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biosimulators · Sep 9, 2024 · 73acb10 · 73acb10
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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/doctrees/verification.doctree b/documentation/build/doctrees/verification.doctree
diff --git a/documentation/build/html/_modules/bio_compose.html b/documentation/build/html/_modules/bio_compose.html
@@ -41,17 +41,11 @@
   </form>
 </div>
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/_modules/bio_compose/bundles.html b/documentation/build/html/_modules/bio_compose/bundles.html
@@ -41,17 +41,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/_modules/bio_compose/composer.html b/documentation/build/html/_modules/bio_compose/composer.html
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/_modules/bio_compose/data_model.html b/documentation/build/html/_modules/bio_compose/data_model.html
@@ -41,17 +41,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul>
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-</ul>
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diff --git a/documentation/build/html/_modules/bio_compose/processing_tools.html b/documentation/build/html/_modules/bio_compose/processing_tools.html
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul>
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-</ul>
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diff --git a/documentation/build/html/_modules/bio_compose/runner.html b/documentation/build/html/_modules/bio_compose/runner.html
@@ -41,17 +41,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/_modules/bio_compose/verifier.html b/documentation/build/html/_modules/bio_compose/verifier.html
@@ -41,17 +41,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/_modules/index.html b/documentation/build/html/_modules/index.html
@@ -41,17 +41,11 @@
   </form>
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         </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">Installation</span></p>
+              <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>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
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diff --git a/documentation/build/html/_sources/index.rst.txt b/documentation/build/html/_sources/index.rst.txt
@@ -12,20 +12,10 @@ Create, execute, and introspect reproducible composite simulations of dynamic bi
 
 .. toctree::
    :maxdepth: 2
-   :caption: Installation
+   :caption: Contents
 
    installation
-
-.. toctree::
-   :maxdepth: 2
-   :caption: Getting Started
-
    verification
    simulation_runs
-
-.. toctree::
-   :maxdepth: 2
-   :caption: BioCompose modules
-
    modules
 
diff --git a/documentation/build/html/_sources/verification.rst.txt b/documentation/build/html/_sources/verification.rst.txt
@@ -1,7 +1,6 @@
 Verification
 ============
 
-
 Running a verification with `bio-compose` can be achieved in a few simple steps.
 
 Running a **OMEX verifications**:

diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
@@ -43,17 +43,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
-<ul>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
+<ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
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diff --git a/documentation/build/html/genindex.html b/documentation/build/html/genindex.html
@@ -41,17 +41,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/index.html b/documentation/build/html/index.html
@@ -43,17 +43,11 @@
   </form>
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         </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">Installation</span></p>
+              <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>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
-<ul>
 <li class="toctree-l1"><a class="reference internal" href="verification.html">Verification</a></li>
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-<p class="caption" role="heading"><span class="caption-text">BioCompose modules</span></p>
-<ul>
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 </ul>
 
@@ -86,21 +80,11 @@ <h1>BioCompose documentation<a class="headerlink" href="#biocompose-documentatio
 <p>Create, execute, and introspect reproducible composite simulations of dynamic biological systems.</p>
 <img alt="BioCompose logo" src="_images/bio_compose.png" />
 <div class="toctree-wrapper compound">
-<p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+<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>
-</ul>
-</div>
-<div class="toctree-wrapper compound">
-<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
-<ul>
 <li class="toctree-l1"><a class="reference internal" href="verification.html">Verification</a></li>
 <li class="toctree-l1"><a class="reference internal" href="simulation_runs.html">Simulation Runs</a></li>
-</ul>
-</div>
-<div class="toctree-wrapper compound">
-<p class="caption" role="heading"><span class="caption-text">BioCompose modules</span></p>
-<ul>
 <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>
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diff --git a/documentation/build/html/installation.html b/documentation/build/html/installation.html
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
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diff --git a/documentation/build/html/modules.html b/documentation/build/html/modules.html
@@ -44,17 +44,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
-<ul>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
+<ul class="current">
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diff --git a/documentation/build/html/py-modindex.html b/documentation/build/html/py-modindex.html
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/search.html b/documentation/build/html/search.html
@@ -44,17 +44,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
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diff --git a/documentation/build/html/searchindex.js b/documentation/build/html/searchindex.js
diff --git a/documentation/build/html/simple_example.html b/documentation/build/html/simple_example.html
@@ -42,17 +42,11 @@
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-              <p class="caption" role="heading"><span class="caption-text">Installation</span></p>
+              <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>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
-<ul>
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-</ul>
-<p class="caption" role="heading"><span class="caption-text">BioCompose modules</span></p>
-<ul>
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diff --git a/documentation/build/html/simulation_runs.html b/documentation/build/html/simulation_runs.html
@@ -44,17 +44,11 @@
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-</ul>
-<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
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diff --git a/documentation/build/html/verification.html b/documentation/build/html/verification.html
@@ -44,17 +44,11 @@
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-<ul>
-<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
-</ul>
-<p class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Contents</span></p>
 <ul class="current">
+<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="#">Verification</a></li>
 <li class="toctree-l1"><a class="reference internal" href="simulation_runs.html">Simulation Runs</a></li>
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