vivarium-public-health 4.0.2__tar.gz → 4.1.1__tar.gz

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**4.1.1 - 05/23/25**
+
+  - Feature: Update Observer to use super class get_configuration method
+
+**4.1.0 - 05/20/25**
+
+  - Feature: Update RateTransition to have configuration key for rate conversion type
+
 **4.0.2 - 05/01/25**
 
   - Bugfix: Fix configuration key for untracking age in FertilityCrudeBirthRate

vivarium_public_health-4.1.1/Jenkinsfile

@@ -0,0 +1,6 @@
+@Library("vivarium_build_utils") _
+reusable_pipeline(
+    scheduled_branches: ["main"], 
+    upstream_repos: ["vivarium", "layered_config_tree", "risk_distributions"],
+    run_mypy: false,
+)

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.0.2
+Version: 4.1.1
 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>=3.2.3
+Requires-Dist: vivarium>=3.4.3
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/setup.py

@@ -42,7 +42,7 @@ if __name__ == "__main__":
         long_description = f.read()
 
     install_requirements = [
-        "vivarium>=3.2.3",
+        "vivarium>=3.4.3",
         "layered_config_tree>=1.0.1",
         "loguru",
         "numpy<2.0.0",

vivarium_public_health-4.1.1/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.1.1"

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health/disease/model.py

@@ -14,14 +14,16 @@ from functools import partial
 from typing import Any
 
 import pandas as pd
+from layered_config_tree import ConfigurationError
 from vivarium.framework.engine import Builder
+from vivarium.framework.event import Event
 from vivarium.framework.population import SimulantData
 from vivarium.framework.state_machine import Machine
 from vivarium.types import DataInput, LookupTableData
 
 from vivarium_public_health.disease.exceptions import DiseaseModelError
 from vivarium_public_health.disease.state import BaseDiseaseState, SusceptibleState
-from vivarium_public_health.disease.transition import TransitionString
+from vivarium_public_health.disease.transition import RateTransition, TransitionString
 
 
 class DiseaseModel(Machine):
@@ -118,6 +120,18 @@ class DiseaseModel(Machine):
             required_resources=["age", "sex"],
         )
 
+    def on_post_setup(self, event: Event) -> None:
+        conversion_types = set()
+        for state in self.states:
+            for transition in state.transition_set.transitions:
+                if isinstance(transition, RateTransition):
+                    conversion_types.add(transition.rate_conversion_type)
+        if len(conversion_types) > 1:
+            raise ConfigurationError(
+                "All transitions in a disease model must have the same rate conversion type."
+                f" Found: {conversion_types}."
+            )
+
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
         """Initialize the simulants in the population.
 

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health/disease/transition.py

@@ -48,6 +48,7 @@ class RateTransition(Transition):
                 "data_sources": {
                     "transition_rate": self._rate_source,
                 },
+                "rate_conversion_type": "linear",
             },
         }
 
@@ -143,6 +144,7 @@ class RateTransition(Transition):
             component=self,
             required_resources=lookup_columns + ["alive", self.joint_paf],
         )
+        self.rate_conversion_type = self.configuration["rate_conversion_type"]
 
     #################
     # Setup methods #
@@ -184,7 +186,12 @@ class RateTransition(Transition):
     ##################
 
     def _probability(self, index: pd.Index) -> pd.Series:
-        return pd.Series(rate_to_probability(self.transition_rate(index)))
+        return pd.Series(
+            rate_to_probability(
+                self.transition_rate(index),
+                rate_conversion_type=self.rate_conversion_type,
+            )
+        )
 
 
 class ProportionTransition(Transition):

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health/results/disability.py

@@ -34,7 +34,7 @@ class DisabilityObserver(PublicHealthObserver):
     .. code-block:: yaml
 
         configuration:
-            observers:
+            stratification:
                 disability:
                     exclude:
                         - "sex"
@@ -128,20 +128,6 @@ class DisabilityObserver(PublicHealthObserver):
             cause for cause in causes_of_disability if cause.state_id not in excluded_causes
         ]
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification.disability
-
     def register_observations(self, builder: Builder) -> None:
         """Register an observation for years lived with disability."""
         cause_pipelines = [

