vivarium-public-health 3.1.0__py3-none-any.whl → 3.1.2__py3-none-any.whl

vivarium_public_health/risks/distributions.py

@@ -9,7 +9,7 @@ exposure distributions.
 """
 
 from abc import ABC, abstractmethod
-from typing import Callable, Dict, List, Optional, Union
+from collections.abc import Callable
 
 import numpy as np
 import pandas as pd
@@ -38,7 +38,7 @@ class RiskExposureDistribution(Component, ABC):
         self,
         risk: EntityString,
         distribution_type: str,
-        exposure_data: Optional[Union[int, float, pd.DataFrame]] = None,
+        exposure_data: int | float | pd.DataFrame | None = None,
     ) -> None:
         super().__init__()
         self.risk = risk
@@ -51,14 +51,14 @@ class RiskExposureDistribution(Component, ABC):
     # Setup methods #
     #################
 
-    def get_configuration(self, builder: "Builder") -> Optional[LayeredConfigTree]:
+    def get_configuration(self, builder: "Builder") -> LayeredConfigTree | None:
         return builder.configuration[self.risk]
 
     @abstractmethod
     def build_all_lookup_tables(self, builder: "Builder") -> None:
         raise NotImplementedError
 
-    def get_exposure_data(self, builder: Builder) -> Union[int, float, pd.DataFrame]:
+    def get_exposure_data(self, builder: Builder) -> int | float | pd.DataFrame:
         if self._exposure_data is not None:
             return self._exposure_data
         return self.get_data(builder, self.configuration["data_sources"]["exposure"])
@@ -92,11 +92,11 @@ class EnsembleDistribution(RiskExposureDistribution):
     ##############
 
     @property
-    def columns_created(self) -> List[str]:
+    def columns_created(self) -> list[str]:
         return [self._propensity]
 
     @property
-    def initialization_requirements(self) -> Dict[str, List[str]]:
+    def initialization_requirements(self) -> dict[str, list[str]]:
         return {
             "requires_columns": [],
             "requires_values": [],
@@ -265,7 +265,7 @@ class ContinuousDistribution(RiskExposureDistribution):
 
 class PolytomousDistribution(RiskExposureDistribution):
     @property
-    def categories(self) -> List[str]:
+    def categories(self) -> list[str]:
         # These need to be sorted so the cumulative sum is in the ocrrect order of categories
         # and results are therefore reproducible and correct
         return sorted(self.lookup_tables["exposure"].value_columns)
@@ -286,8 +286,8 @@ class PolytomousDistribution(RiskExposureDistribution):
         )
 
     def get_exposure_value_columns(
-        self, exposure_data: Union[int, float, pd.DataFrame]
-    ) -> Optional[List[str]]:
+        self, exposure_data: int | float | pd.DataFrame
+    ) -> list[str] | None:
         if isinstance(exposure_data, pd.DataFrame):
             return list(exposure_data["parameter"].unique())
         return None
@@ -342,7 +342,7 @@ class DichotomousDistribution(RiskExposureDistribution):
         )
         self.lookup_tables["paf"] = self.build_lookup_table(builder, 0.0)
 
-    def get_exposure_data(self, builder: Builder) -> Union[int, float, pd.DataFrame]:
+    def get_exposure_data(self, builder: Builder) -> int | float | pd.DataFrame:
         exposure_data = super().get_exposure_data(builder)
 
         if isinstance(exposure_data, (int, float)):
@@ -373,8 +373,8 @@ class DichotomousDistribution(RiskExposureDistribution):
         return exposure_data
 
     def get_exposure_value_columns(
-        self, exposure_data: Union[int, float, pd.DataFrame]
-    ) -> Optional[List[str]]:
+        self, exposure_data: int | float | pd.DataFrame
+    ) -> list[str] | None:
         if isinstance(exposure_data, pd.DataFrame):
             return self.get_value_columns(exposure_data)
         return None
@@ -470,9 +470,9 @@ def clip(q):
 
 
 def get_risk_distribution_parameter(
-    value_columns_getter: Callable[[Union[pd.DataFrame]], List[str]],
-    data: Union[float, pd.DataFrame],
-) -> Union[float, pd.Series]:
+    value_columns_getter: Callable[[pd.DataFrame], list[str]],
+    data: float | pd.DataFrame,
+) -> float | pd.Series:
     if isinstance(data, pd.DataFrame):
         value_columns = value_columns_getter(data)
         if len(value_columns) > 1:

vivarium_public_health/risks/effect.py

@@ -7,9 +7,9 @@ This module contains tools for modeling the relationship between risk
 exposure models and disease models.
 
