test table of contents

_site.yml

@@ -1,5 +1,3 @@
-name: "data-carpentry-week"
-output_dir: "."
 navbar:
   left:
     - text: "Home"
@@ -32,3 +30,11 @@ navbar:
       menu:
         - text: "Refresh Day 4"
           href: refresh_day4.html    
+output_dir: "."
+output:
+  html_document:
+    highlight: pygments
+    toc: true
+    toc_float:
+      collapsed: false
+    css: style.css

about.Rmd

@@ -7,8 +7,8 @@ title: "About"
 This website was built entirely using `R` and `RStudio`-- the same tools you are learning in this very course.
 
 For this course, we embrace the spirit of [collaborative lesson development](https://github.com/swcarpentry/collaborative-lesson-development). We leverage the community's effort to develop effective approaches to teach this material, and draw lessons from the following open sources:
-- [Data Carpentry: R for data analysis and visualization of Ecological Data](http://www.datacarpentry.org/R-ecology-lesson/)
-- [Data Carpentry for Biologists](http://www.datacarpentry.org/semester-biology/)
+* [Data Carpentry: R for data analysis and visualization of Ecological Data](http://www.datacarpentry.org/R-ecology-lesson/)
+* [Data Carpentry for Biologists](http://www.datacarpentry.org/semester-biology/)
 
 
 ## About the Instructors

about.html

@@ -270,7 +270,7 @@ <h1 class="title toc-ignore">About</h1>
 <div id="about-the-course-website" class="section level2">
 <h2>About the Course Website</h2>
 <p>This website was built entirely using <code>R</code> and <code>RStudio</code>– the same tools you are learning in this very course.</p>
-<p>For this course, we embrace the spirit of <a href="https://github.com/swcarpentry/collaborative-lesson-development">collaborative lesson development</a>. We leverage the community’s effort to develop effective approaches to teach this material, and draw lessons from the following open sources: - <a href="http://www.datacarpentry.org/R-ecology-lesson/">Data Carpentry: R for data analysis and visualization of Ecological Data</a> - <a href="http://www.datacarpentry.org/semester-biology/">Data Carpentry for Biologists</a></p>
+<p>For this course, we embrace the spirit of <a href="https://github.com/swcarpentry/collaborative-lesson-development">collaborative lesson development</a>. We leverage the community’s effort to develop effective approaches to teach this material, and draw lessons from the following open sources: * <a href="http://www.datacarpentry.org/R-ecology-lesson/">Data Carpentry: R for data analysis and visualization of Ecological Data</a> * <a href="http://www.datacarpentry.org/semester-biology/">Data Carpentry for Biologists</a></p>
 </div>
 <div id="about-the-instructors" class="section level2">
 <h2>About the Instructors</h2>

index.html

@@ -20,23 +20,11 @@
 <script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
 <script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
 <script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
+<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
+<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
+<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
 <script src="site_libs/navigation-1.1/tabsets.js"></script>
-<link href="site_libs/highlightjs-1.1/default.css" rel="stylesheet" />
-<script src="site_libs/highlightjs-1.1/highlight.js"></script>
 
-<style type="text/css">code{white-space: pre;}</style>
-<style type="text/css">
-  pre:not([class]) {
-    background-color: white;
-  }
-</style>
-<script type="text/javascript">
-if (window.hljs && document.readyState && document.readyState === "complete") {
-   window.setTimeout(function() {
-      hljs.initHighlighting();
-   }, 0);
-}
-</script>
 
 
 
@@ -67,6 +55,7 @@
 }
 </style>
 
+<link rel="stylesheet" href="style.css" type="text/css" />
 
 </head>
 
@@ -162,6 +151,107 @@
 
 
 
