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mesoscope · Jul 16, 2024 · b547b4a · b547b4a
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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: e79b02e7e37ee12e96f31fe460804991
+config: 04f5bf5aef507cba4eeec16b87a1bc78
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/RECIPE_SCHEMA.html b/RECIPE_SCHEMA.html
@@ -16,7 +16,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -480,7 +480,7 @@ <h3>example ingredient<a class="headerlink" href="#example-ingredient" title="Li
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
   <div>
     <h3><a href="index.html">Table of Contents</a></h3>
@@ -595,7 +595,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -610,7 +610,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack.html b/_modules/cellpack.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -60,7 +60,7 @@ <h1>Source code for cellpack</h1><div class="highlight"><pre>
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -76,7 +76,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -92,7 +92,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack.html b/_modules/cellpack/autopack.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -709,7 +709,7 @@ <h1>Source code for cellpack.autopack</h1><div class="highlight"><pre>
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -725,7 +725,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
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-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -742,7 +742,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack/AWSHandler.html b/_modules/cellpack/autopack/AWSHandler.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
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       <ul>
         <li class="right" style="margin-right: 10px">
@@ -208,7 +208,7 @@ <h1>Source code for cellpack.autopack.AWSHandler</h1><div class="highlight"><pre
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -224,7 +224,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
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-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -242,7 +242,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack/Analysis.html b/_modules/cellpack/autopack/Analysis.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1575,7 +1575,7 @@ <h1>Source code for cellpack.autopack.Analysis</h1><div class="highlight"><pre>
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -1591,7 +1591,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
     </div>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1609,7 +1609,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack/BaseGrid.html b/_modules/cellpack/autopack/BaseGrid.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1001,7 +1001,7 @@ <h1>Source code for cellpack.autopack.BaseGrid</h1><div class="highlight"><pre>
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -1017,7 +1017,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
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-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
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         <li class="right" style="margin-right: 10px">
@@ -1035,7 +1035,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack/Compartment.html b/_modules/cellpack/autopack/Compartment.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -3343,7 +3343,7 @@ <h1>Source code for cellpack.autopack.Compartment</h1><div class="highlight"><pr
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -3359,7 +3359,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
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-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
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         <li class="right" style="margin-right: 10px">
@@ -3377,7 +3377,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack/DBRecipeHandler.html b/_modules/cellpack/autopack/DBRecipeHandler.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -964,7 +964,7 @@ <h1>Source code for cellpack.autopack.DBRecipeHandler</h1><div class="highlight"
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -980,7 +980,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
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-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -998,7 +998,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack/Environment.html b/_modules/cellpack/autopack/Environment.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
       <ul>
         <li class="right" style="margin-right: 10px">
@@ -1126,13 +1126,8 @@ <h1>Source code for cellpack.autopack.Environment</h1><div class="highlight"><pr
         <span class="n">ingredient_type</span> <span class="o">=</span> <span class="n">arguments</span><span class="p">[</span><span class="s2">&quot;type&quot;</span><span class="p">]</span>
         <span class="n">ingredient_class</span> <span class="o">=</span> <span class="n">ingredient</span><span class="o">.</span><span class="n">get_ingredient_class</span><span class="p">(</span><span class="n">ingredient_type</span><span class="p">)</span>
         <span class="n">ingr</span> <span class="o">=</span> <span class="n">ingredient_class</span><span class="p">(</span><span class="o">**</span><span class="n">arguments</span><span class="p">)</span>
-        <span class="k">if</span> <span class="p">(</span>
-            <span class="s2">&quot;gradient&quot;</span> <span class="ow">in</span> <span class="n">arguments</span>
-            <span class="ow">and</span> <span class="n">arguments</span><span class="p">[</span><span class="s2">&quot;gradient&quot;</span><span class="p">]</span> <span class="o">!=</span> <span class="s2">&quot;&quot;</span>
-            <span class="ow">and</span> <span class="n">arguments</span><span class="p">[</span><span class="s2">&quot;gradient&quot;</span><span class="p">]</span> <span class="o">!=</span> <span class="s2">&quot;None&quot;</span>
-        <span class="p">):</span>
-            <span class="n">ingr</span><span class="o">.</span><span class="n">gradient</span> <span class="o">=</span> <span class="n">arguments</span><span class="p">[</span><span class="s2">&quot;gradient&quot;</span><span class="p">]</span>
-            <span class="c1"># TODO: allow ingrdients to have multiple gradients</span>
+        <span class="k">if</span> <span class="s2">&quot;gradient&quot;</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
+            <span class="n">ingr</span> <span class="o">=</span> <span class="n">Gradient</span><span class="o">.</span><span class="n">update_ingredient_gradient</span><span class="p">(</span><span class="n">ingr</span><span class="p">,</span> <span class="n">arguments</span><span class="p">)</span>
         <span class="k">if</span> <span class="s2">&quot;results&quot;</span> <span class="ow">in</span> <span class="n">arguments</span><span class="p">:</span>
             <span class="n">ingr</span><span class="o">.</span><span class="n">results</span> <span class="o">=</span> <span class="n">arguments</span><span class="p">[</span><span class="s2">&quot;results&quot;</span><span class="p">]</span>
         <span class="n">ingr</span><span class="o">.</span><span class="n">initialize_mesh</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mesh_store</span><span class="p">)</span>
@@ -3201,7 +3196,7 @@ <h1>Source code for cellpack.autopack.Environment</h1><div class="highlight"><pr
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
         <div class="sphinxsidebarwrapper">
 <search id="searchbox" style="display: none" role="search">
   <h3 id="searchlabel">Quick search</h3>
@@ -3217,7 +3212,7 @@ <h3 id="searchlabel">Quick search</h3>
       </div>
       <div class="clearer"></div>
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-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
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         <li class="right" style="margin-right: 10px">
@@ -3235,7 +3230,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>
diff --git a/_modules/cellpack/autopack/FirebaseHandler.html b/_modules/cellpack/autopack/FirebaseHandler.html
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="../../../genindex.html" />
     <link rel="search" title="Search" href="../../../search.html" /> 
   </head><body>
-    <div class="related" role="navigation" aria-label="related navigation">
+    <div class="related" role="navigation" aria-label="Related">
       <h3>Navigation</h3>
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         <li class="right" style="margin-right: 10px">
@@ -374,7 +374,7 @@ <h1>Source code for cellpack.autopack.FirebaseHandler</h1><div class="highlight"
           </div>
         </div>
       </div>
-      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+      <div class="sphinxsidebar" role="navigation" aria-label="Main">
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   <h3 id="searchlabel">Quick search</h3>
@@ -390,7 +390,7 @@ <h3 id="searchlabel">Quick search</h3>
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+    <div class="related" role="navigation" aria-label="Related">
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@@ -408,7 +408,7 @@ <h3>Navigation</h3>
     </div>
     <div class="footer" role="contentinfo">
     &#169; Copyright 2021, Megan Riel-Mehan.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.4.
     </div>
   </body>
 </html>