From 03e94f1735b0a62e78c70e8f5a11300eb18d2e1d Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 19 Sep 2024 15:37:54 +0000
Subject: [PATCH 1/2] Latest docs build.

---
 docs/build/html/.doctrees/environment.pickle  | Bin 1314815 -> 1314815 bytes
 .../tut_toggle_switch.doctree                 | Bin 11179 -> 11185 bytes
 .../tut_toggle_switch.rst.txt                 |   4 ++--
 docs/build/html/searchindex.js                |   2 +-
 .../tut_toggle_switch/tut_toggle_switch.html  |   2 +-
 5 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/build/html/.doctrees/environment.pickle b/docs/build/html/.doctrees/environment.pickle
index 072883dfdb481cedcd24029eadb4e7df41005af5..e276889a24a59377f3fe9dffc68ead839a03a45a 100644
GIT binary patch
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diff --git a/docs/build/html/.doctrees/tutorials/tut_toggle_switch/tut_toggle_switch.doctree b/docs/build/html/.doctrees/tutorials/tut_toggle_switch/tut_toggle_switch.doctree
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diff --git a/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt b/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt
index e9550fbfe..e68601760 100644
--- a/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt
+++ b/docs/build/html/_sources/tutorials/tut_toggle_switch/tut_toggle_switch.rst.txt
@@ -8,7 +8,7 @@ First, in a Python script that uses GillesPy2 to perform model simulation, we be
 .. code-block:: python
 
  import gillespy2
- 
+
 
 Next, we define a model. This is a model based on a publication by Gardner et al. in Nature, 1999, and represents a genetic toggle switch in Escherichia coli.  In GillesPy2, a model is expressed as an object having the parent class ``Model``.  Components of the model, such as the reactions, molecular species, and characteristics such as the time span for simulation, are all defined within the subclass definition.  The following Python code represents our model using GillesPy2's facility:
 
@@ -77,7 +77,7 @@ And here is a plot of the deterministic simulation results:
 
 .. code-block:: python
 
- d_results.plot(title="Stochastic Switch")
+ d_results.plot(title="Deterministic Switch")
 
 
 .. image:: ode.png
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
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+++ b/docs/build/html/searchindex.js
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diff --git a/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html b/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html
index 1c62b485b..a2af6b15c 100644
--- a/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html
+++ b/docs/build/html/tutorials/tut_toggle_switch/tut_toggle_switch.html
@@ -160,7 +160,7 @@ <h1>Tutorial: ODE vs. SSA<a class="headerlink" href="#tutorial-ode-vs-ssa" title
 </div>
 <img alt="../../_images/stochastic.png" class="align-center" src="../../_images/stochastic.png" />
 <p>And here is a plot of the deterministic simulation results:</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">d_results</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;Stochastic Switch&quot;</span><span class="p">)</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">d_results</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">title</span><span class="o">=</span><span class="s2">&quot;Deterministic Switch&quot;</span><span class="p">)</span>
 </pre></div>
 </div>
 <img alt="../../_images/ode.png" class="align-center" src="../../_images/ode.png" />

From 5541061087fdb0549f1bcb18555183cbc2504874 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 19 Sep 2024 18:52:55 +0000
Subject: [PATCH 2/2] Latest docs build.

