vivarium-public-health 3.0.11__tar.gz → 3.1.1__tar.gz

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/.github/workflows/build.yml

@@ -14,7 +14,7 @@ jobs:
   build:
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11"]
     uses: 
       ihmeuw/vivarium_build_utils/.github/workflows/build.yml@main
     with:

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/CHANGELOG.rst

@@ -1,3 +1,12 @@
+**3.1.1 - 11/12/24**
+
+ - Feature: Rename DiseaseModel initial_state to residual_state
+ - Refactor: Use callables rather than strings to define lookup table builders
+
+**3.1.0 - 11/07/24**
+
+ - Drop support for python 3.9
+
 **3.0.11 - 11/07/24**
 
  - Add ScaledPopulation component to population package

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.11
+Version: 3.1.1
 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>=3.0.3
+Requires-Dist: vivarium>=3.2.0
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/docs/nitpick-exceptions

@@ -11,6 +11,7 @@ py:class pandas.core.series.Series
 py:class pandas.core.generic.PandasObject
 # layered-config-tree
 py:class layered_config_tree.main.LayeredConfigTree
+py:class vivarium.framework.values.pipeline.Pipeline
 
 # TODO: Need to revisit this. Nitpicking here to avoid failing builds on 3.9 in LBWSGRisk
 py:class PopulationView
@@ -22,4 +23,3 @@ py:class Builder
 py:class SimulantData
 py:class Event
 py:class LookupTable
-py:class Pipeline

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/setup.py

@@ -15,7 +15,7 @@ if __name__ == "__main__":
         long_description = f.read()
 
     install_requirements = [
-        "vivarium>=3.0.3",
+        "vivarium>=3.2.0",
         "layered_config_tree>=1.0.1",
         "loguru",
         "numpy<2.0.0",

vivarium_public_health-3.1.1/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.1.1"

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health/disease/model.py

@@ -8,7 +8,8 @@ function is to provide coordination across a set of disease states and
 transitions at simulation initialization and during transitions.
 
 """
-
+import warnings
+from collections.abc import Iterable
 from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 import numpy as np
@@ -38,7 +39,7 @@ class DiseaseModel(Machine):
         return {
             f"{self.name}": {
                 "data_sources": {
-                    "cause_specific_mortality_rate": "self::load_cause_specific_mortality_rate"
+                    "cause_specific_mortality_rate": self.load_cause_specific_mortality_rate,
                 },
             },
         }
@@ -79,16 +80,35 @@ class DiseaseModel(Machine):
         initial_state: Optional[BaseDiseaseState] = None,
         get_data_functions: Optional[Dict[str, Callable]] = None,
         cause_type: str = "cause",
+        states: Iterable[BaseDiseaseState] = (),
+        residual_state: BaseDiseaseState | None = None,
         **kwargs,
     ):
-        super().__init__(cause, **kwargs)
+        super().__init__(cause, states=states, **kwargs)
         self.cause = cause
         self.cause_type = cause_type
 
         if initial_state is not None:
-            self.initial_state = initial_state.state_id
+            warnings.warn(
+                "In the future, the 'initial_state' argument to DiseaseModel"
+                " will be used to initialize all simulants into that state. To"
+                " retain the current behavior of defining a residual state, use"
+                " the 'residual_state' argument.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+
+            if residual_state:
+                raise DiseaseModelError(
+                    "A DiseaseModel cannot be initialized with both"
+                    " 'initial_state and 'residual_state'."
+                )
+
+            self.residual_state = initial_state.state_id
+        elif residual_state is not None:
+            self.residual_state = residual_state.state_id
         else:
-            self.initial_state = self._get_default_initial_state()
+            self.residual_state = self._get_default_residual_state()
 
         self._get_data_functions = (
             get_data_functions if get_data_functions is not None else {}
@@ -135,7 +155,7 @@ class DiseaseModel(Machine):
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
         population = self.population_view.subview(["age", "sex"]).get(pop_data.index)
 
-        assert self.initial_state in {s.state_id for s in self.states}
+        assert self.residual_state in {s.state_id for s in self.states}
 
         if pop_data.user_data["sim_state"] == "setup":  # simulation start
             if self.configuration_age_start != self.configuration_age_end != 0:
@@ -176,7 +196,7 @@ class DiseaseModel(Machine):
             )
         else:
             condition_column = pd.Series(
-                self.initial_state, index=population.index, name=self.state_column
+                self.residual_state, index=population.index, name=self.state_column
             )
         self.population_view.update(condition_column)
 
