StochSS · briandrawert · Aug 15, 2022 · Jul 25, 2022 · Jul 26, 2022 · Jul 27, 2022
diff --git a/README.md b/README.md
@@ -88,7 +88,7 @@ def create_birth_death(parameter_values=None):
 
     # Define domain points and attributes of a regional space for simulation.
     domain = spatialpy.Domain.create_2D_domain(
-        xlim=(0, 1), ylim=(0, 1), nx=10, ny=10, type_id=model.HABITAT, fixed=True
+        xlim=(0, 1), ylim=(0, 1), numx=10, numy=10, type_id=model.HABITAT, fixed=True
     )
     model.add_domain(domain)
 

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: dcc482ab068f3e2527755562cc1c17ff
+config: 8b8c7260a070827b00291bef99cea017
 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 1.0.2 documentation</title>
+    <title>Overview: module code &#8212; SpatialPy 1.1.0 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/spatialpy_alabaster_customizations.css" />
@@ -89,22 +89,21 @@ <h3 id="searchlabel">Quick search</h3>
           <div class="body" role="main">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="collections.html">collections</a></li>
-<li><a href="itertools.html">itertools</a></li>
-<li><a href="plotly/offline/offline.html">plotly.offline.offline</a></li>
-<li><a href="scipy/spatial/kdtree.html">scipy.spatial.kdtree</a></li>
-<li><a href="spatialpy/core/boundarycondition.html">spatialpy.core.boundarycondition</a></li>
+<ul><li><a href="spatialpy/core/boundarycondition.html">spatialpy.core.boundarycondition</a></li>
 <li><a href="spatialpy/core/cleanup.html">spatialpy.core.cleanup</a></li>
 <li><a href="spatialpy/core/datafunction.html">spatialpy.core.datafunction</a></li>
 <li><a href="spatialpy/core/domain.html">spatialpy.core.domain</a></li>
 <li><a href="spatialpy/core/geometry.html">spatialpy.core.geometry</a></li>
 <li><a href="spatialpy/core/initialcondition.html">spatialpy.core.initialcondition</a></li>
+<li><a href="spatialpy/core/lattice.html">spatialpy.core.lattice</a></li>
 <li><a href="spatialpy/core/model.html">spatialpy.core.model</a></li>
 <li><a href="spatialpy/core/parameter.html">spatialpy.core.parameter</a></li>
 <li><a href="spatialpy/core/reaction.html">spatialpy.core.reaction</a></li>
 <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/timespan.html">spatialpy.core.timespan</a></li>
+<li><a href="spatialpy/core/transformation.html">spatialpy.core.transformation</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>

diff --git a/docs/build/html/_modules/spatialpy/core/boundarycondition.html b/docs/build/html/_modules/spatialpy/core/boundarycondition.html
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 1.0.2 documentation</title>
+    <title>spatialpy.core.cleanup &#8212; SpatialPy 1.1.0 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/spatialpy_alabaster_customizations.css" />
@@ -127,7 +127,7 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
     <span class="sd">&#39;&#39;&#39;</span>
 <span class="sd">    Cleanup all tempfiles in spatialpy core.</span>
 <span class="sd">    &#39;&#39;&#39;</span>
-    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="kn">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
+    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="k">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</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>
     <span class="n">core_dir</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">tempdir</span><span class="p">,</span> <span class="s2">&quot;spatialpy_core&quot;</span><span class="p">)</span>
@@ -142,7 +142,7 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
 <span class="sd">    :param build_dir: Path to the build directory to be removed. (optional)</span>
 <span class="sd">    :type build_dir: string</span>
 <span class="sd">    &#39;&#39;&#39;</span>
-    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="kn">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
+    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="k">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
 
     <span class="k">if</span> <span class="n">build_dir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">build_dir</span><span class="p">)</span>
@@ -164,7 +164,7 @@ <h1>Source code for spatialpy.core.cleanup</h1><div class="highlight"><pre>
 <span class="sd">    :param result_dir: Path to the result directory to be removed. (optional)</span>
 <span class="sd">    :type result_dir: string</span>
 <span class="sd">    &#39;&#39;&#39;</span>
-    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="kn">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
+    <span class="kn">from</span> <span class="nn">spatialpy.core</span> <span class="k">import</span> <span class="n">log</span> <span class="c1"># pylint: disable=import-outside-toplevel</span>
 
     <span class="k">if</span> <span class="n">result_dir</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
         <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">result_dir</span><span class="p">)</span>

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 1.0.2 documentation</title>
+    <title>spatialpy.core.datafunction &#8212; SpatialPy 1.1.0 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/spatialpy_alabaster_customizations.css" />
@@ -106,7 +106,7 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
 
 <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>
+<span class="kn">from</span> <span class="nn">spatialpy.core.spatialpyerror</span> <span class="k">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>
     <span class="sd">&quot;&quot;&quot;</span>
@@ -118,7 +118,7 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
 <span class="sd">    :raises DataFunctionError: If a name is not provided.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
         <span class="k">if</span> <span class="n">name</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">name</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -137,7 +137,7 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
 <span class="sd">        :returns: Value of function at this spatial location.</span>
 <span class="sd">        :rtype: float</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">raise</span> <span class="n">DataFunctionError</span><span class="p">(</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">: DataFunction.map() must be implemented.&quot;</span><span class="p">)</span></div></div>
+        <span class="k">raise</span> <span class="n">DataFunctionError</span><span class="p">(</span><span class="n">f</span><span class="s2">&quot;</span><span class="si">{self.name}</span><span class="s2">: DataFunction.map() must be implemented.&quot;</span><span class="p">)</span></div></div>
 </pre></div>
 
           </div>