Converted to using Jekyll

.gitignore

@@ -3,3 +3,6 @@
 **/.DS_Store
 **/_.DS_Store
 .idea/
+_site
+.sass-cache
+.jekyll-metadata

Gemfile

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+source "https://rubygems.org"
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+#     bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "jekyll", "~> 3.6.2"
+
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.0"
+
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+# gem "github-pages", group: :jekyll_plugins
+
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+  gem "jekyll-feed", "~> 0.6"
+end
+
+# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+

_config.yml

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+# Site settings
+# These are used to personalize your new site. If you look in the HTML files,
+# you will see them accessed via {{ site.title }}, {{ site.email }}, and so on.
+# You can create any custom variable you would like, and they will be accessible
+# in the templates via {{ site.myvariable }}.
+title: PAIR Website
+email: [email protected]
+description: >- # this means to ignore newlines until "baseurl:"
+  Write an awesome description for your new site here. You can edit this
+  line in _config.yml. It will appear in your document head meta (for
+  Google search results) and in your feed.xml site description.
+baseurl: "" # the subpath of your site, e.g. /blog
+url: "" # the base hostname & protocol for your site, e.g. http://example.com
+twitter_username: jekyllrb
+github_username:  jekyll
+
+# Build settings
+markdown: kramdown
+theme: minima
+plugins:
+  - jekyll-feed
+
+collections:
+  people:
+    output: true
+
+defaults:
+  -
+    scope:
+      path: ""
+      type: "pages"
+    values:
+      layout: "base"
+  -
+    scope:
+      path: "publications"
+      type: "pages" 
+    values:
+      layout: "publication" # overrides previous default layout
+
+# Exclude from processing.
+# The following items will not be processed, by default. Create a custom list
+# to override the default setting.
+# exclude:
+#   - Gemfile
+#   - Gemfile.lock
+#   - node_modules
+#   - vendor/bundle/
+#   - vendor/cache/
+#   - vendor/gems/
+#   - vendor/ruby/

_includes/entry-date.html

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+{%- unless page.layout == 'collection' -%}
+  <time class="entry-date dt-published" datetime="{{ entry.date | date_to_xmlschema }}">
+    {%- assign date_format = site.date_format | default: "%B %-d, %Y" -%}
+    {{ entry.date | date: date_format }}
+  </time>
+{%- endunless -%}

_includes/entry.html

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+<li class="entry-card"><article><a href="{{ site.url }}{{ post.url }}">{{ post.title }} <span class="entry-date"><time datetime="{{ post.date | date_to_xmlschema }}">{{ post.date | date: "%B %d, %Y" }}</time></span>{% if   post.excerpt %} <span class="excerpt">{{ post.excerpt | remove: '\[ ... \]' | remove: '\( ... \)' | markdownify | strip_html | strip_newlines | escape_once }}</span>{% endif %}</a></article></li>  

_includes/feed-footer.html

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+<p><a href="{{ site.url }}{{ post.url }}">{{ post.title | xml_escape }}</a> was originally published by {{ site.owner.name }} at <a href="{{ site.url }}">{{ site.title }}</a> on {{ post.date | date: "%B %d, %Y" }}.</p>

_includes/footer.html

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+<!-- Footer -->
+<footer>
+    <div class="row">
+        <div class="col-lg-12">
+            <p></p>
+        </div>
+    </div>
+</footer>
+
+<!-- Global footer snippet start -->
+<div id="global-footer">
+    <div class="container">
+        <div class="row">
+            <div id="bottom-logo" class="span2">
+                <a href="http://www.stanford.edu">
+                    <img src="https://www.stanford.edu/su-identity/images/[email protected]" alt="Stanford University"
+                         width="105" height="49"/>
+                </a>
+            </div>
+            <!-- #bottom-logo end -->
+            <div id="bottom-text" class="span10">
+                <ul>
+                    <li class="home"><a href="http://www.stanford.edu">SU Home</a></li>
+                    <li class="maps alt"><a href="http://visit.stanford.edu/plan/maps.html">Maps &amp; Directions</a></li>
+                    <li class="search-stanford"><a href="http://www.stanford.edu/search/">Search Stanford</a></li>
+                    <li class="terms alt"><a href="http://www.stanford.edu/site/terms.html">Terms of Use</a></li>
+                    <li class="emergency-info"><a href="http://emergency.stanford.edu">Emergency Info</a></li>
+                </ul>
+            </div> <!-- .bottom-text end -->
+            <div class="clear"></div>
+            <p class="copyright vcard">&copy; <span class="fn org">Stanford University</span>, <span class="adr"> <span
+                        class="locality">Stanford</span>, <span class="region">California</span> <span
+                        class="postal-code">94305</span></span>.&nbsp;&nbsp;
+                <span id="copyright-complaint"><a href="https://uit.stanford.edu/security/copyright-infringement" class="copyright-complaint">Copyright Complaints.</a></span>&nbsp;&nbsp;
+                <span id="copyright-complaint">This page was last updated on <?php echo date("F d, Y", filemtime("index.php")); ?>.</span>
+            </p>
+        </div> <!-- .row end -->
+    </div> <!-- .container end -->
+</div> <!-- global-footer end -->
+<!-- Global footer snippet end -->

