update for dup

biosimulators · Sep 3, 2024 · 2e8785f · 2e8785f
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diff --git a/documentation/build/doctrees/environment.pickle b/documentation/build/doctrees/environment.pickle
diff --git a/documentation/build/doctrees/index.doctree b/documentation/build/doctrees/index.doctree
diff --git a/documentation/build/html/_modules/bio_compose/bundles.html b/documentation/build/html/_modules/bio_compose/bundles.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/_modules/bio_compose/composer.html b/documentation/build/html/_modules/bio_compose/composer.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/_modules/bio_compose/data_model.html b/documentation/build/html/_modules/bio_compose/data_model.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/_modules/bio_compose/processing_tools.html b/documentation/build/html/_modules/bio_compose/processing_tools.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/_modules/bio_compose/runner.html b/documentation/build/html/_modules/bio_compose/runner.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/_modules/bio_compose/verifier.html b/documentation/build/html/_modules/bio_compose/verifier.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/_modules/index.html b/documentation/build/html/_modules/index.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/_sources/index.rst.txt b/documentation/build/html/_sources/index.rst.txt
@@ -13,7 +13,6 @@ Create, execute, and introspect reproducible composite simulations of dynamic bi
    :caption: Contents:
 
    installation
-   modules
 
 .. automodule:: bio_compose
    :members:

diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
@@ -20,8 +20,7 @@
         <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" />
-    <link rel="prev" title="bio_compose" href="modules.html" /> 
+    <link rel="search" title="Search" href="search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -44,43 +43,8 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="modules.html">bio_compose</a><ul class="current">
-<li class="toctree-l2 current"><a class="current reference internal" href="#">bio_compose package</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#submodules">Submodules</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#module-bio_compose.bundles">bio_compose.bundles module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.bundles.BioBundle"><code class="docutils literal notranslate"><span class="pre">BioBundle</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#module-bio_compose.composer">bio_compose.composer module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.composer.Composer"><code class="docutils literal notranslate"><span class="pre">Composer</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#module-bio_compose.data_model">bio_compose.data_model module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.data_model.Api"><code class="docutils literal notranslate"><span class="pre">Api</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.data_model.RequestError"><code class="docutils literal notranslate"><span class="pre">RequestError</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.data_model.save_plot"><code class="docutils literal notranslate"><span class="pre">save_plot()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#module-bio_compose.processing_tools">bio_compose.processing_tools module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.processing_tools.generate_color_gradient"><code class="docutils literal notranslate"><span class="pre">generate_color_gradient()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#module-bio_compose.runner">bio_compose.runner module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.runner.SimulationRunner"><code class="docutils literal notranslate"><span class="pre">SimulationRunner</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#module-bio_compose.verifier">bio_compose.verifier module</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.verifier.Verifier"><code class="docutils literal notranslate"><span class="pre">Verifier</span></code></a></li>
-<li class="toctree-l4"><a class="reference internal" href="#bio_compose.verifier.test_verifier"><code class="docutils literal notranslate"><span class="pre">test_verifier()</span></code></a></li>
-</ul>
-</li>
-<li class="toctree-l3"><a class="reference internal" href="#module-bio_compose">Module contents</a></li>
-</ul>
-</li>
-</ul>
-</li>
 </ul>
 
         </div>
@@ -97,7 +61,6 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="modules.html">bio_compose</a></li>
       <li class="breadcrumb-item active">bio_compose package</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/bio_compose.rst.txt" rel="nofollow"> View page source</a>
@@ -572,9 +535,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="modules.html" class="btn btn-neutral float-left" title="bio_compose" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-    </div>
+          <footer>
 
   <hr/>
 

diff --git a/documentation/build/html/genindex.html b/documentation/build/html/genindex.html
@@ -44,7 +44,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/index.html b/documentation/build/html/index.html
@@ -46,7 +46,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">bio_compose</a></li>
 </ul>
 
         </div>
@@ -80,10 +79,6 @@ <h1>BioCompose documentation<a class="headerlink" href="#biocompose-documentatio
 <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">bio_compose</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="bio_compose.html">bio_compose package</a></li>
-</ul>
-</li>
 </ul>
 </div>
 <span class="target" id="module-bio_compose"></span></section>

diff --git a/documentation/build/html/installation.html b/documentation/build/html/installation.html
@@ -21,7 +21,6 @@
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="bio_compose" href="modules.html" />
     <link rel="prev" title="BioCompose documentation" href="index.html" /> 
 </head>
 
@@ -47,7 +46,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">bio_compose</a></li>
 </ul>
 
         </div>
@@ -93,7 +91,6 @@ <h1>Installation<a class="headerlink" href="#installation" title="Link to this h
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="index.html" class="btn btn-neutral float-left" title="BioCompose documentation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="modules.html" class="btn btn-neutral float-right" title="bio_compose" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

diff --git a/documentation/build/html/modules.html b/documentation/build/html/modules.html
@@ -20,9 +20,7 @@
         <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" />
-    <link rel="next" title="bio_compose package" href="bio_compose.html" />
-    <link rel="prev" title="Installation" href="installation.html" /> 
+    <link rel="search" title="Search" href="search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -45,12 +43,8 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">bio_compose</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="bio_compose.html">bio_compose package</a></li>
-</ul>
-</li>
 </ul>
 
         </div>
@@ -159,10 +153,7 @@ <h1>bio_compose<a class="headerlink" href="#bio-compose" title="Link to this hea
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="installation.html" class="btn btn-neutral float-left" title="Installation" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="bio_compose.html" class="btn btn-neutral float-right" title="bio_compose package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
 
   <hr/>
 

diff --git a/documentation/build/html/py-modindex.html b/documentation/build/html/py-modindex.html
@@ -47,7 +47,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">bio_compose</a></li>
 </ul>
 
         </div>

diff --git a/documentation/build/html/search.html b/documentation/build/html/search.html
@@ -47,7 +47,6 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="modules.html">bio_compose</a></li>
 </ul>
 
         </div>