StochSS · BryanRumsey · Apr 14, 2022 · Mar 7, 2022 · Mar 8, 2022 · Mar 8, 2022
diff --git a/README.md b/README.md
@@ -1,13 +1,13 @@
 <p align="left">
-<img src="https://raw.githubusercontent.com/StochSS/SpatialPy/main/logo/SpatialPy_logo.png">
+<img src="https://raw.githubusercontent.com/StochSS/SpatialPy/main/.graphics/SpatialPy_logo.png">
 </p>
 
 SpatialPy is a Python 3 package for simulation of spatial deterministic/stochastic reaction-diffusion-advection problems embedded in Lagrangian reference frame particle based fluid dynamics domain
 
 This package is intended to replace the PyURDME software https://github.com/pyurdme/pyurdme and will feature both a NSM solver for RDME simulation on static domains and a sSSA-SDPD particle based fluid dynamics solver as described in the publication "A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection–diffusion–reaction problems" by Drawert, Jacob, Li, Yi, Petzold https://www.sciencedirect.com/science/article/pii/S0021999118307101
 
 <table><tr><td><b>
-<img width="20%" align="right" src="https://raw.githubusercontent.com/SpatialPy/SpatialPy/develop/.graphics/stochss-logo.png">
+<img width="20%" align="right" src="https://raw.githubusercontent.com/SpatialPy/SpatialPy/main/.graphics/stochss-logo.png">
 <a href="https://docs.google.com/forms/d/12tAH4f8CJ-3F-lK44Q9uQHFio_mGoK0oY829q5lD7i4/viewform">PLEASE REGISTER AS A USER</a>, so that we can prove SpatialPy has many users when we seek funding to support development. SpatialPy is part of the <a href="http://www.stochss.org">StochSS</a> project.
 </td></tr></table>
 
@@ -25,9 +25,11 @@ Table of contents
   - [_Using the source code repository_](#using-the-source-code-repository)
 - [Usage](#usage)
   - [_Simple example to illustrate the use of SpatialPy_](#simple-example-to-illustrate-the-use-of-spatialpy)
+<!--
   - [_Docker environment_](#docker-environment)
   - [_Debugging_](#debugging)
   - [_Profiling_](#profiling)
+-->
 - [Getting help](#getting-help)
 - [Contributing](#contributing)
 - [License](#license)
@@ -72,8 +74,8 @@ SpatialPy provides simple object-oriented abstractions for defining a model of a
 
 The `run()` method can be customized using keyword arguments to select different solvers, random seed, data return type and more.  For more detailed examples on how to use SpatialPy, please see the Jupyter notebooks contained in the [examples](https://github.com/StochSS/SpatialPy/tree/main/examples) subdirectory.
 
-
-### Docker environment
+<!-- 
+### Docker environment (DOES NOT WORK)
 
 You can use Docker to create a repeatable environment for developing and debugging SpatialPy. The supplied Dockerfile starts a jupyter server with SpatialPy dependencies installed.
 
@@ -102,6 +104,7 @@ You can invoke `solver.run_debugger()` anytime after you instantiate a solver in
 ### Profiling
 
 To enable profiling, both `solver.compile()` and `solver.run()` need to be invoked with `profile=True`. If you don't run `solver.compile()` explicitly, invoking `solver.run()` with `profile=True` will run `compile()` correctly for you.
+-->
 
