deploy: 3b0905d

molssi-seamm · Oct 15, 2024 · 45cf745 · 45cf745
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diff --git a/.buildinfo b/.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: edd266f8b85f32302a9b56e7c8909917
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 727a346649e8f140a23ff6388ebd638b
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/_modules/index.html b/_modules/index.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>Overview: module code &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/loop_step/loop.html b/_modules/loop_step/loop.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>loop_step.loop &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>loop_step.loop &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>
@@ -632,7 +632,7 @@ <h1>Source code for loop_step.loop</h1><div class="highlight"><pre>
         <span class="n">next_node</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">loop_node</span><span class="p">()</span>
         <span class="k">while</span> <span class="n">next_node</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">next_node</span> <span class="o">!=</span> <span class="n">join_node</span><span class="p">:</span>
             <span class="n">text</span> <span class="o">+=</span> <span class="s2">&quot;</span><span class="se">\n\n</span><span class="s2">&quot;</span>
-            <span class="n">text</span> <span class="o">+=</span> <span class="n">__</span><span class="p">(</span><span class="n">next_node</span><span class="o">.</span><span class="n">description_text</span><span class="p">(),</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span> <span class="o">*</span> <span class="s2">&quot; &quot;</span><span class="p">)</span><span class="o">.</span><span class="fm">__str__</span><span class="p">()</span>
+            <span class="n">text</span> <span class="o">+=</span> <span class="nb">str</span><span class="p">(</span><span class="n">__</span><span class="p">(</span><span class="n">next_node</span><span class="o">.</span><span class="n">description_text</span><span class="p">(),</span> <span class="n">indent</span><span class="o">=</span><span class="mi">4</span> <span class="o">*</span> <span class="s2">&quot; &quot;</span><span class="p">,</span> <span class="n">wrap</span><span class="o">=</span><span class="kc">False</span><span class="p">))</span>
             <span class="n">next_node</span> <span class="o">=</span> <span class="n">next_node</span><span class="o">.</span><span class="n">next</span><span class="p">()</span>
 
         <span class="k">return</span> <span class="n">text</span></div>

diff --git a/_modules/loop_step/loop_parameters.html b/_modules/loop_step/loop_parameters.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>loop_step.loop_parameters &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>loop_step.loop_parameters &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/loop_step/loop_step.html b/_modules/loop_step/loop_step.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>loop_step.loop_step &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>loop_step.loop_step &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_modules/loop_step/tk_loop.html b/_modules/loop_step/tk_loop.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>loop_step.tk_loop &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>loop_step.tk_loop &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -45,8 +45,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../../_static/copybutton.js?v=f281be69"></script>

diff --git a/_static/basic.css b/_static/basic.css
@@ -1,12 +1,5 @@
 /*
- * basic.css
- * ~~~~~~~~~
- *
  * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 /* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
 /* -- search page ----------------------------------------------------------- */
 
 ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
+    margin-top: 10px;
 }
 
 ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
+    padding: 5px 0;
 }
 
 ul.search li a {

diff --git a/_static/doctools.js b/_static/doctools.js
@@ -1,12 +1,5 @@
 /*
- * doctools.js
- * ~~~~~~~~~~~
- *
  * Base JavaScript utilities for all Sphinx HTML documentation.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 

diff --git a/_static/documentation_options.js b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '2024.8.23',
+    VERSION: '2024.10.15',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/_static/language_data.js b/_static/language_data.js
@@ -1,13 +1,6 @@
 /*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 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"];

diff --git a/_static/searchtools.js b/_static/searchtools.js
@@ -1,12 +1,5 @@
 /*
- * searchtools.js
- * ~~~~~~~~~~~~~~~~
- *
  * Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 
@@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") {
     // and returns the new score.
     /*
     score: result => {
-      const [docname, title, anchor, descr, score, filename] = result
+      const [docname, title, anchor, descr, score, filename, kind] = result
       return score
     },
     */
@@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") {
   };
 }
 
