Merge branch 'dev' of /~https://github.com/biosimulators/Biosimulators_…

…MASSpy into dev
biosimulators · Oct 24, 2024 · e17fbc7 · e17fbc7
2 parents c650cba + ccafcfe
commit e17fbc7
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diff --git a/docs/_static/scripts/bootstrap.js.map b/docs/_static/scripts/bootstrap.js.map
diff --git a/docs/_static/scripts/fontawesome.js b/docs/_static/scripts/fontawesome.js
diff --git a/docs/_static/scripts/fontawesome.js.LICENSE.txt b/docs/_static/scripts/fontawesome.js.LICENSE.txt
@@ -0,0 +1,5 @@
+/*!
+ * Font Awesome Free 6.5.2 by @fontawesome - https://fontawesome.com
+ * License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License)
+ * Copyright 2024 Fonticons, Inc.
+ */
diff --git a/docs/_static/scripts/fontawesome.js.map b/docs/_static/scripts/fontawesome.js.map
diff --git a/docs/_static/scripts/pydata-sphinx-theme.js b/docs/_static/scripts/pydata-sphinx-theme.js
diff --git a/docs/_static/scripts/pydata-sphinx-theme.js.map b/docs/_static/scripts/pydata-sphinx-theme.js.map
diff --git a/docs/_static/styles/pydata-sphinx-theme.css b/docs/_static/styles/pydata-sphinx-theme.css
diff --git a/docs/_static/styles/pydata-sphinx-theme.css.map b/docs/_static/styles/pydata-sphinx-theme.css.map
diff --git a/docs/_static/vendor/fontawesome/webfonts/fa-brands-400.ttf b/docs/_static/vendor/fontawesome/webfonts/fa-brands-400.ttf
diff --git a/docs/_static/vendor/fontawesome/webfonts/fa-brands-400.woff2 b/docs/_static/vendor/fontawesome/webfonts/fa-brands-400.woff2
diff --git a/docs/_static/vendor/fontawesome/webfonts/fa-regular-400.ttf b/docs/_static/vendor/fontawesome/webfonts/fa-regular-400.ttf
diff --git a/docs/_static/vendor/fontawesome/webfonts/fa-regular-400.woff2 b/docs/_static/vendor/fontawesome/webfonts/fa-regular-400.woff2
diff --git a/docs/_static/vendor/fontawesome/webfonts/fa-solid-900.ttf b/docs/_static/vendor/fontawesome/webfonts/fa-solid-900.ttf
diff --git a/docs/_static/vendor/fontawesome/webfonts/fa-solid-900.woff2 b/docs/_static/vendor/fontawesome/webfonts/fa-solid-900.woff2
diff --git a/docs/_static/webpack-macros.html b/docs/_static/webpack-macros.html
@@ -2,30 +2,23 @@
   AUTO-GENERATED from webpack.config.js, do **NOT** edit by hand.
   These are re-used in layout.html
 -->
-{# Load FontAwesome icons #}
-{% macro head_pre_icons() %}
-  <link href="{{ pathto('_static/vendor/fontawesome/6.5.2/css/all.min.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-  <link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-solid-900.woff2', 1) }}" />
-<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2', 1) }}" />
-<link rel="preload" as="font" type="font/woff2" crossorigin href="{{ pathto('_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2', 1) }}" />
-{% endmacro %}
 
 {% macro head_pre_assets() %}
   <!-- Loaded before other Sphinx assets -->
-  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/bootstrap.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
+  <link href="{{ pathto('_static/styles/theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+<link href="{{ pathto('_static/styles/pydata-sphinx-theme.css', 1) }}?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
 {% endmacro %}
 
 {% macro head_js_preload() %}
+  <!-- So that users can add custom icons -->
+  <script src="{{ pathto('_static/scripts/fontawesome.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=dfe6caa3a7d634c4db9b" />
-<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=dfe6caa3a7d634c4db9b" />
-  <script src="{{ pathto('_static/vendor/fontawesome/6.5.2/js/all.min.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
+  <link rel="preload" as="script" href="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
+<link rel="preload" as="script" href="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549" />
 {% endmacro %}
 
 {% macro body_post() %}
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
-<script src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=dfe6caa3a7d634c4db9b"></script>
+  <script defer src="{{ pathto('_static/scripts/bootstrap.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
+<script defer src="{{ pathto('_static/scripts/pydata-sphinx-theme.js', 1) }}?digest=26a4bc78f4c0ddb94549"></script>
 {% endmacro %}
diff --git a/docs/about.html b/docs/about.html
@@ -16,25 +16,28 @@
     document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
     document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
   </script>
-
-  <!-- Loaded before other Sphinx assets -->
-  <link href="_static/styles/theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-<link href="_static/styles/bootstrap.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-<link href="_static/styles/pydata-sphinx-theme.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
+  <!-- 
+    this give us a css class that will be invisible only if js is disabled 
+  -->
+  <noscript>
+    <style>
+      .pst-js-only { display: none !important; }
 
+    </style>
+  </noscript>
 
-  <link href="_static/vendor/fontawesome/6.5.2/css/all.min.css?digest=dfe6caa3a7d634c4db9b" rel="stylesheet" />
-  <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-solid-900.woff2" />
-<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-brands-400.woff2" />
-<link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.5.2/webfonts/fa-regular-400.woff2" />
+  <!-- Loaded before other Sphinx assets -->
+  <link href="_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+<link href="_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
 
