chore: Updating compiled documentation [skip ci]

biosimulators · Jan 20, 2022 · 7e5eba1 · 7e5eba1
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commit 7e5eba1
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Showing 20 changed files with 488 additions and 329 deletions.
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -757,6 +757,7 @@ span.pre {
     -ms-hyphens: none;
     -webkit-hyphens: none;
     hyphens: none;
+    white-space: nowrap;
 }
 
 div[class*="highlight-"] {

diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -264,6 +264,9 @@ var Documentation = {
   hideSearchWords : function() {
     $('#searchbox .highlight-link').fadeOut(300);
     $('span.highlighted').removeClass('highlighted');
+    var url = new URL(window.location);
+    url.searchParams.delete('highlight');
+    window.history.replaceState({}, '', url);
   },
 
   /**

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: '0.1.82',
+    VERSION: '0.1.83',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js
@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_static/scripts/pydata-sphinx-theme.js b/docs/_static/scripts/pydata-sphinx-theme.js
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */

diff --git a/docs/_static/styles/pydata-sphinx-theme.css b/docs/_static/styles/pydata-sphinx-theme.css
diff --git a/docs/_static/styles/theme.css b/docs/_static/styles/theme.css
@@ -0,0 +1,134 @@
+/* Provided by Sphinx's 'basic' theme, and included in the final set of assets */
+@import "../basic.css";
+
+:root {
+  /*****************************************************************************
+  * Theme config
+  **/
+  --pst-header-height: 60px;
+
+  /*****************************************************************************
+  * Font size
+  **/
+  --pst-font-size-base: 15px; /* base font size - applied at body / html level */
+
+  /* heading font sizes */
+  --pst-font-size-h1: 36px;
+  --pst-font-size-h2: 32px;
+  --pst-font-size-h3: 26px;
+  --pst-font-size-h4: 21px;
+  --pst-font-size-h5: 18px;
+  --pst-font-size-h6: 16px;
+
+  /* smaller then heading font sizes*/
+  --pst-font-size-milli: 12px;
+
+  --pst-sidebar-font-size: 0.9em;
+  --pst-sidebar-caption-font-size: 0.9em;
+
+  /*****************************************************************************
+  * Font family
+  **/
+  /* These are adapted from https://systemfontstack.com/ */
+  --pst-font-family-base-system: -apple-system, BlinkMacSystemFont, Segoe UI,
+    "Helvetica Neue", Arial, sans-serif, Apple Color Emoji, Segoe UI Emoji,
+    Segoe UI Symbol;
+  --pst-font-family-monospace-system: "SFMono-Regular", Menlo, Consolas, Monaco,
+    Liberation Mono, Lucida Console, monospace;
+
+  --pst-font-family-base: var(--pst-font-family-base-system);
+  --pst-font-family-heading: var(--pst-font-family-base);
+  --pst-font-family-monospace: var(--pst-font-family-monospace-system);
+
+  /*****************************************************************************
+  * Color
+  *
+  * Colors are defined in rgb string way, "red, green, blue"
+  **/
+  --pst-color-primary: 19, 6, 84;
+  --pst-color-success: 40, 167, 69;
+  --pst-color-info: 0, 123, 255; /*23, 162, 184;*/
+  --pst-color-warning: 255, 193, 7;
+  --pst-color-danger: 220, 53, 69;
+  --pst-color-text-base: 51, 51, 51;
+
+  --pst-color-h1: var(--pst-color-primary);
+  --pst-color-h2: var(--pst-color-primary);
+  --pst-color-h3: var(--pst-color-text-base);
+  --pst-color-h4: var(--pst-color-text-base);
+  --pst-color-h5: var(--pst-color-text-base);
+  --pst-color-h6: var(--pst-color-text-base);
+  --pst-color-paragraph: var(--pst-color-text-base);
+  --pst-color-link: 0, 91, 129;
+  --pst-color-link-hover: 227, 46, 0;
+  --pst-color-headerlink: 198, 15, 15;
+  --pst-color-headerlink-hover: 255, 255, 255;
+  --pst-color-preformatted-text: 34, 34, 34;
+  --pst-color-preformatted-background: 250, 250, 250;
+  --pst-color-inline-code: 232, 62, 140;
+
+  --pst-color-active-navigation: 19, 6, 84;
+  --pst-color-navbar-link: 77, 77, 77;
+  --pst-color-navbar-link-hover: var(--pst-color-active-navigation);
+  --pst-color-navbar-link-active: var(--pst-color-active-navigation);
+  --pst-color-sidebar-link: 77, 77, 77;
+  --pst-color-sidebar-link-hover: var(--pst-color-active-navigation);
+  --pst-color-sidebar-link-active: var(--pst-color-active-navigation);
+  --pst-color-sidebar-expander-background-hover: 244, 244, 244;
