Homepage setup for schleppe lab blog

_includes/anchor_headings.html

@@ -0,0 +1,174 @@
+{% capture headingsWorkspace %}
+  {% comment %}
+    Copyright (c) 2018 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 1.0.13
+      https://github.com/allejo/jekyll-anchor-headings
+
+    "Be the pull request you wish to see in the world." ~Ben Balter
+
+    Usage:
+      {% include anchor_headings.html html=content anchorBody="#" %}
+
+    Parameters:
+      * html          (string) - the HTML of compiled markdown generated by kramdown in Jekyll
+
+    Optional Parameters:
+      * beforeHeading (bool)   : false  - Set to true if the anchor should be placed _before_ the heading's content
+      * headerAttrs   (string) :  ''    - Any custom HTML attributes that will be added to the heading tag; you may NOT use `id`;
+                                          the `%heading%` and `%html_id%` placeholders are available
+      * anchorAttrs   (string) :  ''    - Any custom HTML attributes that will be added to the `<a>` tag; you may NOT use `href`, `class` or `title`;
+                                          the `%heading%` and `%html_id%` placeholders are available
+      * anchorBody    (string) :  ''    - The content that will be placed inside the anchor; the `%heading%` placeholder is available
+      * anchorClass   (string) :  ''    - The class(es) that will be used for each anchor. Separate multiple classes with a space
+      * anchorTitle   (string) :  ''    - The `title` attribute that will be used for anchors
+      * h_min         (int)    :  1     - The minimum header level to build an anchor for; any header lower than this value will be ignored
+      * h_max         (int)    :  6     - The maximum header level to build an anchor for; any header greater than this value will be ignored
+      * bodyPrefix    (string) :  ''    - Anything that should be inserted inside of the heading tag _before_ its anchor and content
+      * bodySuffix    (string) :  ''    - Anything that should be inserted inside of the heading tag _after_ its anchor and content
+      * generateId    (true)   :  false - Set to true if a header without id should generate an id to use.
+
+    Output:
+      The original HTML with the addition of anchors inside of all of the h1-h6 headings.
+  {% endcomment %}
+
+  {% assign minHeader = include.h_min | default: 1 %}
+  {% assign maxHeader = include.h_max | default: 6 %}
+  {% assign beforeHeading = include.beforeHeading %}
+  {% assign headerAttrs = include.headerAttrs %}
+  {% assign nodes = include.html | split: '<h' %}
+
+  {% capture edited_headings %}{% endcapture %}
+
+  {% for _node in nodes %}
+    {% capture node %}{{ _node | strip }}{% endcapture %}
+
+    {% if node == "" %}
+      {% continue %}
+    {% endif %}
+
+    {% assign nextChar = node | replace: '"', '' | strip | slice: 0, 1 %}
+    {% assign headerLevel = nextChar | times: 1 %}
+
+    <!-- If the level is cast to 0, it means it's not a h1-h6 tag, so let's see if we need to fix it -->
+    {% if headerLevel == 0 %}
+      <!-- Split up the node based on closing angle brackets and get the first one. -->
+      {% assign firstChunk = node | split: '>' | first %}
+
+      <!-- If the first chunk does NOT contain a '<', that means we've broken another HTML tag that starts with 'h' -->
+      {% unless firstChunk contains '<' %}
+        {% capture node %}<h{{ node }}{% endcapture %}
+      {% endunless %}
+
+      {% capture edited_headings %}{{ edited_headings }}{{ node }}{% endcapture %}
+      {% continue %}
+    {% endif %}
+
