include_groups=False in data_transformations .apply (#531)

Author: stevebachmeier

CHANGELOG.rst

@@ -1,3 +1,7 @@
+**4.2.5 - 07/18/25**
+
+  - Hush FutureWarnings: add include_groups=False to apply call in StratifiedObservation
+
 **4.2.4 - 07/16/25**
 
   - Support pinning of vivarium_build_utils; pin vivarium_build_utils>=1.1.0,<2.0.0

setup.py

@@ -47,7 +47,7 @@
         "layered_config_tree>=3.2.0",
         "loguru",
         "numpy<2.0.0",
-        "pandas",
+        "pandas>=2.2.0",
         "scipy",
         "tables",
         "risk_distributions>=2.0.11",

src/vivarium_public_health/population/data_transformations.py

@@ -54,21 +54,27 @@ def assign_demographic_proportions(
 
     population_data["P(sex, location, age| year)"] = (
         population_data.groupby("year_start", as_index=False)
-        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
+        .apply(
+            lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum(), include_groups=False
+        )
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )
 
     population_data["P(sex, location | age, year)"] = (
         population_data.groupby(["age", "year_start"], as_index=False)
-        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
+        .apply(
+            lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum(), include_groups=False
+        )
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )
 
     population_data["P(age | year, sex, location)"] = (
         population_data.groupby(["year_start", "sex", "location"], as_index=False)
-        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
+        .apply(
+            lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum(), include_groups=False
+        )
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )