vivarium-public-health 4.3.8__tar.gz → 4.3.10__tar.gz

{vivarium_public_health-4.3.8 → vivarium_public_health-4.3.10}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**4.3.10 - 09/23/25**
+
+  - Bugfix: Fix bug in PublicHealthObserver to retain stratification columns in results
+
+**4.3.9 - 09/16/25**
+
+  - Bugfix: require alive column in register_transition_count_observation()
+
 **4.3.8 - 09/10/25**
 
   - Pin vivarium<4.0.0

{vivarium_public_health-4.3.8/src/vivarium_public_health.egg-info → vivarium_public_health-4.3.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.8
+Version: 4.3.10
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers

vivarium_public_health-4.3.10/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.3.10"

{vivarium_public_health-4.3.8 → vivarium_public_health-4.3.10}/src/vivarium_public_health/results/disease.py

@@ -198,6 +198,7 @@ class DiseaseObserver(PublicHealthObserver):
             name=f"transition_count_{self.disease}",
             pop_filter=pop_filter,
             requires_columns=[
+                "alive",
                 self.previous_state_column_name,
                 self.disease,
             ],

{vivarium_public_health-4.3.8 → vivarium_public_health-4.3.10}/src/vivarium_public_health/results/observer.py

@@ -12,6 +12,7 @@ from collections.abc import Callable
 
 import pandas as pd
 from vivarium.framework.engine import Builder
+from vivarium.framework.event import Event
 from vivarium.framework.results import Observer
 
 from vivarium_public_health.results.columns import COLUMNS
@@ -30,7 +31,7 @@ class PublicHealthObserver(Observer):
         self,
         builder: Builder,
         name: str,
-        pop_filter: str,
+        pop_filter: str = "tracked==True",
         when: str = "collect_metrics",
         requires_columns: list[str] = [],
         requires_values: list[str] = [],
@@ -38,6 +39,7 @@ class PublicHealthObserver(Observer):
         excluded_stratifications: list[str] = [],
         aggregator_sources: list[str] | None = None,
         aggregator: Callable[[pd.DataFrame], float | pd.Series] = len,
+        to_observe: Callable[[Event], bool] = lambda event: True,
     ) -> None:
         """Registers an adding observation to the results system.
 
@@ -73,6 +75,9 @@ class PublicHealthObserver(Observer):
             List of population view columns to be used in the `aggregator`.
         aggregator
             Function that computes the quantity for this observation.
+        to_observe
+            Function that takes an event and returns a boolean indicating whether
+            the observation should be performed for that event.
         """
         builder.results.register_adding_observation(
             name=name,
@@ -85,6 +90,7 @@ class PublicHealthObserver(Observer):
             excluded_stratifications=excluded_stratifications,
             aggregator_sources=aggregator_sources,
             aggregator=aggregator,
+            to_observe=to_observe,
         )
 
     def format_results(self, measure: str, results: pd.DataFrame) -> pd.DataFrame:
@@ -134,7 +140,7 @@ class PublicHealthObserver(Observer):
     def format(self, measure: str, results: pd.DataFrame) -> pd.DataFrame:
         """Format results.
 
-        This method should be overwritten in subclasses to provide custom formatting
+        This method can be overwritten in subclasses to provide custom formatting
         for the results.
 
         Parameters
@@ -148,12 +154,12 @@ class PublicHealthObserver(Observer):
         -------
             The formatted results.
         """
-        return results
+        return results.reset_index()
 
     def get_measure_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
         """Get the 'measure' column.
 
-        This method should be overwritten in subclasses to provide the 'measure' column.
+        This method can be overwritten in subclasses to provide the 'measure' column.
 
         Parameters
         ----------
@@ -171,7 +177,7 @@ class PublicHealthObserver(Observer):
     def get_entity_type_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
         """Get the 'entity_type' column.
 
-        This method should be overwritten in subclasses to provide the 'entity_type' column.
+        This method can be overwritten in subclasses to provide the 'entity_type' column.
 
         Parameters
         ----------
@@ -189,7 +195,7 @@ class PublicHealthObserver(Observer):
     def get_entity_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
         """Get the 'entity' column.
 
-        This method should be overwritten in subclasses to provide the 'entity' column.
+        This method can be overwritten in subclasses to provide the 'entity' column.
 
         Parameters
         ----------
@@ -207,7 +213,7 @@ class PublicHealthObserver(Observer):
     def get_sub_entity_column(self, measure: str, results: pd.DataFrame) -> pd.Series:
         """Get the 'sub_entity' column.
 
-        This method should be overwritten in subclasses to provide the 'sub_entity' column.
+        This method can be overwritten in subclasses to provide the 'sub_entity' column.
 
         Parameters
         ----------

{vivarium_public_health-4.3.8 → vivarium_public_health-4.3.10/src/vivarium_public_health.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.8
+Version: 4.3.10
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers

{vivarium_public_health-4.3.8 → vivarium_public_health-4.3.10}/tests/results/test_disability_observer.py

@@ -72,6 +72,7 @@ def test_disability_observer_setup(mocker):
         excluded_stratifications=observer.configuration.exclude,
         aggregator_sources=cause_pipelines,
         aggregator=observer.disability_weight_aggregator,
+        to_observe=mocker.ANY,
     )
 
     assert set(observer.disability_classes) == set([DiseaseState, RiskAttributableDisease])

vivarium_public_health-4.3.8/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.3.8"