+    {% capture _closingTag %}</h{{ headerLevel }}>{% endcapture %}
+    {% assign _workspace = node | split: _closingTag %}
+    {% capture _hAttrToStrip %}{{ _workspace[0] | split: '>' | first }}>{% endcapture %}
+    {% assign header = _workspace[0] | replace: _hAttrToStrip, '' %}
+    {% assign escaped_header = header | strip_html | strip %}
+
+    {% assign _classWorkspace = _workspace[0] | split: 'class="' %}
+    {% assign _classWorkspace = _classWorkspace[1] | split: '"' %}
+    {% assign _html_class = _classWorkspace[0] %}
+
+    {% if _html_class contains "no_anchor" %}
+      {% assign skip_anchor = true %}
+    {% else %}
+      {% assign skip_anchor = false %}
+    {% endif %}
+
+    {% assign _idWorkspace = _workspace[0] | split: 'id="' %}
+    {% if _idWorkspace[1] %}
+      {% assign _idWorkspace = _idWorkspace[1] | split: '"' %}
+      {% assign html_id = _idWorkspace[0] %}
+      {% assign h_attrs = headerAttrs %}
+    {% elsif include.generateId %}
+      <!-- If the header did not have an id we create one. -->
+      {% assign html_id = escaped_header | slugify %}
+      {% if html_id == "" %}
+        {% assign html_id = false %}
+      {% endif %}
+      <!-- Append the generated id to other potential header attributes. -->
+      {% capture h_attrs %}{{ headerAttrs }} id="%html_id%"{% endcapture %}
+    {% endif %}
+
+    <!-- Build the anchor to inject for our heading -->
+    {% capture anchor %}{% endcapture %}
+
+    {% if skip_anchor == false and html_id and headerLevel >= minHeader and headerLevel <= maxHeader %}
+      {% if h_attrs %}
+        {% capture _hAttrToStrip %}{{ _hAttrToStrip | split: '>' | first }} {{ h_attrs | strip | replace: '%heading%', escaped_header | replace: '%html_id%', html_id }}>{% endcapture %}
+      {% endif %}
+
+      {% capture anchor %}href="#{{ html_id }}"{% endcapture %}
+
+      {% if include.anchorClass %}
+        {% capture anchor %}{{ anchor }} class="{{ include.anchorClass }}"{% endcapture %}
+      {% endif %}
+
+      {% if include.anchorTitle %}
+        {% capture anchor %}{{ anchor }} title="{{ include.anchorTitle | replace: '%heading%', escaped_header }}"{% endcapture %}
+      {% endif %}
+
+      {% if include.anchorAttrs %}
+        {% capture anchor %}{{ anchor }} {{ include.anchorAttrs | replace: '%heading%', escaped_header | replace: '%html_id%', html_id }}{% endcapture %}
+      {% endif %}
+
+      {% capture anchor %}<a {{ anchor }}>{{ include.anchorBody | replace: '%heading%', escaped_header | default: '' }}</a>{% endcapture %}
+
+      <!-- In order to prevent adding extra space after a heading, we'll let the 'anchor' value contain it -->
+      {% if beforeHeading %}
+        {% capture anchor %}{{ anchor }} {% endcapture %}
+      {% else %}
+        {% capture anchor %} {{ anchor }}{% endcapture %}
+      {% endif %}
+    {% endif %}
+
+    {% capture new_heading %}
+<h{{ _hAttrToStrip }}
+  {{ include.bodyPrefix }}
+  {% if beforeHeading %}
+    {{ anchor }}{{ header }}
+  {% else %}
+    {{ header }}{{ anchor }}
+  {% endif %}
+  {{ include.bodySuffix }}
+</h{{ headerLevel }}>
+    {% endcapture %}
+
+    <!--
+    If we have content after the `</hX>` tag, then we'll want to append that here so we don't lost any content.
+    -->
+    {% assign chunkCount = _workspace | size %}
+    {% if chunkCount > 1 %}
+      {% capture new_heading %}{{ new_heading }}{{ _workspace | last }}{% endcapture %}
+    {% endif %}
+
+    {% capture edited_headings %}{{ edited_headings }}{{ new_heading }}{% endcapture %}
+  {% endfor %}
+{% endcapture %}{% assign headingsWorkspace = '' %}{{ edited_headings | strip }}

