json
+  - petridish.gemspec
+
+# FRONTMATTER DEFAULTS
+defaults:
+  - scope:
+      path: ""
+    values:
+      layout: default                   # Use default.html layout by default for all files
+  - scope:
+      type: posts
+    values:
+      permalink: "/blog/:year/:slug/"   # Use /blog/yyyy/{filename}/ as permalink for all posts

data/_data/custom-navigation.yml

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+# Links listed below will be included in your site's navbar (navigation at the top)
+
+- text: "Courses 2022" # Note that users can reach the homepage by clicking the site's title on the left in the navbar
+  href: /docs/custom-navigation/
+- text: Courses
+  menu:
+  - text: Course 1
+    href: true
+  - text: Course 2
+    href: true
+- text: Exercises
+  href: true
+

data/_data/footer.yml

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+# Footer content is organized in columns, with the first one reserved for social icons (defined in _config.yml).
+# You can also add a small print license statement at the bottom.
+
+# Columns (the more you add, the narrower they will be)
+columns:
+  - description:
+    links:
+    - text: Name of project partner 1
+      href: http://example.com
+      new_window: true
+    - text: Prestigious and long name of project partner 2
+      href: http://example.com
+      new_window: true
+
+  - description: > # E.g. funding acknowledgement. Can be Markdown
+      This project is made with ❤ for open source.
+      See [`_data/footer.yml`](https://raw.githubusercontent.com/peterdesmet/petridish/master/_data/footer.yml)
+      to customize this text.
+    links:
+
+# Small print license statement to add at the bottom of the footer. Can be Markdown
+# Will be prefixed by "© {{ site.author }}" if defined in _config.yml
+license: >
+  Content on this site is licensed under a [CC BY 4.0 License](http://creativecommons.org/licenses/by/4.0/).
+  \| Theme: [Petridish](https://github.com/peterdesmet/petridish)

data/_data/navigation.yml

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+# Links listed below will be included in your site's navbar (navigation at the top)
+
+- text: Home # Note that users can also reach the homepage by clicking the site's title on the left in the navbar
+  href: /
+- text: About
+  href: /about/
+- text: Team
+  href: /team/
+- text: Blog
+  href: /blog/
+- text: Documentation
+  menu: # Dropdown menu (one level deep only)
+  - text: Installation
+    href: /docs/installation/
+  - text: Configuration
+    href: /docs/configuration/
+  - href: /docs/markdown/ # Undefined "text" will automatically get the title of the page at "href" (here "Markdown")
+  - text: "---" # Divider to separate blocks of menu items (at least 3 "-")
+  - text: "Dropdown header" # Title for block of menu items
+  - text: Page with custom navigation
+    href: /docs/custom-navigation/
+- text: GitHub
+  href: https://github.com/peterdesmet/petridish/
+  new_window: true

data/_data/team.yml

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+# Project team members listed below will appear on the /team page
+
+- name: Philip J. Fry
+  role: Delivery boy # Will appear next to name
+  image: assets/theme/images/fry_ethan-hoover-311143-unsplash.jpg # Can be external link
+  description: > # Can be Markdown
+    Protagonist, from the 20th century. Many times great-uncle to Professor Hubert Farnsworth.
+  orcid: 0000-0000-0000-0000
+  researchgate: researchgate_username
+  googlescholar: googlescholar_username
+  twitter: twitter_username
+  mastodon: https://mastodon.social/@mastodon_username
+  github: github_username
+  email: name@example.com
+
+- name: Turanga Leela
+  role: Captain
+  description: >
+    Mutant cyclops. Leela is spaceship captain, pilot, and head of all 
+    aviation services on board the [Planet Express Ship](https://en.wikipedia.org/wiki/Planet_Express_Ship). 
+
+- name: Professor Hubert J. Farnsworth
+  role: CEO & Owner
+  image: assets/theme/images/farnsworth_angelo-abear-1662775-unsplash.jpg
+  description: >
+    Many times great-nephew of Fry. Tenured professor of [Mars University](https://en.wikipedia.org/wiki/Mars_University).

