vivarium-public-health 4.3.2__tar.gz → 4.3.4__tar.gz

{vivarium_public_health-4.3.2 → vivarium_public_health-4.3.4}/.gitignore

@@ -114,7 +114,4 @@ src/vivarium_public_health/_version.py
 tests/proportion_test_diagnostics.csv
 
 # macOS
-*.DS_Store
-
-# Visual Studio Code project settings
-.vscode/
+*.DS_Store

{vivarium_public_health-4.3.2 → vivarium_public_health-4.3.4}/CHANGELOG.rst

@@ -1,8 +1,16 @@
-**4.3.2 - 07/30/25**
+**4.3.4 - 07/31/25**
+
+  - Modify futurewarning fix from v4.2.6 to not require pandas>=2.2.0
+
+**4.3.3 - 07/30/25**
+
+  - Revert changes from v4.3.0-4.3.2
+
+**4.3.2 - 07/30/25** (withdrawn)
 
   - Support RiskEffect backwards compatibility with v4.2.x
 
-**4.3.1 - 07/30/25**
+**4.3.1 - 07/30/25** (withdrawn)
 
   - Bugfix: reference correct entity name in LBWSG get_current_exposure method
   - Support backwards compatibility with v4.2.x

{vivarium_public_health-4.3.2 → vivarium_public_health-4.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.2
+Version: 4.3.4
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -31,7 +31,7 @@ Requires-Dist: vivarium>=3.4.3
 Requires-Dist: layered_config_tree>=3.2.0
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0
-Requires-Dist: pandas>=2.2.0
+Requires-Dist: pandas
 Requires-Dist: scipy
 Requires-Dist: tables
 Requires-Dist: risk_distributions>=2.0.11

vivarium_public_health-4.3.4/docs/source/api_reference/risks/distributions.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.risks.distributions

{vivarium_public_health-4.3.2 → vivarium_public_health-4.3.4}/setup.py

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

{vivarium_public_health-4.3.2 → vivarium_public_health-4.3.4}/src/vivarium_public_health/__init__.py

@@ -46,13 +46,7 @@ from vivarium_public_health.risks import (
     Risk,
     RiskEffect,
 )
-from vivarium_public_health.treatment import (
-    AbsoluteShift,
-    Intervention,
-    InterventionEffect,
-    LinearScaleUp,
-    TherapeuticInertia,
-)
+from vivarium_public_health.treatment import AbsoluteShift, LinearScaleUp, TherapeuticInertia
 
 __all__ = [
     __author__,

vivarium_public_health-4.3.4/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.3.4"

{vivarium_public_health-4.3.2 → vivarium_public_health-4.3.4}/src/vivarium_public_health/population/data_transformations.py

@@ -52,29 +52,28 @@ def assign_demographic_proportions(
     if include_sex != "Both":
         population_data.loc[population_data.sex != include_sex, "value"] = 0.0
 
+    year_start_groups = population_data.groupby("year_start", as_index=False)
     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(), include_groups=False
-        )
+        year_start_groups[year_start_groups.obj.columns]
+        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )
 
+    age_year_start_groups = population_data.groupby(["age", "year_start"], as_index=False)
     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(), include_groups=False
-        )
+        age_year_start_groups[age_year_start_groups.obj.columns]
+        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )
 
+    year_start_sex_location_groups = population_data.groupby(
+        ["year_start", "sex", "location"], as_index=False
+    )
     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(), include_groups=False
-        )
+        year_start_sex_location_groups[year_start_sex_location_groups.obj.columns]
+        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )
@@ -584,8 +583,8 @@ def rescale_final_age_bin(builder, population_data):
 
 def validate_crude_birth_rate_data(builder, data_year_max):
     population_config = builder.configuration.population.to_dict()
-    untracking_age = population_config.get("untracking_age")
-    age_end = population_config.get("age_end")
+    untracking_age = population_config.get("untracking_age", None)
+    age_end = population_config.get("age_end", None)
     if untracking_age and age_end and age_end != untracking_age:
         raise ValueError(
             "If you specify an exit age, the initial population age end must be the same "

{vivarium_public_health-4.3.2 → vivarium_public_health-4.3.4}/src/vivarium_public_health/results/__init__.py

