Built site for gh-pages

UCSB-Library-Research-Data-Services · Feb 16, 2024 · c67f4d5 · c67f4d5
1 parent 0c520fb
commit c67f4d5
Show file tree

Hide file tree

Showing 30 changed files with 4,154 additions and 693 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-1dec6c52
+ed5c2c40
diff --git a/01-handson_github_website.html b/01-handson_github_website.html
diff --git a/02-handson_github_rstudio.html b/02-handson_github_rstudio.html
diff --git a/03-handson_github_workflows.html b/03-handson_github_workflows.html
diff --git a/coding.html b/coding.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-1.3.450">
+<meta name="generator" content="quarto-1.4.550">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -47,7 +47,12 @@
   "collapse-after": 3,
   "panel-placement": "end",
   "type": "overlay",
-  "limit": 20,
+  "limit": 50,
+  "keyboard-shortcut": [
+    "f",
+    "/",
+    "s"
+  ],
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -56,6 +61,7 @@
     "search-more-match-text": "more match in this document",
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
+    "search-text-placeholder": "",
     "search-detached-cancel-button-title": "Cancel",
     "search-submit-button-title": "Submit",
     "search-label": "Search"
@@ -69,34 +75,34 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
-      <div class="navbar-brand-container">
+      <div class="navbar-brand-container mx-auto">
     <a class="navbar-brand" href="./index.html">
     <span class="navbar-title">Designing a Reproducible and Collaborative Lab (RCL)</span>
     </a>
   </div>
-        <div class="quarto-navbar-tools ms-auto">
-    <a href="https://github.com/UCSB-Library-Research-Data-Services/reproducible-lab" rel="" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-github"></i></a>
+        <div class="quarto-navbar-tools">
+    <a href="https://github.com/UCSB-Library-Research-Data-Services/reproducible-lab" title="" class="quarto-navigation-tool px-1" aria-label=""><i class="bi bi-github"></i></a>
 </div>
           <div id="quarto-search" class="" title="Search"></div>
       </div> <!-- /container-fluid -->
     </nav>
   <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,#quarto-sidebar-glass" 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" 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="./coding.html">Coding as a Lab</a></li><li class="breadcrumb-item"><a href="./coding.html">Code as scientific product</a></li></ol></nav>
-      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
-      </a>
+        <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./coding.html">Coding as a Lab</a></li><li class="breadcrumb-item"><a href="./coding.html">Code as scientific product</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>
     </div>
   </nav>
 </header>
 <!-- content -->
 <div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
 <!-- sidebar -->
-  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation docked overflow-auto">
+  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation docked overflow-auto">
     <div class="sidebar-menu-container"> 
     <ul class="list-unstyled mt-1">
         <li class="sidebar-item">
@@ -228,6 +234,23 @@
   <a href="./github_template.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Repository template</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 collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="false">
+ <span class="menu-text">Managing your Research data</span></a>
+          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="false" aria-label="Toggle section">
+            <i class="bi bi-chevron-right ms-2"></i>
+          </a> 
+      </div>
+      <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth2 ">  
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./data_mgmt.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">What is data management?</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -236,7 +259,7 @@
     </ul>
     </div>
 </nav>
-<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
+<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">
         <nav id="TOC" role="doc-toc" class="toc-active">
@@ -250,7 +273,7 @@ <h2 id="toc-title">On this page</h2>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
-<header id="title-block-header" class="quarto-title-block default">
+<header id="title-block-header" class="quarto-title-block default"><nav class="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./coding.html">Coding as a Lab</a></li><li class="breadcrumb-item"><a href="./coding.html">Code as scientific product</a></li></ol></nav>
 <div class="quarto-title">
 <h1 class="title">Code as scientific product</h1>
 </div>
@@ -265,8 +288,10 @@ <h1 class="title">Code as scientific product</h1>
   </div>
 