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+    static get index() { return  "index"; }
+    static get object() { return "object"; }
+    static get text() { return "text"; }
+    static get title() { return "title"; }
+}
+
 const _removeChildren = (element) => {
   while (element && element.lastChild) element.removeChild(element.lastChild);
 };
@@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
   const contentRoot = document.documentElement.dataset.content_root;
 
-  const [docName, title, anchor, descr, score, _filename] = item;
+  const [docName, title, anchor, descr, score, _filename, kind] = item;
 
   let listItem = document.createElement("li");
+  // Add a class representing the item's type:
+  // can be used by a theme's CSS selector for styling
+  // See SearchResultKind for the class names.
+  listItem.classList.add(`kind-${kind}`);
   let requestUrl;
   let linkUrl;
   if (docBuilder === "dirhtml") {
@@ -115,8 +120,10 @@ const _finishSearch = (resultCount) => {
       "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
     );
   else
-    Search.status.innerText = _(
-      "Search finished, found ${resultCount} page(s) matching the search query."
+    Search.status.innerText = Documentation.ngettext(
+      "Search finished, found one page matching the search query.",
+      "Search finished, found ${resultCount} pages matching the search query.",
+      resultCount,
     ).replace('${resultCount}', resultCount);
 };
 const _displayNextItem = (
@@ -138,7 +145,7 @@ const _displayNextItem = (
   else _finishSearch(resultCount);
 };
 // Helper function used by query() to order search results.
-// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
 // Order the results by score (in opposite order of appearance, since the
 // `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
 const _orderResultsByScoreThenName = (a, b) => {
@@ -248,6 +255,7 @@ const Search = {
     searchSummary.classList.add("search-summary");
     searchSummary.innerText = "";
     const searchList = document.createElement("ul");
+    searchList.setAttribute("role", "list");
     searchList.classList.add("search");
 
     const out = document.getElementById("search-results");
@@ -318,7 +326,7 @@ const Search = {
     const indexEntries = Search._index.indexentries;
 
     // Collect multiple result groups to be sorted separately and then ordered.
-    // Each is an array of [docname, title, anchor, descr, score, filename].
+    // Each is an array of [docname, title, anchor, descr, score, filename, kind].
     const normalResults = [];
     const nonMainIndexResults = [];
 
@@ -337,6 +345,7 @@ const Search = {
             null,
             score + boost,
             filenames[file],
+            SearchResultKind.title,
           ]);
         }
       }
@@ -354,6 +363,7 @@ const Search = {
             null,
             score,
             filenames[file],
+            SearchResultKind.index,
           ];
           if (isMain) {
             normalResults.push(result);
@@ -475,6 +485,7 @@ const Search = {
         descr,
         score,
         filenames[match[0]],
+        SearchResultKind.object,
       ]);
     };
     Object.keys(objects).forEach((prefix) =>
@@ -585,6 +596,7 @@ const Search = {
         null,
         score,
         filenames[file],
+        SearchResultKind.text,
       ]);
     }
     return results;

diff --git a/api/index.html b/api/index.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>API Documentation &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>API Documentation &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -46,8 +46,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=f281be69"></script>

diff --git a/api/loop_step.html b/api/loop_step.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>loop_step package &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>loop_step package &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -46,8 +46,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=f281be69"></script>

diff --git a/api/modules.html b/api/modules.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>loop_step &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>loop_step &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -46,8 +46,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="../_static/documentation_options.js?v=0280db91"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="../_static/copybutton.js?v=f281be69"></script>

diff --git a/authors.html b/authors.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Development Team &#8212; SEAMM Loop Plug-in 2024.8.23 documentation</title>
+    <title>Development Team &#8212; SEAMM Loop Plug-in 2024.10.15 documentation</title>
 
 
 
@@ -46,8 +46,8 @@
 })(window,document,'script','dataLayer','GTM-PQXXTJ2');</script>
 <!-- End Google Tag Manager -->
 
-    <script src="_static/documentation_options.js?v=0280db91"></script>
-    <script src="_static/doctools.js?v=9a2dae69"></script>
+    <script src="_static/documentation_options.js?v=4ddceb86"></script>
+    <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="_static/clipboard.min.js?v=a7894cd8"></script>
     <script src="_static/copybutton.js?v=f281be69"></script>