vivarium-public-health 4.0.1__tar.gz → 4.1.0__tar.gz

{vivarium_public_health-4.0.1 → vivarium_public_health-4.1.0}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**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
+
 **4.0.1 - 03/21/25**
 
  - Feature: Update required resources for all components

{vivarium_public_health-4.0.1 → vivarium_public_health-4.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.0.1
+Version: 4.1.0
 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>=3.4.0
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-4.0.1 → vivarium_public_health-4.1.0}/setup.py

@@ -42,7 +42,7 @@ if __name__ == "__main__":
         long_description = f.read()
 
     install_requirements = [
-        "vivarium>=3.2.3",
+        "vivarium>=3.4.0",
         "layered_config_tree>=1.0.1",
         "loguru",
         "numpy<2.0.0",

vivarium_public_health-4.1.0/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.1.0"

{vivarium_public_health-4.0.1 → vivarium_public_health-4.1.0}/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-4.0.1 → vivarium_public_health-4.1.0}/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-4.0.1 → vivarium_public_health-4.1.0}/src/vivarium_public_health/population/data_transformations.py

@@ -561,22 +561,24 @@ def get_live_births_per_year(builder):
 
 
 def rescale_final_age_bin(builder, population_data):
-    exit_age = builder.configuration.population.to_dict().get("exit_age", None)
-    if exit_age:
-        population_data = population_data.loc[population_data["age_start"] < exit_age].copy()
-        cut_bin_idx = exit_age <= population_data["age_end"]
+    untracking_age = builder.configuration.population.to_dict().get("untracking_age", None)
+    if untracking_age:
+        population_data = population_data.loc[
+            population_data["age_start"] < untracking_age
+        ].copy()
+        cut_bin_idx = untracking_age <= population_data["age_end"]
         cut_age_start = population_data.loc[cut_bin_idx, "age_start"]
         cut_age_end = population_data.loc[cut_bin_idx, "age_end"]
-        population_data.loc[cut_bin_idx, "value"] *= (exit_age - cut_age_start) / (
+        population_data.loc[cut_bin_idx, "value"] *= (untracking_age - cut_age_start) / (
             cut_age_end - cut_age_start
         )
-        population_data.loc[cut_bin_idx, "age_end"] = exit_age
+        population_data.loc[cut_bin_idx, "age_end"] = untracking_age
     return population_data
 
 
 def validate_crude_birth_rate_data(builder, data_year_max):
-    exit_age = builder.configuration.population.to_dict().get("exit_age", None)
-    if exit_age and builder.configuration.population.age_end != exit_age:
+    untracking_age = builder.configuration.population.to_dict().get("untracking_age", None)
+    if untracking_age and builder.configuration.population.age_end != untracking_age:
         raise ValueError(
             "If you specify an exit age, the initial population age end must be the same "
             "for the crude birth rate calculation to work."

{vivarium_public_health-4.0.1 → vivarium_public_health-4.1.0}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.0.1
+Version: 4.1.0
 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>=3.4.0
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-4.0.1 → vivarium_public_health-4.1.0}/src/vivarium_public_health.egg-info/requires.txt

@@ -1,4 +1,4 @@
-vivarium>=3.2.3
+vivarium>=3.4.0
 layered_config_tree>=1.0.1
 loguru
 numpy<2.0.0

{vivarium_public_health-4.0.1 → vivarium_public_health-4.1.0}/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-4.0.1/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.0.1"