Component Standardization Refactor (#72)

* Component Refactor: Pregnancy + Children (#68)

* update vivarium

* pin VPH

* refactor birth recorder

* refactor LBWSG Distribution

* unrefactor NewChildren for now

* refactor pregnancy.py

* lint

* remove diseasestate refactor

* refactor NewChildren

* lint

* remove a setup super call

* do LB instead of full pin

* remove newchildren columns created

* add new children columns to pregnancy creation

* remove references to new_children.columns_created

* undo comment out

* Refactor Observers (#71)

* refactor observers

* lint

* Refactor Anemia, Hemoglobin, Others (#70)

* refactor hemoglobin

* refactor anemia

* refactor maternal BMI

* refactor intervention

* lint

* Refactor Disorders (#69)

* update vivarium

* pin VPH

* refactor birth recorder

* refactor LBWSG Distribution

* unrefactor NewChildren for now

* refactor pregnancy.py

* lint

* remove diseasestate refactor

* refactor NewChildren

* lint

* remove a setup super call

* do LB instead of full pin

* remove newchildren columns created

* add new children columns to pregnancy creation

* remove references to new_children.columns_created

* update vivarium

* refactor birth recorder

* unrefactor NewChildren for now

* refactor pregnancy.py

* lint

* remove diseasestate refactor

* start mortality refactor

* refactor the exclusionstates

* refactor maternal disorders

* fix bug

* fix imports

* refactor mortality

* outline methods

* lint

* model reflects current status

* include diseaseobservers for free

* refactor morbidity

* add morbidity

* remove newchildren columns created

* remove references to new_children.columns_created

* fix bug

* Revert "Merge branch 'feature/pnast/MIC-4416-pregnancy-refactor' into feature/pnast-MIC-4416-refactor-disorders"

This reverts commit 68cba01, reversing
changes made to 62ce0bf.

* add is_non_zero

* revert erroneous changes

* revert model spec

* comment out diseaseobserver

* lint

* Update CHANGELOG.rst

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**1.0.1 - 10/02/23**
+
+ - Refactor to use vivarium Components
+
 **1.0.0 - 09/18/23**
 
  - Release to 1.0.0 with Wave 1 production runs

setup.py

@@ -17,9 +17,9 @@
         long_description = f.read()
 
     install_requirements = [
-        "gbd_mapping==3.1.1",
-        "vivarium==1.2.2",
-        "vivarium_public_health==1.0.2",
+        "gbd_mapping>=3.1.1",
+        "vivarium>=2.0.0",
+        "vivarium_public_health>=2.0.0",
         "click",
         "jinja2",
         "loguru",
@@ -32,8 +32,8 @@
 
     # use "pip install -e .[dev]" to install required components + extra components
     data_requires = [
-        "vivarium_cluster_tools==1.3.10",
-        "vivarium_inputs[data]==4.1.1",
+        "vivarium_cluster_tools>=1.3.12",
+        "vivarium_inputs[data]>=4.1.1",
     ]
 
     test_requirements = ["pytest"]

src/vivarium_gates_nutrition_optimization/components/children.py

@@ -1,9 +1,10 @@
 from datetime import datetime
 from pathlib import Path
-from typing import Tuple
+from typing import List, Tuple
 
 import numpy as np
 import pandas as pd
+from vivarium import Component
 from vivarium.framework.engine import Builder
 from vivarium.framework.event import Event
 from vivarium_cluster_tools.utilities import mkdir
@@ -15,21 +16,18 @@
 )
 
 
-class NewChildren:
-    def __init__(self):
-        self.lbwsg = LBWSGDistribution()
-
-    @property
-    def name(self):
-        return "child_status"
+class NewChildren(Component):
+    ##############
+    # Properties #
+    ##############
 
     @property
-    def sub_components(self):
+    def sub_components(self) -> List[str]:
         return [self.lbwsg]
 
-    @property
-    def columns_created(self):
-        return ["sex_of_child", "birth_weight", "gestational_age"]
+    def __init__(self):
+        super().__init__()
+        self.lbwsg = LBWSGDistribution()
 
     def setup(self, builder: Builder):
         self.randomness = builder.randomness.get_stream(self.name)
@@ -47,7 +45,7 @@ def empty(self, index: pd.Index) -> pd.DataFrame:
             index=index,
         )
 
-    def generate_children(self, index: pd.Index):
+    def generate_children(self, index: pd.Index) -> pd.DataFrame:
         sex_of_child = self.randomness.choice(
             index,
             choices=["Male", "Female"],
@@ -65,11 +63,7 @@ def generate_children(self, index: pd.Index):
         )
 
 
-class LBWSGDistribution:
-    @property
-    def name(self):
-        return "lbwsg_distribution"
-
+class LBWSGDistribution(Component):
     def setup(self, builder: Builder):
         self.randomness = builder.randomness.get_stream(self.name)
         self.exposure = builder.data.load(data_keys.LBWSG.EXPOSURE).set_index("sex")
@@ -142,23 +136,14 @@ def _parse_description(description: str) -> Tuple:
         return *birth_weight, *gestational_age
 
 
-class BirthRecorder:
-    @property
-    def name(self):
-        return "birth_recorder"
-
-    #################
-    # Setup methods #
-    #################
-
-    # noinspection PyAttributeOutsideInit
-    def setup(self, builder: Builder) -> None:
-        self.output_path = self._build_output_path(builder)
-        self.randomness = builder.randomness.get_stream(self.name)
-
-        self.births = []
+class BirthRecorder(Component):
+    ##############
+    # Properties #
+    ##############
 
-        required_columns = [
+    @property
+    def columns_required(self) -> List[str]:
+        return [
             "pregnancy",
             "previous_pregnancy",
             "pregnancy_outcome",
@@ -168,10 +153,15 @@ def setup(self, builder: Builder) -> None:
             "maternal_bmi_anemia_category",
             "intervention",
         ]
-        self.population_view = builder.population.get_view(required_columns)
 
-        builder.event.register_listener("collect_metrics", self.on_collect_metrics)
-        builder.event.register_listener("simulation_end", self.write_output)
+    #################
+    # Setup methods #
+    #################
+
+    # noinspection PyAttributeOutsideInit
+    def setup(self, builder: Builder) -> None:
+        self.output_path = self._build_output_path(builder)
+        self.births = []
 
     def on_collect_metrics(self, event: Event):
         pop = self.population_view.get(event.index)
@@ -207,7 +197,7 @@ def on_collect_metrics(self, event: Event):
         self.births.append(new_births)
 
     # noinspection PyUnusedLocal
-    def write_output(self, event: Event) -> None:
+    def on_simulation_end(self, event: Event) -> None:
         births_data = pd.concat(self.births)
         births_data.to_hdf(f"{self.output_path}.hdf", key="data")
         births_data.to_csv(f"{self.output_path}.csv")