vivarium-public-health 3.0.6__tar.gz → 3.0.8__tar.gz

{vivarium_public_health-3.0.6 → vivarium_public_health-3.0.8}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**3.0.8 - 09/12/24**
+
+ - Fix broken tests in RiskAttributableDisease due to changes in how to set population_view
+
+**3.0.7 - 09/10/24**
+
+ - Properly create the population_view in RateTransition
+
 **3.0.6 - 09/04/24**
 
  - Fix bug that was occurring when RiskEffect's rr_source was a float or DataFrame

{vivarium_public_health-3.0.6/src/vivarium_public_health.egg-info → vivarium_public_health-3.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.6
+Version: 3.0.8
 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>=3.0.0
+Requires-Dist: vivarium>=3.0.3
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-3.0.6 → vivarium_public_health-3.0.8}/setup.py

@@ -15,7 +15,7 @@ if __name__ == "__main__":
         long_description = f.read()
 
     install_requirements = [
-        "vivarium>=3.0.0",
+        "vivarium>=3.0.3",
         "layered_config_tree>=1.0.1",
         "loguru",
         "numpy<2.0.0",

vivarium_public_health-3.0.8/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.0.8"

{vivarium_public_health-3.0.6 → vivarium_public_health-3.0.8}/src/vivarium_public_health/disease/transition.py

@@ -7,7 +7,7 @@ This module contains tools to model transitions between disease states.
 
 """
 
-from typing import TYPE_CHECKING, Any, Callable, Dict, Union
+from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Union
 
 import pandas as pd
 from vivarium.framework.engine import Builder
@@ -48,6 +48,10 @@ class RateTransition(Transition):
             },
         }
 
+    @property
+    def columns_required(self) -> Optional[List[str]]:
+        return ["alive"]
+
     @property
     def transition_rate_pipeline_name(self) -> str:
         if "incidence_rate" in self._get_data_functions:
@@ -100,8 +104,6 @@ class RateTransition(Transition):
             preferred_post_processor=union_post_processor,
         )
 
-        self.population_view = builder.population.get_view(["alive"])
-
     #################
     # Setup methods #
     #################

{vivarium_public_health-3.0.6 → vivarium_public_health-3.0.8/src/vivarium_public_health.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.6
+Version: 3.0.8
 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>=3.0.0
+Requires-Dist: vivarium>=3.0.3
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-3.0.6 → vivarium_public_health-3.0.8}/src/vivarium_public_health.egg-info/requires.txt

@@ -1,4 +1,4 @@
-vivarium>=3.0.0
+vivarium>=3.0.3
 layered_config_tree>=1.0.1
 loguru
 numpy<2.0.0

{vivarium_public_health-3.0.6 → vivarium_public_health-3.0.8}/tests/disease/test_special_disease.py

@@ -13,7 +13,7 @@ def disease_mock(mocker):
     def disease_with_distribution(distribution):
         test_disease = RiskAttributableDisease("cause.test_cause", "risk_factor.test_risk")
         test_disease.distribution = distribution
-        test_disease.population_view = mocker.Mock()
+        test_disease._population_view = mocker.Mock()
         test_disease.excess_mortality_rate = mocker.Mock()
         return test_disease
 

vivarium_public_health-3.0.6/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "3.0.6"