 Getting help
 ------------

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
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: 9eb3e1c2ecc65d7c728e939f73f722a8
+config: dcc482ab068f3e2527755562cc1c17ff
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/.doctrees/classes/spatialpy.core.doctree b/docs/build/html/.doctrees/classes/spatialpy.core.doctree
diff --git a/docs/build/html/.doctrees/classes/spatialpy.doctree b/docs/build/html/.doctrees/classes/spatialpy.doctree
diff --git a/docs/build/html/.doctrees/classes/spatialpy.solvers.doctree b/docs/build/html/.doctrees/classes/spatialpy.solvers.doctree
diff --git a/docs/build/html/.doctrees/classes/spatialpy.stochss.doctree b/docs/build/html/.doctrees/classes/spatialpy.stochss.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/index.html b/docs/build/html/_modules/index.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; SpatialPy 1.0 documentation</title>
+    <title>Overview: module code &#8212; SpatialPy 1.0.2 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/spatialpy_alabaster_customizations.css" />
@@ -105,6 +105,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="spatialpy/core/result.html">spatialpy.core.result</a></li>
 <li><a href="spatialpy/core/spatialpyerror.html">spatialpy.core.spatialpyerror</a></li>
 <li><a href="spatialpy/core/species.html">spatialpy.core.species</a></li>
+<li><a href="spatialpy/core/visualization.html">spatialpy.core.visualization</a></li>
 <li><a href="spatialpy/core/vtkreader.html">spatialpy.core.vtkreader</a></li>
 <li><a href="spatialpy/solvers/build_expression.html">spatialpy.solvers.build_expression</a></li>
 <li><a href="spatialpy/solvers/solver.html">spatialpy.solvers.solver</a></li>
@@ -125,10 +126,10 @@ <h1>All modules for which code is available</h1>
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2019-2022.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.1.1</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.4.0</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>

diff --git a/docs/build/html/_modules/spatialpy/core/boundarycondition.html b/docs/build/html/_modules/spatialpy/core/boundarycondition.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>spatialpy.core.boundarycondition &#8212; SpatialPy 1.0 documentation</title>
+    <title>spatialpy.core.boundarycondition &#8212; SpatialPy 1.0.2 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/spatialpy_alabaster_customizations.css" />
@@ -91,23 +91,21 @@ <h3 id="searchlabel">Quick search</h3>
           <div class="body" role="main">
 
   <h1>Source code for spatialpy.core.boundarycondition</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;</span>
-<span class="sd">SpatialPy is a Python 3 package for simulation of</span>
-<span class="sd">spatial deterministic/stochastic reaction-diffusion-advection problems</span>
-<span class="sd">Copyright (C) 2019 - 2022 SpatialPy developers.</span>
+<span></span><span class="c1"># SpatialPy is a Python 3 package for simulation of</span>
+<span class="c1"># spatial deterministic/stochastic reaction-diffusion-advection problems</span>
+<span class="c1"># Copyright (C) 2019 - 2022 SpatialPy developers.</span>
 
-<span class="sd">This program is free software: you can redistribute it and/or modify</span>
-<span class="sd">it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as</span>
-<span class="sd">published by the Free Software Foundation.</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 Version 3 as</span>
+<span class="c1"># published by the Free Software Foundation.</span>
 
-<span class="sd">This program is distributed in the hope that it will be useful,</span>
-<span class="sd">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
-<span class="sd">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
-<span class="sd">GNU GENERAL PUBLIC LICENSE Version 3 for more details.</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 Version 3 for more details.</span>
 
-<span class="sd">You should have received a copy of the GNU General Public License</span>
-<span class="sd">along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
-<span class="sd">&#39;&#39;&#39;</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">from</span> <span class="nn">spatialpy.core.spatialpyerror</span> <span class="kn">import</span> <span class="n">BoundaryConditionError</span>
 
@@ -274,10 +272,10 @@ <h1>Source code for spatialpy.core.boundarycondition</h1><div class="highlight">
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2019-2022.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.1.1</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.4.0</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>

diff --git a/docs/build/html/_modules/spatialpy/core/cleanup.html b/docs/build/html/_modules/spatialpy/core/cleanup.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>spatialpy.core.cleanup &#8212; SpatialPy 1.0 documentation</title>
+    <title>spatialpy.core.cleanup &#8212; SpatialPy 1.0.2 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/spatialpy_alabaster_customizations.css" />
@@ -91,23 +91,21 @@ <h3 id="searchlabel">Quick search</h3>
           <div class="body" role="main">
 
