update docs

fastlmm · Feb 6, 2024 · 5b6e8ec · 5b6e8ec
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Showing 15 changed files with 160 additions and 101 deletions.
diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 0ffcf54393a856012dadc0b1563f2c43
+config: bf1d0a21c26d9c55c442915740521680
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_modules/bed_reader/_open_bed.html b/docs/_modules/bed_reader/_open_bed.html
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,16 +3,16 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; Bed Reader 1.0.1-beta.2 documentation</title>
+  <title>Overview: module code &mdash; Bed Reader 1.0.1-beta.5 documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
-        <script src="../_static/doctools.js"></script>
-        <script src="../_static/sphinx_highlight.js"></script>
+        <script src="../_static/documentation_options.js?v=8c107f28"></script>
+        <script src="../_static/doctools.js?v=888ff710"></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" /> 
@@ -30,7 +30,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.1-beta.2
+                1.0.1-beta.5
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">

diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -11,6 +11,7 @@
 ################################
 
 .. currentmodule:: bed_reader
+
 Read and write the PLINK BED format, simply and efficiently.
 
 Features:

diff --git a/docs/_static/basic.css b/docs/_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,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,5 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.0.1-beta.2',
+const DOCUMENTATION_OPTIONS = {
+    VERSION: '1.0.1-beta.5',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_static/searchtools.js b/docs/_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/docs/_static/sphinx_highlight.js b/docs/_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();
+});
diff --git a/docs/cloud_urls.html b/docs/cloud_urls.html
@@ -4,16 +4,16 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Cloud URL Examples &mdash; Bed Reader 1.0.1-beta.2 documentation</title>
+  <title>Cloud URL Examples &mdash; Bed Reader 1.0.1-beta.5 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
+        <script src="_static/documentation_options.js?v=8c107f28"></script>
+        <script src="_static/doctools.js?v=888ff710"></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" />
@@ -32,7 +32,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.1-beta.2
+                1.0.1-beta.5
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -79,7 +79,7 @@
            <div itemprop="articleBody">
 
   <section id="cloud-url-examples">
-<h1>Cloud URL Examples<a class="headerlink" href="#cloud-url-examples" title="Permalink to this heading"></a></h1>
+<h1>Cloud URL Examples<a class="headerlink" href="#cloud-url-examples" title="Link to this heading"></a></h1>
 <p><em>Table of Contents</em>:</p>
 <ul class="simple">
 <li><p><a class="reference external" href="#http-section">Http</a></p></li>
@@ -93,7 +93,7 @@ <h1>Cloud URL Examples<a class="headerlink" href="#cloud-url-examples" title="Pe
 <p>To specify a file in the cloud, you must specify URL string plus optional cloud options.</p>
 <p>The exact details depend on the cloud service. We’ll look at <cite>http</cite>, at <cite>local files</cite>, and at <cite>AWS S3</cite>.</p>
 <section id="http-section">
-<span id="id1"></span><h2>Http<a class="headerlink" href="#http-section" title="Permalink to this heading"></a></h2>
+<span id="id1"></span><h2>Http<a class="headerlink" href="#http-section" title="Link to this heading"></a></h2>
 <p>You can read *.bed files from web sites directly. For small files, access will be fast. For medium-sized files,
 you may need to extend the default <cite>timeout</cite>.</p>
 <p>Reading from large files can also be practical and even fast under these conditions:</p>
@@ -199,11 +199,11 @@ <h1>Cloud URL Examples<a class="headerlink" href="#cloud-url-examples" title="Pe
 </div>
 </section>
 <section id="local-file-section">
-<span id="id2"></span><h2>Local File<a class="headerlink" href="#local-file-section" title="Permalink to this heading"></a></h2>
+<span id="id2"></span><h2>Local File<a class="headerlink" href="#local-file-section" title="Link to this heading"></a></h2>
 <p>We can specify a local file as if it is in the cloud. This is a great way to test cloud functions. For real work and better efficiency, however,
 use the file’s path rather than its URL.</p>
 <section id="local-file-url">
-<h3>Local File URL<a class="headerlink" href="#local-file-url" title="Permalink to this heading"></a></h3>
+<h3>Local File URL<a class="headerlink" href="#local-file-url" title="Link to this heading"></a></h3>
 <p>The URL for a local file takes the form <cite>file:///{encoded_file_name}</cite>. No cloud options are needed.</p>
 <p><em>Example:</em></p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
@@ -227,7 +227,7 @@ <h3>Local File URL<a class="headerlink" href="#local-file-url" title="Permalink
 </section>
 </section>
 <section id="aws-section">
-<span id="id3"></span><h2>AWS S3<a class="headerlink" href="#aws-section" title="Permalink to this heading"></a></h2>
+<span id="id3"></span><h2>AWS S3<a class="headerlink" href="#aws-section" title="Link to this heading"></a></h2>
 <p>Let’s look next at reading a file (or part of a file) from AWS S3.</p>
 <p>The URL for an AWS S3 file takes the form <cite>s3://{bucket_name}/{s3_path}</cite>.</p>
 <p>AWS forbids putting some needed information in the URL. Instead, that information must go into a string-to-string

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -3,16 +3,16 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; Bed Reader 1.0.1-beta.2 documentation</title>
+  <title>Index &mdash; Bed Reader 1.0.1-beta.5 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-        <script src="_static/doctools.js"></script>
-        <script src="_static/sphinx_highlight.js"></script>
+        <script src="_static/documentation_options.js?v=8c107f28"></script>
+        <script src="_static/doctools.js?v=888ff710"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" /> 
@@ -30,7 +30,7 @@
             Bed Reader
           </a>
               <div class="version">
-                1.0.1-beta.2
+                1.0.1-beta.5
               </div>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">