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nmfs-opensci · Dec 3, 2024 · 60e6741 · 60e6741
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-388aaefc
+8432fb72
diff --git a/coc.html b/coc.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-1.6.39">
+<meta name="generator" content="quarto-1.5.55">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -37,12 +37,12 @@
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="site_libs/quarto-html/anchor.min.js"></script>
 <link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting-dark-d166b450ba5a8e9f7a0ab969bf6592c1.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
 <script src="site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="site_libs/bootstrap/bootstrap-34f0718a046e1c696f050a04181c961f.min.css" rel="stylesheet" append-hash="true" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
-<link href="site_libs/bootstrap/bootstrap-dark-23c114e9f269a5bcf5260e6b10ff2021.min.css" rel="prefetch" append-hash="true" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
+<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
+<link href="site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -260,12 +260,6 @@
   <a href="./tutorials/tutorial-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Dynamic output in Quarto files: Code, Tables, and Figures</span></a>
   </div>
-</li>
-          <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./tutorials/tutorial-4.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Cross-references, bibliography and citations in Quarto files</span></a>
-  </div>
 </li>
       </ul>
   </li>
@@ -580,6 +574,8 @@ <h2 class="anchored" data-anchor-id="reporting-a-violation">Reporting a violatio
   });
   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')
@@ -690,6 +686,7 @@ <h2 class="anchored" data-anchor-id="reporting-a-violation">Reporting a violatio
       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 {

diff --git a/content/01-accessing-jupyterhub.html b/content/01-accessing-jupyterhub.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-1.6.39">
+<meta name="generator" content="quarto-1.5.55">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -37,12 +37,12 @@
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="../site_libs/quarto-html/anchor.min.js"></script>
 <link href="../site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark-d166b450ba5a8e9f7a0ab969bf6592c1.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
 <script src="../site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="../site_libs/bootstrap/bootstrap-34f0718a046e1c696f050a04181c961f.min.css" rel="stylesheet" append-hash="true" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
-<link href="../site_libs/bootstrap/bootstrap-dark-23c114e9f269a5bcf5260e6b10ff2021.min.css" rel="prefetch" append-hash="true" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
+<link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
+<link href="../site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -260,12 +260,6 @@
   <a href="../tutorials/tutorial-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Dynamic output in Quarto files: Code, Tables, and Figures</span></a>
   </div>
-</li>
-          <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../tutorials/tutorial-4.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Cross-references, bibliography and citations in Quarto files</span></a>
-  </div>
 </li>
       </ul>
   </li>
@@ -559,6 +553,8 @@ <h3 class="anchored" data-anchor-id="accepting-the-invite">Accepting the invite<
   });
   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')
@@ -669,6 +665,7 @@ <h3 class="anchored" data-anchor-id="accepting-the-invite">Accepting the invite<
       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 {

diff --git a/content/01-intro-to-jupyterhub.html b/content/01-intro-to-jupyterhub.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-1.6.39">
+<meta name="generator" content="quarto-1.5.55">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -37,12 +37,12 @@
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="../site_libs/quarto-html/anchor.min.js"></script>
 <link href="../site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark-d166b450ba5a8e9f7a0ab969bf6592c1.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
 <script src="../site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="../site_libs/bootstrap/bootstrap-34f0718a046e1c696f050a04181c961f.min.css" rel="stylesheet" append-hash="true" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
-<link href="../site_libs/bootstrap/bootstrap-dark-23c114e9f269a5bcf5260e6b10ff2021.min.css" rel="prefetch" append-hash="true" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
+<link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
+<link href="../site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -260,12 +260,6 @@
   <a href="../tutorials/tutorial-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Dynamic output in Quarto files: Code, Tables, and Figures</span></a>
   </div>
-</li>
-          <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../tutorials/tutorial-4.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Cross-references, bibliography and citations in Quarto files</span></a>
-  </div>
 </li>
       </ul>
   </li>
@@ -709,6 +703,8 @@ <h3 class="anchored" data-anchor-id="acknowledgements">Acknowledgements</h3>
   });
   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')
@@ -819,6 +815,7 @@ <h3 class="anchored" data-anchor-id="acknowledgements">Acknowledgements</h3>
       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 {

diff --git a/content/01-repro-reports.html b/content/01-repro-reports.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-1.6.39">
+<meta name="generator" content="quarto-1.5.55">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -37,12 +37,12 @@
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="../site_libs/quarto-html/anchor.min.js"></script>
 <link href="../site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark-d166b450ba5a8e9f7a0ab969bf6592c1.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
 <script src="../site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="../site_libs/bootstrap/bootstrap-34f0718a046e1c696f050a04181c961f.min.css" rel="stylesheet" append-hash="true" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
-<link href="../site_libs/bootstrap/bootstrap-dark-23c114e9f269a5bcf5260e6b10ff2021.min.css" rel="prefetch" append-hash="true" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
+<link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
+<link href="../site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -260,12 +260,6 @@
   <a href="../tutorials/tutorial-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Dynamic output in Quarto files: Code, Tables, and Figures</span></a>
   </div>
-</li>
-          <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../tutorials/tutorial-4.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Cross-references, bibliography and citations in Quarto files</span></a>
-  </div>
 </li>
       </ul>
   </li>
@@ -562,6 +556,8 @@ <h3 class="anchored" data-anchor-id="examples-of-nmfs-reproducible-reports">Exam
   });
   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')
@@ -672,6 +668,7 @@ <h3 class="anchored" data-anchor-id="examples-of-nmfs-reproducible-reports">Exam
       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 {

diff --git a/content/02-git-2.html b/content/02-git-2.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-1.6.39">
+<meta name="generator" content="quarto-1.5.55">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -35,12 +35,12 @@
 <script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="../site_libs/quarto-html/anchor.min.js"></script>
 <link href="../site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-e26003cea8cd680ca0c55a263523d882.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark-d166b450ba5a8e9f7a0ab969bf6592c1.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-text-highlighting-styles">
+<link href="../site_libs/quarto-html/quarto-syntax-highlighting-dark.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-text-highlighting-styles">
 <script src="../site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="../site_libs/bootstrap/bootstrap-34f0718a046e1c696f050a04181c961f.min.css" rel="stylesheet" append-hash="true" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
-<link href="../site_libs/bootstrap/bootstrap-dark-23c114e9f269a5bcf5260e6b10ff2021.min.css" rel="prefetch" append-hash="true" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
+<link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" class="quarto-color-scheme" id="quarto-bootstrap" data-mode="light">
+<link href="../site_libs/bootstrap/bootstrap-dark.min.css" rel="prefetch" class="quarto-color-scheme quarto-color-alternate" id="quarto-bootstrap" data-mode="dark">
 <script id="quarto-search-options" type="application/json">{
   "location": "navbar",
   "copy-button": false,
@@ -258,12 +258,6 @@
   <a href="../tutorials/tutorial-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Dynamic output in Quarto files: Code, Tables, and Figures</span></a>
   </div>
-</li>
-          <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="../tutorials/tutorial-4.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text">Cross-references, bibliography and citations in Quarto files</span></a>
-  </div>
 </li>
       </ul>
   </li>
@@ -602,6 +596,8 @@ <h3 class="anchored" data-anchor-id="step-3-trigger-git-to-ask-for-your-password
   });
   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')
@@ -712,6 +708,7 @@ <h3 class="anchored" data-anchor-id="step-3-trigger-git-to-ask-for-your-password
       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 {