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1.8.2 Release
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briandrawert authored Apr 27, 2023
2 parents 662926a + ae9fd73 commit de40702
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# 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: 714161441d2f0842325605e90e4c0783
config: 6224f6c27785099ae9bf97ec5ae27f60
tags: 645f666f9bcd5a90fca523b33c5a78b7
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.8.2 documentation</title>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.cleanup &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.cleanup &#8212; GillesPy2 1.8.2 documentation</title>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.events &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.events &#8212; GillesPy2 1.8.2 documentation</title>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.8.2 documentation</title>
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<head>
<meta charset="utf-8" />
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<title>gillespy2.core.gillespyError &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.gillespyError &#8212; GillesPy2 1.8.2 documentation</title>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.gillespySolver &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.gillespySolver &#8212; GillesPy2 1.8.2 documentation</title>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.jsonify &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.jsonify &#8212; GillesPy2 1.8.2 documentation</title>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.liveGraphing &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.liveGraphing &#8212; GillesPy2 1.8.2 documentation</title>
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24 changes: 21 additions & 3 deletions docs/build/html/_modules/gillespy2/core/model.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.model &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.model &#8212; GillesPy2 1.8.2 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
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Expand Down Expand Up @@ -175,10 +175,14 @@ <h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
<span class="k">except</span> <span class="ne">ImportError</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
<span class="k">raise</span> <span class="ne">ImportError</span><span class="p">(</span><span class="s1">&#39;SBML conversion not imported successfully&#39;</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">err</span>

<span class="k">return</span> <span class="n">convert</span><span class="p">(</span>
<span class="p">(</span><span class="n">model</span><span class="p">,</span><span class="n">errs</span><span class="p">)</span> <span class="o">=</span> <span class="n">convert</span><span class="p">(</span>
<span class="n">filename</span><span class="p">,</span> <span class="n">model_name</span><span class="o">=</span><span class="n">name</span><span class="p">,</span> <span class="n">gillespy_model</span><span class="o">=</span><span class="n">gillespy_model</span><span class="p">,</span>
<span class="n">report_silently_with_sbml_error</span><span class="o">=</span><span class="n">report_silently_with_sbml_error</span>
<span class="p">)</span></div>
<span class="p">)</span>
<span class="k">if</span> <span class="n">model</span><span class="o">.</span><span class="n">tspan</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">model</span><span class="o">.</span><span class="n">timespan</span><span class="p">(</span><span class="n">gillespy2</span><span class="o">.</span><span class="n">TimeSpan</span><span class="o">.</span><span class="n">linspace</span><span class="p">(</span><span class="n">t</span><span class="o">=</span><span class="mi">1</span><span class="p">))</span>

<span class="k">return</span> <span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">errs</span><span class="p">)</span></div>


<div class="viewcode-block" id="export_SBML"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.model.export_SBML">[docs]</a><span class="k">def</span> <span class="nf">export_SBML</span><span class="p">(</span><span class="n">gillespy_model</span><span class="p">,</span> <span class="n">filename</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
Expand Down Expand Up @@ -318,6 +322,8 @@ <h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
<span class="n">print_string</span> <span class="o">+=</span> <span class="n">decorate</span><span class="p">(</span><span class="s1">&#39;Species&#39;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">species</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">listOfSpecies</span><span class="o">.</span><span class="n">values</span><span class="p">()):</span>
<span class="n">print_string</span> <span class="o">+=</span> <span class="s1">&#39;</span><span class="se">\n</span><span class="s1">&#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">species</span><span class="p">)</span>
<span class="k">if</span> <span class="n">species</span><span class="o">.</span><span class="n">mode</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">print_string</span> <span class="o">+=</span> <span class="s1">&#39; (&#39;</span> <span class="o">+</span> <span class="n">species</span><span class="o">.</span><span class="n">mode</span> <span class="o">+</span> <span class="s1">&#39;)&#39;</span>
<span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">listOfParameters</span><span class="p">):</span>
<span class="n">print_string</span> <span class="o">+=</span> <span class="n">decorate</span><span class="p">(</span><span class="s1">&#39;Parameters&#39;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">parameter</span> <span class="ow">in</span> <span class="nb">sorted</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">listOfParameters</span><span class="o">.</span><span class="n">values</span><span class="p">()):</span>
Expand Down Expand Up @@ -345,6 +351,8 @@ <h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
<span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">tspan</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">print_string</span> <span class="o">+=</span> <span class="n">decorate</span><span class="p">(</span><span class="s1">&#39;Timespan&#39;</span><span class="p">)</span>
<span class="n">print_string</span> <span class="o">+=</span> <span class="nb">str</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">tspan</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">print_string</span> <span class="o">+=</span> <span class="n">decorate</span><span class="p">(</span><span class="s1">&#39;No Timespan found&#39;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">print_string</span>

