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graphcore-research · Mar 13, 2024 · 68b55a3 · 68b55a3
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diff --git a/API_reference.html b/API_reference.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="./">
 <head>
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
@@ -16,9 +16,9 @@
 
         <script src="_static/jquery.js?v=5d32c60e"></script>
         <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js?v=b3ba4146"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
-        <script src="_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -80,7 +80,7 @@
            <div itemprop="articleBody">
 
   <section id="api-reference">
-<h1>API Reference<a class="headerlink" href="#api-reference" title="Permalink to this heading"></a></h1>
+<h1>API Reference<a class="headerlink" href="#api-reference" title="Link to this heading"></a></h1>
 <table class="autosummary longtable docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/kg_topology_toolbox.topology_toolbox.html#module-kg_topology_toolbox.topology_toolbox" title="kg_topology_toolbox.topology_toolbox"><code class="xref py py-obj docutils literal notranslate"><span class="pre">kg_topology_toolbox.topology_toolbox</span></code></a></p></td>

diff --git a/_modules/index.html b/_modules/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -15,9 +15,9 @@
 
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=b3ba4146"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
-        <script src="../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 

diff --git a/_modules/kg_topology_toolbox/topology_toolbox.html b/_modules/kg_topology_toolbox/topology_toolbox.html
diff --git a/_modules/kg_topology_toolbox/utils.html b/_modules/kg_topology_toolbox/utils.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en">
+<html class="writer-html5" lang="en" data-content_root="../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
@@ -15,9 +15,9 @@
 
         <script src="../../_static/jquery.js?v=5d32c60e"></script>
         <script src="../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script data-url_root="../../" id="documentation_options" src="../../_static/documentation_options.js?v=b3ba4146"></script>
+        <script src="../../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../_static/sphinx_highlight.js?v=4825356b"></script>
+        <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
@@ -87,7 +87,9 @@ <h1>Source code for kg_topology_toolbox.utils</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">scipy.sparse</span> <span class="kn">import</span> <span class="n">coo_array</span><span class="p">,</span> <span class="n">csc_array</span><span class="p">,</span> <span class="n">csr_array</span>
 
 
-<div class="viewcode-block" id="jaccard_similarity"><a class="viewcode-back" href="../../generated/kg_topology_toolbox.utils.jaccard_similarity.html#kg_topology_toolbox.utils.jaccard_similarity">[docs]</a><span class="k">def</span> <span class="nf">jaccard_similarity</span><span class="p">(</span>
+<div class="viewcode-block" id="jaccard_similarity">
+<a class="viewcode-back" href="../../generated/kg_topology_toolbox.utils.jaccard_similarity.html#kg_topology_toolbox.utils.jaccard_similarity">[docs]</a>
+<span class="k">def</span> <span class="nf">jaccard_similarity</span><span class="p">(</span>
     <span class="n">entities_1</span><span class="p">:</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">],</span> <span class="n">entities_2</span><span class="p">:</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">int32</span><span class="p">]</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
@@ -103,7 +105,10 @@ <h1>Source code for kg_topology_toolbox.utils</h1><div class="highlight"><pre>
     <span class="k">return</span> <span class="nb">float</span><span class="p">(</span><span class="n">intersection</span> <span class="o">/</span> <span class="n">union</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="composition_count"><a class="viewcode-back" href="../../generated/kg_topology_toolbox.utils.composition_count.html#kg_topology_toolbox.utils.composition_count">[docs]</a><span class="k">def</span> <span class="nf">composition_count</span><span class="p">(</span>
+
+<div class="viewcode-block" id="composition_count">
+<a class="viewcode-back" href="../../generated/kg_topology_toolbox.utils.composition_count.html#kg_topology_toolbox.utils.composition_count">[docs]</a>
+<span class="k">def</span> <span class="nf">composition_count</span><span class="p">(</span>
     <span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">chunk_size</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">workers</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">directed</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;A helper function to compute the composition count of a graph.</span>
@@ -167,6 +172,7 @@ <h1>Source code for kg_topology_toolbox.utils</h1><div class="highlight"><pre>
         <span class="p">]</span>
 
     <span class="k">return</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">df_composition_list</span><span class="p">)</span></div>
+
 </pre></div>
 
            </div>

diff --git a/_static/basic.css b/_static/basic.css
@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

diff --git a/_static/searchtools.js b/_static/searchtools.js
@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**

diff --git a/_static/sphinx_highlight.js b/_static/sphinx_highlight.js
@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});