Merge pull request #921 from StochSS/develop

Release 1.8.1
StochSS · Mar 7, 2023 · 662926a · 662926a
2 parents fa89882 + 3dd682b
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diff --git a/COPYRIGHT b/COPYRIGHT
@@ -1,5 +1,5 @@
 GillesPy2 is a Python 3 package for stochastic simulation of biochemical systems.
-Copyright (C) 2019-2022 GillesPy2 developers.
+Copyright (C) 2019-2023 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

diff --git a/docs/build/html/.buildinfo b/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: 2006784203741c89b203814ea55dd5b3
+config: 714161441d2f0842325605e90e4c0783
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/.doctrees/classes/gillespy2.core.doctree b/docs/build/html/.doctrees/classes/gillespy2.core.doctree
diff --git a/docs/build/html/.doctrees/classes/gillespy2.solvers.doctree b/docs/build/html/.doctrees/classes/gillespy2.solvers.doctree
diff --git a/docs/build/html/.doctrees/classes/gillespy2.solvers.stochkit.doctree b/docs/build/html/.doctrees/classes/gillespy2.solvers.stochkit.doctree
diff --git a/docs/build/html/.doctrees/environment.pickle b/docs/build/html/.doctrees/environment.pickle
diff --git a/docs/build/html/.doctrees/index.doctree b/docs/build/html/.doctrees/index.doctree
diff --git a/docs/build/html/_modules/gillespy2/core/assignmentrule.html b/docs/build/html/_modules/gillespy2/core/assignmentrule.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -187,7 +187,7 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>

diff --git a/docs/build/html/_modules/gillespy2/core/cleanup.html b/docs/build/html/_modules/gillespy2/core/cleanup.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.cleanup &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.cleanup &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -146,7 +146,7 @@ <h1>Source code for gillespy2.core.cleanup</h1><div class="highlight"><pre>
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>

diff --git a/docs/build/html/_modules/gillespy2/core/events.html b/docs/build/html/_modules/gillespy2/core/events.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.events &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.events &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -396,7 +396,7 @@ <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>

diff --git a/docs/build/html/_modules/gillespy2/core/functiondefinition.html b/docs/build/html/_modules/gillespy2/core/functiondefinition.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -200,7 +200,7 @@ <h1>Source code for gillespy2.core.functiondefinition</h1><div class="highlight"
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>

diff --git a/docs/build/html/_modules/gillespy2/core/gillespyError.html b/docs/build/html/_modules/gillespy2/core/gillespyError.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.gillespyError &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.gillespyError &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -219,7 +219,7 @@ <h1>Source code for gillespy2.core.gillespyError</h1><div class="highlight"><pre
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>

diff --git a/docs/build/html/_modules/gillespy2/core/gillespySolver.html b/docs/build/html/_modules/gillespy2/core/gillespySolver.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.gillespySolver &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.gillespySolver &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -284,7 +284,7 @@ <h1>Source code for gillespy2.core.gillespySolver</h1><div class="highlight"><pr
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>

diff --git a/docs/build/html/_modules/gillespy2/core/jsonify.html b/docs/build/html/_modules/gillespy2/core/jsonify.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.jsonify &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.jsonify &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -538,7 +538,7 @@ <h1>Source code for gillespy2.core.jsonify</h1><div class="highlight"><pre>
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>

diff --git a/docs/build/html/_modules/gillespy2/core/liveGraphing.html b/docs/build/html/_modules/gillespy2/core/liveGraphing.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>gillespy2.core.liveGraphing &#8212; GillesPy2 1.8.0 documentation</title>
+    <title>gillespy2.core.liveGraphing &#8212; GillesPy2 1.8.1 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" />
@@ -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) 2019-2022 GillesPy2 developers.</span>
+<span class="c1"># Copyright (C) 2019-2023 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>
@@ -393,7 +393,7 @@ <h1>Source code for gillespy2.core.liveGraphing</h1><div class="highlight"><pre>
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2017-2023.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>