Update Demographics from_X() style functions to be class methods to support proper inheritance (Fix #30)

emod_api/demographics/demographics_base.py

@@ -261,10 +261,7 @@ def _verify_node_name_uniqueness(self):
 
     @property
     def _all_nodes(self) -> List[Node]:
-        # only HIV is using a default node object right now, malaria currently uses self.raw
-        # None protection if users are using self.raw default node access
-        default_node = [] if self.default_node is None else [self.default_node]
-        all_nodes = self.nodes + default_node
+        all_nodes = self.nodes + [self.default_node]
         return all_nodes
 
     @property

emod_api/demographics/demographics_overlay.py

@@ -12,28 +12,30 @@ class DemographicsOverlay(DemographicsBase):
     """
 
     def __init__(self,
+                 default_node: OverlayNode,
                  nodes: list[OverlayNode] = None,
-                 idref: str = None,
-                 default_node: OverlayNode = None):
+                 idref: str = None):
         """
-        A class to create demographic overlays.
-        Args:
-            nodes: Overlay is applied to these nodes.
-            idref: a name used to indicate files (demographics, climate, and migration) are used together
-            individual_attributes: Object of type
-                :py:obj:`emod_api:emod_api.demographics.PropertiesAndAttributes.IndividualAttributes
-                to overwrite individual attributes
-            node_attributes:  Object of type
-                :py:obj:`emod_api:emod_api.demographics.PropertiesAndAttributes.NodeAttributes
-                to overwrite individual attributes
-            default_node: (OverlayNode) An optional node to use for default settings.
+        An object representation of an EMOD demographics overlay input (file). The contents are interpreted by EMOD
+        at runtime as overrides to the canonical/primary demographics input file.
 
+        Args:
+            default_node: (OverlayNode) Contains default settings for nodes in the overlay.
+            nodes (List[OverlayNode]): Overlay is applied to these nodes. Default is no nodes.
+            idref (str): a name used to indicate files (demographics, climate, and migration) are used together
         """
-        super(DemographicsOverlay, self).__init__(nodes=nodes, idref=idref, default_node=default_node)
+        nodes = [] if nodes is None else nodes
+        super().__init__(nodes=nodes, idref=idref, default_node=default_node)
 
-    def to_file(self, file_name="demographics_overlay.json"):
+    def to_file(self, file_name: str = "demographics_overlay.json") -> None:
         """
-        Write the contents of the instance to an EMOD-compatible (JSON) file.
+        Writes the DemographicsOverlay to an EMOD-compatible json file.
+
+        Args:
+            file_name (str): The filepath to write to.
+
+        Returns:
+            Nothing
         """
         with open(file_name, "w") as demo_override_f:
             json.dump(self.to_dict(), demo_override_f)

emod_api/demographics/properties_and_attributes.py

@@ -151,15 +151,15 @@ class NoSuchIndividualPropertyException(Exception):
     # TODO: this constructor call is WEIRD. it should take a list of IndividualProperties instead and remove
     #  "if is None" checks on self.individual_properties (None should auto goes to [] in constructor)
     #  https://github.com/InstituteforDiseaseModeling/emod-api/issues/685
-    def __init__(self, individual_property: IndividualProperty = None):
+    def __init__(self, individual_properties: List[IndividualProperty] = None):
         """
         https://docs.idmod.org/projects/emod-generic/en/latest/model-properties.html
 
         Args:
-            individual_property:
+            individual_properties:
         """
         super().__init__()
-        self.individual_properties = [individual_property] if individual_property else None
+        self.individual_properties = individual_properties if individual_properties else []
 
     def add(self, individual_property: IndividualProperty, overwrite=False) -> None:
         if self.individual_properties is None:
@@ -207,8 +207,6 @@ def __getitem__(self, index: int):
         return self.individual_properties[index]
 
     def __len__(self):
-        if not self.individual_properties:
-            return 0
         return len(self.individual_properties)
 
 

tests/test_config_demog.py

@@ -19,7 +19,7 @@ def get_config_as_object(self):
     def reset_config(self):
         self.config = self.get_config_as_object()
 
-    # TODO: restore when working on issue #43 dealing with moving emodpy distribuiton classes down to emod-api
+    # TODO: restore when working on issue #43 dealing with moving emodpy distribution classes down to emod-api
     # def test_set_birth_rate_config(self):
     #     demog = Demographics.from_template_node()
     #     self.config.parameters.Enable_Birth = 0  # since it is 1 by default
@@ -28,15 +28,15 @@ def reset_config(self):
     #     demog.implicits[-1](self.config)
     #     self.assertEqual(self.config.parameters.Birth_Rate_Dependence, "POPULATION_DEP_RATE")
 
-    # TODO: restore when working on issue #43 dealing with moving emodpy distribuiton classes down to emod-api
+    # TODO: restore when working on issue #43 dealing with moving emodpy distribution classes down to emod-api
     # def test_set_mortality_rate_config(self):
     #     for index in range(2):
     #         demog = Demographics.from_template_node()
     #         if index:
     #             demog.SetMortalityRate(0.75)
     #         demog.implicits[-1](self.config)
 
-    # TODO: restore when working on issue #43 dealing with moving emodpy distribuiton classes down to emod-api
+    # TODO: restore when working on issue #43 dealing with moving emodpy distribution classes down to emod-api
     # def test_set_mortality_distribution(self):
     #     demog = Demographics.from_template_node()
     #
@@ -47,7 +47,7 @@ def reset_config(self):
     #     demog.implicits[-2](self.config)
     #     self.assertEqual(self.config.parameters.Death_Rate_Dependence, "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER")
 
-    # TODO: restore when working on issue #43 dealing with moving emodpy distribuiton classes down to emod-api
+    # TODO: restore when working on issue #43 dealing with moving emodpy distribution classes down to emod-api
     # def test_set_age_distribution(self):
     #     demog = Demographics.from_template_node()
     #     self.assertEqual(self.config.parameters.Age_Initialization_Distribution_Type, "DISTRIBUTION_OFF")

tests/test_demog_send_over_pipes.py

@@ -3,10 +3,13 @@
 import json
 import unittest
 import emod_api.demographics.demographics as Demog
+from emod_api.demographics.demographics import Demographics
 import emod_api.demographics.pre_defined_distributions as Distributions
 import tempfile
 import copy
 
+from emod_api.demographics.node import Node
+
 thisplatform = sys.platform
 
 
@@ -19,11 +22,10 @@ def setUpClass(cls):
         cls.create_large_demog(cls)
 
     def create_large_demog(cls):
-        print('called once before any tests in class')
-        # Large demographics object.
         num_node = 1000
-        print("Creating big complex demographics.")
-        cls.large_demog = Demog.from_params(tot_pop=10000000, num_nodes=num_node)
+        nodes = [Node(lat=0, lon=0, pop=10000, forced_id=i+1) for i in range(num_node)]
+        cls.large_demog = Demographics(nodes=nodes)
+
 
         for node_id in range(num_node):
             cls.large_demog.SetFertilityOverTimeFromParams(years_region1=100, years_region2=10, start_rate=0.3, inflection_rate=0.25, end_rate=0.1, node_ids=[node_id + 1])
@@ -32,7 +34,6 @@ def create_large_demog(cls):
 
         # Large Expected Results Dictionary
         cls.large_expected = cls.large_demog.to_dict()
-        print(f"Total of nodes: {cls.large_expected['Metadata']['NodeCount']} ... file size is aprox 54 MB")
 
     @unittest.skipIf(thisplatform.startswith("win"), "Not valid on Windows")
     def test_linux_send_over_file(self):