+  --pst-color-sidebar-caption: 77, 77, 77;
+  --pst-color-toc-link: 119, 117, 122;
+  --pst-color-toc-link-hover: var(--pst-color-active-navigation);
+  --pst-color-toc-link-active: var(--pst-color-active-navigation);
+
+  /*****************************************************************************
+  * Icon
+  **/
+
+  /* font awesome icons*/
+  --pst-icon-check-circle: "\f058";
+  --pst-icon-info-circle: "\f05a";
+  --pst-icon-exclamation-triangle: "\f071";
+  --pst-icon-exclamation-circle: "\f06a";
+  --pst-icon-times-circle: "\f057";
+  --pst-icon-lightbulb: "\f0eb";
+
+  /*****************************************************************************
+  * Admonitions
+  **/
+
+  --pst-color-admonition-default: var(--pst-color-info);
+  --pst-color-admonition-note: var(--pst-color-info);
+  --pst-color-admonition-attention: var(--pst-color-warning);
+  --pst-color-admonition-caution: var(--pst-color-warning);
+  --pst-color-admonition-warning: var(--pst-color-warning);
+  --pst-color-admonition-danger: var(--pst-color-danger);
+  --pst-color-admonition-error: var(--pst-color-danger);
+  --pst-color-admonition-hint: var(--pst-color-success);
+  --pst-color-admonition-tip: var(--pst-color-success);
+  --pst-color-admonition-important: var(--pst-color-success);
+
+  --pst-icon-admonition-default: var(--pst-icon-info-circle);
+  --pst-icon-admonition-note: var(--pst-icon-info-circle);
+  --pst-icon-admonition-attention: var(--pst-icon-exclamation-circle);
+  --pst-icon-admonition-caution: var(--pst-icon-exclamation-triangle);
+  --pst-icon-admonition-warning: var(--pst-icon-exclamation-triangle);
+  --pst-icon-admonition-danger: var(--pst-icon-exclamation-triangle);
+  --pst-icon-admonition-error: var(--pst-icon-times-circle);
+  --pst-icon-admonition-hint: var(--pst-icon-lightbulb);
+  --pst-icon-admonition-tip: var(--pst-icon-lightbulb);
+  --pst-icon-admonition-important: var(--pst-icon-exclamation-circle);
+
+  /*****************************************************************************
+  * versionmodified
+  **/
+
+  --pst-color-versionmodified-default: var(--pst-color-info);
+  --pst-color-versionmodified-added: var(--pst-color-success);
+  --pst-color-versionmodified-changed: var(--pst-color-warning);
+  --pst-color-versionmodified-deprecated: var(--pst-color-danger);
+
+  --pst-icon-versionmodified-default: var(--pst-icon-exclamation-circle);
+  --pst-icon-versionmodified-added: var(--pst-icon-exclamation-circle);
+  --pst-icon-versionmodified-changed: var(--pst-icon-exclamation-circle);
+  --pst-icon-versionmodified-deprecated: var(--pst-icon-exclamation-circle);
+}
diff --git a/docs/_static/webpack-macros.html b/docs/_static/webpack-macros.html
@@ -1,25 +1,28 @@
-<!-- these macros are generated by "yarn build:production". do not edit by hand. -->
-{% macro head_pre_icons() %}
-  <link rel="stylesheet"
-    href="{{ pathto('_static/vendor/fontawesome/5.13.0/css/all.min.css', 1) }}">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="{{ pathto('_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2', 1) }}">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="{{ pathto('_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2', 1) }}">
-{% endmacro %}
+<!--
+    All these macros are auto-generated and must **NOT** be edited by hand.
+    See the webpack.config.js file, to learn more about how this is generated.
+  -->
+  {% macro head_pre_icons() %}
+    <link rel="stylesheet"
+      href="{{ pathto('_static/vendor/fontawesome/5.13.0/css/all.min.css', 1) }}">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="{{ pathto('_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2', 1) }}">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="{{ pathto('_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2', 1) }}">
+  {% endmacro %}
 
-{% macro head_pre_fonts() %}
-{% endmacro %}
+  {% macro head_pre_fonts() %}
+  {% endmacro %}
 
-{% macro head_pre_bootstrap() %}
-  <link href="{{ pathto('_static/css/theme.css', 1) }}" rel="stylesheet">
-  <link href="{{ pathto('_static/css/index.ff1ffe594081f20da1ef19478df9384b.css', 1) }}" rel="stylesheet">
-{% endmacro %}
+  {% macro head_pre_bootstrap() %}
+    <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=1999514e3f237ded88cf" rel="stylesheet">
+<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=1999514e3f237ded88cf" rel="stylesheet">
+  {% endmacro %}
 
