Merge pull request #203 from StochSS/repo-restucture

Repo restructure

spatialpy/__init__.py

@@ -22,13 +22,9 @@
 import sys
 if (sys.version_info < (3,0)):
     raise Exception("SpatialPy only works in Python 3.0 and higher")
+from .__version__ import __version__, __title__, __description__, __url__
+from .__version__ import __author__, __email__
+from .__version__ import __license__, __copyright__
 
-from spatialpy.Model import *
-from spatialpy.Solver import *
-from spatialpy.Geometry import *
-from spatialpy.Domain import *
-from spatialpy.DataFunction import DataFunction
-from spatialpy.InitialCondition import *
-from spatialpy.BoundaryCondition import BoundaryCondition
-from spatialpy.VTKReader import *
-from spatialpy.cleanup import *
+from spatialpy.core import *
+from spatialpy.solvers import *

spatialpy/BoundaryCondition.py → spatialpy/core/BoundaryCondition.py

@@ -17,7 +17,8 @@
 '''
 
 import numpy
-from spatialpy.Model import ModelError
+
+from spatialpy.core.spatialpyError import BoundaryConditionError
 
 
 class BoundaryCondition():
@@ -102,9 +103,9 @@ def expression(self):
             :rtype: str
     """
         if( self.species is not None and self.property is not None):
-            raise ModelError("Can not set both species and property")
+            raise BoundaryConditionError("Can not set both species and property")
         if self.value is None:
-            raise ModelError("Must set value")
+            raise BoundaryConditionError("Must set value")
         cond=[]
         if(self.xmin is not None): cond.append("(me->x[0] >= {0})".format(self.xmin))
         if(self.xmax is not None): cond.append("(me->x[0] <= {0})".format(self.xmax))
@@ -113,14 +114,14 @@ def expression(self):
         if(self.zmin is not None): cond.append("(me->x[2] >= {0})".format(self.zmin))
         if(self.zmax is not None): cond.append("(me->x[2] <= {0})".format(self.zmax))
         if(self.type_id is not None): cond.append("(me->type == {0})".format(int(self.type_id)))
-        if(len(cond)==0): raise ModelError('need at least one condition on the BoundaryCondition')
+        if(len(cond)==0): raise BoundaryConditionError('need at least one condition on the BoundaryCondition')
         bcstr = "if(" + '&&'.join(cond) + "){"
         if self.species is not None:
             if self.deterministic:
                 s_ndx = self.model.species_map[self.model.listOfSpecies[self.species]]
                 bcstr += "me->C[{0}] = {1};".format(s_ndx,self.value)
             else:
-                raise Exception("BoundaryConditions don't work for stochastic species yet")
+                raise BoundaryConditionError("BoundaryConditions don't work for stochastic species yet")
         elif self.property is not None:
             if(self.property == 'v'):
                 for i in range(3):
@@ -130,6 +131,6 @@ def expression(self):
             elif(self.property == 'rho'):
                 bcstr+= "me->rho={0};".format(self.value)
             else:
-                raise Exception("Unable handle boundary condition for property '{0}'".format(self.property))
+                raise BoundaryConditionError("Unable handle boundary condition for property '{0}'".format(self.property))
         bcstr+= "}"
         return bcstr

spatialpy/DataFunction.py → spatialpy/core/DataFunction.py

@@ -15,7 +15,7 @@
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 '''
-
+from spatialpy.core.spatialpyError import DataFunctionError
 
 class DataFunction():
     """ Abstract class used to constuct the data function. """
@@ -24,7 +24,7 @@ def __init__(self, name=None):
         if name is not None:
             self.name = name
         if self.name is None:
-            raise Exception("DataFunction must have a 'name'")
+            raise DataFunctionError("DataFunction must have a 'name'")
 
     def map(self, x):
         """
@@ -39,6 +39,6 @@ def map(self, x):
         :returns: value of function at this spatial location.
         :rtype: float
         """
-        raise Exception("DataFunction.map() must be implemented.")
+        raise DataFunctionError("DataFunction.map() must be implemented.")
 
 

spatialpy/Domain.py → spatialpy/core/Domain.py

@@ -22,8 +22,7 @@
 import numpy
 from scipy.spatial import KDTree
 
-from spatialpy.Result import _plotly_iterate
-
+from spatialpy.core.spatialpyError import DomainError
 
 class Domain():
     """ Domain class for SpatialPy.  A domain defines points and attributes of a regional space for simulation.
@@ -360,6 +359,7 @@ def plot_types(self, width=None, height=None, colormap=None, size=5, title=None,
         :param use_matplotlib: Whether or not to plot the proprties results using matplotlib.
         :type use_matplotlib: bool
         '''
+        from spatialpy.core.Result import _plotly_iterate
 
         if use_matplotlib:
             width = 6.4 if width in (None, "auto") else width
@@ -557,7 +557,7 @@ def read_stochss_subdomain_file(self, filename):
                     (ndx,type_id) = line.rstrip().split(',')
                     self.type[int(ndx)] = int(type_id)
                 except ValueError as e:
-                    raise ModelError(f"Could not read in subdomain file, error on line {ln}: {line}")
+                    raise DomainError(f"Could not read in subdomain file, error on line {ln}: {line}")
 
 
     @classmethod
@@ -751,8 +751,3 @@ def create_2D_domain(cls, xlim, ylim, nx, ny, type_id=1, mass=1.0, nu=1.0, rho=N
 
         # return model ref
         return obj
-
-
-
-class DomainError(Exception):
-    pass

spatialpy/Geometry.py → spatialpy/core/Geometry.py

@@ -15,6 +15,7 @@
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
 '''
+from spatialpy.core.spatialpyError import GeometryError
 
 class Geometry:
     """ Geometry class provides a method for tagging parts of the spatial domain as separate parts"""
@@ -23,7 +24,7 @@ def __init__(self):
         pass
 
     def inside(self, x, on_boundary):
-        raise Exception("Subclasses of spatialpy.Geometry must implement the inside() method")
+        raise GeometryError("Subclasses of spatialpy.Geometry must implement the inside() method")
 
 
 class GeometryAll(Geometry):

spatialpy/InitialCondition.py → spatialpy/core/InitialCondition.py

@@ -17,7 +17,8 @@
 '''
 
 import numpy
-from spatialpy.Model import ModelError
+
+from spatialpy.core.spatialpyError import InitialConditionError
 
 
 class InitialCondition():
@@ -27,7 +28,7 @@ class InitialCondition():
     """
 
     def apply(self, model):
-        raise ModelError("spatialpy.InitialCondition subclasses must implement apply()")
+        raise InitialConditionError("spatialpy.InitialCondition subclasses must implement apply()")
 
 #TODO: implement InitialConditionFromResult()
 
@@ -102,7 +103,7 @@ def apply(self, model):
                 if model.domain.type[i] in self.types:
                     allowed_voxels.append(i)
             nvox = len(allowed_voxels)
-            if nvox==0: raise ModelError("ScatterInitialCondition has zero voxels to scatter in. Species={0} count={1} types={2}".format(self.species.name, self.count, self.types))
+            if nvox==0: raise InitialConditionError("ScatterInitialCondition has zero voxels to scatter in. Species={0} count={1} types={2}".format(self.species.name, self.count, self.types))
             for mol in range(self.count):
                 v_ndx = numpy.random.randint(0, nvox)
                 vtx = allowed_voxels[v_ndx]