Built site for gh-pages

OuhscBbmc · Oct 27, 2024 · 7c7e972 · 7c7e972
1 parent 7ea9e2f
commit 7c7e972
Show file tree

Hide file tree

Showing 11 changed files with 1,021 additions and 30 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-f4dcd538
+60c06bea
diff --git a/chapters/support.md b/chapters/support.md
@@ -15,7 +15,6 @@ author:
     affiliation-url: https://ouhsc.edu/bbmc/
     email: [email protected]
     orcid: 0000-0002-5613-5006
-    attributes:
 
 
 csl: ../assets/csl/apa-7e.csl

diff --git a/index.html b/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.551">
+<meta name="generator" content="quarto-1.5.57">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -31,6 +31,7 @@
 <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="./trouble/login.html" rel="next">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -166,13 +167,13 @@
   <header id="quarto-header" class="headroom fixed-top">
   <nav class="quarto-secondary-nav">
     <div class="container-fluid d-flex">
-      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
         <i class="bi bi-layout-text-sidebar-reverse"></i>
       </button>
         <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./index.html">Welcome</a></li></ol></nav>
-        <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
+        <a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
         </a>
-      <button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
+      <button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
         <i class="bi bi-search"></i>
       </button>
     </div>
@@ -188,17 +189,17 @@
         <div class="sidebar-tools-main tools-wide">
     <a href="https://github.com/OuhscBbmc/redcap-manual-1" title="Source Code" class="quarto-navigation-tool px-1" aria-label="Source Code"><i class="bi bi-github"></i></a>
     <div class="dropdown">
-      <a href="" title="Share" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Share"><i class="bi bi-share"></i></a>
+      <a href="" title="Share" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" role="link" aria-label="Share"><i class="bi bi-share"></i></a>
       <ul class="dropdown-menu" aria-labelledby="quarto-navigation-tool-dropdown-0">
           <li>
             <a class="dropdown-item sidebar-tools-main-item" href="https://twitter.com/intent/tweet?url=|url|">
-              <i class="bi bi-bi-twitter pe-1"></i>
+              <i class="bi bi-twitter pe-1"></i>
             Twitter
             </a>
           </li>
           <li>
             <a class="dropdown-item sidebar-tools-main-item" href="https://www.facebook.com/sharer/sharer.php?u=|url|">
-              <i class="bi bi-bi-facebook pe-1"></i>
+              <i class="bi bi-facebook pe-1"></i>
             Facebook
             </a>
           </li>
@@ -221,6 +222,23 @@
  <span class="menu-text">Welcome</span></a>
   </div>
 </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-1" role="navigation" aria-expanded="true">
+ <span class="menu-text">Troubleshooting</span></a>
+          <a class="sidebar-item-toggle text-start" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" role="navigation" 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="./trouble/login.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Can’t log in</span></span></a>
+  </div>
+</li>
+      </ul>
+  </li>
     </ul>
     </div>
 </nav>
@@ -485,18 +503,7 @@ <h2 class="anchored" data-anchor-id="sec-welcome-licensing">Licensing</h2>
     }
     return false;
   }
-  const clipboard = new window.ClipboardJS('.code-copy-button', {
-    text: function(trigger) {
-      const codeEl = trigger.previousElementSibling.cloneNode(true);
-      for (const childEl of codeEl.children) {
-        if (isCodeAnnotation(childEl)) {
-          childEl.remove();
-        }
-      }
-      return codeEl.innerText;
-    }
-  });
-  clipboard.on('success', function(e) {
+  const onCopySuccess = function(e) {
     // button target
     const button = e.trigger;
     // don't keep focus
@@ -528,15 +535,37 @@ <h2 class="anchored" data-anchor-id="sec-welcome-licensing">Licensing</h2>
     }, 1000);
     // clear code selection
     e.clearSelection();
+  }
+  const getTextToCopy = function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+  }
+  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
+    text: getTextToCopy
   });
+  clipboard.on('success', onCopySuccess);
+  if (window.document.getElementById('quarto-embedded-source-code-modal')) {
+    // For code content inside modals, clipBoardJS needs to be initialized with a container option
+    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
+    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
+      text: getTextToCopy,
+      container: window.document.getElementById('quarto-embedded-source-code-modal')
+    });
+    clipboardModal.on('success', onCopySuccess);
+  }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
       var filterRegex = new RegExp('/' + window.location.host + '/');
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
     // Inspect non-navigation links and adorn them if external
- 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {
@@ -864,6 +893,15 @@ <h2 class="anchored" data-anchor-id="sec-welcome-licensing">Licensing</h2>
   }
 });
 </script>
+<nav class="page-navigation">
+  <div class="nav-page nav-page-previous">
+  </div>
+  <div class="nav-page nav-page-next">
+      <a href="./trouble/login.html" class="pagination-link" aria-label="Can't log in">
+        <span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Can’t log in</span></span> <i class="bi bi-arrow-right-short"></i>
+      </a>
+  </div>
+</nav>
 </div> <!-- /content -->
 <footer class="footer">
   <div class="nav-footer">

diff --git a/search.json b/search.json
@@ -1,4 +1,15 @@
 [
+  {
+    "objectID": "trouble/login.html",
+    "href": "trouble/login.html",
+    "title": "1  Can’t log in",
+    "section": "",
+    "text": "Chapter Leads: Thomas Wilson",
+    "crumbs": [
+      "Troubleshooting",
+      "<span class='chapter-number'>1</span>  <span class='chapter-title'>Can't log in</span>"
+    ]
+  },
   {
     "objectID": "index.html",
     "href": "index.html",

