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docs/build/html/.doctrees/classes/gillespy2.core.doctree

@@ -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="kc">None</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>
+<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>
 <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>
 
@@ -400,6 +400,12 @@ <h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
 
 <span class="sd">        :param stamp: Allows the user to optionally &quot;tag&quot; the directory (not included files). Default is timestamp.</span>
 <span class="sd">        :type stamp: str</span>
+
+<span class="sd">        :param verbose: Print useful informataion.</span>
+<span class="sd">        :type verbose: str</span>
+
+<span class="sd">        :returns: Path to the observed data files.</span>
+<span class="sd">        :rtype: str</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">stamp</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="n">now</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">now</span><span class="p">()</span>
@@ -408,13 +414,13 @@ <h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
             <span class="n">identifier</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_validate_title</span><span class="p">(</span><span class="n">show_title</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
         <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="k">if</span> <span class="n">path</span> <span class="ow">is</span> <span class="kc">None</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="s2">&quot;.&quot;</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">identifier</span><span class="p">)</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">stamp</span><span class="p">))</span>
-        <span class="k">else</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="nb">str</span><span class="p">(</span><span class="n">identifier</span><span class="p">)</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">stamp</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">postfix</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>
         <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">,</span> <span class="nb">list</span><span class="p">):</span>
-            <span class="n">os</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">directory</span><span class="p">)</span>
+            <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">directory</span><span class="p">)</span>
             <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">trajectory</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="p">):</span>  <span class="c1"># write each CSV file</span>
                 <span class="n">filename</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">directory</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">identifier</span><span class="p">)</span><span class="o">+</span><span class="nb">str</span><span class="p">(</span><span class="n">i</span><span class="p">)</span><span class="o">+</span><span class="s2">&quot;.csv&quot;</span><span class="p">)</span>
                 <span class="n">field_names</span> <span class="o">=</span> <span class="p">[]</span>
@@ -427,7 +433,8 @@ <h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
                         <span class="n">this_line</span><span class="o">=</span><span class="p">[]</span>
                         <span class="k">for</span> <span class="n">species</span> <span class="ow">in</span> <span class="n">trajectory</span><span class="p">:</span>  <span class="c1"># build one line of the CSV file</span>
                             <span class="n">this_line</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">trajectory</span><span class="p">[</span><span class="n">species</span><span class="p">][</span><span class="n">j</span><span class="p">])</span>
-                        <span class="n">csv_writer</span><span class="o">.</span><span class="n">writerow</span><span class="p">(</span><span class="n">this_line</span><span class="p">)</span>  <span class="c1"># write one line of the CSV file</span></div>
+                        <span class="n">csv_writer</span><span class="o">.</span><span class="n">writerow</span><span class="p">(</span><span class="n">this_line</span><span class="p">)</span>  <span class="c1"># write one line of the CSV file</span>
+        <span class="k">return</span> <span class="n">directory</span></div>
 
 <div class="viewcode-block" id="Results.plot"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.results.Results.plot">[docs]</a>    <span class="k">def</span> <span class="nf">plot</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">xaxis_label</span><span class="o">=</span><span class="s2">&quot;Time&quot;</span><span class="p">,</span> <span class="n">xscale</span><span class="o">=</span><span class="s1">&#39;linear&#39;</span><span class="p">,</span> <span class="n">yscale</span><span class="o">=</span><span class="s1">&#39;linear&#39;</span><span class="p">,</span> <span class="n">yaxis_label</span><span class="o">=</span><span class="s2">&quot;Value&quot;</span><span class="p">,</span>
              <span class="n">style</span><span class="o">=</span><span class="s2">&quot;default&quot;</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">show_title</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">show_legend</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">multiple_graphs</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>

docs/build/html/.doctrees/environment.pickle

@@ -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">None</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><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">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>
 <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>
@@ -2458,8 +2458,15 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 name.</p></li>
 <li><p><strong>path</strong> (<em>str</em>) – the location for the new directory and included files. Defaults to model location.</p></li>
 <li><p><strong>stamp</strong> (<em>str</em>) – Allows the user to optionally “tag” the directory (not included files). Default is timestamp.</p></li>
+<li><p><strong>verbose</strong> (<em>str</em>) – Print useful informataion.</p></li>
 </ul>
 </dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Path to the observed data files.</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>str</p>
+</dd>
 </dl>
 </dd></dl>
 
@@ -4560,7 +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">None</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><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">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>
 <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>
@@ -4569,8 +4576,15 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 name.</p></li>
 <li><p><strong>path</strong> (<em>str</em>) – the location for the new directory and included files. Defaults to model location.</p></li>
 <li><p><strong>stamp</strong> (<em>str</em>) – Allows the user to optionally “tag” the directory (not included files). Default is timestamp.</p></li>
+<li><p><strong>verbose</strong> (<em>str</em>) – Print useful informataion.</p></li>
 </ul>
 </dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>Path to the observed data files.</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>str</p>
+</dd>
 </dl>
 </dd></dl>