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health/results/disease.py

@@ -66,19 +66,6 @@ class DiseaseObserver(PublicHealthObserver):
     # Properties #
     ##############
 
-    @property
-    def configuration_defaults(self) -> dict[str, Any]:
-        """A dictionary containing the defaults for any configurations managed by
-        this component.
-        """
-        return {
-            "stratification": {
-                self.disease: super().configuration_defaults["stratification"][
-                    self.get_configuration_name()
-                ]
-            }
-        }
-
     @property
     def columns_created(self) -> list[str]:
         """Columns created by this observer."""
@@ -122,19 +109,8 @@ class DiseaseObserver(PublicHealthObserver):
         self.entity = self.disease_model.cause
         self.transition_stratification_name = f"transition_{self.disease}"
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification[self.disease]
+    def get_configuration_name(self) -> str:
+        return self.disease
 
     def register_observations(self, builder: Builder) -> None:
         """Register stratifications and observations.

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health/results/mortality.py

@@ -136,20 +136,6 @@ class MortalityObserver(PublicHealthObserver):
             SimpleCause("other_causes", "other_causes", "cause"),
         ]
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification[self.get_configuration_name()]
-
     def register_observations(self, builder: Builder) -> None:
         """Register stratifications and observations.
 

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health/results/risk.py

@@ -58,19 +58,6 @@ class CategoricalRiskObserver(PublicHealthObserver):
     # Properties #
     ##############
 
-    @property
-    def configuration_defaults(self) -> dict[str, Any]:
-        """A dictionary containing the defaults for any configurations managed by
-        this component.
-        """
-        return {
-            "stratification": {
-                f"{self.risk}": super().configuration_defaults["stratification"][
-                    self.get_configuration_name()
-                ]
-            }
-        }
-
     @property
     def columns_required(self) -> list[str] | None:
         """The columns required by this observer."""
@@ -101,19 +88,8 @@ class CategoricalRiskObserver(PublicHealthObserver):
         self.step_size = builder.time.step_size()
         self.categories = builder.data.load(f"risk_factor.{self.risk}.categories")
 
-    def get_configuration(self, builder: Builder) -> LayeredConfigTree:
-        """Get the stratification configuration for this observer.
-
-        Parameters
-        ----------
-        builder
-            The builder object for the simulation.
-
-        Returns
-        -------
-            The stratification configuration for this observer.
-        """
-        return builder.configuration.stratification[self.risk]
+    def get_configuration_name(self) -> str:
+        return self.risk
 
     def register_observations(self, builder: Builder) -> None:
         """Register a stratification and observation.

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.0.2
+Version: 4.1.1
 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>=3.2.3
+Requires-Dist: vivarium>=3.4.3
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/src/vivarium_public_health.egg-info/requires.txt

@@ -1,4 +1,4 @@
-vivarium>=3.2.3
+vivarium>=3.4.3
 layered_config_tree>=1.0.1
 loguru
 numpy<2.0.0

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/tests/disease/test_disease.py

