Merge pull request #229 from StochSS/doc-edits

small doc update

Author: briandrawert

docs/build/html/.doctrees/classes/spatialpy.core.doctree

@@ -124,7 +124,7 @@ <h1>Source code for spatialpy.core.boundarycondition</h1><div class="highlight">
 <span class="sd">         - type_id: type (subdomain) of the partciles</span>
 <span class="sd">    Targets (one of the following must be set):</span>
 <span class="sd">        property: (str), &#39;nu&#39;, &#39;rho&#39;,&#39;v&#39;</span>
-<span class="sd">        species: (str) name of a chemical species.</span>
+<span class="sd">        species: (str) name of a chemical species. \</span>
 <span class="sd">                   Must also set deterministic=True/False flag.</span>
 
 <span class="sd">    :param xmin: x-axis coordinate lower bound of **condition**</span>
@@ -152,15 +152,15 @@ <h1>Source code for spatialpy.core.boundarycondition</h1><div class="highlight">
 <span class="sd">    and applies to deterministic simulation. **BoundaryCondition not yet implemeneted for Stochastic Species**.</span>
 <span class="sd">    :type deterministic: bool</span>
 
-<span class="sd">    :param target: Set **target** to properties, can be &#39;nu&#39; &#39;rho&#39; or &#39;v&#39; or species name</span>
+<span class="sd">    :param target: Set **target** to properties, can be &#39;nu&#39; &#39;rho&#39; or &#39;v&#39; or species name \</span>
 <span class="sd">    If species name, determinstic must also be set to True/False.</span>
 <span class="sd">    :type target: str</span>
 
 <span class="sd">    :param value: Value property will take in region defined by the conditions</span>
 <span class="sd">    :type value: float or float[3]</span>
 
 <span class="sd">    :param model: Target model of boundary condition</span>
-<span class="sd">    :type model: spatialpy.Model.Model</span>
+<span class="sd">    :type model: spatialpy.core.model.Model</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">xmin</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">xmax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ymin</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">ymax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">zmin</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">zmax</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>

docs/build/html/.doctrees/classes/spatialpy.solvers.doctree

@@ -116,6 +116,8 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
 
 <span class="sd">    :param name: Name of the Data Function.</span>
 <span class="sd">    :type name: str</span>
+
+<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>
@@ -128,11 +130,11 @@ <h1>Source code for spatialpy.core.datafunction</h1><div class="highlight"><pre>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        This method must be overridden by the DataFunction subclass.</span>
 
-<span class="sd">        NOTE: The spatial location is evaulated at t=0 and is not</span>
-<span class="sd">              reevaluated as the fluid domain moves over time.</span>
+<span class="sd">        NOTE: The spatial location is evaulated at t=0 and is not \</span>
+<span class="sd">              re-evaluated as the fluid domain moves over time.</span>
 
-<span class="sd">        :param point: The x,y,z position</span>
-<span class="sd">        :type point: vector of 3 doubles</span>
+<span class="sd">        :param point: The x, y, z position.</span>
+<span class="sd">        :type point: float[3]</span>
 
 <span class="sd">        :returns: Value of function at this spatial location.</span>
 <span class="sd">        :rtype: float</span>

docs/build/html/.doctrees/classes/spatialpy.stochss.doctree

@@ -150,7 +150,7 @@ <h1>Source code for spatialpy.core.geometry</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="GeometryExterior"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.geometry.GeometryExterior">[docs]</a><span class="k">class</span> <span class="nc">GeometryExterior</span><span class="p">(</span><span class="n">Geometry</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Mark particles that are on the edge of the domain.</span>
-<span class="sd">    only works for meshes that define triangles and tetrahedrons.</span>
+<span class="sd">    only works for domains that define triangles and tetrahedrons.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 <div class="viewcode-block" id="GeometryExterior.inside"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.geometry.GeometryExterior.inside">[docs]</a>    <span class="k">def</span> <span class="nf">inside</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">point</span><span class="p">,</span> <span class="n">on_boundary</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
@@ -168,7 +168,7 @@ <h1>Source code for spatialpy.core.geometry</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="GeometryInterior"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.geometry.GeometryInterior">[docs]</a><span class="k">class</span> <span class="nc">GeometryInterior</span><span class="p">(</span><span class="n">Geometry</span><span class="p">):</span>
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Mark particles that are not on the edge of the domain.</span>
-<span class="sd">    Only works for meshes that define triangles and tetrahedrons.</span>
+<span class="sd">    Only works for domains that define triangles and tetrahedrons.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 <div class="viewcode-block" id="GeometryInterior.inside"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.geometry.GeometryInterior.inside">[docs]</a>    <span class="k">def</span> <span class="nf">inside</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">point</span><span class="p">,</span> <span class="n">on_boundary</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>