 """
-
+from collections.abc import Callable
 from importlib import import_module
-from typing import Any, Callable, Dict, List, Tuple, Union
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -58,7 +58,7 @@ class RiskEffect(Component):
         return f"risk_effect.{risk.name}_on_{target}"
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         """Default values for any configurations managed by this component."""
         return {
             self.name: {
@@ -150,7 +150,7 @@ class RiskEffect(Component):
         self,
         builder: Builder,
         configuration=None,
-    ) -> Union[str, float, pd.DataFrame]:
+    ) -> str | float | pd.DataFrame:
         if configuration is None:
             configuration = self.configuration
 
@@ -173,8 +173,8 @@ class RiskEffect(Component):
         return rr_data
 
     def get_filtered_data(
-        self, builder: "Builder", data_source: Union[str, float, pd.DataFrame]
-    ) -> Union[float, pd.DataFrame]:
+        self, builder: "Builder", data_source: str | float | pd.DataFrame
+    ) -> float | pd.DataFrame:
         data = super().get_data(builder, data_source)
 
         if isinstance(data, pd.DataFrame):
@@ -191,8 +191,8 @@ class RiskEffect(Component):
         return data
 
     def process_categorical_data(
-        self, builder: Builder, rr_data: Union[str, float, pd.DataFrame]
-    ) -> Tuple[Union[str, float, pd.DataFrame], List[str]]:
+        self, builder: Builder, rr_data: str | float | pd.DataFrame
+    ) -> tuple[str | float | pd.DataFrame, list[str]]:
         if not isinstance(rr_data, pd.DataFrame):
             cat1 = builder.data.load("population.demographic_dimensions")
             cat1["parameter"] = "cat1"
@@ -347,7 +347,7 @@ class NonLogLinearRiskEffect(RiskEffect):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         """Default values for any configurations managed by this component."""
         return {
             self.name: {
@@ -419,7 +419,7 @@ class NonLogLinearRiskEffect(RiskEffect):
         self,
         builder: Builder,
         configuration=None,
-    ) -> Union[str, float, pd.DataFrame]:
+    ) -> str | float | pd.DataFrame:
         if configuration is None:
             configuration = self.configuration
 

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-3.1.0.dist-info → vivarium_public_health-3.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.1.0
+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
@@ -26,7 +26,7 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
-Requires-Dist: vivarium >=3.0.3
+Requires-Dist: vivarium >=3.2.0
 Requires-Dist: layered-config-tree >=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy <2.0.0

vivarium_public_health-3.1.2.dist-info/RECORD

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+vivarium_public_health/mslt/intervention.py,sha256=jgzyDYEypsJDlKeLHDDqcgiwiCTA31VIz7_keS-Jww4,10325
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+vivarium_public_health/mslt/population.py,sha256=LnN9ch_FoPGNbKeIT5BaEFfeAn5itZgZ0q_ZEaZTJEI,7211
+vivarium_public_health/plugins/__init__.py,sha256=oBW_zfgG_LbwfgTDjUe0btfy9FaDvAbtXho1zQFnz0Y,76
+vivarium_public_health/plugins/parser.py,sha256=WoUisq0d-PfJtSzKYZ6C-s-fYdQpNiRBE14vKaYE27Y,32921
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+vivarium_public_health/population/add_new_birth_cohorts.py,sha256=Xc3NukpbZQpXCtGJsaaN4_arSjOMZ1YJHGyAVTUhGjU,9034
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+vivarium_public_health/population/mortality.py,sha256=komiAsM4ONm6emChAbkiMTYey-5jbnUKjq4B4Q1DOnM,10223
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+vivarium_public_health/results/disease.py,sha256=NwKDtHNEjPJUB-DqhE-gVCC1TNRbX5qbQBDL06XT3Pg,12517
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+vivarium_public_health/results/risk.py,sha256=VArTuuW-xoeuE-EkgAIMVb5la_YGRulIPMLoOmsMnik,6597
+vivarium_public_health/results/simple_cause.py,sha256=ibdE6KwhDfQWntCVkOEooBcmUydEoupmd3_poHSHyu8,1007
+vivarium_public_health/results/stratification.py,sha256=4I3YGHVabNAZENE7YboOtWsWU4X-8LUBJ9iwYMbpl6E,5387
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+vivarium_public_health/risks/effect.py,sha256=BN7XzmCutG5yCIcw9uxl_yKBTtqrL_Y4trrj5wND62w,20735
+vivarium_public_health/risks/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
+vivarium_public_health/treatment/magic_wand.py,sha256=zGIhrNgB9q6JD7fHlvbDQb3H5e_N_QsROO4Y0kl_JQM,1955
+vivarium_public_health/treatment/scale_up.py,sha256=hVz0ELXDqlpcExI31rKdepxqcW_hy2hZSa6qCzv6udU,7020
+vivarium_public_health/treatment/therapeutic_inertia.py,sha256=8Z97s7GfcpfLu1U1ESJSqeEk4L__a3M0GbBV21MFg2s,2346
+vivarium_public_health-3.1.2.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-3.1.2.dist-info/METADATA,sha256=m30cn1jwJksbLgxSqetpor3zYnZZdHQ6BqDBQ3l2hnA,4061
+vivarium_public_health-3.1.2.dist-info/WHEEL,sha256=R06PA3UVYHThwHvxuRWMqaGcr-PuniXahwjmQRFMEkY,91
+vivarium_public_health-3.1.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-3.1.2.dist-info/RECORD,,

{vivarium_public_health-3.1.0.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-3.1.0.dist-info/RECORD

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