Moved migration in celltype class

MANIFEST.in

@@ -0,0 +1,2 @@
+recursive-include examples *.py *.ipynb
+recursive-include tests *.py

biosim/animal.py

@@ -7,6 +7,10 @@
 
 
 class Animal:
+    """
+    This is the class level documentation
+    :return None
+    """
     _params = {}
 
     @classmethod
@@ -15,6 +19,12 @@ def set_parameters(cls, params):
         cls._params.update(params)
 
     def __init__(self, age=0, weight=None):
+        """
+        This is for the init function
+        :param age:  age
+        :param weight: wt
+        :return
+        """
         self.age = age
         birth_weight = np.random.normal(self._params['w_birth'], self._params['sigma_birth'])
         # print(birth_weight)
@@ -171,9 +181,5 @@ def hunts(self, herb_sorted_list ):
 
         return dead_herb_list
 
-if __name__ == "__main__":
-    h = Herbivore(weight = 50)
-    print(h.__class__.__name__)
-    # print( list( set(h) - set([]) ) )
 
 

biosim/celltype.py

@@ -83,6 +83,30 @@ def make_animals_age(self):
         for anim in self.carn_list:
             anim.get_older()
 
+    def migration_prepare(self): # to be called once for all cell at the beginning
+        for anim in self.herb_list + self.carn_list:
+            anim.has_migrated = False
+
+    def migration_master(self, object_matrix):
+        if not isinstance(self, Water):
+            adjacent_cells = self.adjacent_cells( object_matrix)
+            dict_of_migrants = self.emigrants_list(adjacent_cells)
+
+            for migrating_cell, values in dict_of_migrants.items():
+                if not isinstance(migrating_cell, Water) and values:
+                    migrating_cell.add_immigrants(values)
+                    self.remove_emigrants(values)
+
+    def adjacent_cells(self, object_matrix):
+        x = self.row
+        y = self.col
+        adjacent_cells = []
+        for i in (-1, 1):
+            adjacent_cells.append(object_matrix[x + i][y])
+            adjacent_cells.append(object_matrix[x][y + i])
+
+        return adjacent_cells
+
     def emigrants_list(self, adjacent_cells): #takes in adjacent cells
         dct = {}
         listofanim =  [anim for anim in self.carn_list + self.herb_list if anim.migrates() and