   <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;</span>
-<span class="sd">SpatialPy is a Python 3 package for simulation of</span>
-<span class="sd">spatial deterministic/stochastic reaction-diffusion-advection problems</span>
-<span class="sd">Copyright (C) 2019 - 2022 SpatialPy developers.</span>
+<span></span><span class="c1"># SpatialPy is a Python 3 package for simulation of</span>
+<span class="c1"># spatial deterministic/stochastic reaction-diffusion-advection problems</span>
+<span class="c1"># Copyright (C) 2019 - 2022 SpatialPy developers.</span>
 
-<span class="sd">This program is free software: you can redistribute it and/or modify</span>
-<span class="sd">it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as</span>
-<span class="sd">published by the Free Software Foundation.</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 Version 3 as</span>
+<span class="c1"># published by the Free Software Foundation.</span>
 
-<span class="sd">This program is distributed in the hope that it will be useful,</span>
-<span class="sd">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
-<span class="sd">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
-<span class="sd">GNU GENERAL PUBLIC LICENSE Version 3 for more details.</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 Version 3 for more details.</span>
 
-<span class="sd">You should have received a copy of the GNU General Public License</span>
-<span class="sd">along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
-<span class="sd">&#39;&#39;&#39;</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>
@@ -196,10 +194,10 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2019-2022.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.1.1</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.4.0</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>

diff --git a/docs/build/html/_modules/spatialpy/core/datafunction.html b/docs/build/html/_modules/spatialpy/core/datafunction.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>spatialpy.core.datafunction &#8212; SpatialPy 1.0 documentation</title>
+    <title>spatialpy.core.datafunction &#8212; SpatialPy 1.0.2 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/spatialpy_alabaster_customizations.css" />
@@ -91,23 +91,21 @@ <h3 id="searchlabel">Quick search</h3>
           <div class="body" role="main">
 
   <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
-<span></span><span class="sd">&#39;&#39;&#39;</span>
-<span class="sd">SpatialPy is a Python 3 package for simulation of</span>
-<span class="sd">spatial deterministic/stochastic reaction-diffusion-advection problems</span>
-<span class="sd">Copyright (C) 2019 - 2022 SpatialPy developers.</span>
-
-<span class="sd">This program is free software: you can redistribute it and/or modify</span>
-<span class="sd">it under the terms of the GNU GENERAL PUBLIC LICENSE Version 3 as</span>
-<span class="sd">published by the Free Software Foundation.</span>
-
-<span class="sd">This program is distributed in the hope that it will be useful,</span>
-<span class="sd">but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
-<span class="sd">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
-<span class="sd">GNU GENERAL PUBLIC LICENSE Version 3 for more details.</span>
-
-<span class="sd">You should have received a copy of the GNU General Public License</span>
-<span class="sd">along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span>
-<span class="sd">&#39;&#39;&#39;</span>
+<span></span><span class="c1"># SpatialPy is a Python 3 package for simulation of</span>
+<span class="c1"># spatial deterministic/stochastic reaction-diffusion-advection problems</span>
+<span class="c1"># Copyright (C) 2019 - 2022 SpatialPy 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 Version 3 as</span>
+<span class="c1"># published by the Free Software Foundation.</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 Version 3 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">from</span> <span class="nn">spatialpy.core.spatialpyerror</span> <span class="kn">import</span> <span class="n">DataFunctionError</span>
 
 <div class="viewcode-block" id="DataFunction"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.datafunction.DataFunction">[docs]</a><span class="k">class</span> <span class="nc">DataFunction</span><span class="p">():</span>
@@ -156,10 +154,10 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
     <div class="clearer"></div>
   </div>
     <div class="footer">
-      &copy;Copyright (C) 2017-2022.
+      &copy;Copyright (C) 2019-2022.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.1.1</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 4.4.0</a>
       &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
 
     </div>