redoing with bs3

Makefile

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+_config.yml: _config_header.yml registry/ontologies.yml
+	cat $^ > $@

_config_header.yml

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+name: Uberon
+markdown: redcarpet
+pygments: true
+baseurl: /
+imgurl: /images
+speciesAOs: [xao, zfa]

_includes/JB/analytics

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+{% include JB/is_production %}
+
+{% if is_production and site.JB.analytics.provider and page.JB.analytics != false %}
+
+{% case site.JB.analytics.provider %}
+{% when "gauges" %}
+  {% include JB/analytics-providers/gauges %}
+{% when "google" %}
+  {% include JB/analytics-providers/google %}
+{% when "getclicky" %}
+  {% include JB/analytics-providers/getclicky %}
+{% when "mixpanel" %}
+  {% include JB/analytics-providers/mixpanel %}
+{% when "piwik" %}
+  {% include JB/analytics-providers/piwik %}
+{% when "custom" %}
+  {% include custom/analytics %}
+{% endcase %}
+
+{% endif %}

_includes/JB/analytics-providers/gauges

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+<script type="text/javascript">
+  var _gauges = _gauges || [];
+  (function() {
+    var t   = document.createElement('script');
+    t.type  = 'text/javascript';
+    t.async = true;
+    t.id    = 'gauges-tracker';
+    t.setAttribute('data-site-id', '{{ site.JB.analytics.gauges.site_id }}');
+    t.src = '//secure.gaug.es/track.js';
+    var s = document.getElementsByTagName('script')[0];
+    s.parentNode.insertBefore(t, s);
+  })();
+</script>

_includes/JB/analytics-providers/getclicky

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+<script type="text/javascript">
+var clicky_site_ids = clicky_site_ids || [];
+clicky_site_ids.push({{ site.JB.analytics.getclicky.site_id }});
+(function() {
+  var s = document.createElement('script');
+  s.type = 'text/javascript';
+  s.async = true;
+  s.src = '//static.getclicky.com/js';
+  ( document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0] ).appendChild( s );
+})();
+</script>
+<noscript><p><img alt="Clicky" width="1" height="1" src="//in.getclicky.com/{{ site.JB.analytics.getclicky.site_id }}ns.gif" /></p></noscript>

_includes/JB/analytics-providers/google

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+<script type="text/javascript">
+  var _gaq = _gaq || [];
+  _gaq.push(['_setAccount', '{{ site.JB.analytics.google.tracking_id }}']);
+  _gaq.push(['_trackPageview']);
+
+  (function() {
+    var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+    ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+    var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+  })();
+</script>

_includes/JB/analytics-providers/google-universal

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+<script>
+  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+  })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
+
+  ga('create', {{ site.JB.analytics.googleUA.tracking_id }}', {% if site.JB.analytics.googleUA.property_name %}{{ site.JB.analytics.googleUA.property_name }}{% else %}'auto'{% endif %});
+  ga('send', 'pageview');
+</script>

_includes/JB/analytics-providers/mixpanel

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+<script type="text/javascript">
+    var mpq = [];
+    mpq.push(["init", "{{ site.JB.analytics.mixpanel.token}}"]);
+    (function(){var b,a,e,d,c;b=document.createElement("script");b.type="text/javascript";
+    b.async=true;b.src=(document.location.protocol==="https:"?"https:":"http:")+
+    "//api.mixpanel.com/site_media/js/api/mixpanel.js";a=document.getElementsByTagName("script")[0];
+    a.parentNode.insertBefore(b,a);e=function(f){return function(){mpq.push(
+    [f].concat(Array.prototype.slice.call(arguments,0)))}};d=["init","track","track_links",
+    "track_forms","register","register_once","identify","name_tag","set_config"];for(c=0;c<
+    d.length;c++){mpq[d[c]]=e(d[c])}})();
+</script>

