Updating compiled documentation

biosimulators · Mar 3, 2021 · 97b9618 · 97b9618
1 parent b07d921
commit 97b9618
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Showing 28 changed files with 2,770 additions and 755 deletions.
diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js
@@ -29,9 +29,14 @@ if (!window.console || !console.firebug) {
 
 /**
  * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
  */
 jQuery.urldecode = function(x) {
-  return decodeURIComponent(x).replace(/\+/g, ' ');
+  if (!x) {
+    return x
+  }
+  return decodeURIComponent(x.replace(/\+/g, ' '));
 };
 
 /**

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.1.39',
+    VERSION: '0.1.40',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js
@@ -13,7 +13,8 @@
 var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
 
 
-/* Non-minified version JS is _stemmer.js if file is provided */ 
+/* Non-minified version is copied as a separate JS file, is available */
+
 /**
  * Porter Stemmer
  */
@@ -199,7 +200,6 @@ var Stemmer = function() {
 
 
 
-
 var splitChars = (function() {
     var result = {};
     var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,

diff --git a/docs/_static/pygments.css b/docs/_static/pygments.css
@@ -1,7 +1,7 @@
 pre { line-height: 125%; }
-td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
-span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
-td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+td.linenos .normal { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: inherit; background-color: transparent; padding-left: 5px; padding-right: 5px; }
+td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 .highlight .hll { background-color: #ffffcc }
 .highlight { background: #eeffcc; }

diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -248,7 +248,7 @@ var Search = {
       // results left, load the summary and display it
       if (results.length) {
         var item = results.pop();
-        var listItem = $('<li style="display:none"></li>');
+        var listItem = $('<li></li>');
         var requestUrl = "";
         var linkUrl = "";
         if (DOCUMENTATION_OPTIONS.BUILDER === 'dirhtml') {
@@ -273,9 +273,9 @@ var Search = {
         if (item[3]) {
           listItem.append($('<span> (' + item[3] + ')</span>'));
           Search.output.append(listItem);
-          listItem.slideDown(5, function() {
+          setTimeout(function() {
             displayNextItem();
-          });
+          }, 5);
         } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
           $.ajax({url: requestUrl,
                   dataType: "text",
@@ -285,16 +285,16 @@ var Search = {
                       listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
                     }
                     Search.output.append(listItem);
-                    listItem.slideDown(5, function() {
+                    setTimeout(function() {
                       displayNextItem();
-                    });
+                    }, 5);
                   }});
         } else {
           // no source available, just display title
           Search.output.append(listItem);
-          listItem.slideDown(5, function() {
+          setTimeout(function() {
             displayNextItem();
-          });
+          }, 5);
         }
       }
       // search finished, update title and status message
@@ -379,6 +379,13 @@ var Search = {
     return results;
   },
 
+  /**
+   * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions
+   */
+  escapeRegExp : function(string) {
+    return string.replace(/[.*+\-?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string
+  },
+
   /**
    * search for full-text terms in the index
    */
@@ -402,13 +409,14 @@ var Search = {
       ];
       // add support for partial matches
       if (word.length > 2) {
+        var word_regex = this.escapeRegExp(word);
         for (var w in terms) {
-          if (w.match(word) && !terms[word]) {
+          if (w.match(word_regex) && !terms[word]) {
             _o.push({files: terms[w], score: Scorer.partialTerm})
           }
         }
         for (var w in titleterms) {
-          if (w.match(word) && !titleterms[word]) {
+          if (w.match(word_regex) && !titleterms[word]) {
               _o.push({files: titleterms[w], score: Scorer.partialTitle})
           }
         }