vivarium-public-health 3.1.1__py3-none-any.whl → 3.1.2__py3-none-any.whl

vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -9,7 +9,8 @@ implementation that has been used in several public health models.
 """
 
 import pickle
-from typing import Any, Callable, Dict, List, Optional, Tuple
+from collections.abc import Callable
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -39,7 +40,7 @@ class LBWSGDistribution(PolytomousDistribution):
         super().setup(builder)
         self.category_intervals = self.get_category_intervals(builder)
 
-    def get_category_intervals(self, builder: Builder) -> Dict[str, Dict[str, pd.Interval]]:
+    def get_category_intervals(self, builder: Builder) -> dict[str, dict[str, pd.Interval]]:
         """Gets the intervals for each category.
 
         Parameters
@@ -51,7 +52,7 @@ class LBWSGDistribution(PolytomousDistribution):
         -------
             The intervals for each category.
         """
-        categories: Dict[str, str] = builder.data.load(f"{self.risk}.categories")
+        categories: dict[str, str] = builder.data.load(f"{self.risk}.categories")
         category_intervals = {
             axis: {
                 category: self._parse_description(axis, description)
@@ -96,8 +97,8 @@ class LBWSGDistribution(PolytomousDistribution):
         self,
         axis: str,
         propensity: pd.Series,
-        categorical_propensity: Optional[pd.Series] = None,
-        categorical_exposure: Optional[pd.Series] = None,
+        categorical_propensity: pd.Series | None = None,
+        categorical_exposure: pd.Series | None = None,
     ) -> pd.Series:
         """Calculate continuous exposures from propensities for a single axis.
 
@@ -199,13 +200,13 @@ class LBWSGRisk(Risk):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         configuration_defaults = super().configuration_defaults
         configuration_defaults[self.name]["distribution_type"] = "lbwsg"
         return configuration_defaults
 
     @property
-    def columns_created(self) -> List[str]:
+    def columns_created(self) -> list[str]:
         return [self.get_exposure_column_name(axis) for axis in self.AXES]
 
     #####################
@@ -224,15 +225,15 @@ class LBWSGRisk(Risk):
     # Setup methods #
     #################
 
-    def get_propensity_pipeline(self, builder: Builder) -> Optional[Pipeline]:
+    def get_propensity_pipeline(self, builder: Builder) -> Pipeline | None:
         # Propensity only used on initialization; not being saved to avoid a cycle
         return None
 
-    def get_exposure_pipeline(self, builder: Builder) -> Optional[Pipeline]:
+    def get_exposure_pipeline(self, builder: Builder) -> Pipeline | None:
         # Exposure only used on initialization; not being saved to avoid a cycle
         return None
 
-    def get_birth_exposure_pipelines(self, builder: Builder) -> Dict[str, Pipeline]:
+    def get_birth_exposure_pipelines(self, builder: Builder) -> dict[str, Pipeline]:
         required_columns = get_lookup_columns(
             self.exposure_distribution.lookup_tables.values()
         )
@@ -291,15 +292,15 @@ class LBWSGRiskEffect(RiskEffect):
     ##############
 
     @property
-    def columns_created(self) -> List[str]:
+    def columns_created(self) -> list[str]:
         return self.rr_column_names
 
     @property
-    def columns_required(self) -> Optional[List[str]]:
+    def columns_required(self) -> list[str] | None:
         return ["age", "sex"] + self.lbwsg_exposure_column_names
 
     @property
-    def initialization_requirements(self) -> Dict[str, List[str]]:
+    def initialization_requirements(self) -> dict[str, list[str]]:
         return {
             "requires_columns": ["sex"] + self.lbwsg_exposure_column_names,
             "requires_values": [],
@@ -307,7 +308,7 @@ class LBWSGRiskEffect(RiskEffect):
         }
 
     @property
-    def rr_column_names(self) -> List[str]:
+    def rr_column_names(self) -> list[str]:
         return [self.relative_risk_column_name(age_group) for age_group in self.age_intervals]
 
     #####################
@@ -356,7 +357,7 @@ class LBWSGRiskEffect(RiskEffect):
 
     def get_population_attributable_fraction_source(
         self, builder: Builder
-    ) -> Tuple[pd.DataFrame, List[str]]:
+    ) -> tuple[pd.DataFrame, list[str]]:
         paf_key = f"{self.risk}.population_attributable_fraction"
         paf_data = builder.data.load(paf_key)
         return paf_data, builder.data.value_columns()(paf_key)
@@ -376,7 +377,7 @@ class LBWSGRiskEffect(RiskEffect):
             requires_values=[self.relative_risk_pipeline_name],
         )
 
-    def get_age_intervals(self, builder: Builder) -> Dict[str, pd.Interval]:
+    def get_age_intervals(self, builder: Builder) -> dict[str, pd.Interval]:
         age_bins = builder.data.load("population.age_bins").set_index("age_start")
         exposure = builder.data.load(f"{self.risk}.exposure")
         exposure = exposure[exposure["age_end"] > 0]

vivarium_public_health/treatment/magic_wand.py

@@ -8,7 +8,7 @@ level by providing direct shifts to epidemiological measures.
 