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diff --git a/docs/build/html/.doctrees/environment.pickle b/docs/build/html/.doctrees/environment.pickle
index e276889a24a59377f3fe9dffc68ead839a03a45a..9c951c38eecd747c7cbb8fef9b1e3d03b40c395f 100644
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diff --git a/docs/build/html/_modules/gillespy2/core/model.html b/docs/build/html/_modules/gillespy2/core/model.html
index 0273d918d..4e049436d 100644
--- a/docs/build/html/_modules/gillespy2/core/model.html
+++ b/docs/build/html/_modules/gillespy2/core/model.html
@@ -1768,8 +1768,8 @@ <h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
             <span class="n">doc</span> <span class="o">=</span> <span class="n">eTree</span><span class="o">.</span><span class="n">tostring</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">document</span><span class="p">)</span>
             <span class="n">xmldoc</span> <span class="o">=</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">doc</span><span class="p">)</span>
             <span class="n">ugly_xml</span> <span class="o">=</span> <span class="n">xmldoc</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">(</span><span class="n">indent</span><span class="o">=</span><span class="s1">&#39;  &#39;</span><span class="p">)</span>
-            <span class="n">text_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s2">&quot;&gt;</span><span class="se">\n</span><span class="s2">\s+([^&lt;&gt;\s].*?)</span><span class="se">\n</span><span class="s2">\s+&lt;/&quot;</span><span class="p">,</span> <span class="n">re</span><span class="o">.</span><span class="n">DOTALL</span><span class="p">)</span>
-            <span class="n">pretty_xml</span> <span class="o">=</span> <span class="n">text_re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s2">&quot;&gt;\g&lt;1&gt;&lt;/&quot;</span><span class="p">,</span> <span class="n">ugly_xml</span><span class="p">)</span>
+            <span class="n">text_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;&gt;\n\s+([^&lt;&gt;\s].*?)\n\s+&lt;/&quot;</span><span class="p">,</span> <span class="n">re</span><span class="o">.</span><span class="n">DOTALL</span><span class="p">)</span>
+            <span class="n">pretty_xml</span> <span class="o">=</span> <span class="n">text_re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;&gt;\g&lt;1&gt;&lt;/&quot;</span><span class="p">,</span> <span class="n">ugly_xml</span><span class="p">)</span>
             <span class="k">return</span> <span class="n">pretty_xml</span></div>
 
     <span class="k">def</span> <span class="nf">__species_to_element</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>
diff --git a/docs/build/html/_modules/gillespy2/core/results.html b/docs/build/html/_modules/gillespy2/core/results.html
index d33d3d7a5..d04691ab0 100644
--- a/docs/build/html/_modules/gillespy2/core/results.html
+++ b/docs/build/html/_modules/gillespy2/core/results.html
@@ -387,7 +387,7 @@ <h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
             <span class="k">return</span> <span class="n">results</span>
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;number_of_trajectories must be non-negative and non-zero&quot;</span><span class="p">)</span></div>
 
-<div class="viewcode-block" id="Results.to_csv"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.results.Results.to_csv">[docs]</a>    <span class="k">def</span> <span class="nf">to_csv</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="s2">&quot;.&quot;</span><span class="p">,</span> <span class="n">nametag</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">stamp</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">postfix</span><span class="o">=</span><span class="s2">&quot;.odf&quot;</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+<div class="viewcode-block" id="Results.to_csv"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.results.Results.to_csv">[docs]</a>    <span class="k">def</span> <span class="nf">to_csv</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">path</span><span class="o">=</span><span class="s2">&quot;.&quot;</span><span class="p">,</span> <span class="n">nametag</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">stamp</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">suffix</span><span class="o">=</span><span class="s2">&quot;.odf&quot;</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Outputs the Results to one or more .csv files in a new directory.</span>
 
@@ -415,7 +415,7 @@ <h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
         <span class="k">else</span><span class="p">:</span>
             <span class="n">identifier</span> <span class="o">=</span> <span class="n">nametag</span>
 
-        <span class="n">directory</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">identifier</span><span class="si">}</span><span class="s2">-</span><span class="si">{</span><span class="n">stamp</span><span class="si">}{</span><span class="n">postfix</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="n">directory</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">identifier</span><span class="si">}</span><span class="s2">-</span><span class="si">{</span><span class="n">stamp</span><span class="si">}{</span><span class="n">suffix</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="k">if</span> <span class="n">verbose</span><span class="p">:</span>
             <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Writing data to: </span><span class="si">{</span><span class="n">directory</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="c1"># multiple trajectories</span>
diff --git a/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html b/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
index 7ce016f82..e75b674ff 100644
--- a/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
+++ b/docs/build/html/_modules/gillespy2/solvers/numpy/CLE_solver.html
@@ -163,7 +163,7 @@ <h1>Source code for gillespy2.solvers.numpy.CLE_solver</h1><div class="highlight
         <span class="bp">self</span><span class="o">.</span><span class="n">is_instantiated</span> <span class="o">=</span> <span class="kc">True</span>
 