@@ -1,7 +1,6 @@
 from .columns import COLUMNS
 from .disability import DisabilityObserver
 from .disease import DiseaseObserver
-from .intervention import CategoricalInterventionObserver
 from .mortality import MortalityObserver
 from .observer import PublicHealthObserver
 from .risk import CategoricalRiskObserver

vivarium_public_health-4.3.2/src/vivarium_public_health/exposure/exposure.py → vivarium_public_health-4.3.4/src/vivarium_public_health/risks/base_risk.py

@@ -1,5 +1,14 @@
-from abc import ABC, abstractmethod
-from typing import Any, NamedTuple
+"""
+===================
+Risk Exposure Model
+===================
+
+This module contains tools for modeling categorical and continuous risk
+exposure.
+
+"""
+
+from typing import Any
 
 import pandas as pd
 from vivarium import Component
@@ -10,23 +19,73 @@ from vivarium.framework.randomness import RandomnessStream
 from vivarium.framework.resource import Resource
 from vivarium.framework.values import Pipeline
 
-from vivarium_public_health.exposure.distributions import (
+from vivarium_public_health.risks.data_transformations import get_exposure_post_processor
+from vivarium_public_health.risks.distributions import (
     ContinuousDistribution,
     DichotomousDistribution,
     EnsembleDistribution,
-    ExposureDistribution,
     PolytomousDistribution,
+    RiskExposureDistribution,
 )
-from vivarium_public_health.risks.data_transformations import get_exposure_post_processor
 from vivarium_public_health.utilities import EntityString, get_lookup_columns
 
 
-class Exposure(Component, ABC):
-    """A base class to store common functionality for for risk-like health factors.
+class Risk(Component):
+    """A model for a risk factor defined by either a continuous or a categorical value.
+
+    For example,
+
+    #. high systolic blood pressure as a risk where the SBP is not dichotomized
+       into hypotension and normal but is treated as the actual SBP
+       measurement.
+    #. smoking as two categories: current smoker and non-smoker.
+
+    This component can source data either from builder.data or from parameters
+    supplied in the configuration. If data is derived from the configuration, it
+    must be an integer or float expressing the desired exposure level or a
+    covariate name that is intended to be used as a proxy. For example, for a
+    risk named "risk", the configuration could look like this:
+
+    .. code-block:: yaml
+
+       configuration:
+           risk:
+               exposure: 1.0
+
+    or
+
+    .. code-block:: yaml
+
+       configuration:
+           risk:
+               exposure: proxy_covariate
 
-    This class is used to define the determinant of models health factors such as
-    risks and the exposure to these risks, or interventions and the available coverage
-    for these interventions.
+    For polytomous risks, you can also provide an optional 'rebinned_exposed'
+    block in the configuration to indicate that the risk should be rebinned
+    into a dichotomous risk. That block should contain a list of the categories
+    that should be rebinned into a single exposed category in the resulting
+    dichotomous risk. For example, for a risk named "risk" with categories
+    cat1, cat2, cat3, and cat4 that you wished to rebin into a dichotomous risk
+    with an exposed category containing cat1 and cat2 and an unexposed category
+    containing cat3 and cat4, the configuration could look like this:
+
+    .. code-block:: yaml
+
+       configuration:
+           risk:
+              rebinned_exposed: ['cat1', 'cat2']
+
+    For alternative risk factors, you must provide a 'category_thresholds'
+    block in the in configuration to dictate the thresholds that should be
+    used to bin the continuous distributions. Note that this is mutually
+    exclusive with providing 'rebinned_exposed' categories. For a risk named
+    "risk", the configuration could look like:
+
+    .. code-block:: yaml
+
+       configuration:
+           risk:
+               category_thresholds: [7, 8, 9]
 
     """
 
@@ -45,18 +104,18 @@ class Exposure(Component, ABC):
 
     @property
     def name(self) -> str:
-        return self.entity
+        return self.risk
 
     @property
     def configuration_defaults(self) -> dict[str, Any]:
         return {
             self.name: {
                 "data_sources": {
-                    f"{self.exposure_type}": f"{self.entity}.{self.exposure_type}",
-                    "ensemble_distribution_weights": f"{self.entity}.exposure_distribution_weights",
-                    "exposure_standard_deviation": f"{self.entity}.exposure_standard_deviation",
+                    "exposure": f"{self.risk}.exposure",
+                    "ensemble_distribution_weights": f"{self.risk}.exposure_distribution_weights",
+                    "exposure_standard_deviation": f"{self.risk}.exposure_standard_deviation",
                 },
-                "distribution_type": f"{self.entity}.distribution",
+                "distribution_type": f"{self.risk}.distribution",
                 # rebinned_exposed only used for DichotomousDistribution
                 "rebinned_exposed": [],
                 "category_thresholds": [],
@@ -74,42 +133,27 @@ class Exposure(Component, ABC):
     def initialization_requirements(self) -> list[str | Resource]:
         return [self.randomness]
 
