Parameter name as diffusion coefficient

spatialpy/core/model.py

@@ -318,6 +318,15 @@ def compile_prep(self):
         self.__update_diffusion_restrictions()
         self.__apply_initial_conditions()
         self.__resolve_parameters()
+
+        sanitized_params = self.sanitized_parameter_names()
+        for species in self.listOfSpecies.values():
+            diff_coeff = species.diffusion_coefficient
+            if isinstance(diff_coeff, str):
+                if diff_coeff not in sanitized_params:
+                    raise ModelError(f"Parameterm {diff_coeff} doesn't exist.")
+                species.diffusion_coefficient = sanitized_params[diff_coeff]
+
         self.__get_expression_utility()
         stoich_matrix = self.__create_stoichiometric_matrix()
         dep_graph = self.__create_dependency_graph()

spatialpy/core/species.py

@@ -40,9 +40,9 @@ def __init__(self, name=None, diffusion_coefficient=None, restrict_to=None):
 
         if  diffusion_coefficient is None:
             raise SpeciesError("Species must have a diffusion_coefficient.")
-        if not (isinstance(diffusion_coefficient, (Parameter, float, int)) or \
+        if not (isinstance(diffusion_coefficient, (Parameter, str, float, int)) or \
                     type(diffusion_coefficient).__name__ == 'Parameter'):
-            raise SpeciesError("Diffusion coefficient must be a spatialpy.Parameter, float, or int.")
+            raise SpeciesError("Diffusion coefficient must be a spatialpy.Parameter, str, float, or int.")
         if isinstance(diffusion_coefficient, (float, int)) and diffusion_coefficient < 0:
             raise SpeciesError("Diffusion coefficient must be non-negative.")
 
@@ -73,9 +73,9 @@ def set_diffusion_coefficient(self, diffusion_coefficient):
 
         :raises SpeciesError: If diffusion_coefficient is negative or not a valid type.
         """
-        if not (isinstance(diffusion_coefficient, (Parameter, float, int)) or \
+        if not (isinstance(diffusion_coefficient, (Parameter, str, float, int)) or \
                             type(diffusion_coefficient).__name__ == 'Parameter'):
-            raise SpeciesError("Diffusion coefficient must be a spatialpy.Parameter, float, or int.")
+            raise SpeciesError("Diffusion coefficient must be a spatialpy.Parameter, str, float, or int.")
         if diffusion_coefficient < 0:
             raise SpeciesError("Diffusion coefficient must be non-negative.")
 

test/test_species.py

@@ -65,10 +65,10 @@ def test_constructor__parameter_diffusion_coefficient(self):
         self.assertIsInstance(species.diffusion_coefficient, Parameter)
 
 
-    def test_constructor__diffusion_coefficient_not_int_or_float(self):
-        """ Test the Species constructor with non-int or non-float diffusion_coefficient. """
+    def test_constructor__diffusion_coefficient_not_str_int_or_float(self):
+        """ Test the Species constructor with non-str, non-int, or non-float diffusion_coefficient. """
         with self.assertRaises(SpeciesError):
-            species = Species(name="test_species", diffusion_coefficient="0")
+            species = Species(name="test_species", diffusion_coefficient=[0])
 
 
     def test_constructor__restrict_to_not_accepted_type(self):
@@ -111,8 +111,8 @@ def test_set_diffusion_coefficient__negative_diffusion_coefficient(self):
             species.set_diffusion_coefficient(diffusion_coefficient=-1)
 
 
-    def test_set_diffusion_coefficient__diffusion_coefficient_not_int_or_float(self):
-        """ Test Species.set_diffusion_coefficient method with non-int or non-float diffusion_coefficient. """
+    def test_set_diffusion_coefficient__diffusion_coefficient_not_str_int_or_float(self):
+        """ Test Species.set_diffusion_coefficient method with non-str, non-int, or non-float diffusion_coefficient. """
         species = Species(name="test_species", diffusion_coefficient=0)
         with self.assertRaises(SpeciesError):
-            species.set_diffusion_coefficient(diffusion_coefficient="1")
+            species.set_diffusion_coefficient(diffusion_coefficient=[0])