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v1.7.0 Documentation Update #858

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Aug 10, 2022
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v1.7.0 Documentation Update #858

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9987e41
Updated docs for v1.7.0 release.
BryanRumsey Aug 9, 2022
a258970
Merge branch 'develop' of https://github.com/StochSS/GillesPy2 into d…
BryanRumsey Aug 10, 2022
80c7efa
Updated the basic usage rst file.
BryanRumsey Aug 10, 2022
04a636c
updated docs take 2.
BryanRumsey Aug 10, 2022
cf202ac
Updated the toggle switch tutorial.
BryanRumsey Aug 10, 2022
750b5cb
Updated docs take 3.
BryanRumsey Aug 10, 2022
4d4cf6b
Updated the toggle switch tutorial again.....
BryanRumsey Aug 10, 2022
b55123e
Updated docs take 4.
BryanRumsey Aug 10, 2022
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2 changes: 1 addition & 1 deletion docs/build/html/.buildinfo
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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: 3660d62a689826af0ef6e8b2cfa373ce
config: d1441d39ddf6f2630e9183ea6bf3095a
tags: 645f666f9bcd5a90fca523b33c5a78b7
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5 changes: 3 additions & 2 deletions docs/build/html/_modules/gillespy2/core/assignmentrule.html
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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 1.6.9 documentation</title>
<title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.6.10 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />
Expand Down Expand Up @@ -146,7 +146,8 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
<span class="bp">self</span><span class="o">.</span><span class="n">formula</span> <span class="o">=</span> <span class="n">formula</span>

<span class="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">variable</span> <span class="o">+</span> <span class="s1">&#39;: &#39;</span> <span class="o">+</span> <span class="bp">self</span><span class="o">.</span><span class="n">formula</span>
<span class="n">var_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">variable</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">variable</span><span class="p">,</span> <span class="nb">str</span><span class="p">)</span> <span class="k">else</span> <span class="bp">self</span><span class="o">.</span><span class="n">variable</span><span class="o">.</span><span class="n">name</span>
<span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="si">}</span><span class="s2">: Var: </span><span class="si">{</span><span class="n">var_name</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">formula</span><span class="si">}</span><span class="s2">&quot;</span>

<div class="viewcode-block" id="AssignmentRule.sanitized_formula"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.assignmentrule.AssignmentRule.sanitized_formula">[docs]</a> <span class="k">def</span> <span class="nf">sanitized_formula</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">species_mappings</span><span class="p">,</span> <span class="n">parameter_mappings</span><span class="p">):</span>
<span class="n">names</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">species_mappings</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span> <span class="o">+</span> <span class="nb">list</span><span class="p">(</span><span class="n">parameter_mappings</span><span class="o">.</span><span class="n">keys</span><span class="p">()),</span> <span class="n">key</span><span class="o">=</span><span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="nb">len</span><span class="p">(</span><span class="n">x</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.cleanup &#8212; GillesPy2 1.6.9 documentation</title>
<title>gillespy2.core.cleanup &#8212; GillesPy2 1.6.10 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />
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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 1.6.9 documentation</title>
<title>gillespy2.core.events &#8212; GillesPy2 1.6.10 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.functiondefinition &#8212; GillesPy2 1.6.9 documentation</title>
<title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.6.10 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />
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24 changes: 22 additions & 2 deletions docs/build/html/_modules/gillespy2/core/gillespyError.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.gillespyError &#8212; GillesPy2 1.6.9 documentation</title>
<title>gillespy2.core.gillespyError &#8212; GillesPy2 1.6.10 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css" />
Expand Down Expand Up @@ -125,11 +125,27 @@ <h1>Source code for gillespy2.core.gillespyError</h1><div class="highlight"><pre
<span class="k">pass</span></div>


<div class="viewcode-block" id="ParameterError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.ParameterError">[docs]</a><span class="k">class</span> <span class="nc">ParameterError</span><span class="p">(</span><span class="n">ModelError</span><span class="p">):</span>
<span class="k">pass</span></div>


<div class="viewcode-block" id="ReactionError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.ReactionError">[docs]</a><span class="k">class</span> <span class="nc">ReactionError</span><span class="p">(</span><span class="n">ModelError</span><span class="p">):</span>
<span class="k">pass</span></div>


<div class="viewcode-block" id="ParameterError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.ParameterError">[docs]</a><span class="k">class</span> <span class="nc">ParameterError</span><span class="p">(</span><span class="n">ModelError</span><span class="p">):</span>
<div class="viewcode-block" id="RateRuleError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.RateRuleError">[docs]</a><span class="k">class</span> <span class="nc">RateRuleError</span><span class="p">(</span><span class="n">ModelError</span><span class="p">):</span>
<span class="k">pass</span></div>


<div class="viewcode-block" id="AssignmentRuleError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.AssignmentRuleError">[docs]</a><span class="k">class</span> <span class="nc">AssignmentRuleError</span><span class="p">(</span><span class="n">ModelError</span><span class="p">):</span>
<span class="k">pass</span></div>


<span class="k">class</span> <span class="nc">EventError</span><span class="p">(</span><span class="n">ModelError</span><span class="p">):</span>
<span class="k">pass</span>


<div class="viewcode-block" id="FunctionDefinitionError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.FunctionDefinitionError">[docs]</a><span class="k">class</span> <span class="nc">FunctionDefinitionError</span><span class="p">(</span><span class="n">ModelError</span><span class="p">):</span>
<span class="k">pass</span></div>


Expand Down Expand Up @@ -185,6 +201,10 @@ <h1>Source code for gillespy2.core.gillespyError</h1><div class="highlight"><pre

<div class="viewcode-block" id="ValidationError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.ValidationError">[docs]</a><span class="k">class</span> <span class="nc">ValidationError</span><span class="p">(</span><span class="n">ResultsError</span><span class="p">):</span>
<span class="k">pass</span></div>


<div class="viewcode-block" id="SBMLError"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.gillespyError.SBMLError">[docs]</a><span class="k">class</span> <span class="nc">SBMLError</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
<span class="k">pass</span></div>
</pre></div>

</div>
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