diff --git a/site_libs/bootstrap/bootstrap-dark.min.css b/site_libs/bootstrap/bootstrap-dark.min.css
diff --git a/site_libs/bootstrap/bootstrap.min.css b/site_libs/bootstrap/bootstrap.min.css
diff --git a/site_libs/quarto-html/quarto-syntax-highlighting.css b/site_libs/quarto-html/quarto-syntax-highlighting.css
diff --git a/site_libs/quarto-html/quarto.js b/site_libs/quarto-html/quarto.js
@@ -94,7 +94,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
       if (link.href.indexOf("#") !== -1) {
         const anchor = link.href.split("#")[1];
         const heading = window.document.querySelector(
-          `[data-anchor-id=${anchor}]`
+          `[data-anchor-id="${anchor}"]`
         );
         if (heading) {
           // Add the class
@@ -134,8 +134,10 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
       window.innerHeight + window.pageYOffset >=
       window.document.body.offsetHeight
     ) {
+      // This is the no-scroll case where last section should be the active one
       sectionIndex = 0;
     } else {
+      // This finds the last section visible on screen that should be made active
       sectionIndex = [...sections].reverse().findIndex((section) => {
         if (section) {
           return window.pageYOffset >= section.offsetTop - sectionMargin;
@@ -317,6 +319,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
           for (const child of el.children) {
             child.style.opacity = 0;
             child.style.overflow = "hidden";
+            child.style.pointerEvents = "none";
           }
 
           nexttick(() => {
@@ -358,6 +361,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
 
               const clone = child.cloneNode(true);
               clone.style.opacity = 1;
+              clone.style.pointerEvents = null;
               clone.style.display = null;
               toggleContents.append(clone);
             }
@@ -432,6 +436,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
           for (const child of el.children) {
             child.style.opacity = 1;
             child.style.overflow = null;
+            child.style.pointerEvents = null;
           }
 
           const placeholderEl = window.document.getElementById(
@@ -739,6 +744,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
     // Process the collapse state if this is an UL
     if (el.tagName === "UL") {
       if (tocOpenDepth === -1 && depth > 1) {
+        // toc-expand: false
         el.classList.add("collapse");
       } else if (
         depth <= tocOpenDepth ||
@@ -757,10 +763,9 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
   };
 
   // walk the TOC and expand / collapse any items that should be shown
-
   if (tocEl) {
-    walk(tocEl, 0);
     updateActiveLink();
+    walk(tocEl, 0);
   }
 
   // Throttle the scroll event and walk peridiocally
@@ -779,6 +784,10 @@ window.document.addEventListener("DOMContentLoaded", function (_event) {
   window.addEventListener(
     "resize",
     throttle(() => {
+      if (tocEl) {
+        updateActiveLink();
+        walk(tocEl, 0);
+      }
       if (!isReaderMode()) {
         hideOverlappedSidebars();
       }

diff --git a/site_libs/quarto-nav/quarto-nav.js b/site_libs/quarto-nav/quarto-nav.js
@@ -5,9 +5,45 @@ const headroomChanged = new CustomEvent("quarto-hrChanged", {
   composed: false,
 });
 
+const announceDismiss = () => {
+  const annEl = window.document.getElementById("quarto-announcement");
+  if (annEl) {
+    annEl.remove();
+
+    const annId = annEl.getAttribute("data-announcement-id");
+    window.localStorage.setItem(`quarto-announce-${annId}`, "true");
+  }
+};
+
+const announceRegister = () => {
+  const annEl = window.document.getElementById("quarto-announcement");
+  if (annEl) {
+    const annId = annEl.getAttribute("data-announcement-id");
+    const isDismissed =
+      window.localStorage.getItem(`quarto-announce-${annId}`) || false;
+    if (isDismissed) {
+      announceDismiss();
+      return;
+    } else {
+      annEl.classList.remove("hidden");
+    }
+
+    const actionEl = annEl.querySelector(".quarto-announcement-action");
+    if (actionEl) {
+      actionEl.addEventListener("click", function (e) {
+        e.preventDefault();
+        // Hide the bar immediately
+        announceDismiss();
+      });
+    }
+  }
+};
+
 window.document.addEventListener("DOMContentLoaded", function () {
   let init = false;
 
+  announceRegister();
+
   // Manage the back to top button, if one is present.
   let lastScrollTop = window.pageYOffset || document.documentElement.scrollTop;
   const scrollDownBuffer = 5;

diff --git a/site_libs/quarto-search/quarto-search.js b/site_libs/quarto-search/quarto-search.js
@@ -1275,7 +1275,11 @@ async function fuseSearch(query, fuse, fuseOptions) {
 
   // If we don't have a subfuse and the query is long enough, go ahead
   // and create a subfuse to use for subsequent queries
-  if (now - then > kFuseMaxWait && subSearchFuse === undefined) {
+  if (
+    now - then > kFuseMaxWait &&
+    subSearchFuse === undefined &&
+    resultsRaw.length < fuseOptions.limit
+  ) {
     subSearchTerm = query;
     subSearchFuse = new window.Fuse([], kFuseIndexOptions);
     resultsRaw.forEach((rr) => {