_includes/JB/analytics-providers/piwik

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+<script type="text/javascript">
+  var pkBaseURL = (("https:" == document.location.protocol) ? "https://{{ site.JB.analytics.piwik.baseURL }}/" : "http://{{ site.JB.analytics.piwik.baseURL }}/");
+  document.write(unescape("%3Cscript src='" + pkBaseURL + "piwik.js' type='text/javascript'%3E%3C/script%3E"));
+</script><script type="text/javascript">
+  try {
+    var piwikTracker = Piwik.getTracker(pkBaseURL + "piwik.php", {{ site.JB.analytics.piwik.idsite }});
+    piwikTracker.trackPageView();
+    piwikTracker.enableLinkTracking();
+  } catch( err ) {}
+</script><noscript><p><img src="http://{{ site.JB.analytics.piwik.baseURL }}/piwik.php?idsite={{ site.JB.analytics.piwik.idsite }}" style="border:0" alt="" /></p></noscript>

_includes/JB/categories_list

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+{% comment %}<!--
+The categories_list include is a listing helper for categories.
+Usage:
+  1) assign the 'categories_list' variable to a valid array of tags.
+  2) include JB/categories_list
+  example:
+    <ul>
+  	  {% assign categories_list = site.categories %}  
+  	  {% include JB/categories_list %}
+  	</ul>
+
+  Notes: 
+    Categories can be either a Hash of Category objects (hashes) or an Array of category-names (strings).
+    The encapsulating 'if' statement checks whether categories_list is a Hash or Array.
+    site.categories is a Hash while page.categories is an array.
+
+  This helper can be seen in use at: ../_layouts/default.html
+-->{% endcomment %}
+
+{% if site.JB.categories_list.provider == "custom" %}
+  {% include custom/categories_list %}
+{% else %}
+  {% if categories_list.first[0] == null %}
+    {% for category in categories_list %} 
+    	<li><a href="{{ BASE_PATH }}{{ site.JB.categories_path }}#{{ category }}-ref">
+    		{{ category | join: "/" }} <span>{{ site.categories[category].size }}</span>
+    	</a></li>
+    {% endfor %}
+  {% else %}
+    {% for category in categories_list %} 
+    	<li><a href="{{ BASE_PATH }}{{ site.JB.categories_path }}#{{ category[0] }}-ref">
+    		{{ category[0] | join: "/" }} <span>{{ category[1].size }}</span>
+    	</a></li>
+    {% endfor %}
+  {% endif %}
+{% endif %}
+{% assign categories_list = nil %}

_includes/JB/comments

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+{% if site.JB.comments.provider and page.comments != false %}
+
+{% case site.JB.comments.provider %}
+{% when "disqus" %}
+  {% include JB/comments-providers/disqus %}
+{% when "livefyre" %}
+  {% include JB/comments-providers/livefyre %}
+{% when "intensedebate" %}
+  {% include JB/comments-providers/intensedebate %}
+{% when "facebook" %}
+  {% include JB/comments-providers/facebook %}
+{% when "duoshuo" %}
+  {% include JB/comments-providers/duoshuo %}
+{% when "custom" %}
+  {% include custom/comments %}
+{% endcase %}
+
+{% endif %}

_includes/JB/comments-providers/disqus

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+<div id="disqus_thread"></div>
+<script type="text/javascript">
+    {% include JB/is_production %}
+    {% if is_production == false %}var disqus_developer = 1;{% endif %}
+    var disqus_shortname = '{{ site.JB.comments.disqus.short_name }}'; // required: replace example with your forum shortname
+    {% if page.wordpress_id %}var disqus_identifier = '{{page.wordpress_id}} {{site.production_url}}/?p={{page.wordpress_id}}';{% endif %}
+    /* * * DON'T EDIT BELOW THIS LINE * * */
+    (function() {
+        var dsq = document.createElement('script'); dsq.type = 'text/javascript'; dsq.async = true;
+        dsq.src = 'http://' + disqus_shortname + '.disqus.com/embed.js';
+        (document.getElementsByTagName('head')[0] || document.getElementsByTagName('body')[0]).appendChild(dsq);
+    })();
+</script>
+<noscript>Please enable JavaScript to view the <a href="http://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
+<a href="http://disqus.com" class="dsq-brlink">blog comments powered by <span class="logo-disqus">Disqus</span></a>