data/_includes/card.html

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+{% if item.background.first %}
+  {% assign background = item.background.img %}
+{% else %}
+  {% assign background = item.background %}
+{% endif %}
+
+<div class="card" data-tags="{% for tag in item.tags %}{{ tag | downcase | strip }}|{% endfor %}">
+  <a href="{{ item.url | relative_url }}">
+    {% if item.background %}
+      <img class="card-img-top" src="{{ background | relative_url }}" alt="Background image">  
+    {% else %}
+      <div class="card-img-top bg-secondary"></div>
+    {% endif %}
+  </a>
+
+  <div class="card-body position-relative">
+    <h5 class="card-title">
+      <a class="stretched-link" href="{{ item.url | relative_url }}">{{ item.title }}</a>
+    </h5>
+
+    {% if item.collection == 'posts' %}
+      <h6 class="card-subtitle">{{ item.date | date: '%B %d, %Y' }}</h6>
+    {% endif %}
+
+    <div class="card-text">
+      {% if item.description %}
+        {{ item.description | markdownify | strip_html | truncatewords: 20 }}
+      {% else %}
+        {{ item.excerpt | strip_html | truncatewords: 20 }}
+      {% endif %}
+    </div>
+  </div>
+
+  {% if item.collection == 'posts' and item.tags and site.archive_permalink %}
+    <div class="card-footer">
+      {% for tag in item.tags %}
+        <a class="badge{% if site.rounded_corners != false %} rounded-pill{% endif %}" href="{{ site.archive_permalink | relative_url }}?tag={{ tag | url_encode }}">{{ tag }}</a>
+      {% endfor %}
+    </div>
+  {% endif %}
+</div>

data/_includes/footer.html

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+<footer>
+  <div class="container">
+    <div class="row">
+      {% if site.social %}
+        <div class="col-lg">
+          <ul class="list-inline">
+            {% if site.social.email %}
+              <li class="list-inline-item">
+                <a href="mailto:{{ site.social.email }}">
+                  <span class="fa-stack fa-lg">
+                    <i class="fas fa-circle fa-stack-2x"></i>
+                    <i class="far fa-envelope fa-stack-1x fa-inverse"></i>
+                  </span>
+                </a>
+              </li>
+            {% endif %}
+
+            {% if site.social.twitter %}
+              <li class="list-inline-item">
+                <a href="https://twitter.com/{{ site.social.twitter }}">
+                  <span class="fa-stack fa-lg">
+                    <i class="fas fa-circle fa-stack-2x"></i>
+                    <i class="fab fa-twitter fa-stack-1x fa-inverse"></i>
+                  </span>
+                </a>
+              </li>
+            {% endif %}
+
+            {% if site.social.mastodon %}
+              <li class="list-inline-item">
+                <a rel="me" href="{{ site.social.mastodon }}">
+                  <span class="fa-stack fa-lg">
+                    <i class="fas fa-circle fa-stack-2x"></i>
+                    <i class="fab fa-mastodon fa-stack-1x fa-inverse"></i>
+                  </span>
+                </a>
+              </li>
+            {% endif %}
+
+            {% if site.social.facebook %}
+              <li class="list-inline-item">
+                <a red="me" href="{{ site.social.facebook }}">
+                  <span class="fa-stack fa-lg">
+                    <i class="fas fa-circle fa-stack-2x"></i>
+                    <i class="fab fa-facebook fa-stack-1x fa-inverse"></i>
+                  </span>
+                </a>
+              </li>
+            {% endif %}
+
+            {% if site.social.github %}
+              <li class="list-inline-item">
+                <a href="https://github.com/{{ site.social.github }}">
+                  <span class="fa-stack fa-lg">
+                    <i class="fas fa-circle fa-stack-2x"></i>
+                    <i class="fab fa-github fa-stack-1x fa-inverse"></i>
+                  </span>
+                </a>
+              </li>
+            {% endif %}
+
+            {% if site.archive_permalink %}
+              <li class="list-inline-item">
+                <a href="{{ '/feed.xml' | absolute_url }}">
+                  <span class="fa-stack fa-lg">
+                    <i class="fas fa-circle fa-stack-2x"></i>
+                    <i class="fas fa-rss fa-stack-1x fa-inverse"></i>
+                  </span>
+                </a>
+              </li>
+            {% endif %}
+          </ul>
+        </div>
+      {% endif %}
+
+      {% for col in site.data.footer.columns %}
+        <div class="col-lg">
+          {{ col.description | markdownify }}
+
+          {% if col.links %}
+            <ul class="fa-ul">
+              {% for item in col.links %}
+                <li>
+                  <i class="fa-li fa fa-chevron-circle-right"></i>
+                  <a href="{{ item.href | relative_url }}"{% if item.new_window %} target="_blank"{% endif %}>{{ item.text }}</a>
+                </li>
+              {% endfor %}
+            </ul>
+          {% endif %}
+        </div>
+      {% endfor %}
+    </div>
+
+    <div class="small mt-2">
+      {% if site.author %}
+        <p>© {{ site.author }}</p>
+      {% endif %}
+      {% if site.data.footer.license %}
+        {{ site.data.footer.license | markdownify }}
+      {% endif %}
+      {% if site.github_edit %}
+        {% if site.github_edit contains '' %}
+          {% assign branch = site.github_edit %}
+        {% else %}
+          {% assign branch = 'main' %}
+        {% endif %}
+        <p>
+          <a href="{{ site.github.repository_url }}/edit/{{ branch }}/{{ page.path }}">
+            <i class="fas fa-edit"></i> Edit this page
+          </a>
+        </p>
+      {% endif %}
+    </div>
+  </div>
+</footer>
+
+<script src="{{ '/assets/theme/js/anchor.min.js' | relative_url }}"></script>
+<script>
+  // Show anchors when hovering over headings, using anchor.js
+  (function () {
+    const headings = ".content h2[id], .content h3[id], .content h4[id], .content h5[id], .content h6[id]";
+    anchors.options = { placement: "right" };
+    anchors.add(headings);
+  })();
+</script>