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="_static/css/biosimulators.css?v=ff938351" />
 
+  <!-- So that users can add custom icons -->
+  <script src="_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
   <!-- Pre-loaded scripts that we'll load fully later -->
-  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b" />
-<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
-  <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
+  <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
+<link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
 
     <script src="_static/documentation_options.js?v=01f34227"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
@@ -47,6 +50,7 @@
     <link rel="prev" title="biosimulators_masspy package" href="source/biosimulators_masspy.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
+  <meta name="docsearch:version" content="0.1.0" />
   </head>
 
 
@@ -62,36 +66,24 @@
     <i class="fa-solid fa-arrow-up"></i>Back to top</button>
 
 
-  <input type="checkbox"
-          class="sidebar-toggle"
-          id="pst-primary-sidebar-checkbox"/>
-  <label class="overlay overlay-primary" for="pst-primary-sidebar-checkbox"></label>
-
-  <input type="checkbox"
-          class="sidebar-toggle"
-          id="pst-secondary-sidebar-checkbox"/>
-  <label class="overlay overlay-secondary" for="pst-secondary-sidebar-checkbox"></label>
-
-  <div class="search-button__wrapper">
-    <div class="search-button__overlay"></div>
-    <div class="search-button__search-container">
+  <dialog id="pst-search-dialog">
+
 <form class="bd-search d-flex align-items-center"
       action="search.html"
       method="get">
   <i class="fa-solid fa-magnifying-glass"></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"
          autocorrect="off"
          autocapitalize="off"
          spellcheck="false"/>
   <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
-</form></div>
-  </div>
+</form>
+  </dialog>
 
   <div class="pst-async-banner-revealer d-none">
   <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
@@ -125,7 +117,7 @@
 
 
     <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators-MASSpy 0.1.0 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators-MASSpy 0.1.0 documentation - Home"/>`);</script>
+    <img src="_static/biosimulators-logo.svg" class="logo__image only-dark pst-js-only" alt="BioSimulators-MASSpy 0.1.0 documentation - Home"/>
 
 
 </a></div>
@@ -140,15 +132,11 @@
         <div class="navbar-item navbar-persistent--container">
 
 
- <script>
- document.write(`
-   <button class="btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
-    <i class="fa-solid fa-magnifying-glass"></i>
-    <span class="search-button__default-text">Search</span>
-    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
-   </button>
- `);
- </script>
+<button class="btn search-button-field search-button__button pst-js-only" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <i class="fa-solid fa-magnifying-glass"></i>
+ <span class="search-button__default-text">Search</span>
+ <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+</button>
         </div>
 
 
@@ -199,15 +187,11 @@
 
     <div class="navbar-persistent--mobile">
 
- <script>
- document.write(`
-   <button class="btn search-button-field search-button__button" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
-    <i class="fa-solid fa-magnifying-glass"></i>
-    <span class="search-button__default-text">Search</span>
-    <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
-   </button>
- `);
- </script>
+<button class="btn search-button-field search-button__button pst-js-only" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <i class="fa-solid fa-magnifying-glass"></i>
+ <span class="search-button__default-text">Search</span>
+ <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+</button>
     </div>
 
 
@@ -226,7 +210,8 @@
 
 
 
-      <div class="bd-sidebar-primary bd-sidebar">
+      <dialog id="pst-primary-sidebar-modal"></dialog>
+      <div id="pst-primary-sidebar" class="bd-sidebar-primary bd-sidebar">
 
 
 
@@ -290,7 +275,6 @@
   <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"
@@ -329,8 +313,6 @@
 
         <div class="header-article-item">
 
-
-
 <nav aria-label="Breadcrumb" class="d-print-none">
   <ul class="bd-breadcrumbs">
 
@@ -339,7 +321,7 @@
         <i class="fa-solid fa-home"></i>
       </a>
     </li>
-    <li class="breadcrumb-item active" aria-current="page">About...</li>
+    <li class="breadcrumb-item active" aria-current="page"><span class="ellipsis">About BioSimulators-MASSpy</span></li>
   </ul>
 </nav>
 </div>
@@ -383,7 +365,8 @@ <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" t
 
 
 
-                <div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
+                <dialog id="pst-secondary-sidebar-modal"></dialog>
+                <div id="pst-secondary-sidebar" class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
 
 
   <div class="sidebar-secondary-item">
@@ -438,8 +421,8 @@ <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" t
   </div>
 
   <!-- Scripts loaded after <body> so the DOM is not blocked -->
-  <script src="_static/scripts/bootstrap.js?digest=dfe6caa3a7d634c4db9b"></script>
-<script src="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b"></script>
+  <script defer src="_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
+<script defer src="_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
 
   <footer class="bd-footer">
 <div class="bd-footer__inner bd-page-width">
@@ -472,7 +455,7 @@ <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" t
 
         <div class="footer-item">
 <p class="theme-version">
-  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.15.4.
+  Built with the <a href="https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html">PyData Sphinx Theme</a> 0.16.0.
 </p></div>
 
     </div>