vivarium-public-health 4.3.10__tar.gz → 4.3.12__tar.gz

{vivarium_public_health-4.3.10 → vivarium_public_health-4.3.12}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**4.3.12 - 10/06/25**
+
+  - Register event_year as a stratification in the ResultsStratifier
+
+**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

{vivarium_public_health-4.3.10/src/vivarium_public_health.egg-info → vivarium_public_health-4.3.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.10
+Version: 4.3.12
 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-4.3.12/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.3.12"

{vivarium_public_health-4.3.10 → vivarium_public_health-4.3.12}/src/vivarium_public_health/results/stratification.py

@@ -62,15 +62,14 @@ class ResultsStratifier(Component):
             is_vectorized=True,
             requires_columns=["current_time"],
         )
-        # TODO [MIC-4232]: simulants occasionally have event year of end_year_year+1 if the end time plus step size
-        #  lands in the next year. possible solution detailed in ticket
-        # builder.results.register_stratification(
-        #     "event_year",
-        #     [str(year) for year in range(self.start_year, self.end_year + 1)],
-        #     mapper=self.map_year,
-        #     is_vectorized=True,
-        #     requires_columns=["event_time"],
-        # )
+        builder.results.register_stratification(
+            "event_year",
+            [str(year) for year in range(self.start_year, self.end_year + 2)],
+            excluded_categories=[str(self.end_year + 1)],
+            mapper=self.map_year,
+            is_vectorized=True,
+            requires_columns=["event_time"],
+        )
         # TODO [MIC-3892]: simulants occasionally have entrance year of start_year-1 if the start time minus step size
         #  lands in the previous year. possible solution detailed in ticket
         # builder.results.register_stratification(

{vivarium_public_health-4.3.10 → vivarium_public_health-4.3.12}/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-4.3.10 → vivarium_public_health-4.3.12/src/vivarium_public_health.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.10
+Version: 4.3.12
 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 → vivarium_public_health-4.3.12}/tests/results/test_stratification.py

@@ -104,13 +104,14 @@ def test_results_stratifier_register_stratifications(mocker):
         is_vectorized=True,
         requires_columns=["current_time"],
     )
-    # builder.results.register_stratification.assert_any_call(
-    #     "event_year",
-    #     years_list,
-    #     mapper=rs.map_year,
-    #     is_vectorized=True,
-    #     requires_columns=["event_time"],
-    # )
+    builder.results.register_stratification.assert_any_call(
+        "event_year",
+        years_list + [str(int(years_list[-1]) + 1)],
+        excluded_categories=[str(int(years_list[-1]) + 1)],
+        mapper=rs.map_year,
+        is_vectorized=True,
+        requires_columns=["event_time"],
+    )
     # builder.results.register_stratification.assert_any_call(
     #     "entrance_year",
     #     years_list,
@@ -129,7 +130,7 @@ def test_results_stratifier_register_stratifications(mocker):
     builder.results.register_stratification.assert_any_call(
         "sex", ["Female", "Male"], requires_columns=["sex"]
     )
-    assert builder.results.register_stratification.call_count == 3
+    assert builder.results.register_stratification.call_count == 4
 
 
 def test_results_stratifier_map_age_groups():

{vivarium_public_health-4.3.10 → vivarium_public_health-4.3.12}/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-4.3.10/src/vivarium_public_health/_version.py

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