Merge pull request #909 from StochSS/develop

Release 1.8.0
StochSS · Feb 9, 2023 · c82e36c · c82e36c
2 parents efa0ced + 97f0116
commit c82e36c
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Showing 92 changed files with 935 additions and 773 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,5 @@
 recursive-include gillespy2/solvers/cpp/c_base/ *
+recursive-include gillespy2/solvers/cpp/build/ SConstruct
 include requirements.txt
 include LICENSE
 include COPYRIGHT

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: a445821264fd5d4d13e4b1c30c83c950
+config: 2006784203741c89b203814ea55dd5b3
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/.doctrees/classes/gillespy2.solvers.cpp.build.doctree b/docs/build/html/.doctrees/classes/gillespy2.solvers.cpp.build.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 1.7.2 documentation</title>
+    <title>gillespy2.core.assignmentrule &#8212; GillesPy2 1.8.0 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" />
@@ -124,7 +124,7 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
 <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="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>
 
@@ -151,7 +151,7 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
         <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="sd">&#39;&#39;&#39;</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">        Sanitize the assignment rule formula.</span>
 
 <span class="sd">        :param species_mappings: Mapping of species names to sanitized species names.</span>
@@ -191,7 +191,7 @@ <h1>Source code for gillespy2.core.assignmentrule</h1><div class="highlight"><pr
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>
 

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 1.7.2 documentation</title>
+    <title>gillespy2.core.cleanup &#8212; GillesPy2 1.8.0 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" />
@@ -123,7 +123,7 @@ <h1>Source code for gillespy2.core.cleanup</h1><div class="highlight"><pre>
 <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="w">    </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>
@@ -150,7 +150,7 @@ <h1>Source code for gillespy2.core.cleanup</h1><div class="highlight"><pre>
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>
 

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 1.7.2 documentation</title>
+    <title>gillespy2.core.events &#8212; GillesPy2 1.8.0 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" />
@@ -127,7 +127,7 @@ <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">gillespy2.core.gillespyError</span> <span class="kn">import</span> <span class="n">EventError</span>
 
 <div class="viewcode-block" id="EventAssignment"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.events.EventAssignment">[docs]</a><span class="k">class</span> <span class="nc">EventAssignment</span><span class="p">(</span><span class="n">Jsonify</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    An EventAssignment describes a change to be performed to the current model</span>
 <span class="sd">    simulation.  This is assignment can either be fired at the time its</span>
 <span class="sd">    associated trigger changes from false to true, or after a specified delay,</span>
@@ -183,7 +183,7 @@ <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
         <span class="k">raise</span> <span class="ne">AttributeError</span></div>
 
 <div class="viewcode-block" id="EventTrigger"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.events.EventTrigger">[docs]</a><span class="k">class</span> <span class="nc">EventTrigger</span><span class="p">(</span><span class="n">Jsonify</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Trigger detects changes in model/environment conditions in order to fire an</span>
 <span class="sd">    event.  A Trigger contains an expression, a mathematical function which can</span>
 <span class="sd">    be evaluated to a boolean value within a model&#39;s namespace.  Upon</span>
@@ -221,7 +221,7 @@ <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">expression</span>
 
 <div class="viewcode-block" id="EventTrigger.sanitized_expression"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.events.EventTrigger.sanitized_expression">[docs]</a>    <span class="k">def</span> <span class="nf">sanitized_expression</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="sd">&#39;&#39;&#39;</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">        Sanitize the event trigger expression.</span>
 
 <span class="sd">        :param species_mappings: Mapping of species names to sanitized species names.</span>
@@ -243,7 +243,7 @@ <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">sanitized_expression</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>
 
 <div class="viewcode-block" id="Event"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.events.Event">[docs]</a><span class="k">class</span> <span class="nc">Event</span><span class="p">(</span><span class="n">Jsonify</span><span class="p">):</span>
-    <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    An Event can be given as an assignment_expression (function) or directly</span>
 <span class="sd">    as a value (scalar). If given an assignment_expression, it should be</span>
 <span class="sd">    understood as evaluable in the namespace of a parent Model.</span>
@@ -363,7 +363,7 @@ <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">print_string</span>
 
 <div class="viewcode-block" id="Event.add_assignment"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.events.Event.add_assignment">[docs]</a>    <span class="k">def</span> <span class="nf">add_assignment</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">assignment</span><span class="p">):</span>
-        <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Adds an EventAssignment or a list of EventAssignment.</span>
 
 <span class="sd">        :param assignment: The event or list of events to be added to this event.</span>
@@ -400,7 +400,7 @@ <h1>Source code for gillespy2.core.events</h1><div class="highlight"><pre>
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>
 

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 1.7.2 documentation</title>
+    <title>gillespy2.core.functiondefinition &#8212; GillesPy2 1.8.0 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" />
@@ -126,7 +126,7 @@ <h1>Source code for gillespy2.core.functiondefinition</h1><div class="highlight"
 <span class="kn">from</span> <span class="nn">gillespy2.core.gillespyError</span> <span class="kn">import</span> <span class="n">FunctionDefinitionError</span>
 
 <div class="viewcode-block" id="FunctionDefinition"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.functiondefinition.FunctionDefinition">[docs]</a><span class="k">class</span> <span class="nc">FunctionDefinition</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="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Object representation defining an evaluable function to be used during</span>
 <span class="sd">    simulation of a GillesPy2 model</span>
 
@@ -156,15 +156,15 @@ <h1>Source code for gillespy2.core.functiondefinition</h1><div class="highlight"
         <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">: Args: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="si">}</span><span class="s2">, Expression: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">function_string</span><span class="si">}</span><span class="s2">&quot;</span>
 
 <div class="viewcode-block" id="FunctionDefinition.get_arg_string"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.functiondefinition.FunctionDefinition.get_arg_string">[docs]</a>    <span class="k">def</span> <span class="nf">get_arg_string</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
-        <span class="sd">&quot;&quot;&quot;</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Convert function&#39;s argument list into a comma-separated formatted string.</span>
 
 <span class="sd">        :returns: Argument list as a comma-separated formatted string.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="s1">&#39;,&#39;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">args</span><span class="p">)</span></div>
 
 <div class="viewcode-block" id="FunctionDefinition.sanitized_function"><a class="viewcode-back" href="../../../classes/gillespy2.core.html#gillespy2.core.functiondefinition.FunctionDefinition.sanitized_function">[docs]</a>    <span class="k">def</span> <span class="nf">sanitized_function</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="sd">&#39;&#39;&#39;</span>
+<span class="w">        </span><span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">        Sanitize the function definition function.</span>
 
 <span class="sd">        :param species_mappings: Mapping of species names to sanitized species names.</span>
@@ -204,7 +204,7 @@ <h1>Source code for gillespy2.core.functiondefinition</h1><div class="highlight"
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>
 

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 1.7.2 documentation</title>
+    <title>gillespy2.core.gillespyError &#8212; GillesPy2 1.8.0 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" />
@@ -223,7 +223,7 @@ <h1>Source code for gillespy2.core.gillespyError</h1><div class="highlight"><pre
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 5.3.0</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.13</a>
 
     </div>