_includes/disqus_comments.html

@@ -0,0 +1,20 @@
+{%- if page.comments != false and jekyll.environment == "production" -%}
+
+  <div id="disqus_thread"></div>
+  <script>
+    var disqus_config = function () {
+      this.page.url = '{{ page.url | absolute_url }}';
+      this.page.identifier = '{{ page.url | absolute_url }}';
+    };
+
+    (function() {
+      var d = document, s = d.createElement('script');
+
+      s.src = 'https://{{ site.disqus.shortname }}.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 -%}

_includes/footer.html

@@ -0,0 +1,28 @@
+<footer class="site-footer h-card">
+  <data class="u-url" href="{{ "/" | relative_url }}"></data>
+
+  <div class="wrapper">
+    <div class="footer-col-wrapper">
+      <div class="footer-col footer-col-1">
+        <ul class="contact-list">
+          <li class="p-name">
+            {%- if site.author -%}
+              {{ site.author | escape }}
+            {%- else -%}
+              {{ site.title | escape }}
+            {%- endif -%}
+            </li>
+            {%- if site.email -%}
+            <li><a class="u-email" href="mailto:{{ site.email }}">{{ site.email }}</a></li>
+            {%- endif -%}
+        </ul>
+      </div>
+
+      <div class="footer-col footer-col-2">
+        {%- include social.html -%}
+      </div>
+    </div>
+
+  </div>
+
+</footer>

_includes/head.html

@@ -0,0 +1,9 @@
+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  {%- seo -%}
+  <link rel="stylesheet" href="{{ "/assets/style.css" | relative_url }}">
+
+  {%- feed_meta -%}
+</head>

_includes/header.html

@@ -0,0 +1,30 @@
+<header class="site-header" role="banner">
+
+  <div class="wrapper">
+    {%- assign default_paths = site.pages | map: "path" -%}
+    {%- assign page_paths = site.header_pages | default: default_paths -%}
+    <a class="site-title" rel="author" href="{{ "/" | relative_url }}">{{ site.title | escape }}</a>
+
+    {%- if page_paths -%}
+      <nav class="site-nav">
+        <input type="checkbox" id="nav-trigger" class="nav-trigger" />
+        <label for="nav-trigger">
+          <span class="menu-icon">
+            <svg viewBox="0 0 18 15" width="18px" height="15px">
+              <path d="M18,1.484c0,0.82-0.665,1.484-1.484,1.484H1.484C0.665,2.969,0,2.304,0,1.484l0,0C0,0.665,0.665,0,1.484,0 h15.032C17.335,0,18,0.665,18,1.484L18,1.484z M18,7.516C18,8.335,17.335,9,16.516,9H1.484C0.665,9,0,8.335,0,7.516l0,0 c0-0.82,0.665-1.484,1.484-1.484h15.032C17.335,6.031,18,6.696,18,7.516L18,7.516z M18,13.516C18,14.335,17.335,15,16.516,15H1.484 C0.665,15,0,14.335,0,13.516l0,0c0-0.82,0.665-1.483,1.484-1.483h15.032C17.335,12.031,18,12.695,18,13.516L18,13.516z"/>
+            </svg>
+          </span>
+        </label>
+
+        <div class="trigger">
+          {%- for path in page_paths -%}
+            {%- assign my_page = site.pages | where: "path", path | first -%}
+            {%- if my_page.title -%}
+            <a class="page-link" href="{{ my_page.url | relative_url }}">{{ my_page.title | escape }}</a>
+            {%- endif -%}
+          {%- endfor -%}
+        </div>
+      </nav>
+    {%- endif -%}
+  </div>
+</header>

_includes/icon-github.html

@@ -0,0 +1 @@
+<a href="https://github.com/{{ include.username }}"><span class="icon icon--github">{% include icon-github.svg %}</span><span class="username">{{ include.username }}</span></a>

_includes/icon-github.svg

@@ -0,0 +1 @@
+<svg viewBox="0 0 16 16" width="16px" height="16px"><path fill="#828282" d="M7.999,0.431c-4.285,0-7.76,3.474-7.76,7.761 c0,3.428,2.223,6.337,5.307,7.363c0.388,0.071,0.53-0.168,0.53-0.374c0-0.184-0.007-0.672-0.01-1.32 c-2.159,0.469-2.614-1.04-2.614-1.04c-0.353-0.896-0.862-1.135-0.862-1.135c-0.705-0.481,0.053-0.472,0.053-0.472 c0.779,0.055,1.189,0.8,1.189,0.8c0.692,1.186,1.816,0.843,2.258,0.645c0.071-0.502,0.271-0.843,0.493-1.037 C4.86,11.425,3.049,10.76,3.049,7.786c0-0.847,0.302-1.54,0.799-2.082C3.768,5.507,3.501,4.718,3.924,3.65 c0,0,0.652-0.209,2.134,0.796C6.677,4.273,7.34,4.187,8,4.184c0.659,0.003,1.323,0.089,1.943,0.261 c1.482-1.004,2.132-0.796,2.132-0.796c0.423,1.068,0.157,1.857,0.077,2.054c0.497,0.542,0.798,1.235,0.798,2.082 c0,2.981-1.814,3.637-3.543,3.829c0.279,0.24,0.527,0.713,0.527,1.437c0,1.037-0.01,1.874-0.01,2.129 c0,0.208,0.14,0.449,0.534,0.373c3.081-1.028,5.302-3.935,5.302-7.362C15.76,3.906,12.285,0.431,7.999,0.431z"/></svg>

