2.0-ified direct demograhpics __init__ instantiation including DemographicsOverlay (Fix #29) (#43)

* Reworked direct demograhpics __init__ instantiation to only use Node objects, including similar DemographicsOverlay update. Commented/deactivated many tests that will be fixed in following issues/PRs (Fix #29)

Author: ckirkman-IDM

emod_api/demographics/demographics.py

@@ -9,9 +9,8 @@
 import os
 import pandas as pd
 
-from typing import List, Dict
+from typing import List
 
-from emod_api.demographics import demographics_templates as DT
 from emod_api.demographics.node import Node
 from emod_api.demographics.properties_and_attributes import NodeAttributes
 from emod_api.demographics.demographics_base import DemographicsBase
@@ -273,37 +272,17 @@ def from_pop_csv(pop_filename_in,
 
 class Demographics(DemographicsBase):
     """
-    This class is a container of data necessary to produce a EMOD-valid demographics input file. It can be initialized
-    from an existing valid demographics.joson type file or from an array of valid Nodes.
+    This class is a container of data necessary to produce a EMOD-valid demographics input file.
     """
-    def __init__(self, nodes: List[Node], idref: str = "Gridded world grump2.5arcmin", base_file: str = None,
-                 default_node: Node = None):
+    def __init__(self, nodes: List[Node], idref: str = "Gridded world grump2.5arcmin", default_node: Node = None):
         """
         A class to create demographics.
         :param nodes: list of Nodes
         :param idref: A name/reference
-        :param base_file: A demographics file in json format
         :default_node: An optional node to use for default settings.
         """
         super().__init__(nodes=nodes, idref=idref, default_node=default_node)
 
-        # HIV is expected to pass a default node. Malaria is not (for now).
-        if default_node is None:
-            if base_file:
-                with open(base_file, "rb") as src:
-                    self.raw = json.load(src)
-            else:
-                # adding and using this default configuration (True) as malaria may use it; I don't know. HIV does not.
-                self.SetMinimalNodeAttributes()
-                DT.NoInitialPrevalence(self)  # does this need to be called?
-                DT.InitAgeUniform(self)
-
-    def to_dict(self) -> Dict:
-        self.verify_demographics_integrity()
-        self.raw["Nodes"] = [node.to_dict() for node in self.nodes]
-        self.raw["Metadata"]["NodeCount"] = len(self.nodes)
-        return self.raw
-
     def generate_file(self, name="demographics.json"):
         """
         Write the contents of the instance to an EMOD-compatible (JSON) file.

emod_api/demographics/demographics_base.py

@@ -38,9 +38,10 @@ class DuplicateNodeNameException(Exception):
         pass
 
     def __init__(self, nodes: List[Node], idref: str, default_node: Node = None):
+        """
+        Passed-in default nodes are optional. If one is not passed in, one will be created.
+        """
         super().__init__(idref=idref)
-        # TODO: node ids should be required to be UNIQUE to prevent later failures when running EMOD. Any update to
-        #  self.nodes should trigger a check/error if needed.
         self.nodes = nodes
         self.implicits = list()
         self.migration_files = list()
@@ -50,33 +51,28 @@ def __init__(self, nodes: List[Node], idref: str, default_node: Node = None):
             if node.id <= 0:
                 raise InvalidNodeIdException(f"Non-default nodes must have integer ids > 0 . Found id: {node.id}")
 
-        # Build the default node if not provided
-        metadata = self.generate_headers()
-        if default_node is None:  # use raw attribute, current malaria/other disease style
-            # currently all non-HIV disease route
-            self.default_node = None
-            self.metadata = None
-            self.raw = {"Defaults": dict(), "Metadata": metadata}
-            self.raw["Defaults"]["NodeAttributes"] = dict()
-            self.raw["Defaults"]["IndividualAttributes"] = dict()
-            self.raw["Defaults"]["NodeID"] = 0
-            self.raw["Defaults"]["IndividualProperties"] = list()
-            # TODO: remove the following setting of birth_rate on the default node once this EMOD binary issue is fixed
-            #  https://github.com/InstituteforDiseaseModeling/DtkTrunk/issues/4009
-            self.raw["Defaults"]["NodeAttributes"]["BirthRate"] = 0
-        else:  # HIV style
-            self.default_node = default_node
-            self.default_node.name = self.DEFAULT_NODE_NAME
-            if self.default_node.id != 0:
-                raise InvalidNodeIdException(f"Default nodes must have an id of 0. It is {self.default_node.id} .")
-            self.metadata = metadata
-            # TODO: remove the following setting of birth_rate on the default node once this EMOD binary issue is fixed
-            #  https://github.com/InstituteforDiseaseModeling/DtkTrunk/issues/4009
-            self.get_node_by_id(node_id=0).birth_rate = 0
+        # Build the default node if not provided and then perform some setup/verification
+        default_node = self._generate_default_node() if default_node is None else default_node
+        self.default_node = default_node
+        self.default_node.name = self.DEFAULT_NODE_NAME
+        if self.default_node.id != 0:
+            raise InvalidNodeIdException(f"Default nodes must have an id of 0. It is {self.default_node.id} .")
+        self.metadata = self.generate_headers()
+        # TODO: remove the following setting of birth_rate on the default node once this EMOD binary issue is fixed
+        #  https://github.com/InstituteforDiseaseModeling/DtkTrunk/issues/4009
+        if self.default_node.birth_rate is None:
+            self.default_node.birth_rate = 0
 