-{% macro head_js_preload() %}
-  <link rel="preload" as="script" href="{{ pathto('_static/js/index.be7d3bbb2ef33a8344ce.js', 1) }}">
-{% endmacro %}
+  {% macro head_js_preload() %}
+    <link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=1999514e3f237ded88cf">
+  {% endmacro %}
 
-{% macro body_post() %}
-  <script src="{{ pathto('_static/js/index.be7d3bbb2ef33a8344ce.js', 1) }}"></script>
-{% endmacro %}
+  {% macro body_post() %}
+    <script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=1999514e3f237ded88cf"></script>
+  {% endmacro %}
diff --git a/docs/about.html b/docs/about.html
@@ -6,29 +6,29 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
-    <title>About the BioSimulators test suite &#8212; BioSimulators test suite 0.1.82 documentation</title>
+    <title>About the BioSimulators test suite &#8212; BioSimulators test suite 0.1.83 documentation</title>
 
-  <link href="_static/css/theme.css" rel="stylesheet">
-  <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
-
+    <link href="_static/styles/theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
+<link href="_static/styles/pydata-sphinx-theme.css?digest=1999514e3f237ded88cf" rel="stylesheet">
+  
 
-  <link rel="stylesheet"
-    href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
-  <link rel="preload" as="font" type="font/woff2" crossorigin
-    href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
-
+    <link rel="stylesheet"
+      href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2">
+    <link rel="preload" as="font" type="font/woff2" crossorigin
+      href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
+  
 
 
-
+  
 
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="_static/css/blank.css" />
+    <link rel="stylesheet" type="text/css" href="_static/styles/pydata-sphinx-theme.css" />
     <link rel="stylesheet" type="text/css" href="_static/css/biosimulators.css" />
 
-  <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
-
+    <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf">
+  
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
     <script src="_static/underscore.js"></script>
@@ -87,22 +87,16 @@
       <div class="navbar-end-item">
         <ul id="navbar-icon-links" class="navbar-nav" aria-label="Quick links">
         <li class="nav-item">
-          <a class="nav-link" href="https://github.com/biosimulators/Biosimulators_test_suite" rel="noopener" target="_blank" title="GitHub">
-            <span><i class="fab fa-github"></i></span>
-            <label class="sr-only">GitHub</label>
-          </a>
+          <a class="nav-link" href="https://github.com/biosimulators/Biosimulators_test_suite" rel="noopener" target="_blank" title="GitHub"><span><i class="fab fa-github"></i></span>
+            <label class="sr-only">GitHub</label></a>
         </li>
         <li class="nav-item">
-          <a class="nav-link" href="https://twitter.com/biosimulators" rel="noopener" target="_blank" title="Twitter">
-            <span><i class="fab fa-twitter"></i></span>
-            <label class="sr-only">Twitter</label>
-          </a>
+          <a class="nav-link" href="https://twitter.com/biosimulators" rel="noopener" target="_blank" title="Twitter"><span><i class="fab fa-twitter"></i></span>
+            <label class="sr-only">Twitter</label></a>
         </li>
         <li class="nav-item">
-          <a class="nav-link" href="mailto:[email protected]" rel="noopener" target="_blank" title="Email">
-            <span><i class="fas fa-envelope"></i></span>
-            <label class="sr-only">Email</label>
-          </a>
+          <a class="nav-link" href="mailto:[email protected]" rel="noopener" target="_blank" title="Email"><span><i class="fas fa-envelope"></i></span>
+            <label class="sr-only">Email</label></a>
         </li>
       </ul>
       </div>
@@ -118,14 +112,18 @@
 
 
             <!-- Only show if we have sidebars configured, else just a small margin  -->
-            <div class="col-12 col-md-3 bd-sidebar"><form class="bd-search d-flex align-items-center" action="search.html" method="get">
+            <div class="col-12 col-md-3 bd-sidebar">
+              <div class="sidebar-start-items"><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
   <input type="search" class="form-control" name="q" id="search-input" placeholder="Enter text to search for ..." aria-label="Enter text to search for ..." autocomplete="off" >
 </form><nav class="bd-links" id="bd-docs-nav" aria-label="Main navigation">
   <div class="bd-toc-item active">
 
   </div>
 </nav>
+              </div>
+              <div class="sidebar-end-items">
+              </div>
             </div>
 
 
@@ -229,8 +227,8 @@ <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" t
       </div>
     </div>
 
-  <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
-<footer class="footer mt-5 mt-md-0">
+    <script src="_static/scripts/pydata-sphinx-theme.js?digest=1999514e3f237ded88cf"></script>
+  <footer class="footer mt-5 mt-md-0">
   <div class="container">
 
     <div class="footer-item">