     <span class="k">def</span> <span class="nf">__get_reactions</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">step</span><span class="p">,</span> <span class="n">curr_state</span><span class="p">,</span> <span class="n">curr_time</span><span class="p">,</span> <span class="n">save_time</span><span class="p">,</span> <span class="n">propensities</span><span class="p">,</span> <span class="n">reactions</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Helper Function to get reactions fired from t to t+tau.  </span>
 <span class="sd">        </span>
 <span class="sd">        In the equation:</span>
diff --git a/docs/build/html/classes/gillespy2.core.html b/docs/build/html/classes/gillespy2.core.html
index d9cd66ead..721e2e338 100644
--- a/docs/build/html/classes/gillespy2.core.html
+++ b/docs/build/html/classes/gillespy2.core.html
@@ -2449,7 +2449,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="gillespy2.core.results.Results.to_csv">
-<span class="sig-name descname"><span class="pre">to_csv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nametag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stamp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">postfix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.odf'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gillespy2/core/results.html#Results.to_csv"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gillespy2.core.results.Results.to_csv" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">to_csv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nametag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stamp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">suffix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.odf'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gillespy2/core/results.html#Results.to_csv"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gillespy2.core.results.Results.to_csv" title="Permalink to this definition">¶</a></dt>
 <dd><p>Outputs the Results to one or more .csv files in a new directory.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -4567,7 +4567,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="py method">
 <dt class="sig sig-object py" id="gillespy2.core.Results.to_csv">
-<span class="sig-name descname"><span class="pre">to_csv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nametag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stamp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">postfix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.odf'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gillespy2/core/results.html#Results.to_csv"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gillespy2.core.Results.to_csv" title="Permalink to this definition">¶</a></dt>
+<span class="sig-name descname"><span class="pre">to_csv</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nametag</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stamp</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">suffix</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.odf'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/gillespy2/core/results.html#Results.to_csv"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#gillespy2.core.Results.to_csv" title="Permalink to this definition">¶</a></dt>
 <dd><p>Outputs the Results to one or more .csv files in a new directory.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index bb155c43a..328559b6d 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["classes/gillespy2", "classes/gillespy2.core", "classes/gillespy2.sbml", "classes/gillespy2.solvers", "classes/gillespy2.solvers.auto", "classes/gillespy2.solvers.cpp", "classes/gillespy2.solvers.cpp.build", "classes/gillespy2.solvers.cython", "classes/gillespy2.solvers.numpy", "classes/gillespy2.solvers.stochkit", "classes/gillespy2.solvers.utilities", "classes/gillespy2.stochss", "getting_started/basic_usage/basic_usage", "getting_started/installation/installation", "index", "tutorials/tut_michaelis_menten/tut_michaelis_menten", "tutorials/tut_sbml/tut_sbml", "tutorials/tut_toggle_switch/tut_toggle_switch"], "filenames": ["classes/gillespy2.rst", "classes/gillespy2.core.rst", "classes/gillespy2.sbml.rst", "classes/gillespy2.solvers.rst", "classes/gillespy2.solvers.auto.rst", "classes/gillespy2.solvers.cpp.rst", "classes/gillespy2.solvers.cpp.build.rst", "classes/gillespy2.solvers.cython.rst", "classes/gillespy2.solvers.numpy.rst", 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"sanitized_formula": [0, 1], "cleanup": 0, "cleanup_tempfil": [0, 1], "event": [0, 3, 8], "add_assign": [0, 1], "eventassign": [0, 1], "eventtrigg": [0, 1], "sanitized_express": [0, 1], "functiondefinit": 0, "get_arg_str": [0, 1], "sanitized_funct": [0, 1], "gillespyerror": 0, "assignmentruleerror": [0, 1], "builderror": [0, 1], "directoryerror": [0, 1], "eventerror": [0, 1], "executionerror": [0, 1], "functiondefinitionerror": [0, 1], "invalidmodelerror": [0, 1], "invalidstochmlerror": [0, 1], "modelerror": [0, 1], "parametererror": [0, 1], "rateruleerror": [0, 1], "reactionerror": [0, 1], "resultserror": [0, 1], "sbmlerror": [0, 1], "simulationerror": [0, 1], "simulationtimeouterror": [0, 1], "solvererror": [0, 1], "specieserror": [0, 1], "stochmlimporterror": [0, 1], "timespanerror": [0, 1], "validationerror": [0, 1], "gillespysolv": [0, 3, 5, 8], "get_solver_set": [0, 1, 3, 5, 8], "get_supported_featur": [0, 1, 3, 5, 8], "get_supported_integrator_opt": [0, 1, 3, 5], "name": [0, 1, 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