Merge pull request #962 from StochSS/develop

Release 1.8.3

.github/workflows/run-full-tests.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-versions: [ '3.7', '3.8', '3.9', '3.10' ]
+        python-versions: [ '3.10', '3.11', '3.12' ]
 
     steps:
     - name: Initialize environment

.github/workflows/run-integration-tests.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Install Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.7'
+        python-version: '3.12'
 
     # see: https://github.com/actions/virtual-environments/pull/5729
     # GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.

.github/workflows/run-system-tests.yml

@@ -18,7 +18,7 @@ jobs:
     - name: Install Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.7'
+        python-version: '3.12'
 
     # see: https://github.com/actions/virtual-environments/pull/5729
     # GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.

.github/workflows/run-unit-tests.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Install Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.7'
+        python-version: '3.12'
 
     # see: https://github.com/actions/virtual-environments/pull/5729
     # GHA recently upgrading MinGW to v11.20, which seems to break things in that environment.

AUTHORS

@@ -21,3 +21,5 @@ Ethan Green
 Josh Cooper
 Matthew Dippel
 Joshua Fisher-Caudill
+Ben Blamey
+

COPYRIGHT

@@ -1,5 +1,5 @@
 GillesPy2 is a Python 3 package for stochastic simulation of biochemical systems.
-Copyright (C) 2019-2023 GillesPy2 developers.
+Copyright (C) 2019-2024 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

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # 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: 6224f6c27785099ae9bf97ec5ae27f60
+config: 1b056b927b45b7771d0f07f5ff9c1698
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_modules/gillespy2/core/assignmentrule.html

@@ -103,7 +103,7 @@ <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) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/cleanup.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <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) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/events.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/functiondefinition.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.functiondefinition</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/gillespyError.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.gillespyError</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/gillespySolver.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.gillespySolver</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/jsonify.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.jsonify</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/liveGraphing.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.liveGraphing</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/model.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>
@@ -1768,8 +1768,8 @@ <h1>Source code for gillespy2.core.model</h1><div class="highlight"><pre>
             <span class="n">doc</span> <span class="o">=</span> <span class="n">eTree</span><span class="o">.</span><span class="n">tostring</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">document</span><span class="p">)</span>
             <span class="n">xmldoc</span> <span class="o">=</span> <span class="n">xml</span><span class="o">.</span><span class="n">dom</span><span class="o">.</span><span class="n">minidom</span><span class="o">.</span><span class="n">parseString</span><span class="p">(</span><span class="n">doc</span><span class="p">)</span>
             <span class="n">ugly_xml</span> <span class="o">=</span> <span class="n">xmldoc</span><span class="o">.</span><span class="n">toprettyxml</span><span class="p">(</span><span class="n">indent</span><span class="o">=</span><span class="s1">&#39;  &#39;</span><span class="p">)</span>
-            <span class="n">text_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="s2">&quot;&gt;</span><span class="se">\n</span><span class="s2">\s+([^&lt;&gt;\s].*?)</span><span class="se">\n</span><span class="s2">\s+&lt;/&quot;</span><span class="p">,</span> <span class="n">re</span><span class="o">.</span><span class="n">DOTALL</span><span class="p">)</span>
-            <span class="n">pretty_xml</span> <span class="o">=</span> <span class="n">text_re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="s2">&quot;&gt;\g&lt;1&gt;&lt;/&quot;</span><span class="p">,</span> <span class="n">ugly_xml</span><span class="p">)</span>
+            <span class="n">text_re</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;&gt;\n\s+([^&lt;&gt;\s].*?)\n\s+&lt;/&quot;</span><span class="p">,</span> <span class="n">re</span><span class="o">.</span><span class="n">DOTALL</span><span class="p">)</span>
+            <span class="n">pretty_xml</span> <span class="o">=</span> <span class="n">text_re</span><span class="o">.</span><span class="n">sub</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;&gt;\g&lt;1&gt;&lt;/&quot;</span><span class="p">,</span> <span class="n">ugly_xml</span><span class="p">)</span>
             <span class="k">return</span> <span class="n">pretty_xml</span></div>
 
     <span class="k">def</span> <span class="nf">__species_to_element</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">species</span><span class="p">):</span>

docs/build/html/_modules/gillespy2/core/parameter.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.parameter</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/raterule.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.raterule</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/reaction.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.reaction</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/results.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>
@@ -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="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>
+<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">suffix</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>
 
@@ -415,7 +415,7 @@ <h1>Source code for gillespy2.core.results</h1><div class="highlight"><pre>
         <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="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="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">suffix</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>

docs/build/html/_modules/gillespy2/core/sortableobject.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.sortableobject</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/species.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.species</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/core/timespan.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.core.timespan</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/solvers/cpp/build/build_engine.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.solvers.cpp.build.build_engine</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/solvers/cpp/build/expression.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.solvers.cpp.build.expression</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>

docs/build/html/_modules/gillespy2/solvers/cpp/build/make.html

@@ -103,7 +103,7 @@ <h3 id="searchlabel">Quick search</h3>
 
   <h1>Source code for gillespy2.solvers.cpp.build.make</h1><div class="highlight"><pre>
 <span></span><span class="c1"># GillesPy2 is a modeling toolkit for biochemical simulation.</span>
-<span class="c1"># Copyright (C) 2019-2023 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2024 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>