_includes/head.html

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+<head>
+
+    <meta charset="utf-8">
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <meta name="viewport" content="width=device-width, initial-scale=1">
+    <meta name="description" content="">
+    <meta name="author" content="">
+    <meta name="HandheldFriendly" content="True">
+    <meta name="MobileOptimized" content="320">
+
+    <title>{% if page.title %}{{ page.title }} &#8211; {% endif %}{{ site.title }}</title>
+    {% if page.excerpt %}<meta name="description" content="{{ page.excerpt | strip_html }}">{% endif %}
+    {% if page.tags %}<meta name="keywords" content="{{ page.tags | join: ', ' }}">{% endif %}
+
+    {% include open-graph.html %}
+
+    <link rel="canonical" href="{{ canonical }}">
+
+    <!-- Bootstrap Core CSS -->
+    <link href="/assets/css/bootstrap.min.css" rel="stylesheet">
+
+    <!-- Custom CSS -->
+    <link href="/assets/css/modern-business.css" rel="stylesheet">
+
+    <!-- Custom Fonts -->
+    <link href="/assets/font-awesome/css/font-awesome.min.css" rel="stylesheet" type="text/css">
+    <link href="https://fonts.googleapis.com/css?family=Roboto" rel="stylesheet">
+
+    <link href="https://www.stanford.edu/su-identity/css/su-identity.css" rel="stylesheet">
+    <link href="https://fonts.googleapis.com/css?family=Source+Sans+Pro:300,400,700" rel="stylesheet" type="text/css">
+
+    {% if page.extra_css %}    
+      {% for extraCSS in page.extra_css %}    
+	       <link rel="stylesheet" href="{{extraCSS}}">
+      {% endfor %}
+    {% endif %}
+
+    <!-- 16x16 -->
+    <link rel="shortcut icon" href="{{ site.url }}/images/favicon.ico">
+    <!-- 32x32 -->
+    <link rel="shortcut icon" href="{{ site.url }}/images/favicon.png">
+
+    <!-- HTML5 Shim and Respond.js IE8 support of HTML5 elements and media queries -->
+    <!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
+    <!--[if lt IE 9]>
+        <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
+        <script src="https://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js"></script>
+    <![endif]-->
+
+    <!--[if lt IE 9]>
+    <script src="js/html5shiv.js"></script>
+    <![endif]-->
+    <!--[if IE 8]>
+      <link rel="stylesheet" type="text/css" href="https://www.stanford.edu/su-identity/css/ie/ie8.css" />
+    <![endif]-->
+    <!--[if IE 7]>
+      <link rel="stylesheet" type="text/css" href="https://www.stanford.edu/su-identity/css/ie/ie7.css" />
+    <![endif]-->
+</head>