@@ -197,7 +217,7 @@ class DiseaseModel(Machine):
     # Helper functions #
     ####################
 
-    def _get_default_initial_state(self):
+    def _get_default_residual_state(self):
         susceptible_states = [s for s in self.states if isinstance(s, SusceptibleState)]
         if len(susceptible_states) != 1:
             raise DiseaseModelError("Disease model must have exactly one SusceptibleState.")
@@ -219,7 +239,7 @@ class DiseaseModel(Machine):
         weights = np.array(weights).T
         weights_bins = np.cumsum(weights, axis=1)
 
-        state_names = [s.state_id for s in states] + [self.initial_state]
+        state_names = [s.state_id for s in states] + [self.residual_state]
 
         return state_names, weights_bins
 

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health/disease/special_disease.py

@@ -14,7 +14,6 @@ from typing import Any, Dict, List, Optional
 
 import pandas as pd
 from vivarium import Component
-from vivarium.framework.engine import Builder
 from vivarium.framework.event import Event
 from vivarium.framework.population import SimulantData
 from vivarium.framework.values import list_combiner, union_post_processor
@@ -101,8 +100,8 @@ class RiskAttributableDisease(Component):
             self.name: {
                 "data_sources": {
                     "raw_disability_weight": f"{self.cause}.disability_weight",
-                    "cause_specific_mortality_rate": "self::load_cause_specific_mortality_rate_data",
-                    "excess_mortality_rate": "self::load_excess_mortality_rate_data",
+                    "cause_specific_mortality_rate": self.load_cause_specific_mortality_rate_data,
+                    "excess_mortality_rate": self.load_excess_mortality_rate_data,
                     "population_attributable_fraction": 0,
                 },
                 "threshold": None,

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health/disease/state.py

@@ -282,11 +282,11 @@ class DiseaseState(BaseDiseaseState):
         return {
             f"{self.name}": {
                 "data_sources": {
-                    "prevalence": "self::load_prevalence",
-                    "birth_prevalence": "self::load_birth_prevalence",
-                    "dwell_time": "self::load_dwell_time",
-                    "disability_weight": "self::load_disability_weight",
-                    "excess_mortality_rate": "self::load_excess_mortality_rate",
+                    "prevalence": self.load_prevalence,
+                    "birth_prevalence": self.load_birth_prevalence,
+                    "dwell_time": self.load_dwell_time,
+                    "disability_weight": self.load_disability_weight,
+                    "excess_mortality_rate": self.load_excess_mortality_rate,
                 },
             },
         }

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health/disease/transition.py

@@ -43,7 +43,7 @@ class RateTransition(Transition):
         return {
             f"{self.name}": {
                 "data_sources": {
-                    "transition_rate": "self::load_transition_rate",
+                    "transition_rate": self.load_transition_rate,
                 },
             },
         }
@@ -156,7 +156,7 @@ class ProportionTransition(Transition):
         return {
             f"{self.name}": {
                 "data_sources": {
-                    "proportion": "self::load_proportion",
+                    "proportion": self.load_proportion,
                 },
             },
         }

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health/plugins/parser.py

@@ -9,7 +9,7 @@ that can parse configurations of components specific to the Vivarium Public
 Health package.
 
 """
-
+import warnings
 from importlib import import_module
 from typing import Any, Callable, Dict, List, Optional, Union
 
@@ -56,11 +56,13 @@ class CausesConfigurationParser(ComponentConfigurationParser):
     DEFAULT_MODEL_CONFIG = {
         "model_type": f"{DiseaseModel.__module__}.{DiseaseModel.__name__}",
         "initial_state": None,
+        "residual_state": None,
     }
     """Default cause model configuration if it's not explicitly specified.
     
-    If the initial state is not specified, the cause  model must have a state 
-    named 'susceptible'.
+    Initial state and residual state cannot both be provided. If neither initial
+    state nor residual state has been specified, the cause  model must have a
+    state named 'susceptible'.
     """
 
     DEFAULT_STATE_CONFIG = {
@@ -104,7 +106,7 @@ class CausesConfigurationParser(ComponentConfigurationParser):
             causes:
                 cause_1:
                     model_type: vivarium_public_health.disease.DiseaseModel
-                    initial_state: susceptible
+                    residual_state: susceptible
                     states:
                         susceptible:
                             cause_type: cause
@@ -247,11 +249,13 @@ class CausesConfigurationParser(ComponentConfigurationParser):
                 )
 
             model_type = import_by_path(cause_config.model_type)
-            initial_state = states.get(cause_config.initial_state, None)
+            residual_state = states.get(
+                cause_config.residual_state, states.get(cause_config.initial_state, None)
+            )
             model = model_type(
                 cause_name,
-                initial_state=initial_state,
                 states=list(states.values()),
+                residual_state=residual_state,
                 get_data_functions=data_sources,
             )
             cause_models.append(model)
@@ -403,7 +407,14 @@ class CausesConfigurationParser(ComponentConfigurationParser):
     # Validation methods #
     ######################
 