data/_includes/head.html

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+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+
+  {% if page.layout == 'home' %}
+    <title>{{ site.title }}</title>
+  {% else %}
+    <title>{{ page.title }} - {{ site.title }}</title>
+  {% endif %}
+
+  {% comment %}Deprecated variables{% endcomment %} 
+  {% if site.email %}
+    {% assign site.social.email = site.email %}
+  {% endif %}
+  {% if site.twitter_username %}
+    {% assign site.social.twitter = site.twitter_username %}
+  {% endif %}
+  {% if site.github_username %}
+    {% assign site.social.github = site.github_username %}
+  {% endif %}
+
+  {% if page.description %}
+    {% assign description = page.description | markdownify | strip_html | newline_to_br | split: '<br />' | first %}
+  {% endif %}
+  {% if description %}
+    <meta name="description" content="{{ description }}">
+  {% endif %}
+  {% if page.author %}
+    {% assign author = page.author | join: ", " %}
+  {% else %}
+    {% assign author = site.author %}
+  {% endif %}
+  {% if author %}
+    <meta name="author" content="{{ author }}">
+  {% endif %}
+  {% if site.remote_theme %}
+    <meta name="generator" content="Jekyll, theme: {{ site.remote_theme }}">
+  {% endif %}
+
+  <meta property="og:url" content="{{ page.url | absolute_url }}">
+  <meta property="og:type" content="{% if page.collection == 'posts' %}article{% else %}website{% endif %}">
+  <meta property="og:title" content="{{ page.title }}">
+  {% if description %}
+    <meta property="og:description" content="{{ description }}">
+  {% endif %}
+  {% if page.background.first %}
+    {% assign background = page.background.img %}
+  {% else %}
+    {% assign background = page.background %}
+  {% endif %}
+  {% if background %}
+    <meta property="og:image" content="{{ background | absolute_url }}">
+  {% endif %}
+
+  <link rel="icon" type="image/x-icon" href="{{ '/favicon.ico' | absolute_url }}">
+  <!-- Bootstrap CSS is included in main.css -->
+  <link rel="stylesheet" href="{{ '/assets/theme/css/main.css' | relative_url }}">
+  <link rel="stylesheet" href="{{ '/assets/theme/css/fontawesome-all.min.css' | relative_url }}">
+  <link rel="stylesheet" href="{{ '/assets/theme/css/academicons.min.css' | relative_url }}">
+  <link rel="stylesheet" href="{{ '/assets/theme/css/pygments.css' | relative_url }}">
+  {% if site.font_serif != false %}
+    <link href="https://fonts.googleapis.com/css?family=Lora:400,400i,700,700i&display=swap" rel="stylesheet">
+  {% endif %}
+  <link rel="alternate" type="application/rss+xml" title="{{ site.title }} - RSS feed" href="{{ '/feed.xml' | absolute_url }}" >
+  <!-- Javascript libraries: loaded at top so templates can use these -->
+  <script src="{{ '/assets/theme/js/jquery.min.js' | relative_url }}"></script>
+  <script src="{{ '/assets/theme/js/popper.min.js' | relative_url }}"></script>
+  <script src="{{ '/assets/theme/js/bootstrap.min.js' | relative_url }}"></script>
+</head>