_includes/header.html

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+<!-- Header Carousel -->
+<header id="myCarousel" class="carousel slide">
+    <!-- Indicators -->
+    <ol class="carousel-indicators">
+        <li data-target="#myCarousel" data-slide-to="0" class="active"></li>
+        <li data-target="#myCarousel" data-slide-to="1"></li>
+        <li data-target="#myCarousel" data-slide-to="2"></li>
+    </ol>
+
+    <!-- Wrapper for slides -->
+    <div class="carousel-inner">
+      <div class="item active">
+        <div class="fill" style="background-image:url('./img/jumbotron/hh.jpg');"></div>
+          <div class="carousel-caption">
+              <font style="font-size: 54px; line-height: 40px;">Partnership in AI-Assisted Care</font><br/>
+              <font style="font-size: 20px; line-height: 40px;">Improving hand hygiene with computer vision at Lucile Packard Children's Hospital</font>
+          </div>
+      </div>
+        <div class="item">
+          <div class="fill" style="background-image:url('./img/jumbotron/thermal.png');"></div>
+            <div class="carousel-caption">
+              <font style="font-size: 54px; line-height: 40px;">Partnership in AI-Assisted Care</font><br/>
+              <font style="font-size: 20px; line-height: 40px;">Automatically detecting falls with thermal cameras</font>
+            </div>
+        </div>
+        <div class="item">
+          <div class="fill" style="background-image:url('./img/jumbotron/phone.png');"></div>
+            <div class="carousel-caption">
+              <font style="font-size: 54px; line-height: 40px;">Partnership in AI-Assisted Care</font><br/>
+              <font style="font-size: 20px; line-height: 40px;">Analysis of phone-based conversational agents on health and violence reveals new insights</font>
+            </div>
+        </div>
+    </div>
+
+    <!-- Controls -->
+    <a class="left carousel-control" href="#myCarousel" data-slide="prev">
+        <span class="icon-prev"></span>
+    </a>
+    <a class="right carousel-control" href="#myCarousel" data-slide="next">
+        <span class="icon-next"></span>
+    </a>
+</header>

_includes/navigation.html

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+<!-- Brandbar snippet start -->
+<div id="brandbar">
+  <div class="container">
+    <a href="http://www.stanford.edu">
+      <img src="https://www.stanford.edu/su-identity/images/[email protected]" alt="Stanford University" width="152" height="26">
+    </a>
+  </div> <!-- .container end -->
+</div> <!-- #brandbar end -->
+<!-- Brandbar snippet end -->
+
+<!-- Navigation -->
+<nav class="navbar navbar-default" role="navigation">
+    <div class="container">
+        <!-- Brand and toggle get grouped for better mobile display -->
+        <div class="navbar-header">
+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
+                <span class="sr-only">Toggle navigation</span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+                <span class="icon-bar"></span>
+            </button>
+            <a class="navbar-brand" href="index.php">Stanford Partnership in AI-Assisted Care</a>
+        </div>
+        <!-- Collect the nav links, forms, and other content for toggling -->
+        <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
+            <ul class="nav navbar-nav navbar-right">
+                <li><a href="/">Home</a></li>
+                <li><a href="/people">People</a></li>
+                <li class="dropdown">
+                  <a href="#" class="dropdown-toggle" data-toggle="dropdown">Projects <b class="caret"></b></a>
+                  <ul class="dropdown-menu">
+                      <li class="dropdown-item"><a href="projects/hand_hygiene/">Hand Hygiene</a></li>
+                      <li class="dropdown-item"><a href="projects/senior_care/">Senior Well-Being</a></li>
+                      <li class="dropdown-item"><a href="projects/icu/">ICU Clinical Pathway Support</a></li>
+                      <li class="dropdown-item"><a href="projects/surgical_support">Surgical Support</a></li>
+                  </ul>
+              </li>
+               <li><a href="/publications">Publications</a></li>
+            </ul>
+        </div>
+        <!-- /.navbar-collapse -->
+    </div>
+    <!-- /.container -->
+</nav>

_includes/open-graph.html

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+<!-- Twitter Cards -->
+<meta name="twitter:title" content="{% if page.title %}{{ page.title }}{% else %}{{ site.title }}{% endif %}">
+{% if page.excerpt %}<meta name="twitter:description" content="{{ page.excerpt | strip_html }}">{% endif %}
+{% if site.owner.twitter %}<meta name="twitter:site" content="@{{ site.owner.twitter }}">{% endif %}
+{% if author.twitter %}<meta name="twitter:creator" content="@{{ author.twitter }}">{% endif %}
+{% if page.image.feature %}
+<meta name="twitter:card" content="summary_large_image">
+<meta name="twitter:image" content="{{ site.url }}/{{ page.image.feature }}">
+{% else %}
+<meta name="twitter:card" content="summary">
+<meta name="twitter:image" content="{{ site.url }}/images/{{ site.logo }}">
+{% endif %}
+<!-- Open Graph -->
+<meta property="og:locale" content="{{ site.locale }}">
+<meta property="og:type" content="article">
+<meta property="og:title" content="{% if page.title %}{{ page.title }}{% else %}{{ site.title }}{% endif %}">
+{% if page.excerpt %}<meta property="og:description" content="{{ page.excerpt | strip_html }}">{% endif %}
+<meta property="og:url" content="{{ page.url | replace:'index.html','' | prepend: site.url }}">
+<meta property="og:site_name" content="{{ site.title }}">

