Latest docs build.

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/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>