Add files inside docs/

fhdsl · Apr 10, 2024 · c26ef14 · c26ef14
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diff --git a/.DS_Store b/.DS_Store
diff --git a/docs/404.html b/docs/404.html
@@ -79,12 +79,9 @@
     <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
-    <a href="/index.html" class="navbar-brand navbar-brand-logo">
+    <a href="https://hutchdatascience.org" class="navbar-brand navbar-brand-logo">
     <img src="/img/logo.jpeg" alt="" class="navbar-logo">
     </a>
-    <a class="navbar-brand" href="/index.html">
-    <span class="navbar-title">Quarto Based OTTR Course</span>
-    </a>
   </div>
         <div class="quarto-navbar-tools tools-end">
     <a href="https://github.com/fhdsl/ottr" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
@@ -546,13 +543,13 @@ <h1 class="title">Page Not Found</h1>
 <footer class="footer">
   <div class="nav-footer">
     <div class="nav-footer-left">
-<p>This book was built with <a href="https://quarto.org/" style="color: #fff;">Quarto</a> by <a href="https://hutchdatascience.org/" style="color: #fff;">The Fred Hutch Data Science Lab</a></p>
+<p>This book was built with <a href="https://quarto.org/" style="color: #fff;">Quarto</a> by <a href="https://hutchdatascience.org/" style="color: #fff;">The Fred Hutch Data Science Lab</a>.</p>
 </div>   
     <div class="nav-footer-center">
 <p>All illustrations <a href="https://creativecommons.org/licenses/by/4.0/" style="color: #fff;">CC-BY. </a> <br> All other materials <a href="https://creativecommons.org/licenses/by/4.0/" style="color: #fff;"> CC-BY </a> unless noted otherwise.</p>
 <div class="toc-actions"><ul><li><a href="https://github.com/fhdsl/ottr/edit/main/404.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/fhdsl/ottr/issues" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></div>
     <div class="nav-footer-right">
-<p>We value your thoughts and experiences! Please take a moment to share your feedback with us by filling out this <a href="https://docs.google.com/forms/d/e/1FAIpQLSfBvVELBg8lcynKj0TrzMlov1zil-Sbkh9VhMKRcSpeo1xo6g/viewform" style="color: #fff;"> Google Form </a>.</p>
+<p>Please take a moment to share your feedback with us by filling out this <a href="https://docs.google.com/forms/d/e/1FAIpQLSfBvVELBg8lcynKj0TrzMlov1zil-Sbkh9VhMKRcSpeo1xo6g/viewform" style="color: #fff;"> Google Form </a>.</p>
 </div>
   </div>
 </footer>

diff --git a/docs/first-section-new-chapter.html b/docs/first-section-new-chapter.html
@@ -60,7 +60,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./references.html" rel="next">
+<link href="./second-section-new-chapter.html" rel="next">
 <link href="./intro.html" rel="prev">
 <link href="./img/favicon.ico" rel="icon">
 <script src="site_libs/quarto-html/quarto.js"></script>
@@ -154,9 +154,45 @@
       </ul>
 </li>
         <li class="sidebar-item sidebar-item-section">
-      <span class="sidebar-item-text sidebar-link text-start">
- <span class="menu-text">Second Section</span></span>
-  </li>
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
+ <span class="menu-text">Second Section</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./second-section-new-chapter.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">New Chapter</span></span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Third Section</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">
+<li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./third-section-new-chapter.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">New Chapter</span></span></a>
+  </div>
+</li>
+      </ul>
+</li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./conclusion.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Conclusion</span></span></a>
+  </div>
+</li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./references.html" class="sidebar-item-text sidebar-link">
@@ -828,8 +864,8 @@ <h1 class="title">
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./references.html" class="pagination-link" aria-label="References">
-        <span class="nav-page-text">References</span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./second-section-new-chapter.html" class="pagination-link" aria-label="New Chapter">
+        <span class="nav-page-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">New Chapter</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>

diff --git a/docs/img/box_images/dictionary.png b/docs/img/box_images/dictionary.png
diff --git a/docs/img/box_images/github.png b/docs/img/box_images/github.png
diff --git a/docs/img/box_images/note.png b/docs/img/box_images/note.png
diff --git a/docs/img/box_images/thinking_face.png b/docs/img/box_images/thinking_face.png
diff --git a/docs/img/box_images/under_construction.png b/docs/img/box_images/under_construction.png
diff --git a/docs/img/box_images/warning.png b/docs/img/box_images/warning.png
diff --git a/docs/img/hero-image.png b/docs/img/hero-image.png
diff --git a/docs/intro.html b/docs/intro.html
@@ -30,7 +30,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./new-chapter.html" rel="next">
+<link href="./first-section-new-chapter.html" rel="next">
 <link href="./index.html" rel="prev">
 <link href="./img/favicon.ico" rel="icon">
 <script src="site_libs/quarto-html/quarto.js"></script>
@@ -120,11 +120,62 @@
  <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Introduction</span></span></a>
   </div>
 </li>
-        <li class="sidebar-item">
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true">
+ <span class="menu-text">First Section</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./new-chapter.html" class="sidebar-item-text sidebar-link">
+  <a href="./first-section-new-chapter.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">New Chapter</span></span></a>
   </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true">
+ <span class="menu-text">Second Section</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./second-section-new-chapter.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">New Chapter</span></span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item sidebar-item-section">
+      <div class="sidebar-item-container"> 
+            <a class="sidebar-item-text sidebar-link text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true">
+ <span class="menu-text">Third Section</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="true" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth1 show">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./third-section-new-chapter.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">New Chapter</span></span></a>
+  </div>
+</li>
+      </ul>
+  </li>
+        <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./conclusion.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Conclusion</span></span></a>
+  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
@@ -137,9 +188,7 @@
 </nav>
 <div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
-    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar"><div class="quarto-margin-header"><div class="margin-header-item">
-<p>Quarto Based OTTR Course</p>
-</div></div>
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
         <nav id="TOC" role="doc-toc" class="toc-active">
     <h2 id="toc-title">Table of contents</h2>
 
@@ -611,7 +660,7 @@ <h2 data-number="1.3" class="anchored" data-anchor-id="curriculum"><span class="
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./new-chapter.html" class="pagination-link" aria-label="New Chapter">
+      <a href="./first-section-new-chapter.html" class="pagination-link" aria-label="New Chapter">
         <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">New Chapter</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>