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Merged
briandrawert merged 22 commits into from
Apr 14, 2022
Merged

v1.0.2 Release #252

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01d5910
Merge branch 'staging' of https://github.com/StochSS/SpatialPy into d…
BryanRumsey Mar 8, 2022
0c8d9eb
Added visualization module to the package.
BryanRumsey Mar 9, 2022
3ac0310
Added a visualization error to the errors module.
BryanRumsey Mar 9, 2022
f9a0b37
Created new module for visualizing results.
BryanRumsey Mar 14, 2022
832b897
Refactored type ploting to use new visualization module.
BryanRumsey Mar 14, 2022
f395b51
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into d…
BryanRumsey Mar 15, 2022
2b9c9da
Merge branch 'main' of https://github.com/StochSS/SpatialPy into develop
BryanRumsey Mar 15, 2022
e10dbfd
Updated version to v1.0.2.
BryanRumsey Mar 15, 2022
84ac411
Added checkout for matplotlib dependency.
BryanRumsey Mar 15, 2022
963edb1
Merge branch 'develop' of https://github.com/StochSS/SpatialPy into v…
BryanRumsey Mar 15, 2022
049e443
Refactored the species constructor to accept param names as diffusion…
BryanRumsey Mar 15, 2022
afaba18
Updated tests for species.
BryanRumsey Mar 15, 2022
21858b7
Added support for parameter names as accepted values for det_diffusio…
BryanRumsey Mar 16, 2022
455a8c9
Updated tests to account for updated type scope for diffusion coeffic…
BryanRumsey Mar 16, 2022
a0640e0
Added support for species names in initial conditions.
BryanRumsey Apr 6, 2022
faa7b2f
Merge pull request #250 from StochSS/spec-str-init-cond
briandrawert Apr 13, 2022
c78b52a
Merge pull request #249 from StochSS/param-str-diff-coeff
briandrawert Apr 13, 2022
ae8a149
Merge pull request #246 from StochSS/visualization
briandrawert Apr 13, 2022
acc1e43
Fixed copyright in the version file.
BryanRumsey Apr 14, 2022
13d7145
Updated copyright blocks to work with docs.
BryanRumsey Apr 14, 2022
c571bc1
Updated docs.
BryanRumsey Apr 14, 2022
fd2831a
Merge pull request #247 from StochSS/develop
BryanRumsey Apr 14, 2022
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2 changes: 1 addition & 1 deletion 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: 9eb3e1c2ecc65d7c728e939f73f722a8
config: dcc482ab068f3e2527755562cc1c17ff
tags: 645f666f9bcd5a90fca523b33c5a78b7
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<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" />
Expand Down Expand Up @@ -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>
Expand All @@ -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.

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</div>
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32 changes: 15 additions & 17 deletions docs/build/html/_modules/spatialpy/core/boundarycondition.html
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<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" />
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<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>

Expand Down Expand Up @@ -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>
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32 changes: 15 additions & 17 deletions docs/build/html/_modules/spatialpy/core/cleanup.html
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<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" />
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<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>
Expand Down Expand Up @@ -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>
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<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" />
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>
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