_includes/JB/comments-providers/duoshuo

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+<!-- Duoshuo Comment BEGIN -->
+  <div class="ds-thread"{% if page.wordpress_id %} data-thread-key="{{page.wordpress_id}}"{% endif %}></div>
+<script type="text/javascript">
+var duoshuoQuery = {short_name:'{{ site.JB.comments.duoshuo.short_name }}'};
+  (function() {
+    var ds = document.createElement('script');
+    ds.type = 'text/javascript';ds.async = true;
+    ds.src = 'http://static.duoshuo.com/embed.js';
+    ds.charset = 'UTF-8';
+    (document.getElementsByTagName('head')[0] 
+    || document.getElementsByTagName('body')[0]).appendChild(ds);
+  })();
+  </script>
+<!-- Duoshuo Comment END -->

_includes/JB/comments-providers/facebook

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+<div id="fb-root"></div>
+<script>(function(d, s, id) {
+  var js, fjs = d.getElementsByTagName(s)[0];
+  if (d.getElementById(id)) return;
+  js = d.createElement(s); js.id = id;
+  js.src = "//connect.facebook.net/en_US/all.js#xfbml=1&appId={{ site.JB.comments.facebook.appid }}";
+  fjs.parentNode.insertBefore(js, fjs);
+}(document, 'script', 'facebook-jssdk'));</script>
+<div class="fb-comments" data-href="{{ site.production_url }}{{ page.url }}" data-num-posts="{{ site.JB.comments.facebook.num_posts }}" data-width="{{ site.JB.comments.facebook.width }}" data-colorscheme="{{ site.JB.comments.facebook.colorscheme }}"></div>

_includes/JB/comments-providers/intensedebate

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+<script>
+var idcomments_acct = '{{ site.JB.comments.intensedebate.account }}';
+var idcomments_post_id;
+var idcomments_post_url;
+</script>
+<script type="text/javascript" src="http://www.intensedebate.com/js/genericCommentWrapperV2.js"></script>

_includes/JB/comments-providers/livefyre

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+<script type='text/javascript' src='http://zor.livefyre.com/wjs/v1.0/javascripts/livefyre_init.js'></script>
+<script type='text/javascript'>
+    var fyre = LF({
+        site_id: {{ site.JB.comments.livefyre.site_id }}
+    });
+</script>

_includes/JB/feedburner

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+{% if site.author.feedburner != null %}
+<link href="http://feeds.feedburner.com/{{ site.author.feedburner }}" rel="alternate" title="{{ site.title }}" type="application/atom+xml" />
+{% endif %}

_includes/JB/file_exists

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+{% comment %}<!--
+  param:  file = "/example/file.png"
+  return: file_exists_result = true
+
+  examples:
+    {% include JB/file_exists file="/404.html" %}
+    {% if file_exists_result %}Found "/404.html"!{% else %}Did not find "/404.html".{% endif %}
+
+    {% assign filename = "/405.html" %}
+    {% include JB/file_exists file=filename %}
+    {% if file_exists_result %}Found "{{ filename }}"!{% else %}Did not find "{{ filename }}".{% endif %}
+
+  NOTE: the BREAK statement in the FOR loop assumes Liquid >= 2.5.0
+
+-->{% endcomment %}
+
+{% assign file_exists_result = false %}
+
+{% if include.file %}
+	{% for static_file in site.static_files %}
+		{% if static_file.path == include.file %}
+			{% assign file_exists_result = true %}
+			{% break %}
+		{% endif %}
+	{% endfor %}
+{% endif %}

_includes/JB/gist

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+{% comment %}<!--
+The gist include allows you to embed GitHub Gist snippets in your content.
+Usage:
+  1) include JB/gist
+  2) specify the gist_id parameter (REQUIRED)
+  3) specify the gist_file parameter (OPTIONAL)
+  example:
+    <ul>
+  	  {% include JB/gist gist_id="fdcfeaba4f33c172828d" %}
+  	  {% include JB/gist gist_id="fdcfeaba4f33c172828d" gist_file="jekyll-bootstrap.js" %}
+  	</ul>
+-->{% endcomment %}
+
+<div id="gist">
+<script src="https://gist.github.com/{{ include.gist_id }}.js{% if include.gist_file %}?file={{ include.gist_file }}{% endif %}"></script>
+<noscript>
+<pre>https://gist.github.com/{{include.gist_id}}.js{% if include.gist_file %}?file={{include.gist_file}}{% endif %}</pre>
+</noscript>
+</div>

