Albrja/mic-5621/observer-get-configuration (#523)

Albrja/mic-5621/observer-get-configuration

Overrides get_configuration in observers to use super class method
- *Category*: Feature
- *JIRA issue*: https://jira.ihme.washington.edu/browse/MIC-5621

Changes and notes
-override get_configuration for observer classes
-DOES NOT update method for disease and risk observers due to their configuration via self.cause and self.risk and not the observer component name

### Testing
<!--
Details on how code was verified, any unit tests local for the
repo, regression testing, etc. At a minimum, this should include an
integration test for a framework change. Consider: plots, images,
(small) csv file.
-->

Author: albrja

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**4.1.1 - 05/23/25**
+
+  - Feature: Update Observer to use super class get_configuration method
+
 **4.1.0 - 05/20/25**
 
   - Feature: Update RateTransition to have configuration key for rate conversion type

setup.py

@@ -42,7 +42,7 @@
         long_description = f.read()
 
     install_requirements = [
-        "vivarium>=3.4.0",
+        "vivarium>=3.4.3",
         "layered_config_tree>=1.0.1",
         "loguru",
         "numpy<2.0.0",

src/vivarium_public_health/results/disability.py

@@ -34,7 +34,7 @@ class DisabilityObserver(PublicHealthObserver):
     .. code-block:: yaml
 
         configuration:
-            observers:
+            stratification:
                 disability:
                     exclude:
                         - "sex"
@@ -128,20 +128,6 @@ def set_causes_of_disability(self, builder: Builder) -> None:
             cause for cause in causes_of_disability if cause.state_id not in excluded_causes
         ]
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification.disability
-
     def register_observations(self, builder: Builder) -> None:
         """Register an observation for years lived with disability."""
         cause_pipelines = [

src/vivarium_public_health/results/disease.py

@@ -66,19 +66,6 @@ class DiseaseObserver(PublicHealthObserver):
     # Properties #
     ##############
 
-    @property
-    def configuration_defaults(self) -> dict[str, Any]:
-        """A dictionary containing the defaults for any configurations managed by
-        this component.
-        """
-        return {
-            "stratification": {
-                self.disease: super().configuration_defaults["stratification"][
-                    self.get_configuration_name()
-                ]
-            }
-        }
-
     @property
     def columns_created(self) -> list[str]:
         """Columns created by this observer."""
@@ -122,19 +109,8 @@ def setup(self, builder: Builder) -> None:
         self.entity = self.disease_model.cause
         self.transition_stratification_name = f"transition_{self.disease}"
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification[self.disease]
+    def get_configuration_name(self) -> str:
+        return self.disease
 
     def register_observations(self, builder: Builder) -> None:
         """Register stratifications and observations.

src/vivarium_public_health/results/mortality.py

@@ -136,20 +136,6 @@ def set_causes_of_death(self, builder: Builder) -> None:
             SimpleCause("other_causes", "other_causes", "cause"),
         ]
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification[self.get_configuration_name()]
-
     def register_observations(self, builder: Builder) -> None:
         """Register stratifications and observations.
 

src/vivarium_public_health/results/risk.py

@@ -58,19 +58,6 @@ class CategoricalRiskObserver(PublicHealthObserver):
     # Properties #
     ##############
 
-    @property
-    def configuration_defaults(self) -> dict[str, Any]:
-        """A dictionary containing the defaults for any configurations managed by
-        this component.
-        """
-        return {
-            "stratification": {
-                f"{self.risk}": super().configuration_defaults["stratification"][
-                    self.get_configuration_name()
-                ]
-            }
-        }
-
     @property
     def columns_required(self) -> list[str] | None:
         """The columns required by this observer."""
@@ -101,19 +88,8 @@ def setup(self, builder: Builder) -> None:
         self.step_size = builder.time.step_size()
         self.categories = builder.data.load(f"risk_factor.{self.risk}.categories")
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification[self.risk]
+    def get_configuration_name(self) -> str:
+        return self.risk
 
     def register_observations(self, builder: Builder) -> None:
         """Register a stratification and observation.

tests/results/test_disability_observer.py

@@ -39,7 +39,6 @@ def test_disability_observer_setup(mocker):
     observer = DisabilityObserver_()
     builder = mocker.Mock()
     mocker.patch("vivarium.component.Component.build_all_lookup_tables")
-    mocker.patch("vivarium.component.Component.get_configuration")
     builder.results.register_adding_observation = mocker.Mock()
     builder.configuration.time.step_size = 28
     builder.configuration.output_data.results_directory = "some/results/directory"