vivarium-public-health 4.0.1__py3-none-any.whl → 4.1.0__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "4.0.1"
+__version__ = "4.1.0"

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/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.dist-info → vivarium_public_health-4.1.0.dist-info}/METADATA

@@ -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.dist-info → vivarium_public_health-4.1.0.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=v4mcX8QEz7plObRyvTdDblE04TUjya-nJkDSAikxv9Y,22
+vivarium_public_health/_version.py,sha256=jegJMYuSW90VKiMotVdNAakBvYVPirm-A5oeyJVuhH8,22
 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
@@ -21,7 +21,7 @@ vivarium_public_health/plugins/parser.py,sha256=WoUisq0d-PfJtSzKYZ6C-s-fYdQpNiRB
 vivarium_public_health/population/__init__.py,sha256=x_9rB93q64Krw-kbBDI1-_U_JsPO1_QrL03AwiFlwXI,243
 vivarium_public_health/population/add_new_birth_cohorts.py,sha256=x6A60GE_F3I8AgLABNJ-2ziiUj52lAd66uX5yc2vIDI,9038
 vivarium_public_health/population/base_population.py,sha256=kBE0WVSV0aElTJNBmOBqowZlsjhDfnFn2IzNxb3X8CA,18909
-vivarium_public_health/population/data_transformations.py,sha256=yxuZuKZt-s8X6XPULbKWXn2w3kAmNLHYvGQ4sWBKlpc,22216
+vivarium_public_health/population/data_transformations.py,sha256=CEID0uLIJc0xXijlHwnC9Kt8vJMKiIkJtUYcLQbbRRY,22304
 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
@@ -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-4.0.1.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-4.0.1.dist-info/METADATA,sha256=ae5FCmlmfFavN9AVHCL8oZnd8ofEG1wf8puuHDvNUbc,4237
-vivarium_public_health-4.0.1.dist-info/WHEEL,sha256=1tXe9gY0PYatrMPMDd6jXqjfpz_B-Wqm32CPfRC58XU,91
-vivarium_public_health-4.0.1.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-4.0.1.dist-info/RECORD,,
+vivarium_public_health-4.1.0.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-4.1.0.dist-info/METADATA,sha256=PHv-B0x7CeotS3pLGNU-qNqqdMvKeO25QYLQG2xSUZ0,4237
+vivarium_public_health-4.1.0.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
+vivarium_public_health-4.1.0.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-4.1.0.dist-info/RECORD,,

{vivarium_public_health-4.0.1.dist-info → vivarium_public_health-4.1.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (77.0.3)
+Generator: setuptools (80.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any