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Mar 7, 2022
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small doc update #229

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eca4d62
small doc update
seanebum Feb 28, 2022
3372f96
Fixed start here notebook name.
BryanRumsey Mar 1, 2022
a2585ed
Fixed doc strings for boundary conditions.
BryanRumsey Mar 1, 2022
05ad212
Fixed doc strings for boundary conditions.
BryanRumsey Mar 1, 2022
86c3647
Added a missing raises doc tag for data functions.
BryanRumsey Mar 1, 2022
4ca44ad
Updated docs in domain. updated docs.
BryanRumsey Mar 1, 2022
d5d489f
Updated docs in domain. updated docs.
BryanRumsey Mar 1, 2022
dffadb7
Updated docs in domain. updated docs.
BryanRumsey Mar 1, 2022
a9df60e
Updates to Geometry and Initial Condition docs.
BryanRumsey Mar 1, 2022
08b5a36
Updated docs.
BryanRumsey Mar 2, 2022
ac1c46b
Updated docs html files.
BryanRumsey Mar 2, 2022
a09f2e0
Updated docs for initial conditions and model.
BryanRumsey Mar 2, 2022
6e7d788
Updated docs html files.
BryanRumsey Mar 2, 2022
c142a95
Updated docs for reactions.
BryanRumsey Mar 2, 2022
b3639dd
Updated docs html files.
BryanRumsey Mar 2, 2022
0186da3
Updated docs for results.
BryanRumsey Mar 2, 2022
aaa1606
Updated docs html files.
BryanRumsey Mar 2, 2022
4a0d3d3
Updated docs for species.
BryanRumsey Mar 2, 2022
93511d4
Updated docs html files.
BryanRumsey Mar 2, 2022
5f41717
Updated docs for stochss export.
BryanRumsey Mar 2, 2022
dd077f1
Updated docs html files.
BryanRumsey Mar 2, 2022
e9edd02
Updated docs for solver.
BryanRumsey Mar 2, 2022
7d7f806
Updated docs html files.
BryanRumsey Mar 2, 2022
a60534d
update to domain docs
seanebum Mar 7, 2022
637527e
update link to example StartHere notebook
seanebum Mar 7, 2022
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6 changes: 3 additions & 3 deletions docs/build/html/_modules/spatialpy/core/boundarycondition.html
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
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10 changes: 6 additions & 4 deletions docs/build/html/_modules/spatialpy/core/datafunction.html
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Expand Up @@ -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>
Expand All @@ -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>
Expand Down
103 changes: 43 additions & 60 deletions docs/build/html/_modules/spatialpy/core/domain.html
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4 changes: 2 additions & 2 deletions docs/build/html/_modules/spatialpy/core/geometry.html
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Expand Up @@ -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>
Expand All @@ -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>
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17 changes: 10 additions & 7 deletions docs/build/html/_modules/spatialpy/core/initialcondition.html
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Expand Up @@ -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>

Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand All @@ -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>
Expand Down
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