_includes/JB/is_production

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+{% capture jbcache %}{% comment %}
+
+  Determine whether or not the site is being built in a production environment.
+
+  Parameters:
+    None.
+
+  Returns:
+    is_production: [true|false]
+    jb_prod_env: [development|github|other]
+
+  Examples:
+
+    {% include JB/is_production %}
+
+    {% if is_production != true %}
+      <h3>This is Private</h3>
+      <p>I love to watch television in my undies. Don't tell anyone!</p>
+    {% endif %}
+
+    <h3>This is Public</h3>
+    <p>I have no unusual quirks.</p>
+
+{% endcomment %}
+
+{% assign is_production = false %}
+{% assign jb_prod_env = "development" %}
+
+{% if jekyll.environment != "development" %}
+  {% assign is_production = true %}
+  {% assign jb_prod_env = jekyll.environment %}
+{% endif %}
+
+{% if site.github %}
+  {% assign is_production = true %}
+  {% assign jb_prod_env = "github" %}
+{% endif %}
+
+{% endcapture %}{% assign jbcache = nil %}

_includes/JB/liquid_raw

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+{% comment%}<!--
+The liquid_raw helper is a way to display raw liquid code, as opposed to parsing it.
+Normally you'd use Liquid's built in 'raw' tag. 
+The problem is GitHub Jekyll does not support the current Liquid release.
+GitHub Jekyll supports the deprecated 'literal' tag.
+Using one will break the other if you plan to deploy to GitHub pages.
+  see: https://github.com/mojombo/jekyll/issues/425
+
+Since I don't want to mess with Liquid versions, I'll just rewrite the way I 
+intend to give liquid examples. It's not an elegant solution by any means:
+
+Usage: 
+  1) Define a 'text' variable with the block of liquid code you intend to display.
+  2) Pass the text variable to include JB/liquid_raw
+
+  example:
+  {% capture text %}|.% for tag in tags_list %.|
+    <li><a href="|.{ site.var.tags_path }.||.{ tag[0] }.|-ref">|.{ tag[0] }.| <span>|.{tag[1].size}.|</span></a></li>
+  |.% endfor %.|
+
+  |.% assign tags_list = null %.|{% endcapture %}    
+  {% include JB/liquid_raw %}
+
+  As seen here, you must use "|." and ".|" as opening and closing brackets.
+-->{% endcomment%}
+
+{% if site.JB.liquid_raw.provider == "custom" %}
+  {% include custom/liquid_raw %}
+{% else %}
+  <pre><code>{{text | replace:"|.", "&#123;" | replace:".|", "&#125;" | replace:">", "&gt;" | replace:"<", "&lt;" }}</code></pre>
+{% endif %}
+{% assign text = nil %}

_includes/JB/pages_list

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+{% comment %}<!--
+The pages_list include is a listing helper.
+Usage:
+  1) assign the 'pages_list' variable to a valid array of pages or posts.
+  2) include JB/pages_list
+  example:
+    <ul>
+  	  {% assign pages_list = site.pages %}  
+  	  {% include JB/pages_list %}
+  	</ul>
+
+  Grouping: (optional): 
+  	assign the 'group' variable to constrain the list to only pages/posts
+  	in the given group. Note you must define the group manually in the page/post
+  	meta-data to use this feature.
+  	Grouping is mainly helpful for non-post pages.
+  	If you want to group posts, it's easier/better to tag them, then pass the tagged posts array.
+  	i.e. site.tags.cool_tag (this returns an array of posts tagged: cool_tag)
+
+  This helper can be seen in use at: ../_layouts/default.html
+-->{% endcomment %}
+
+{% if site.JB.pages_list.provider == "custom" %}
+  {% include custom/pages_list %}
+{% else %}
+  {% for node in pages_list %}
+    {% if node.title != null %}
+      {% if group == null or group == node.group %}
+      	{% if page.url == node.url %}
+      	<li class="active"><a href="{{ BASE_PATH }}{{node.url}}" class="active">{{node.title}}</a></li>
+      	{% else %}
+      	<li><a href="{{ BASE_PATH }}{{node.url}}">{{node.title}}</a></li>
+      	{% endif %}
+      {% endif %}
+    {% endif %}
+  {% endfor %}
+{% endif %}
+{% assign pages_list = nil %}
+{% assign group = nil %}