data/_includes/header.html

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+{% comment %}background is defined in head.html{% endcomment %}
+{% if background %}
+  <header class="header bg-image" style="background-image: url('{{ background | relative_url }}')">
+{% else %}
+  <header class="header bg-no-image">
+{% endif %}
+    <div class="container">
+      <div class="row">
+        <div class="col-md-10 col-lg-8 position-relative mx-auto">
+          <h1{% if page.layout == 'home' %} class="home"{% endif %}>{{ page.title }}</h1>
+          
+          <div class="lead">{{ page.description | markdownify }}</div>
+          
+          {% if page.collection == 'posts' %}
+            <p class="meta">
+              <time>{{ page.date | date: '%B %d, %Y' }}</time>
+              {% if page.author or page.authors %}
+                &bull; {{ page.author | join: ', ' }}{{ page.authors | join: ', ' }}
+              {% endif %}
+            </p>
+          {% endif %}
+
+          <div class="tags">
+            {% if page.collection == 'posts' and page.tags and site.archive_permalink %}
+              {% for tag in page.tags %}
+              <a class="badge{% if site.rounded_corners != false %} rounded-pill{% endif %}" href="{{ site.archive_permalink | relative_url }}?tag={{ tag | url_encode }}">{{ tag }}</a>
+              {% endfor %}
+            {% endif %}
+          </div>
+        </div>
+      </div>
+    </div>
+    {% if page.background.img and page.background.by %}
+      <div class="caption">
+        {% if page.background.href %}
+          Image by <a href="{{ page.background.href }}">{{ page.background.by }}</a>
+        {% else %}
+          Image by {{ page.background.by }}
+        {% endif %}
+      </div>
+    {% endif %}
+  </header>

data/_includes/navbar.html

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+<nav class="navbar navbar-expand-lg navbar-light bg-light" id="main-nav">
+  <div class="container">
+    <a class="navbar-brand d-flex align-items-center" href="{{'/' | relative_url }}">
+      {% if site.logo %}
+        <img class="me-3" src="{{ site.logo | relative_url }}" alt="{{ site.title }}">
+      {% endif %}
+      {{ site.title }}
+    </a>
+    {% if page.navigation and site.data[page.navigation] %}
+      {% assign navigation = site.data[page.navigation] %}
+    {% elsif site.data.navigation %}
+      {% assign navigation = site.data.navigation %}
+    {% endif %}
+    {% if navigation %}
+      <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar-menu">
+        Menu <i class="fas fa-bars"></i>
+      </button>
+      <div class="collapse navbar-collapse" id="navbar-menu">
+        <ul class="navbar-nav ms-auto">
+          {% for item in navigation %}
+            {% if item.menu %}
+              <li class="nav-item dropdown">
+                <a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">
+                  {{ item.text }}
+                </a>
+                <div class="dropdown-menu dropdown-menu-end">
+                  {% for subitem in item.menu %}
+                    {% if subitem.href %}
+                      {% if subitem.text contains '' %}
+                        {% assign subitem_text = subitem.text %}
+                      {% else %}
+                        {% assign subitem_text = site.pages | where: 'url', subitem.href | map: 'title' | first %}
+                      {% endif %}
+                      <a class="dropdown-item{% if subitem.href == page.url %} active{% endif %}" href="{{ subitem.href | relative_url }}"{% if subitem.new_window %} target="_blank"{% endif %}>{{ subitem_text }}</a>
+                    {% elsif subitem.text contains '---' %}
+                      <div class="dropdown-divider"></div>
+                    {% else %}
+                      <h6 class="dropdown-header">{{ subitem.text }}</h6>
+                    {% endif %}
+                  {% endfor %}
+                </div>
+              </li>
+            {% else %}
+              <li class="navbar-item">
+                {% if item.text contains '' %}
+                  {% assign item_text = item.text %}
+                {% else %}
+                  {% assign item_text = site.pages | where: 'url', item.href | map: 'title' | first %}
+                {% endif %}
+                <a class="nav-link{% if item.href == page.url %} active{% endif %}" href="{{ item.href | relative_url }}"{% if item.new_window %} target="_blank"{% endif %}>{{ item_text }}</a>
+              </li>
+            {% endif %}
+          {% endfor %}
+        </ul>
+      </div>
+    {% endif %}
+  </div>
+</nav>