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sipbs-compbiol · Jun 3, 2024 · 359f357 · 359f357
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Showing 19 changed files with 1,294 additions and 447 deletions.
diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-15c66c27
+fc15bd82
diff --git a/about.html b/about.html
diff --git a/calendar.html b/calendar.html
diff --git a/expectations.html b/expectations.html
diff --git a/figures.html b/figures.html
diff --git a/index.html b/index.html
diff --git a/learning_resources.html b/learning_resources.html
diff --git a/methods.html b/methods.html
diff --git a/online_resources.html b/online_resources.html
diff --git a/presentation.html b/presentation.html
diff --git a/scicomm.html b/scicomm.html
diff --git a/search.json b/search.json
diff --git a/site_libs/bootstrap/bootstrap.min.css b/site_libs/bootstrap/bootstrap.min.css
diff --git a/site_libs/quarto-nav/quarto-nav.js b/site_libs/quarto-nav/quarto-nav.js
@@ -237,6 +237,7 @@ 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/, "/");
       }
     }

diff --git a/site_libs/quarto-search/quarto-search.js b/site_libs/quarto-search/quarto-search.js
@@ -675,6 +675,18 @@ function showCopyLink(query, options) {
 // create the index
 var fuseIndex = undefined;
 var shownWarning = false;
+
+// fuse index options
+const kFuseIndexOptions = {
+  keys: [
+    { name: "title", weight: 20 },
+    { name: "section", weight: 20 },
+    { name: "text", weight: 10 },
+  ],
+  ignoreLocation: true,
+  threshold: 0.1,
+};
+
 async function readSearchData() {
   // Initialize the search index on demand
   if (fuseIndex === undefined) {
@@ -685,17 +697,7 @@ async function readSearchData() {
       shownWarning = true;
       return;
     }
-    // create fuse index
-    const options = {
-      keys: [
-        { name: "title", weight: 20 },
-        { name: "section", weight: 20 },
-        { name: "text", weight: 10 },
-      ],
-      ignoreLocation: true,
-      threshold: 0.1,
-    };
-    const fuse = new window.Fuse([], options);
+    const fuse = new window.Fuse([], kFuseIndexOptions);
 
     // fetch the main search.json
     const response = await fetch(offsetURL("search.json"));
@@ -1226,8 +1228,34 @@ function algoliaSearch(query, limit, algoliaOptions) {
   });
 }
 
-function fuseSearch(query, fuse, fuseOptions) {
-  return fuse.search(query, fuseOptions).map((result) => {
+let subSearchTerm = undefined;
+let subSearchFuse = undefined;
+const kFuseMaxWait = 125;
+
+async function fuseSearch(query, fuse, fuseOptions) {
+  let index = fuse;
+  // Fuse.js using the Bitap algorithm for text matching which runs in
+  // O(nm) time (no matter the structure of the text). In our case this
+  // means that long search terms mixed with large index gets very slow
+  //
+  // This injects a subIndex that will be used once the terms get long enough
+  // Usually making this subindex is cheap since there will typically be
+  // a subset of results matching the existing query
+  if (subSearchFuse !== undefined && query.startsWith(subSearchTerm)) {
+    // Use the existing subSearchFuse
+    index = subSearchFuse;
+  } else if (subSearchFuse !== undefined) {
+    // The term changed, discard the existing fuse
+    subSearchFuse = undefined;
+    subSearchTerm = undefined;
+  }
+
+  // Search using the active fuse
+  const then = performance.now();
+  const resultsRaw = await index.search(query, fuseOptions);
+  const now = performance.now();
+
+  const results = resultsRaw.map((result) => {
     const addParam = (url, name, value) => {
       const anchorParts = url.split("#");
       const baseUrl = anchorParts[0];
@@ -1244,4 +1272,15 @@ function fuseSearch(query, fuse, fuseOptions) {
       crumbs: result.item.crumbs,
     };
   });
+
+  // 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) {
+    subSearchTerm = query;
+    subSearchFuse = new window.Fuse([], kFuseIndexOptions);
+    resultsRaw.forEach((rr) => {
+      subSearchFuse.add(rr.item);
+    });
+  }
+  return results;
 }
diff --git a/sitemap.xml b/sitemap.xml
@@ -1,55 +1,55 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <urlset xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/scicomm.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/presentation.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/thesis.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/learning_resources.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/presentation.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/expectations.html</loc>
+    <lastmod>2024-06-03T14:49:30.721Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/online_resources.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/methods.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/figures.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/index.html</loc>
+    <lastmod>2024-06-03T14:49:30.721Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/time_management.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/thesis.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/software.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/about.html</loc>
+    <lastmod>2024-06-03T14:49:30.681Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/index.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/time_management.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/about.html</loc>
-    <lastmod>2024-01-30T09:13:00.649Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/figures.html</loc>
+    <lastmod>2024-06-03T14:49:30.721Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/expectations.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/calendar.html</loc>
+    <lastmod>2024-06-03T14:49:30.721Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/calendar.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/software.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/methods.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/online_resources.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
   <url>
-    <loc>https://sipbs-compbiol.github.io/bm432-project/learning_resources.html</loc>
-    <lastmod>2024-01-30T09:13:00.689Z</lastmod>
+    <loc>https://sipbs-compbiol.github.io/bm432-project/scicomm.html</loc>
+    <lastmod>2024-06-03T14:49:30.725Z</lastmod>
   </url>
 </urlset>
diff --git a/software.html b/software.html
diff --git a/thesis.html b/thesis.html
diff --git a/time_management.html b/time_management.html