vivarium-public-health 4.3.9__tar.gz → 4.3.11__tar.gz

{vivarium_public_health-4.3.9 → vivarium_public_health-4.3.11}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**4.3.11 - 09/24/25**
+
+  - Refactor: Simplify LBWSG parsing logic
+
+**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()

{vivarium_public_health-4.3.9/src/vivarium_public_health.egg-info → vivarium_public_health-4.3.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.9
+Version: 4.3.11
 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-4.3.11/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.3.11"

{vivarium_public_health-4.3.9 → vivarium_public_health-4.3.11}/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-4.3.9 → vivarium_public_health-4.3.11}/src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -9,6 +9,7 @@ implementation that has been used in several public health models.
 """
 
 import pickle
+import re
 from collections.abc import Callable
 from typing import Any
 
@@ -119,13 +120,12 @@ class LBWSGDistribution(PolytomousDistribution):
             The intervals for each category.
         """
         categories: dict[str, str] = builder.data.load(f"{self.risk}.categories")
-        category_intervals = {
-            axis: {
-                category: self._parse_description(axis, description)
-                for category, description in categories.items()
-            }
-            for axis in [BIRTH_WEIGHT, GESTATIONAL_AGE]
-        }
+        category_intervals = {GESTATIONAL_AGE: {}, BIRTH_WEIGHT: {}}
+
+        for category, description in categories.items():
+            gestation_interval, birth_weight_interval = self._parse_description(description)
+            category_intervals[GESTATIONAL_AGE][category] = gestation_interval
+            category_intervals[BIRTH_WEIGHT][category] = birth_weight_interval
         return category_intervals
 
     ##################
@@ -224,7 +224,7 @@ class LBWSGDistribution(PolytomousDistribution):
     ##################
 
     @staticmethod
-    def _parse_description(axis: str, description: str) -> pd.Interval:
+    def _parse_description(description: str) -> tuple[pd.Interval, pd.Interval]:
         """Parses a string corresponding to a low birth weight and short gestation
         category to an Interval.
 
@@ -235,17 +235,15 @@ class LBWSGDistribution(PolytomousDistribution):
         An example of an edge case of birth weight:
         'Neonatal preterm and LBWSG (estimation years) - [36, 37) wks, [4000, 9999] g'
         """
-        endpoints = {
-            BIRTH_WEIGHT: [
-                float(val)
-                for val in description.split(", [")[1].split(")")[0].split("]")[0].split(", ")
-            ],
-            GESTATIONAL_AGE: [
-                float(val)
-                for val in description.split("- [")[1].split(")")[0].split("+")[0].split(", ")
-            ],
-        }[axis]
-        return pd.Interval(*endpoints, closed="left")  # noqa
+        lbwsg_values = [float(val) for val in re.findall(r"(\d+)", description)]
+        if len(list(lbwsg_values)) != 4:
+            raise ValueError(
+                f"Could not parse LBWSG description '{description}'. Expected 4 numeric values."
+            )
+        return (
+            pd.Interval(*lbwsg_values[:2], closed="left"),  # Gestational Age
+            pd.Interval(*lbwsg_values[2:], closed="left"),  # Birth Weight
+        )
 
 
 class LBWSGRisk(Risk):

{vivarium_public_health-4.3.9 → vivarium_public_health-4.3.11/src/vivarium_public_health.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.9
+Version: 4.3.11
 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-4.3.9 → vivarium_public_health-4.3.11}/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-4.3.9 → vivarium_public_health-4.3.11}/tests/risks/test_low_birth_weight_and_short_gestation.py

@@ -36,8 +36,7 @@ from vivarium_public_health.utilities import to_snake_case
     ],
 )
 def test_parsing_lbwsg_descriptions(description, expected_weight_values, expected_age_values):
-    weight_interval = LBWSGDistribution._parse_description("birth_weight", description)
-    age_interval = LBWSGDistribution._parse_description("gestational_age", description)
+    age_interval, weight_interval = LBWSGDistribution._parse_description(description)
     assert weight_interval.left == expected_weight_values[0]
     assert weight_interval.right == expected_weight_values[1]
     assert age_interval.left == expected_age_values[0]

vivarium_public_health-4.3.9/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.3.9"