_includes/responsive-embed

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+{%- case include.ratio -%}
+  {%- when '21:9' -%}
+    {%- assign ratio_class = 'responsive-embed-21by9' -%}
+  {%- when '16:9' -%}
+    {%- assign ratio_class = 'responsive-embed-16by9' -%}
+  {%- when '4:3' -%}
+    {%- assign ratio_class = 'responsive-embed-4by3' -%}
+  {%- when '1:1' -%}
+    {%- assign ratio_class = 'responsive-embed-1by1' -%}
+  {%- else -%}
+    {%- assign ratio_class = 'responsive-embed-16by9' -%}
+{%- endcase -%}
+
+<div class="responsive-embed {{ ratio_class }}">
+  <iframe src="{{ include.url }}" frameborder="0" allowfullscreen></iframe>
+</div>

_includes/scripts.html

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+<!-- jQuery -->
+<script src="/assets/js/jquery.js"></script>
+
+<!-- Bootstrap Core JavaScript -->
+<script src="/assets/js/bootstrap.min.js"></script>
+
+<!-- Script to Activate the Carousel -->
+<script>
+$('.carousel').carousel({
+    interval: 5000 //changes the speed
+})
+</script>
+
+{% if page.extra_js %}    
+    {% for extraJS in page.extra_js %}    
+    <script src="{{extraJS}}"></script>
+    {% endfor %}
+{% endif %}

_includes/skip-links.html

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+<nav class="skip-links">
+  <h2 class="screen-reader-text">{{ site.data.text[site.locale].skip_links | default: 'Skip links' }}</h2>
+  <ul>
+    <li><a href="#primary-nav" class="screen-reader-shortcut">{{ site.data.text[site.locale].skip_primary_nav | default: 'Skip to primary navigation' }}</a></li>
+    <li><a href="#main" class="screen-reader-shortcut">{{ site.data.text[site.locale].skip_content | default: 'Skip to content' }}</a></li>
+    <li><a href="#footer" class="screen-reader-shortcut">{{ site.data.text[site.locale].skip_footer | default: 'Skip to footer' }}</a></li>
+  </ul>
+</nav>

_includes/social-icons.html

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+<div class="social-icons">
+  {%- for footer_link in site.footer_links -%}
+    {%- if footer_link.url contains "://" -%}
+      {%- assign url = footer_link.url -%}
+    {%- else -%}
+      {%- assign url = footer_link.url | relative_url -%}
+    {%- endif -%}
+    <a class="social-icon" href="{{ url }}"><i class="{{ footer_link.icon | default: 'fas fa-link' }} fa-2x" title="{{ footer_link.title }}"></i></a>
+  {%- endfor -%}
+</div>

_includes/social-share.html

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+<span class="social-share-twitter">
+  <a href="https://twitter.com/intent/tweet?hashtags={{ page.tags | join: ',' | remove: ' ' }}&amp;text={{ page.title | escape | replace:' ','%20' }}&amp;url={{ site.url }}{{ page.url }}{% if author.twitter %}&amp;via={{ author.twitter }}{% endif %}" title="Share on Twitter" itemprop="Twitter"><i class="fa fa-twitter-square"></i> Tweet</a>
+</span>
+<span class="social-share-facebook">
+  <a href="https://www.facebook.com/sharer/sharer.php?u={{ site.url }}{{ page.url }}" title="Share on Facebook" itemprop="Facebook"><i class="fa fa-facebook-square"></i> Like</a>
+</span>

_includes/toc

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+{::options parse_block_html="true" /}
+<div id="entry-table-of-contents" class="toc-wrapper">
+<h2 id="toc-toggle" class="no_toc">
+  {{ site.data.text[site.locale].table_of_contents | default: 'Table of Contents' }} <i class="toc-toggle-icon fas fa-chevron-down"></i>
+</h2>
+1. toc
+{:toc}
+</div>
+{::options parse_block_html="false" /}