Merge pull request #2 from 3mmaRand/draft-core-1

Draft core 1
3mmaRand · Sep 28, 2023 · dd66558 · dd66558
2 parents 8d29a21 + 8e70e61
commit dd66558
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Showing 49 changed files with 15,913 additions and 4,691 deletions.
diff --git a/.github/workflows/quarto-gh-pages-html.yaml b/.github/workflows/quarto-gh-pages-html.yaml
@@ -33,7 +33,12 @@ jobs:
 
       # Install any computing dependency you may need, usually either python and Jupyter or R
       # More specific examples will be shared on quarto-dev/quarto-actions project
-
+
+      - name: Install R package
+        run: |
+          R -e "install.packages('xml2')"
+          R -e "install.packages('downlit')"
+     
       - name: Render book to all format
         # Add any command line argument needed
         run: |

diff --git a/_site/about.html b/_site/about.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-1.3.361">
+<meta name="generator" content="quarto-1.2.269">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -18,7 +18,7 @@
 ul.task-list{list-style: none;}
 ul.task-list li input[type="checkbox"] {
   width: 0.8em;
-  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
+  margin: 0 0.8em 0.2em -1.6em;
   vertical-align: middle;
 }
 </style>
@@ -56,12 +56,12 @@
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
     "search-detached-cancel-button-title": "Cancel",
-    "search-submit-button-title": "Submit",
-    "search-label": "Search"
+    "search-submit-button-title": "Submit"
   }
 }</script>
 
 
+<link rel="stylesheet" href="styles.css">
 </head>
 
 <body class="nav-fixed fullcontent">
@@ -75,29 +75,25 @@
     <span class="navbar-title">Data Analysis for Group Project</span>
     </a>
   </div>
-            <div id="quarto-search" class="" title="Search"></div>
           <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
             <ul class="navbar-nav navbar-nav-scroll me-auto">
   <li class="nav-item">
-    <a class="nav-link" href="./index.html" rel="" target="">
+    <a class="nav-link" href="./index.html">
  <span class="menu-text">Welcome!</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./core/core.html" rel="" target="">
+    <a class="nav-link" href="./core/core.html">
  <span class="menu-text">Core</span></a>
   </li>  
   <li class="nav-item">
-    <a class="nav-link" href="./omics/omics.html" rel="" target="">
+    <a class="nav-link" href="./omics/omics.html">
  <span class="menu-text">Omics</span></a>
   </li>  
 </ul>
-            <div class="quarto-navbar-tools ms-auto">
-    <a href="https://twitter.com/er_13" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
-    <a href="https://github.com/3mmaRand/BIO00088H-data" title="BIO00088H-data GitHub" class="quarto-navigation-tool px-1" aria-label="BIO00088H-data GitHub"><i class="bi bi-github"></i></a>
-</div>
+              <div id="quarto-search" class="" title="Search"></div>
           </div> <!-- /navcollapse -->
       </div> <!-- /container-fluid -->
     </nav>
@@ -159,23 +155,9 @@ <h1 class="title">About</h1>
     icon: icon
   };
   anchorJS.add('.anchored');
-  const isCodeAnnotation = (el) => {
-    for (const clz of el.classList) {
-      if (clz.startsWith('code-annotation-')) {                     
-        return true;
-      }
-    }
-    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;
+    target: function(trigger) {
+      return trigger.previousElementSibling;
     }
   });
   clipboard.on('success', function(e) {
@@ -240,92 +222,6 @@ <h1 class="title">About</h1>
       return note.innerHTML;
     });
   }
-      let selectedAnnoteEl;
-      const selectorForAnnotation = ( cell, annotation) => {
-        let cellAttr = 'data-code-cell="' + cell + '"';
-        let lineAttr = 'data-code-annotation="' +  annotation + '"';
-        const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
-        return selector;
-      }
-      const selectCodeLines = (annoteEl) => {
-        const doc = window.document;
-        const targetCell = annoteEl.getAttribute("data-target-cell");
-        const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
-        const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
-        const lines = annoteSpan.getAttribute("data-code-lines").split(",");
-        const lineIds = lines.map((line) => {
-          return targetCell + "-" + line;
-        })
-        let top = null;
-        let height = null;
-        let parent = null;
-        if (lineIds.length > 0) {
-            //compute the position of the single el (top and bottom and make a div)
-            const el = window.document.getElementById(lineIds[0]);
-            top = el.offsetTop;
-            height = el.offsetHeight;
-            parent = el.parentElement.parentElement;
-          if (lineIds.length > 1) {
-            const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
-            const bottom = lastEl.offsetTop + lastEl.offsetHeight;
-            height = bottom - top;
-          }
-          if (top !== null && height !== null && parent !== null) {
-            // cook up a div (if necessary) and position it 
-            let div = window.document.getElementById("code-annotation-line-highlight");
-            if (div === null) {
-              div = window.document.createElement("div");
-              div.setAttribute("id", "code-annotation-line-highlight");
-              div.style.position = 'absolute';
-              parent.appendChild(div);
-            }
-            div.style.top = top - 2 + "px";
-            div.style.height = height + 4 + "px";
-            let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
-            if (gutterDiv === null) {
-              gutterDiv = window.document.createElement("div");
-              gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
-              gutterDiv.style.position = 'absolute';
-              const codeCell = window.document.getElementById(targetCell);
-              const gutter = codeCell.querySelector('.code-annotation-gutter');
-              gutter.appendChild(gutterDiv);
-            }
-            gutterDiv.style.top = top - 2 + "px";
-            gutterDiv.style.height = height + 4 + "px";
-          }
-          selectedAnnoteEl = annoteEl;
-        }
-      };
-      const unselectCodeLines = () => {
-        const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
-        elementsIds.forEach((elId) => {
-          const div = window.document.getElementById(elId);
-          if (div) {
-            div.remove();
-          }
-        });
-        selectedAnnoteEl = undefined;
-      };
-      // Attach click handler to the DT
-      const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
-      for (const annoteDlNode of annoteDls) {
-        annoteDlNode.addEventListener('click', (event) => {
-          const clickedEl = event.target;
-          if (clickedEl !== selectedAnnoteEl) {
-            unselectCodeLines();
-            const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
-            if (activeEl) {
-              activeEl.classList.remove('code-annotation-active');
-            }
-            selectCodeLines(clickedEl);
-            clickedEl.classList.add('code-annotation-active');
-          } else {
-            // Unselect the line
-            unselectCodeLines();
-            clickedEl.classList.remove('code-annotation-active');
-          }
-        });
-      }
   const findCites = (el) => {
     const parentEl = el.parentElement;
     if (parentEl) {
@@ -364,12 +260,12 @@ <h1 class="title">About</h1>
     }
   }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
-      var filterRegex = new RegExp("^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data");
+      var filterRegex = new RegExp(/^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data/);
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.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)');
+    var links = window.document.querySelectorAll('a: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)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {
@@ -383,9 +279,6 @@ <h1 class="title">About</h1>
 <footer class="footer">
   <div class="nav-footer">
     <div class="nav-footer-left"><code>r cffr::cff_to_bibtex("CITATION.cff")</code></div>   
-    <div class="nav-footer-center">
-      &nbsp;
-    </div>
     <div class="nav-footer-right">
       <ul class="footer-items list-unstyled">
     <li class="nav-item compact">