vivarium-public-health 4.3.0__tar.gz → 4.3.2__tar.gz

{vivarium_public_health-4.3.0 → vivarium_public_health-4.3.2}/.gitignore

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

{vivarium_public_health-4.3.0 → vivarium_public_health-4.3.2}/CHANGELOG.rst

@@ -1,5 +1,15 @@
-**4.3.0 - 07/29/25**
+**4.3.2 - 07/30/25**
 
+  - Support RiskEffect backwards compatibility with v4.2.x
+
+**4.3.1 - 07/30/25**
+
+  - Bugfix: reference correct entity name in LBWSG get_current_exposure method
+  - Support backwards compatibility with v4.2.x
+
+**4.3.0 - 07/29/25** (withdrawn)
+
+  - This release was withdrawn from PyPI.
   - Refactor to create two new abstract classes, Exposure and ExposureEffect
   - Add Intervention and InterventionEffect classes
   - Refactor to pass Exposure component to RiskExposureDistribution classes

{vivarium_public_health-4.3.0 → vivarium_public_health-4.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.0
+Version: 4.3.2
 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-4.3.2/docs/source/api_reference/exposure/data_transformations.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.exposure.data_transformations

vivarium_public_health-4.3.2/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.3.2"

{vivarium_public_health-4.3.0 → vivarium_public_health-4.3.2}/src/vivarium_public_health/risks/base_risk.py

@@ -7,6 +7,7 @@ This module contains tools for modeling categorical and continuous risk
 exposure.
 
 """
+import warnings
 from typing import NamedTuple
 
 from vivarium.framework.engine import Builder
@@ -73,6 +74,24 @@ class Risk(Exposure):
 
     """
 
+    @property
+    def risk(self) -> str:
+        warnings.warn(
+            "The 'risk' attribute is deprecated. Use 'entity' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return self.entity
+
+    @risk.setter
+    def risk(self, value: str) -> None:
+        warnings.warn(
+            "The 'risk' attribute is deprecated. Use 'entity' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        self.entity = value
+
     @property
     def exposure_type(self) -> str:
         """The measure of the risk exposure."""

vivarium_public_health-4.3.2/src/vivarium_public_health/risks/data_transformations.py

@@ -0,0 +1,32 @@
+"""
+==============================
+Data Transformations (Legacy)
+==============================
+
+.. deprecated:: 4.3.0
+   This module is deprecated. Use :mod:`vivarium_public_health.exposure.data_transformations` instead.
+
+Backward compatibility module for risk data_transformations.
+
+This module provides backward compatibility for imports that expect risk
+distribution classes to be in vivarium_public_health.risks.data_transformations.
+
+The actual distribution classes have been moved to:
+vivarium_public_health.exposure.data_transformations
+
+This module will be deprecated in a future version.
+"""
+
+import warnings
+
+# Issue a deprecation warning when this module is imported
+warnings.warn(
+    "Importing from 'vivarium_public_health.risks.data_transformations' is deprecated. "
+    "Please import from 'vivarium_public_health.exposure.data_transformations' instead.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
+# Import all the classes from the new location
+from vivarium_public_health.exposure.data_transformations import *
+from vivarium_public_health.exposure.data_transformations import _rebin_relative_risk_data

vivarium_public_health-4.3.2/src/vivarium_public_health/risks/distributions.py

@@ -0,0 +1,24 @@
+"""
+Backward compatibility module for risk distributions.
+
+This module provides backward compatibility for imports that expect risk
+distribution classes to be in vivarium_public_health.risks.distributions.
+
+The actual distribution classes have been moved to:
+vivarium_public_health.exposure.distributions
+
+This module will be deprecated in a future version.
+"""
+
+import warnings
+
+# Issue a deprecation warning when this module is imported
+warnings.warn(
+    "Importing from 'vivarium_public_health.risks.distributions' is deprecated. "
+    "Please import from 'vivarium_public_health.exposure.distributions' instead.",
+    DeprecationWarning,
+    stacklevel=2,
+)
+
+# Import all the classes from the new location
+from vivarium_public_health.exposure.distributions import *

{vivarium_public_health-4.3.0 → vivarium_public_health-4.3.2}/src/vivarium_public_health/risks/effect.py

@@ -5,6 +5,7 @@ Risk Effect Models
 
 """
 
+import warnings
 from collections.abc import Callable
 from typing import Any
 
@@ -26,6 +27,24 @@ class RiskEffect(ExposureEffect):
 
     """
 
+    @property
+    def risk(self) -> str:
+        warnings.warn(
+            "The 'risk' attribute is deprecated. Use 'entity' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        return self.entity
+
+    @risk.setter
+    def risk(self, value: str) -> None:
+        warnings.warn(
+            "The 'risk' attribute is deprecated. Use 'entity' instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+        self.entity = value
+
     def get_name(self, risk: EntityString, target: TargetString) -> str:
         return f"risk_effect.{risk.name}_on_{target}"
 

{vivarium_public_health-4.3.0 → vivarium_public_health-4.3.2}/src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -364,7 +364,7 @@ class LBWSGRisk(Risk):
 
     def get_current_exposure(self, index: pd.Index) -> pd.DataFrame:
         raise LifeCycleError(
-            f"The {self.risk.name} exposure pipeline should not be called. You probably want to"
+            f"The {self.entity.name} exposure pipeline should not be called. You probably want to"
             f" refer directly one of the exposure columns. During simulant initialization the birth"
             f" exposure pipelines should be used instead."
         )

{vivarium_public_health-4.3.0 → vivarium_public_health-4.3.2}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.0
+Version: 4.3.2
 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-4.3.0 → vivarium_public_health-4.3.2}/src/vivarium_public_health.egg-info/SOURCES.txt

@@ -34,6 +34,7 @@ docs/source/api_reference/disease/models.rst
 docs/source/api_reference/disease/special_disease.rst
 docs/source/api_reference/disease/state.rst
 docs/source/api_reference/disease/transition.rst
+docs/source/api_reference/exposure/data_transformations.rst
 docs/source/api_reference/exposure/distributions.rst
 docs/source/api_reference/exposure/effect.rst
 docs/source/api_reference/exposure/exposure.rst
@@ -91,6 +92,7 @@ src/vivarium_public_health/disease/special_disease.py
 src/vivarium_public_health/disease/state.py
 src/vivarium_public_health/disease/transition.py
 src/vivarium_public_health/exposure/__init__.py
+src/vivarium_public_health/exposure/data_transformations.py
 src/vivarium_public_health/exposure/distributions.py
 src/vivarium_public_health/exposure/effect.py
 src/vivarium_public_health/exposure/exposure.py
@@ -121,6 +123,7 @@ src/vivarium_public_health/results/stratification.py
 src/vivarium_public_health/risks/__init__.py
 src/vivarium_public_health/risks/base_risk.py
 src/vivarium_public_health/risks/data_transformations.py
+src/vivarium_public_health/risks/distributions.py
 src/vivarium_public_health/risks/effect.py
 src/vivarium_public_health/risks/implementations/__init__.py
 src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

vivarium_public_health-4.3.0/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.3.0"