Read through and clean up

DukeStatSci · Aug 19, 2024 · e1b5e0d · e1b5e0d
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Showing 32 changed files with 2,880 additions and 1,889 deletions.
diff --git a/_quarto.yml b/_quarto.yml
@@ -9,10 +9,10 @@ book:
   repo-url: https://github.com/DukeStatSci/ta-manual
   repo-branch: main
   repo-actions: [edit, issue]
+  downloads: [pdf]
   chapters:
     - index.qmd
     - useful-links.qmd
-    - covid19.qmd
     - responsibilities.qmd
     - best-practices.qmd
     - policies.qmd
@@ -26,5 +26,8 @@ format:
   html: 
     mainfont: "Atkinson Hyperlegible"
     toc: true
+    theme:
+      light: [cosmo, style/style.scss]
+      dark: [solar, style/style.scss, style/style-dark.scss]
 
 editor: visual
diff --git a/best-practices.qmd b/best-practices.qmd
diff --git a/covid19.qmd b/covid19.qmd
diff --git a/docs/Duke-Statistical-Science-TA-Manual.pdf b/docs/Duke-Statistical-Science-TA-Manual.pdf
diff --git a/docs/best-practices.html b/docs/best-practices.html
diff --git a/docs/covid19.html b/docs/covid19.html
diff --git a/docs/evaluation-recognition.html b/docs/evaluation-recognition.html
diff --git a/docs/head-ta.html b/docs/head-ta.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/policies.html b/docs/policies.html
diff --git a/docs/resources.html b/docs/resources.html
diff --git a/docs/responsibilities.html b/docs/responsibilities.html
diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/site_libs/bootstrap/bootstrap-dark.min.css b/docs/site_libs/bootstrap/bootstrap-dark.min.css
diff --git a/docs/site_libs/bootstrap/bootstrap.min.css b/docs/site_libs/bootstrap/bootstrap.min.css
diff --git a/docs/site_libs/quarto-html/quarto-syntax-highlighting-dark.css b/docs/site_libs/quarto-html/quarto-syntax-highlighting-dark.css
diff --git a/docs/site_libs/quarto-html/quarto-syntax-highlighting.css b/docs/site_libs/quarto-html/quarto-syntax-highlighting.css
diff --git a/docs/site_libs/quarto-html/quarto.js b/docs/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/docs/site_libs/quarto-nav/quarto-nav.js b/docs/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;
@@ -237,6 +273,7 @@ window.document.addEventListener("DOMContentLoaded", function () {
     const links = window.document.querySelectorAll("a");
     for (let i = 0; i < links.length; i++) {
       if (links[i].href) {
+        links[i].dataset.originalHref = links[i].href;
         links[i].href = links[i].href.replace(/\/index\.html/, "/");
       }
     }