 
+
 </header>
 
+
 <p>Codes are part of the scientific products your Lab is producing. It is thus important to manage, document, and preserve them as you would do for any other of your scientific products. In this session, we will discuss tools and practices that can ease the management of your codes, as well as develop them in a collaborative way.</p>
 <section id="code-repository" class="level2">
 <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
@@ -385,10 +410,9 @@ <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
     // clear code selection
     e.clearSelection();
   });
-  function tippyHover(el, contentFn) {
+  function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
     const config = {
       allowHTML: true,
-      content: contentFn,
       maxWidth: 500,
       delay: 100,
       arrow: false,
@@ -398,8 +422,17 @@ <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
       interactive: true,
       interactiveBorder: 10,
       theme: 'quarto',
-      placement: 'bottom-start'
+      placement: 'bottom-start',
     };
+    if (contentFn) {
+      config.content = contentFn;
+    }
+    if (onTriggerFn) {
+      config.onTrigger = onTriggerFn;
+    }
+    if (onUntriggerFn) {
+      config.onUntrigger = onUntriggerFn;
+    }
     window.tippy(el, config); 
   }
   const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
@@ -413,6 +446,125 @@ <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
       const note = window.document.getElementById(id);
       return note.innerHTML;
     });
+  }
+  const xrefs = window.document.querySelectorAll('a.quarto-xref');
+  const processXRef = (id, note) => {
+    // Strip column container classes
+    const stripColumnClz = (el) => {
+      el.classList.remove("page-full", "page-columns");
+      if (el.children) {
+        for (const child of el.children) {
+          stripColumnClz(child);
+        }
+      }
+    }
+    stripColumnClz(note)
+    if (id === null || id.startsWith('sec-')) {
+      // Special case sections, only their first couple elements
+      const container = document.createElement("div");
+      if (note.children && note.children.length > 2) {
+        container.appendChild(note.children[0].cloneNode(true));
+        for (let i = 1; i < note.children.length; i++) {
+          const child = note.children[i];
+          if (child.tagName === "P" && child.innerText === "") {
+            continue;
+          } else {
+            container.appendChild(child.cloneNode(true));
+            break;
+          }
+        }
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(container);
+        }
+        return container.innerHTML
+      } else {
+        if (window.Quarto?.typesetMath) {
+          window.Quarto.typesetMath(note);
+        }
+        return note.innerHTML;
+      }
+    } else {
+      // Remove any anchor links if they are present
+      const anchorLink = note.querySelector('a.anchorjs-link');
+      if (anchorLink) {
+        anchorLink.remove();
+      }
+      if (window.Quarto?.typesetMath) {
+        window.Quarto.typesetMath(note);
+      }
+      // TODO in 1.5, we should make sure this works without a callout special case
+      if (note.classList.contains("callout")) {
+        return note.outerHTML;
+      } else {
+        return note.innerHTML;
+      }
+    }
+  }
+  for (var i=0; i<xrefs.length; i++) {
+    const xref = xrefs[i];
+    tippyHover(xref, undefined, function(instance) {
+      instance.disable();
+      let url = xref.getAttribute('href');
+      let hash = undefined; 
+      if (url.startsWith('#')) {
+        hash = url;
+      } else {
+        try { hash = new URL(url).hash; } catch {}
+      }
+      if (hash) {
+        const id = hash.replace(/^#\/?/, "");
+        const note = window.document.getElementById(id);
+        if (note !== null) {
+          try {
+            const html = processXRef(id, note.cloneNode(true));
+            instance.setContent(html);
+          } finally {
+            instance.enable();
+            instance.show();
+          }
+        } else {
+          // See if we can fetch this
+          fetch(url.split('#')[0])
+          .then(res => res.text())
+          .then(html => {
+            const parser = new DOMParser();
+            const htmlDoc = parser.parseFromString(html, "text/html");
+            const note = htmlDoc.getElementById(id);
+            if (note !== null) {
+              const html = processXRef(id, note);
+              instance.setContent(html);
+            } 
+          }).finally(() => {
+            instance.enable();
+            instance.show();
+          });
+        }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
+        // This is a special case and we should probably do some content thinning / targeting
+        fetch(url)
+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
+          if (note !== null) {
+            // This should only happen for chapter cross references
+            // (since there is no id in the URL)
+            // remove the first header
+            if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
+              note.children[0].remove();
+            }
+            const html = processXRef(null, note);
+            instance.setContent(html);
+          } 
+        }).finally(() => {
+          instance.enable();
+          instance.show();
+        });
+      }
+    }, function(instance) {
+    });
   }
       let selectedAnnoteEl;
       const selectorForAnnotation = ( cell, annotation) => {
@@ -455,6 +607,7 @@ <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
             }
             div.style.top = top - 2 + "px";
             div.style.height = height + 4 + "px";
+            div.style.left = 0;
             let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
             if (gutterDiv === null) {
               gutterDiv = window.document.createElement("div");
@@ -480,6 +633,32 @@ <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
         });
         selectedAnnoteEl = undefined;
       };
+        // Handle positioning of the toggle
+    window.addEventListener(
+      "resize",
+      throttle(() => {
+        elRect = undefined;
+        if (selectedAnnoteEl) {
+          selectCodeLines(selectedAnnoteEl);
+        }
+      }, 10)
+    );
+    function throttle(fn, ms) {
+    let throttle = false;
+    let timer;
+      return (...args) => {
+        if(!throttle) { // first call gets through
+            fn.apply(this, args);
+            throttle = true;
+        } else { // all the others get throttled
+            if(timer) clearTimeout(timer); // cancel #2
+            timer = setTimeout(() => {
+              fn.apply(this, args);
+              timer = throttle = false;
+            }, ms);
+        }
+      };
+    }
       // Attach click handler to the DT
       const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
       for (const annoteDlNode of annoteDls) {
@@ -541,12 +720,12 @@ <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="./index.html" class="pagination-link">
+      <a href="./index.html" class="pagination-link" aria-label="About RCL">
         <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">About RCL</span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./github_intro.html" class="pagination-link">
+      <a href="./github_intro.html" class="pagination-link" aria-label="Our tools: git &amp; GitHub">
         <span class="nav-page-text">Our tools: git &amp; GitHub</span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
@@ -555,4 +734,5 @@ <h2 class="anchored" data-anchor-id="code-repository">Code repository</h2>
 
 
 
+
 </body></html>