docs/build/html/.doctrees/environment.pickle

@@ -116,11 +116,14 @@ <h1>Source code for spatialpy.core.initialcondition</h1><div class="highlight"><
     <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    Class used to defined initial conditions in SpatialPy.</span>
 <span class="sd">    SubClasses must implement the &#39;apply(model)&#39; method, which</span>
-<span class="sd">    direction modifies the model.u0[species,voxel] matrix.</span>
+<span class="sd">    direction modifies the model.u0[species, voxel] matrix.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 <div class="viewcode-block" id="InitialCondition.apply"><a class="viewcode-back" href="../../../classes/spatialpy.core.html#spatialpy.core.initialcondition.InitialCondition.apply">[docs]</a>    <span class="k">def</span> <span class="nf">apply</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">model</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Set the initial condition of the species to the count.</span>
+
+<span class="sd">        :param model: Model contianing the target species.</span>
+<span class="sd">        :type model: spatialpy.core.model.Model</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">raise</span> <span class="n">InitialConditionError</span><span class="p">(</span><span class="s2">&quot;spatialpy.InitialCondition subclasses must implement apply()&quot;</span><span class="p">)</span></div></div>
 
@@ -129,7 +132,7 @@ <h1>Source code for spatialpy.core.initialcondition</h1><div class="highlight"><
 <span class="sd">    Class used to defined the place initial condition in SpatialPy.</span>
 
 <span class="sd">    :param species: The species to set the initial condition.</span>
-<span class="sd">    :type species: spayialpy.species.Species</span>
+<span class="sd">    :type species: spatialpy.core.species.Species</span>
 
 <span class="sd">    :param count: The initial condition for the target species.</span>
 <span class="sd">    :type count: int</span>
@@ -151,7 +154,7 @@ <h1>Source code for spatialpy.core.initialcondition</h1><div class="highlight"><
 <span class="sd">        Set the initial condition of the species to the count at the location.</span>
 
 <span class="sd">        :param model: Model contianing the target species.</span>
-<span class="sd">        :type model: spatialpy.model.Model</span>
+<span class="sd">        :type model: spatialpy.core.model.Model</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">spec_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">species</span><span class="o">.</span><span class="n">name</span>
         <span class="n">spec_ndx</span> <span class="o">=</span> <span class="kc">None</span>
@@ -167,7 +170,7 @@ <h1>Source code for spatialpy.core.initialcondition</h1><div class="highlight"><
 <span class="sd">    Class used to defined the uniform initial condition in SpatialPy.</span>
 
 <span class="sd">    :param species: The species to set the initial condition.</span>
-<span class="sd">    :type species: spayialpy.species.Species</span>
+<span class="sd">    :type species: spatialpy.core.species.Species</span>
 
 <span class="sd">    :param count: The initial condition for the target species.</span>
 <span class="sd">    :type count: int</span>
@@ -194,7 +197,7 @@ <h1>Source code for spatialpy.core.initialcondition</h1><div class="highlight"><
 <span class="sd">        Set &#39;count&#39; of &#39;species&#39; in over the list of types (all types if None).</span>
 
 <span class="sd">        :param model: Model contianing the target species.</span>
-<span class="sd">        :type model: spatialpy.model.Model</span>
+<span class="sd">        :type model: spatialpy.core.model.Model</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">spec_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">species</span><span class="o">.</span><span class="n">name</span>
         <span class="n">spec_ndx</span> <span class="o">=</span> <span class="kc">None</span>
@@ -219,7 +222,7 @@ <h1>Source code for spatialpy.core.initialcondition</h1><div class="highlight"><
 <span class="sd">    Class used to defined the scatter initial condition in SpatialPy.</span>
 
 <span class="sd">    :param species: The species to set the initial condition.</span>
-<span class="sd">    :type species: spayialpy.species.Species</span>
+<span class="sd">    :type species: spatialpy.core.species.Species</span>
 
 <span class="sd">    :param count: The initial condition for the target species.</span>
 <span class="sd">    :type count: int</span>
@@ -246,7 +249,7 @@ <h1>Source code for spatialpy.core.initialcondition</h1><div class="highlight"><
 <span class="sd">        Scatter &#39;count&#39; of &#39;species&#39; randomly over the list of types (all types if None).</span>
 
 <span class="sd">        :param model: Model contianing the target species.</span>
-<span class="sd">        :type model: spatialpy.model.Model</span>
+<span class="sd">        :type model: spatialpy.core.model.Model</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">spec_name</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">species</span><span class="o">.</span><span class="n">name</span>
         <span class="n">spec_ndx</span> <span class="o">=</span> <span class="kc">None</span>