-    @property
-    @abstractmethod
-    def exposure_type(self) -> str:
-        raise NotImplementedError
-
-    @property
-    @abstractmethod
-    def dichotomous_exposure_category_names(self) -> NamedTuple:
-        """The name of the exposure categories. E.g. "exposed" and "unexposed" or
-        "covered" and "uncovered".
-
-        """
-        raise NotImplementedError
-
     #####################
     # Lifecycle methods #
     #####################
 
-    def __init__(self, entity: str) -> None:
+    def __init__(self, risk: str):
         """
 
         Parameters
         ----------
-        entity
-            the type and name of a entity, specified as "type.name". Type is singular.
-        level_type
-            The type of level for the health factor, e.g., "exposure" or "coverage".
+        risk
+            the type and name of a risk, specified as "type.name". Type is singular.
         """
         super().__init__()
-        self.entity = EntityString(entity)
+        self.risk = EntityString(risk)
         self.distribution_type = None
-        self.randomness_stream_name = f"initial_{self.entity.name}_propensity"
-        self.propensity_column_name = f"{self.entity.name}_propensity"
-        self.propensity_pipeline_name = f"{self.entity.name}.propensity"
-        self.exposure_pipeline_name = f"{self.entity.name}.{self.exposure_type}"
-        self.exposure_column_name = f"{self.entity.name}_{self.exposure_type}"
+
+        self.randomness_stream_name = f"initial_{self.risk.name}_propensity"
+        self.propensity_column_name = f"{self.risk.name}_propensity"
+        self.propensity_pipeline_name = f"{self.risk.name}.propensity"
+        self.exposure_pipeline_name = f"{self.risk.name}.exposure"
+        self.exposure_column_name = f"{self.risk.name}_exposure"
 
     #################
     # Setup methods #
@@ -126,10 +170,17 @@ class Exposure(Component, ABC):
 
         self.randomness = self.get_randomness_stream(builder)
         self.propensity = self.get_propensity_pipeline(builder)
-        self.exposure = self.get_exposure_callable(builder)
-        # This will be overwritten in the Risk class if there is a non-loglinear risk effect
-        # on that risk instance
-        self.create_exposure_column = False
+        self.exposure = self.get_exposure_pipeline(builder)
+
+        # We want to set this to True iff there is a non-loglinear risk effect
+        # on this risk instance
+        self.create_exposure_column = bool(
+            [
+                component
+                for component in builder.components.list_components()
+                if component.startswith(f"non_log_linear_risk_effect.{self.risk.name}_on_")
+            ]
+        )
 
     def get_distribution_type(self, builder: Builder) -> str:
         """Get the distribution type for the risk from the configuration.
@@ -165,7 +216,7 @@ class Exposure(Component, ABC):
             distribution_type = "dichotomous"
         return distribution_type
 
-    def get_exposure_distribution(self, builder: Builder) -> ExposureDistribution:
+    def get_exposure_distribution(self, builder: Builder) -> RiskExposureDistribution:
         """Creates and sets up the exposure distribution component for the Risk
         based on its distribution type.
 
@@ -185,7 +236,7 @@ class Exposure(Component, ABC):
         """
         try:
             exposure_distribution = self.exposure_distributions[self.distribution_type](
-                self, self.distribution_type
+                self.risk, self.distribution_type
             )
         except KeyError:
             raise NotImplementedError(
@@ -210,7 +261,7 @@ class Exposure(Component, ABC):
             required_resources=[self.propensity_column_name],
         )
 
-    def get_exposure_callable(self, builder: Builder) -> Pipeline:
+    def get_exposure_pipeline(self, builder: Builder) -> Pipeline:
         required_columns = get_lookup_columns(
             self.exposure_distribution.lookup_tables.values()
         )
@@ -242,7 +293,7 @@ class Exposure(Component, ABC):
 
     def update_exposure_column(self, index: pd.Index) -> None:
         if self.create_exposure_column:
-            exposure = pd.Series(self.exposure_type(index), name=self.exposure_column_name)
+            exposure = pd.Series(self.exposure(index), name=self.exposure_column_name)
             self.population_view.update(exposure)
 
     ##################################