_includes/icon-twitter.html

@@ -0,0 +1 @@
+<a href="https://twitter.com/{{ include.username }}"><span class="icon icon--twitter">{% include icon-twitter.svg %}</span><span class="username">{{ include.username }}</span></a>

_includes/icon-twitter.svg

@@ -0,0 +1 @@
+<svg viewBox="0 0 16 16" width="16px" height="16px"><path fill="#828282" d="M15.969,3.058c-0.586,0.26-1.217,0.436-1.878,0.515c0.675-0.405,1.194-1.045,1.438-1.809c-0.632,0.375-1.332,0.647-2.076,0.793c-0.596-0.636-1.446-1.033-2.387-1.033c-1.806,0-3.27,1.464-3.27,3.27 c0,0.256,0.029,0.506,0.085,0.745C5.163,5.404,2.753,4.102,1.14,2.124C0.859,2.607,0.698,3.168,0.698,3.767 c0,1.134,0.577,2.135,1.455,2.722C1.616,6.472,1.112,6.325,0.671,6.08c0,0.014,0,0.027,0,0.041c0,1.584,1.127,2.906,2.623,3.206 C3.02,9.402,2.731,9.442,2.433,9.442c-0.211,0-0.416-0.021-0.615-0.059c0.416,1.299,1.624,2.245,3.055,2.271 c-1.119,0.877-2.529,1.4-4.061,1.4c-0.264,0-0.524-0.015-0.78-0.046c1.447,0.928,3.166,1.469,5.013,1.469 c6.015,0,9.304-4.983,9.304-9.304c0-0.142-0.003-0.283-0.009-0.423C14.976,4.29,15.531,3.714,15.969,3.058z"/></svg>

_includes/image.html

@@ -0,0 +1,23 @@
+<!-- _includes/image.html -->
+{% if include.fullwidth %}
+<figure class="fullwidth">
+{% else %}
+<figure>
+{% endif %}
+    {% if include.url %}
+    <a href="{{ include.url }}">
+    {% endif %}
+    <img
+        {% if include.srcabs %}
+            src="{{ include.srcabs }}"
+        {% else %}
+            src="{{ site.baseurl }}/assets/images/{{ include.src }}"
+        {% endif %}
+    alt="{{ include.alt }}">
+    {% if include.url %}
+    </a>
+    {% endif %}
+    {% if include.caption %}
+        <figcaption>{{ include.caption }}</figcaption>
+    {% endif %}
+</figure>

_includes/social.html

@@ -0,0 +1,25 @@
+<ul class="social-media-list">
+  {%- if site.github_username -%}
+  <li>
+    <a
+      href="https://github.com/{{ site.github_username| cgi_escape | escape }}"
+    >
+      <div class="svg-icon">
+        {%- include icon-github.svg -%}
+      </div>
+      <span class="username">{{ site.github_username| escape }}</span>
+    </a>
+  </li>
+  {%- endif -%} {%- if site.twitter_username -%}
+  <li>
+    <a
+      href="https://www.twitter.com/{{ site.twitter_username| cgi_escape | escape }}"
+    >
+      <div class="svg-icon">
+        {%- include icon-twitter.svg -%}
+      </div>
+      <span class="username">{{ site.twitter_username| escape }}</span>
+    </a>
+  </li>
+  {%- endif -%}
+</ul>

_includes/tags.html

@@ -0,0 +1,8 @@
+{%- if page.tags.size > 0 -%}
+  <span class="post-tags">
+    {%- for tag in page.tags -%}
+    #<a href="/tag/{{ tag }}">{{ tag }}</a>&nbsp;
+    {%- endfor -%}
+  </span>
+{%- endif -%}
+