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Merge pull request #731 from StochSS/develop
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Release 1.6.9
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briandrawert authored Apr 14, 2022
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strategy:
matrix:
os: [ ubuntu-latest, macos-latest, windows-latest ]
python-versions: [ '3.6', '3.7', '3.8', '3.9' ]
python-versions: [ '3.7', '3.8', '3.9', '3.10' ]

steps:
- name: Initialize environment
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2 changes: 1 addition & 1 deletion COPYRIGHT
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GillesPy2 is a Python 3 package for stochastic simulation of biochemical systems.
Copyright (C) 2020 GillesPy2 developers.
Copyright (C) 2019-2022 GillesPy2 developers.

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
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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: 85b86bfadf484dc8346375c8ac88a258
config: 3660d62a689826af0ef6e8b2cfa373ce
tags: 645f666f9bcd5a90fca523b33c5a78b7
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59 changes: 42 additions & 17 deletions docs/build/html/_modules/gillespy2/core/assignmentrule.html
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<!DOCTYPE html>

<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
<html lang="en">
<head>
<meta charset="utf-8" />
<title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.5.2 documentation</title>
<link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.6.9 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css" />
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<link rel="search" title="Search" href="../../../search.html" />

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<h3>Navigation</h3>
<p class="caption"><span class="caption-text">Getting started</span></p>
<p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../getting_started/installation/installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../../../getting_started/basic_usage/basic_usage.html">Basic usage</a></li>
</ul>
<p class="caption"><span class="caption-text">Tutorials</span></p>
<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tut_toggle_switch/tut_toggle_switch.html">Tutorial: ODE vs. SSA</a></li>
</ul>
<p class="caption"><span class="caption-text">API reference</span></p>
<p class="caption" role="heading"><span class="caption-text">API reference</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../../../classes/gillespy2.html">gillespy2 package</a></li>
</ul>
Expand All @@ -77,7 +77,7 @@ <h3>Related Topics</h3>
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<h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pre>
<span></span><span class="kn">from</span> <span class="nn">gillespy2.core.sortableobject</span> <span class="k">import</span> <span class="n">SortableObject</span>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2022 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
<span class="c1"># the Free Software Foundation, either version 3 of the License, or</span>
<span class="c1"># (at your option) any later version.</span>

<div class="viewcode-block" id="AssignmentRule"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.assignmentrule.AssignmentRule">[docs]</a><span class="k">class</span> <span class="nc">AssignmentRule</span><span class="p">(</span><span class="n">SortableObject</span><span class="p">):</span>
<span class="c1"># This program is distributed in the hope that it will be useful,</span>
<span class="c1"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<span class="c1"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<span class="c1"># GNU General Public License for more details.</span>

<span class="c1"># You should have received a copy of the GNU General Public License</span>
<span class="c1"># along with this program. If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>

<span class="kn">import</span> <span class="nn">uuid</span>

<span class="kn">from</span> <span class="nn">gillespy2.core.sortableobject</span> <span class="kn">import</span> <span class="n">SortableObject</span>
<span class="kn">from</span> <span class="nn">gillespy2.core.jsonify</span> <span class="kn">import</span> <span class="n">Jsonify</span>


<div class="viewcode-block" id="AssignmentRule"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.assignmentrule.AssignmentRule">[docs]</a><span class="k">class</span> <span class="nc">AssignmentRule</span><span class="p">(</span><span class="n">SortableObject</span><span class="p">,</span> <span class="n">Jsonify</span><span class="p">):</span>
<span class="sd">&quot;&quot;&quot;</span>
<span class="sd"> An AssignmentRule is used to express equations that set the values of</span>
<span class="sd"> variables. This would correspond to a function in the form of x = f(V)</span>

<span class="sd"> :param name: Name of the Rule</span>
<span class="sd"> :type name: str</span>

<span class="sd"> :param variable: Target Species/Parameter to be modified by rule</span>
<span class="sd"> :type variable: str</span>

<span class="sd"> :param formula: String representation of formula to be evaluated</span>
<span class="sd"> :type formula: str</span>
<span class="sd"> &quot;&quot;&quot;</span>

<span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">variable</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">formula</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">variable</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">formula</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">if</span> <span class="n">name</span> <span class="ow">in</span> <span class="p">(</span><span class="kc">None</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">):</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="sa">f</span><span class="s1">&#39;ar</span><span class="si">{</span><span class="n">uuid</span><span class="o">.</span><span class="n">uuid4</span><span class="p">()</span><span class="si">}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s1">&#39;-&#39;</span><span class="p">,</span> <span class="s1">&#39;_&#39;</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
<span class="bp">self</span><span class="o">.</span><span class="n">variable</span> <span class="o">=</span> <span class="n">variable</span>
<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="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>

<span class="k">def</span> <span class="nf">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</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>

<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>
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<div class="clearer"></div>
</div>
<div class="footer">
&copy;Copyright (C) 2017-2020.
&copy;Copyright (C) 2017-2021.

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163 changes: 163 additions & 0 deletions docs/build/html/_modules/gillespy2/core/cleanup.html
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<!DOCTYPE html>

<html lang="en">
<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>
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<h3>Navigation</h3>
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<h1>Source code for gillespy2.core.cleanup</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2022 GillesPy2 developers.</span>

<span class="c1"># This program is free software: you can redistribute it and/or modify</span>
<span class="c1"># it under the terms of the GNU General Public License as published by</span>
<span class="c1"># the Free Software Foundation, either version 3 of the License, or</span>
<span class="c1"># (at your option) any later version.</span>

<span class="c1"># This program is distributed in the hope that it will be useful,</span>
<span class="c1"># but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<span class="c1"># MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
<span class="c1"># GNU General Public License for more details.</span>

<span class="c1"># You should have received a copy of the GNU General Public License</span>
<span class="c1"># along with this program. If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>

<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">shutil</span>
<span class="kn">import</span> <span class="nn">tempfile</span>

<div class="viewcode-block" id="cleanup_tempfiles"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.cleanup.cleanup_tempfiles">[docs]</a><span class="k">def</span> <span class="nf">cleanup_tempfiles</span><span class="p">():</span>
<span class="sd">&#39;&#39;&#39;</span>
<span class="sd"> Cleanup all tempfiles in gillespy2 build.</span>
<span class="sd"> &#39;&#39;&#39;</span>
<span class="n">tempdir</span> <span class="o">=</span> <span class="n">tempfile</span><span class="o">.</span><span class="n">gettempdir</span><span class="p">()</span>
<span class="k">for</span> <span class="n">file_obj</span> <span class="ow">in</span> <span class="n">os</span><span class="o">.</span><span class="n">listdir</span><span class="p">(</span><span class="n">tempdir</span><span class="p">):</span>
<span class="k">if</span> <span class="n">file_obj</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;gillespy2_build&quot;</span><span class="p">):</span>
<span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</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">tempdir</span><span class="p">,</span> <span class="n">file_obj</span><span class="p">))</span></div>
</pre></div>

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