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b53c3e2
Latest docs build.
github-actions[bot] Sep 19, 2024
5990276
Merge branch 'main' of github.com:stochss/gillespy2 into develop
briandrawert Jan 23, 2025
472dfc8
updating python version so docs will build
briandrawert Jan 23, 2025
2deca20
Latest docs build.
github-actions[bot] Jan 23, 2025
dda3275
updating python version
briandrawert Jan 23, 2025
d498de2
Merge branch 'develop' of github.com:stochss/gillespy2 into develop
briandrawert Jan 23, 2025
012954d
Latest docs build.
github-actions[bot] Jan 23, 2025
909eefb
update copyright to 2025
briandrawert Jan 23, 2025
3adcb35
Merge pull request #965 from StochSS/update_copyright_to_2025
briandrawert Jan 23, 2025
382d160
Latest docs build.
github-actions[bot] Jan 23, 2025
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4 changes: 2 additions & 2 deletions .github/workflows/pypi-publish.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.7'
python-version: '3.13.1'

- name: Install dependencies
run: |
Expand All @@ -27,4 +27,4 @@ jobs:
uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
password: ${{ secrets.PYPI_API_TOKEN }}
2 changes: 1 addition & 1 deletion .github/workflows/update-docs.yaml
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Expand Up @@ -18,7 +18,7 @@ jobs:
- name: Install Python
uses: actions/setup-python@v2
with:
python-version: '3.7'
python-version: '3.13.1'

- name: Install Sphinx Dependency
run: |
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4 changes: 2 additions & 2 deletions 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: 1b056b927b45b7771d0f07f5ff9c1698
# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 03b167906d31b77ad3f3cd226f36a62e
tags: 645f666f9bcd5a90fca523b33c5a78b7
4 changes: 4 additions & 0 deletions docs/build/html/.buildinfo.bak
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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: 062d73627145ee1a24339b59898243cb
tags: 645f666f9bcd5a90fca523b33c5a78b7
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81 changes: 42 additions & 39 deletions docs/build/html/_modules/gillespy2/core/assignmentrule.html
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@@ -1,38 +1,36 @@

<!DOCTYPE html>

<html lang="en">
<html lang="en" data-content_root="../../../">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.8.2 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" />
<script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
<script src="../../../_static/jquery.js"></script>
<script src="../../../_static/underscore.js"></script>
<script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
<script src="../../../_static/doctools.js"></script>
<script src="../../../_static/sphinx_highlight.js"></script>
<title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.8.3 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=5ecbeea2" />
<link rel="stylesheet" type="text/css" href="../../../_static/basic.css?v=686e5160" />
<link rel="stylesheet" type="text/css" href="../../../_static/alabaster.css?v=5647dbb4" />
<link rel="stylesheet" type="text/css" href="../../../_static/css/gillespy2_alabaster_customizations.css?v=b3beab4e" />
<script src="../../../_static/documentation_options.js?v=82e6e318"></script>
<script src="../../../_static/doctools.js?v=9bcbadda"></script>
<script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
<link rel="index" title="Index" href="../../../genindex.html" />
<link rel="search" title="Search" href="../../../search.html" />

<link rel="stylesheet" href="../../../_static/custom.css" type="text/css" />

<link rel="apple-touch-icon" href="../../../_static/img/gillespy2-logo.svg" />




<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />

</head><body>
<div class="document">

<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<p class="logo">
<a href="../../../index.html">
<img class="logo" src="../../../_static/img/gillespy2-logo.svg" alt="Logo"/>
<img class="logo" src="../../../_static/img/gillespy2-logo.svg" alt="Logo" />

</a>
</p>
Expand All @@ -51,7 +49,16 @@



<h3>Navigation</h3>

<search id="searchbox" style="display: none" role="search">
<div class="searchformwrapper">
<form class="search" action="../../../search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
<input type="submit" value="Go" />
</form>
</div>
</search>
<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
<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>
Expand All @@ -75,16 +82,6 @@ <h3>Related Topics</h3>
</ul></li>
</ul>
</div>
<div id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../../../search.html" method="get">
<input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
<input type="submit" value="Go" />
</form>
</div>
</div>
<script>document.getElementById('searchbox').style.display = "block"</script>



Expand All @@ -103,7 +100,7 @@ <h3 id="searchlabel">Quick search</h3>

<h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pre>
<span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
<span class="c1"># Copyright (C) 2019-2024 GillesPy2 developers.</span>
<span class="c1"># Copyright (C) 2019-2025 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>
Expand All @@ -118,12 +115,14 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
<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">import</span><span class="w"> </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>
<span class="kn">from</span><span class="w"> </span><span class="nn">gillespy2.core.sortableobject</span><span class="w"> </span><span class="kn">import</span> <span class="n">SortableObject</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">gillespy2.core.jsonify</span><span class="w"> </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>
<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="w"> </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="w"> </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>
Expand All @@ -138,19 +137,21 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
<span class="sd"> :type formula: str</span>
<span class="sd"> &quot;&quot;&quot;</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">def</span><span class="w"> </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="k">def</span> <span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="fm">__str__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</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>
<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="w"> </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="w"> </span><span class="sd">&#39;&#39;&#39;</span>
<span class="sd"> Sanitize the assignment rule formula.</span>

Expand All @@ -170,7 +171,9 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
<span class="n">sanitized_formula</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">formula</span>
<span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">names</span><span class="p">):</span>
<span class="n">sanitized_formula</span> <span class="o">=</span> <span class="n">sanitized_formula</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="n">name</span><span class="p">,</span> <span class="s2">&quot;{&quot;</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;}&quot;</span><span class="p">)</span>
<span class="k">return</span> <span class="n">sanitized_formula</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="n">replacements</span><span class="p">)</span></div></div>
<span class="k">return</span> <span class="n">sanitized_formula</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">*</span><span class="n">replacements</span><span class="p">)</span></div>
</div>

</pre></div>

</div>
Expand All @@ -187,17 +190,17 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
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