 """
 
-from typing import Any, Dict, List, Optional
+from typing import Any
 
 from vivarium import Component
 from vivarium.framework.engine import Builder
@@ -30,13 +30,13 @@ class AbsoluteShift(Component):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         return {
             f"intervention_on_{self.target.name}": self.CONFIGURATION_DEFAULTS["intervention"]
         }
 
     @property
-    def columns_required(self) -> Optional[List[str]]:
+    def columns_required(self) -> list[str] | None:
         return ["age"]
 
     #####################

vivarium_public_health/treatment/scale_up.py

@@ -7,7 +7,8 @@ This module contains tools for applying a linear scale-up to an intervention
 
 """
 
-from typing import Any, Callable, Dict, Tuple
+from collections.abc import Callable
+from typing import Any
 
 import pandas as pd
 from vivarium import Component
@@ -61,7 +62,7 @@ class LinearScaleUp(Component):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         return {self.configuration_key: self.CONFIGURATION_DEFAULTS["treatment"]}
 
     @property
@@ -108,11 +109,11 @@ class LinearScaleUp(Component):
         return builder.time.clock()
 
     # noinspection PyMethodMayBeStatic
-    def get_scale_up_dates(self, builder: Builder) -> Tuple[pd.Timestamp, pd.Timestamp]:
+    def get_scale_up_dates(self, builder: Builder) -> tuple[pd.Timestamp, pd.Timestamp]:
         scale_up_config = builder.configuration[self.configuration_key]["date"]
         return pd.Timestamp(scale_up_config["start"]), pd.Timestamp(scale_up_config["end"])
 
-    def get_scale_up_values(self, builder: Builder) -> Tuple[LookupTable, LookupTable]:
+    def get_scale_up_values(self, builder: Builder) -> tuple[LookupTable, LookupTable]:
         """Get the values at the start and end of the scale-up period.
 
         Parameters
@@ -137,7 +138,7 @@ class LinearScaleUp(Component):
         return get_endpoint_value("start"), get_endpoint_value("end")
 
     # noinspection PyMethodMayBeStatic
-    def get_required_pipelines(self, builder: Builder) -> Dict[str, Pipeline]:
+    def get_required_pipelines(self, builder: Builder) -> dict[str, Pipeline]:
         return {}
 
     def register_intervention_modifiers(self, builder: Builder):

vivarium_public_health/utilities.py

@@ -7,9 +7,8 @@ This module contains utility classes and functions for use across
 vivarium_public_health components.
 
 """
-
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Any, Dict, Iterable, List, Optional, Union
 
 import pandas as pd
 from vivarium.framework.lookup import LookupTable, ScalarValue
@@ -77,7 +76,7 @@ DAYS_PER_YEAR = 365.25
 DAYS_PER_MONTH = DAYS_PER_YEAR / 12
 
 
-def to_time_delta(span_in_days: Union[int, float, str]):
+def to_time_delta(span_in_days: int | float | str):
     span_in_days = float(span_in_days)
     days, remainder = span_in_days // 1, span_in_days % 1
     hours, remainder = (24 * remainder) // 24, (24 * remainder) % 24
@@ -90,7 +89,7 @@ def to_years(time: pd.Timedelta) -> float:
     return time / pd.Timedelta(days=DAYS_PER_YEAR)
 
 
-def is_non_zero(data: Union[Iterable[ScalarValue], ScalarValue, pd.DataFrame]) -> bool:
+def is_non_zero(data: Iterable[ScalarValue] | ScalarValue | pd.DataFrame) -> bool:
     if isinstance(data, pd.DataFrame):
         attribute_sum = data.value.sum()
     elif isinstance(data, Iterable):
@@ -103,7 +102,7 @@ def is_non_zero(data: Union[Iterable[ScalarValue], ScalarValue, pd.DataFrame]) -
 
 def get_lookup_columns(
     lookup_tables: Iterable[LookupTable], necessary_columns: Iterable = ()
-) -> List[str]:
+) -> list[str]:
     necessary_columns = set(necessary_columns)
     for lookup_table in lookup_tables:
         necessary_columns.update(set(lookup_table.key_columns))

{vivarium_public_health-3.1.1.dist-info → vivarium_public_health-3.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.1.1
+Version: 3.1.2
 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-3.1.2.dist-info/RECORD

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{vivarium_public_health-3.1.1.dist-info → vivarium_public_health-3.1.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.4.0)
+Generator: setuptools (75.5.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

vivarium_public_health-3.1.1.dist-info/RECORD

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