-    _CAUSE_KEYS = {"model_type", "initial_state", "states", "transitions", "data_sources"}
+    _CAUSE_KEYS = {
+        "model_type",
+        "initial_state",
+        "states",
+        "transitions",
+        "data_sources",
+        "residual_state",
+    }
     _STATE_KEYS = {
         "state_type",
         "cause_type",
@@ -535,11 +546,28 @@ class CausesConfigurationParser(ComponentConfigurationParser):
             )
         else:
             initial_state = cause_config.get("initial_state", None)
-            if initial_state is not None and initial_state not in states_config:
+            residual_state = cause_config.get("residual_state", None)
+            if initial_state is not None:
+                warnings.warn(
+                    "In the future, the 'initial_state' cause configuration will"
+                    " be used to initialize all simulants into that state. To"
+                    " retain the current behavior of defining a residual state,"
+                    " use the 'residual_state' cause configuration.",
+                    DeprecationWarning,
+                    stacklevel=2,
+                )
+                if residual_state is None:
+                    residual_state = initial_state
+                else:
+                    error_messages.append(
+                        "A cause may not have both 'initial_state and"
+                        " 'residual_state' configurations."
+                    )
+
+            if residual_state is not None and residual_state not in states_config:
                 error_messages.append(
-                    f"Initial state '{cause_config['initial_state']}' for cause "
-                    f"'{cause_name}' must be present in the states for cause "
-                    f"'{cause_name}."
+                    f"Residual state '{residual_state}' for cause '{cause_name}'"
+                    f" must be present in the states for cause '{cause_name}."
                 )
             for state_name, state_config in states_config.items():
                 error_messages += self._validate_state(cause_name, state_name, state_config)

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health/population/mortality.py

@@ -105,7 +105,7 @@ class Mortality(Component):
             "mortality": {
                 "data_sources": {
                     "all_cause_mortality_rate": "cause.all_causes.cause_specific_mortality_rate",
-                    "unmodeled_cause_specific_mortality_rate": "self::load_unmodeled_csmr",
+                    "unmodeled_cause_specific_mortality_rate": self.load_unmodeled_csmr,
                     "life_expectancy": "population.theoretical_minimum_risk_life_expectancy",
                 },
                 "unmodeled_causes": [],

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.11
+Version: 3.1.1
 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>=3.0.3
+Requires-Dist: vivarium>=3.2.0
 Requires-Dist: layered_config_tree>=1.0.1
 Requires-Dist: loguru
 Requires-Dist: numpy<2.0.0

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/src/vivarium_public_health.egg-info/requires.txt

@@ -1,4 +1,4 @@
-vivarium>=3.0.3
+vivarium>=3.2.0
 layered_config_tree>=1.0.1
 loguru
 numpy<2.0.0

{vivarium_public_health-3.0.11 → vivarium_public_health-3.1.1}/tests/plugins/test_parser.py

@@ -1,7 +1,6 @@
 import dataclasses
 from typing import Any, Dict, List, NamedTuple, Tuple, Type
 
-import numpy as np
 import pytest
 import yaml
 from layered_config_tree import LayeredConfigTree
@@ -259,7 +258,7 @@ SIR_MODEL_CONFIG = {
 COMPLEX_MODEL_CONFIG = {
     COMPLEX_MODEL: {
         "model_type": "tests.plugins.test_parser.ComplexModel",
-        "initial_state": STATES.COMPLEX_INFECTED_1.name,
+        "residual_state": STATES.COMPLEX_INFECTED_1.name,
         "data_sources": {"cause_specific_mortality_rate": COMPLEX_MODEL_CSMR},
         "states": {
             STATES.COMPLEX_INFECTED_1.name: {
@@ -541,7 +540,7 @@ def test_disease_model(
 ):
     model = sim_components[model_name]
     assert isinstance(model, expected_model_type)
-    assert model.initial_state == expected_initial_state
+    assert model.residual_state == expected_initial_state
 
     assert model.lookup_tables["cause_specific_mortality_rate"].data == expected_csmr
 

vivarium_public_health-3.0.11/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "3.0.11"