vivarium-public-health 4.0.2__py3-none-any.whl → 4.1.1__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "4.0.2"
+__version__ = "4.1.1"

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/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/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/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/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/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.dist-info → vivarium_public_health-4.1.1.dist-info}/METADATA

@@ -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.dist-info → vivarium_public_health-4.1.1.dist-info}/RECORD

@@ -1,14 +1,14 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=GDeeP-7OlCBwPuv_xQoB1wNmvCaFsqfTB7qnnYApm0w,1343
-vivarium_public_health/_version.py,sha256=1UD6TKg1K_f5rIzHLYHv3Su3o2nPpbEj1lo55M4pjtM,22
+vivarium_public_health/_version.py,sha256=NtWqZUv_8plp1gndoYX_eAqe7K65oPMh-hIvB4Evdc8,22
 vivarium_public_health/utilities.py,sha256=QNXQ6fhAr1HcV-GwKw7wQLz6QyuNxqNvMA-XujKjTgs,3035
 vivarium_public_health/disease/__init__.py,sha256=VUJHDLlE6ngo2qHNQUtZ8OWH5H_T7_ao-xsYKDkRmHw,443
 vivarium_public_health/disease/exceptions.py,sha256=vb30IIV82OiDf2cNZCs_E2rF6mdDDHbnZSND60no5CU,97
-vivarium_public_health/disease/model.py,sha256=RyvQ2I4dF6IMUcCL7IEsGccc3qu9V6o30gcYrb38GoU,9205
+vivarium_public_health/disease/model.py,sha256=hCJ3_AVzw1JSIYGGXJqQ2r5o-f3XrPcNQ4rwwm_7jO4,9862
 vivarium_public_health/disease/models.py,sha256=01UK7yB2zGPFzmlIpvhd-XnGe6vSCMDza3QTidgY7Nc,3479
 vivarium_public_health/disease/special_disease.py,sha256=4tGfnXSVuNYsA7izX9y81ByJe46c4h293szVt7AyPMA,14605
 vivarium_public_health/disease/state.py,sha256=ptcNETOo8a0NRXOdUhZMgCJa2h3Pt5ZElhMOKonkD4c,28560
-vivarium_public_health/disease/transition.py,sha256=jwtg0m03zoFiuwFE-WQFXR1F_E-ridsZ7Og_i-J2Q4E,8963
+vivarium_public_health/disease/transition.py,sha256=HPvv1l322XiQcNXIgDTt3WvytxSbuz_2jyPj-spQE3Y,9209
 vivarium_public_health/mslt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 vivarium_public_health/mslt/delay.py,sha256=_neQ8oL2IhCqH0hiM4Od4Eb8NfYjyjSoniq02PFieTw,22872
 vivarium_public_health/mslt/disease.py,sha256=Kwy7cDqiE9yYCsLV_7pAP7ZOe7GWVHUBe39a-GOInVU,16867
@@ -25,11 +25,11 @@ vivarium_public_health/population/data_transformations.py,sha256=CEID0uLIJc0xXij
 vivarium_public_health/population/mortality.py,sha256=Mtv45FENNY0GlPIoVd3d3pRq01aEh4cjzNXIgEe6hMo,10364
 vivarium_public_health/results/__init__.py,sha256=rKUZGlRXJgEyFY4a_WJeg3XnC0l34S5guYZ0N9JJS4E,319
 vivarium_public_health/results/columns.py,sha256=V-L3JgTcsk51Zx9PcUwSgaE1iZjuGyfZ8aShPjynadU,495
-vivarium_public_health/results/disability.py,sha256=sjZpHXfRRWVFI_OjQpYGfDGQ3hQuoLit6XTsBJXNXvY,9872
-vivarium_public_health/results/disease.py,sha256=grhRK329fFLhIq18Ls_AK9hFu9ptXpefI30kynSMU4o,12521
-vivarium_public_health/results/mortality.py,sha256=-gxA9t1nSuKe1CiBje6Kkl985yAUkRWj3Cl9PFYLcQc,9644
+vivarium_public_health/results/disability.py,sha256=OijmWbPkaxmMT4xJ44rWgPz67lVfcLtEloaNwnOiK_g,9459
+vivarium_public_health/results/disease.py,sha256=ni599TKhV3YKQb8_rlnTVt9tIFq_SiM-z8qaoBEdO6s,11764
+vivarium_public_health/results/mortality.py,sha256=9L8tphHn2BEt5sSDkvSfcAyyhsGA_xylEjTed-fv0YI,9206
 vivarium_public_health/results/observer.py,sha256=ADikaV6TvHVaysWoeux_DcvmzAFT7kpD6KtRSl16SaY,7277
-vivarium_public_health/results/risk.py,sha256=VArTuuW-xoeuE-EkgAIMVb5la_YGRulIPMLoOmsMnik,6597
+vivarium_public_health/results/risk.py,sha256=bPZq2El00MZ5A6ttqA-wvbHLm4E3OZcEZOkqV_GENk4,5838
 vivarium_public_health/results/simple_cause.py,sha256=ibdE6KwhDfQWntCVkOEooBcmUydEoupmd3_poHSHyu8,1007
 vivarium_public_health/results/stratification.py,sha256=4I3YGHVabNAZENE7YboOtWsWU4X-8LUBJ9iwYMbpl6E,5387
 vivarium_public_health/risks/__init__.py,sha256=z8DcnZGxqNVAyFZm2WAV-IVNGvrSS4izju_0DNe2Ghw,212
@@ -43,8 +43,8 @@ vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfV
 vivarium_public_health/treatment/magic_wand.py,sha256=zg4I48G-l9fC6-qjvApbM1zNACJimZlX9ZZ9fdHKwvc,1985
 vivarium_public_health/treatment/scale_up.py,sha256=_bsf9c_yVc7-q_-yBcXimISTUfYzPps1auH0uEf7sfQ,7048
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=ZIHnpuszZwA_BkS53JbSLvpcnX_bqG2knwCUyUgkA9M,2362
-vivarium_public_health-4.0.2.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-4.0.2.dist-info/METADATA,sha256=e4EcxG24wvfLnM-9xIy-SHldnpj7-gx9bNES1x3jS8M,4237
-vivarium_public_health-4.0.2.dist-info/WHEEL,sha256=wXxTzcEDnjrTwFYjLPcsW_7_XihufBwmpiBeiXNBGEA,91
-vivarium_public_health-4.0.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-4.0.2.dist-info/RECORD,,
+vivarium_public_health-4.1.1.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-4.1.1.dist-info/METADATA,sha256=FH3HU37jR-MEZ04qtBFZms8kDqdSop1Wc6wSFNoQVSg,4237
+vivarium_public_health-4.1.1.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+vivarium_public_health-4.1.1.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-4.1.1.dist-info/RECORD,,

{vivarium_public_health-4.0.2.dist-info → vivarium_public_health-4.1.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.1.0)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any