<span class="k">def</span> <span class="fm">__getitem__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">):</span>
Expand Down Expand Up @@ -1395,6 +1403,16 @@ <h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">SimulationError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">solver</span><span class="si">}</span><span class="s2"> is not a valid solver. Reason Given: </span><span class="si">{</span><span class="n">err</span><span class="si">}</span><span class="s2">.&quot;</span><span class="p">)</span> <span class="kn">from</span> <span class="nn">err</span>

<span class="k">if</span> <span class="s2">&quot;integrator&quot;</span> <span class="ow">in</span> <span class="n">solver_args</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">SimulationError</span><span class="p">(</span>
<span class="sa">f</span><span class="s2">&quot;&quot;&quot;</span>
<span class="s2"> The integrator argument to run is only supported by the ODESolver.run method. To use the integrator use:</span>

<span class="s2"> solver = gillespy2.ODESolver(model=model)</span>
<span class="s2"> results = solver.run(integrator=&#39;</span><span class="si">{</span><span class="n">solver_args</span><span class="p">[</span><span class="s1">&#39;integrator&#39;</span><span class="p">]</span><span class="si">}</span><span class="s2">&#39;)</span>
<span class="s2"> &quot;&quot;&quot;</span>
<span class="p">)</span>

<span class="k">try</span><span class="p">:</span>
<span class="k">return</span> <span class="n">solver</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">t</span><span class="o">=</span><span class="n">t</span><span class="p">,</span> <span class="n">increment</span><span class="o">=</span><span class="n">increment</span><span class="p">,</span> <span class="n">timeout</span><span class="o">=</span><span class="n">timeout</span><span class="p">,</span> <span class="o">**</span><span class="n">solver_args</span><span class="p">)</span>
<span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">err</span><span class="p">:</span>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.parameter &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.parameter &#8212; GillesPy2 1.8.2 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
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Expand Down Expand Up @@ -225,7 +225,7 @@ <h1>Source code for gillespy2.core.parameter</h1><div class="highlight"><pre>
<span class="k">if</span> <span class="n">expression</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">ParameterError</span><span class="p">(</span><span class="s2">&quot;initial_value can&#39;t be None type.&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">expression</span><span class="p">,</span> <span class="nb">str</span><span class="p">):</span>
<span class="k">raise</span> <span class="n">ParameterError</span><span class="p">(</span><span class="s2">&quot;expression must be of type str, float, or int.&quot;</span><span class="p">)</span>
<span class="k">raise</span> <span class="n">ParameterError</span><span class="p">(</span><span class="s2">&quot;expression must be of type str.&quot;</span><span class="p">)</span>
<span class="k">if</span> <span class="n">expression</span> <span class="o">==</span> <span class="s2">&quot;&quot;</span><span class="p">:</span>
<span class="k">raise</span> <span class="n">ParameterError</span><span class="p">(</span><span class="s2">&quot;expression can&#39;t be an empty string.&quot;</span><span class="p">)</span></div></div>
</pre></div>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.raterule &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.raterule &#8212; GillesPy2 1.8.2 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.reaction &#8212; GillesPy2 1.8.1 documentation</title>
<title>gillespy2.core.reaction &#8212; GillesPy2 1.8.2 documentation</title>
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