@@ -1,6 +1,9 @@
+from unittest.mock import patch
+
 import numpy as np
 import pandas as pd
 import pytest
+from layered_config_tree import ConfigurationError, LayeredConfigTree
 from vivarium import Component, InteractiveContext
 from vivarium.framework.state_machine import Transition
 from vivarium.framework.utilities import from_yearly
@@ -554,3 +557,101 @@ def test_artifact_transition_keys(mocker, disease):
     # check remission rate
     remissive_transition = with_condition.add_rate_transition(healthy)
     assert remissive_transition._rate_source == f"cause.{cause}.remission_rate"
+
+
+@pytest.mark.parametrize("rate_conversion_type", ["linear", "exponential"])
+def test_transition_rate_to_probability_configuration(
+    base_config: LayeredConfigTree,
+    base_plugins: LayeredConfigTree,
+    disease: str,
+    rate_conversion_type: str,
+):
+    """
+    Test that the transition rate to probability configuration is set correctly.
+    """
+    healthy = BaseDiseaseState("healthy")
+    sick = DiseaseState("sick")
+    key = "sequela.acute_myocardial_infarction_first_2_days.incidence_rate"
+    transition = RateTransition(
+        input_state=healthy,
+        output_state=sick,
+        get_data_functions={"incidence_rate": lambda builder, _: builder.data.load(key)},
+    )
+    healthy.transition_set.append(transition)
+    model = DiseaseModel(disease, initial_state=healthy, states=[healthy, sick])
+
+    base_config.update(
+        {
+            f"{transition.name}": {
+                "rate_conversion_type": rate_conversion_type,
+            }
+        }
+    )
+
+    # Sets the configuration
+    sim = InteractiveContext(
+        components=[TestPopulation(), model],
+        configuration=base_config,
+        plugin_configuration=base_plugins,
+        setup=True,
+    )
+
+    assert transition.rate_conversion_type == rate_conversion_type
+    with patch(
+        "vivarium_public_health.disease.transition.rate_to_probability", return_value=1.0
+    ) as mock_rate_to_probability:
+        idx = pd.Index(list(range(10)))
+        transition._probability(idx)
+
+        mock_rate_to_probability.assert_called_once()
+        args, kwargs = mock_rate_to_probability.call_args
+        assert len(args) == 1
+        assert len(kwargs) == 1
+        assert args[0].index.equals(idx)
+        assert kwargs["rate_conversion_type"] == rate_conversion_type
+
+
+def test_disease_model_rate_conversion_config_error(
+    base_config: LayeredConfigTree,
+    base_plugins: LayeredConfigTree,
+    disease: str,
+):
+    """
+    Test that the transition rate to probability configuration is set correctly.
+    """
+    healthy = BaseDiseaseState("healthy")
+    sick = DiseaseState("sick")
+    key = "sequela.acute_myocardial_infarction_first_2_days.incidence_rate"
+    transition = RateTransition(
+        input_state=healthy,
+        output_state=sick,
+        get_data_functions={"incidence_rate": lambda builder, _: builder.data.load(key)},
+    )
+    another_transition = RateTransition(
+        input_state=sick,
+        output_state=healthy,
+        get_data_functions={"incidence_rate": lambda builder, _: builder.data.load(key)},
+    )
+    healthy.transition_set.append(transition)
+    sick.transition_set.append(another_transition)
+    model = DiseaseModel(disease, initial_state=healthy, states=[healthy, sick])
+
+    base_config.update(
+        {
+            f"{transition.name}": {
+                "rate_conversion_type": "linear",
+            },
+            f"{another_transition.name}": {
+                "rate_conversion_type": "exponential",
+            },
+        }
+    )
+
+    # Sets the configuration
+    with pytest.raises(ConfigurationError):
+        InteractiveContext(
+            components=[TestPopulation(), model],
+            configuration=base_config,
+            plugin_configuration=base_plugins,
+            setup=True,
+        )

{vivarium_public_health-4.0.2 → vivarium_public_health-4.1.1}/tests/results/test_disability_observer.py

@@ -39,7 +39,6 @@ def test_disability_observer_setup(mocker):
     observer = DisabilityObserver_()
     builder = mocker.Mock()
     mocker.patch("vivarium.component.Component.build_all_lookup_tables")
-    mocker.patch("vivarium.component.Component.get_configuration")
     builder.results.register_adding_observation = mocker.Mock()
     builder.configuration.time.step_size = 28
     builder.configuration.output_data.results_directory = "some/results/directory"

vivarium_public_health-4.0.2/Jenkinsfile

@@ -1,4 +0,0 @@
-@Library("vivarium_build_utils") _
-reusable_pipeline(scheduled_branches: ["main"], 
-                  upstream_repos: ["vivarium", "layered_config_tree", "risk_distributions"], 
-                 )

vivarium_public_health-4.0.2/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.0.2"