         # enforce unique node ids and names
         self.verify_demographics_integrity()
 
+    def _generate_default_node(self) -> Node:
+        default_node = Node(lat=0, lon=0, pop=0, name=self.DEFAULT_NODE_NAME, forced_id=0)
+        # TODO: remove the following setting of birth_rate on the default node once this EMOD binary issue is fixed
+        #  https://github.com/InstituteforDiseaseModeling/DtkTrunk/issues/4009
+        default_node.birth_rate = 0
+        return default_node
+
     def _select_node_dicts(self, node_ids=None):
         if node_ids is None:
             node_dicts = [self.raw['Defaults']]
@@ -1060,3 +1056,13 @@ def min_not_nan(x_list):
                      }
         self.implicits.append(DT._set_mortality_age_gender_year)
         return dict_female, dict_male
+
+    def to_dict(self) -> Dict:
+        self.verify_demographics_integrity()
+        demographics_dict = {
+            'Defaults': self.default_node.to_dict(),
+            'Nodes': [node.to_dict() for node in self.nodes],
+            'Metadata': self.metadata
+        }
+        demographics_dict["Metadata"]["NodeCount"] = len(self.nodes)
+        return demographics_dict

emod_api/demographics/demographics_overlay.py

@@ -1,20 +1,20 @@
 import json
 
 from emod_api.demographics.demographics_base import DemographicsBase
+from emod_api.demographics.node import OverlayNode
 
 
 class DemographicsOverlay(DemographicsBase):
     """
-    In contrast to class :py:obj:`emod_api:emod_api.demographics.Demographics` this class does not set any defaults.
-    It inherits from :py:obj:`emod_api:emod_api.demographics.DemographicsBase` so all functions that can be used to
-    create demographics can also be used to create an overlay file. Parameters can be changed/set specifically by
-    passing node_id, individual attributes, and individual attributes to the constructor.
+    This class inherits from :py:obj:`emod_api:emod_api.demographics.DemographicsBase` so all functions that can be used
+    to create demographics can also be used to create an overlay file. The intended use is for a user to pass a
+    self-built default OverlayNode object in to represent the Defaults section in the demographics overlay.
     """
 
-    def __init__(self, nodes: list = None,
+    def __init__(self,
+                 nodes: list[OverlayNode] = None,
                  idref: str = None,
-                 individual_attributes=None,
-                 node_attributes=None):
+                 default_node: OverlayNode = None):
         """
         A class to create demographic overlays.
         Args:
@@ -26,36 +26,10 @@ def __init__(self, nodes: list = None,
             node_attributes:  Object of type
                 :py:obj:`emod_api:emod_api.demographics.PropertiesAndAttributes.NodeAttributes
                 to overwrite individual attributes
-        """
-        super(DemographicsOverlay, self).__init__(nodes=nodes, idref=idref)
-
-        self.individual_attributes = individual_attributes
-        self.node_attributes = node_attributes
-
-        if self.individual_attributes is not None:
-            self.raw["Defaults"]["IndividualAttributes"] = self.individual_attributes.to_dict()
-
-        if self.node_attributes is not None:
-            self.raw["Defaults"]["NodeAttributes"] = self.node_attributes.to_dict()
-
-    def to_dict(self):
-        self.verify_demographics_integrity()
-        d = {"Defaults": dict()}
-        if self.raw["Defaults"]["IndividualAttributes"]:
-            d["Defaults"]["IndividualAttributes"] = self.raw["Defaults"]["IndividualAttributes"]
+            default_node: (OverlayNode) An optional node to use for default settings.
 
-        if self.raw["Defaults"]["NodeAttributes"]:
-            d["Defaults"]["NodeAttributes"] = self.raw["Defaults"]["NodeAttributes"]
-
-        if self.raw["Metadata"]:
-            d["Metadata"] = self.raw["Metadata"]  # there is no metadata class
-            d["Metadata"]["NodeCount"] = len(self.nodes)
-        if self.raw["Defaults"]["IndividualProperties"]:
-            d["Defaults"]["IndividualProperties"] = self.raw["Defaults"]["IndividualProperties"]
-
-        d["Nodes"] = [{"NodeID": n.forced_id} for n in self.nodes]
-
-        return d
+        """
+        super(DemographicsOverlay, self).__init__(nodes=nodes, idref=idref, default_node=default_node)
 
     def to_file(self, file_name="demographics_overlay.json"):
         """