+<script>
+$(document).ready(function ()  {
+
+    // move toc-ignore selectors from section div to header
+    $('div.section.toc-ignore')
+        .removeClass('toc-ignore')
+        .children('h1,h2,h3,h4,h5').addClass('toc-ignore');
+
+    // establish options
+    var options = {
+      selectors: "h1,h2,h3",
+      theme: "bootstrap3",
+      context: '.toc-content',
+      hashGenerator: function (text) {
+        return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
+      },
+      ignoreSelector: ".toc-ignore",
+      scrollTo: 0
+    };
+    options.showAndHide = false;
+    options.smoothScroll = true;
+
+    // tocify
+    var toc = $("#TOC").tocify(options).data("toc-tocify");
+});
+</script>
+
+<style type="text/css">
+
+#TOC {
+  margin: 25px 0px 20px 0px;
+}
+@media (max-width: 768px) {
+#TOC {
+  position: relative;
+  width: 100%;
+}
+}
+
+
+.toc-content {
+  padding-left: 30px;
+  padding-right: 40px;
+}
+
+div.main-container {
+  max-width: 1200px;
+}
+
+div.tocify {
+  width: 20%;
+  max-width: 260px;
+  max-height: 85%;
+}
+
+@media (min-width: 768px) and (max-width: 991px) {
+  div.tocify {
+    width: 25%;
+  }
+}
+
+@media (max-width: 767px) {
+  div.tocify {
+    width: 100%;
+    max-width: none;
+  }
+}
+
+.tocify ul, .tocify li {
+  line-height: 20px;
+}
+
+.tocify-subheader .tocify-item {
+  font-size: 0.90em;
+  padding-left: 25px;
+  text-indent: 0;
+}
+
+.tocify .list-group-item {
+  border-radius: 0px;
+}
+
+.tocify-subheader {
+  display: inline;
+}
+.tocify-subheader .tocify-item {
+  font-size: 0.95em;
+}
+
+</style>
+
+<!-- setup 3col/9col grid for toc_float and main content  -->
+<div class="row-fluid">
+<div class="col-xs-12 col-sm-4 col-md-3">
+<div id="TOC" class="tocify">
+</div>
+</div>
+
+<div class="toc-content col-xs-12 col-sm-8 col-md-9">
+
+
 
 
 <div class="navbar navbar-default  navbar-fixed-top" role="navigation">
@@ -377,6 +467,8 @@ <h2>Contributors</h2>
 
 
 
+</div>
+</div>
 
 </div>
 

logistics.Rmd

@@ -8,10 +8,10 @@ This course is being taught in the Valley Hall teaching facility, located on the
 1. Coffee/tea/water/juice
 1. Code of Conduct
 1. Sticky notes
-  a. Green: I'm finished with the task; I'm ready to move on; Feedback on something that's going well for you
-  a. Red: I have a question; I'm not ready to move on; Feedback on something we can improve
+  + Green: I'm finished with the task; I'm ready to move on; Feedback on something that's going well for you
+  + Red: I have a question; I'm not ready to move on; Feedback on something we can improve
 1. Introductions
-  a. Name
-  a. Affiliation
-  a. Field of study
-  a. Something you made recently that you're proud of
+  + Name
+  + Affiliation
+  + Field of study
+  + Something you made recently that you're proud of

logistics.html

@@ -274,19 +274,19 @@ <h1 class="title toc-ignore">Logistics</h1>
 <li>Code of Conduct</li>
 <li>Sticky notes</li>
 </ol>
-<ol style="list-style-type: lower-alpha">
+<ul>
 <li>Green: I’m finished with the task; I’m ready to move on; Feedback on something that’s going well for you</li>
 <li>Red: I have a question; I’m not ready to move on; Feedback on something we can improve</li>
-</ol>
+</ul>
 <ol style="list-style-type: decimal">
 <li>Introductions</li>
 </ol>
-<ol style="list-style-type: lower-alpha">
+<ul>
 <li>Name</li>
 <li>Affiliation</li>
 <li>Field of study</li>
 <li>Something you made recently that you’re proud of</li>
-</ol>
+</ul>
 
 
 

site_libs/jqueryui-1.11.4/README

@@ -0,0 +1,8 @@
+This a jQuery UI custom build, downloaded from:
+http://jqueryui.com/download/#!version=1.11.4&components=1111111111110111111111111111111111111
+
+It includes all components except the datepicker, because it conflicts with
+bootstrap-datepicker that is packaged with Shiny.
+
+The copy of jQuery that is bundled with the download, under external/, is not
+included because Shiny already has its own copy of jQuery.