Merge branch 'develop' of github.com:StochSS/GillesPy2 into develop

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>

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>

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>

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

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>

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" />