vivarium-public-health 3.0.3__tar.gz → 3.0.5__tar.gz

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/.github/workflows/build.yml

@@ -51,8 +51,9 @@ jobs:
           cat ../vivarium_build_utils/install_dependency_branch.sh
           echo ""
           echo "----------------------------------------"
-          sh ../vivarium_build_utils/install_dependency_branch.sh layered_config_tree ${branch_name}
-          sh ../vivarium_build_utils/install_dependency_branch.sh vivarium ${branch_name}
+          sh ../vivarium_build_utils/install_dependency_branch.sh layered_config_tree ${branch_name} github
+          sh ../vivarium_build_utils/install_dependency_branch.sh vivarium ${branch_name} github
+          sh ../vivarium_build_utils/install_dependency_branch.sh risk_distributions ${branch_name} github
       - name: print environment values
         run: |
           cat $GITHUB_ENV

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/.gitignore

@@ -112,3 +112,6 @@ src/vivarium_public_health/_version.py
 
 # FuzzyChecker diagnostics csv
 tests/proportion_test_diagnostics.csv
+
+# macOS
+*.DS_Store

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/CHANGELOG.rst

@@ -1,10 +1,21 @@
-**3.0.3- 08/20/24**
+**3.0.5 - 08/29/24**
+
+ - Add missing results module-level docstrings
+ - Strengthen the SimpleCause docstring
+ - Rename the SimpleCause class method
+
+**3.0.4 - 08/28/24**
+
+ - Strengthen results docstrings and clean up others throughout
+ - Add mention of NonLogLinearRiskEffect class to risk exposure tutorial
+
+**3.0.3 - 08/20/24**
 
  - Use external script to find matching dependency branches
  - Fix bug when excluding all but one causes of disability from results
  - Update FertilityAgeSpecificRates for new data format of age specific fertility rates
 
-**3.0.2- 08/19/24**
+**3.0.2 - 08/19/24**
 
  - Parameterize the script to find matching dependency branches
 

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/Jenkinsfile

@@ -52,9 +52,6 @@ pipeline {
         script {
           // Use the name of the branch in the build name
           currentBuild.displayName = "#${BUILD_NUMBER} ${GIT_BRANCH}"
-
-          // Tell BitBucket that a build has started.
-          notifyBitbucket()
         }
       }
     }
@@ -139,7 +136,7 @@ pipeline {
 
             stage("Install Package") {
               steps {
-                sh "${ACTIVATE} && make install \"ARGS=${GIT_BRANCH}\""
+                sh "${ACTIVATE} && make install"
               }
             }
 
@@ -198,16 +195,21 @@ pipeline {
               sh "rm -rf ${CONDA_ENV_PATH}"
               // Delete the workspace directory.
               deleteDir()
-              // Tell BitBucket whether the build succeeded or failed.
-              script {
-                notifyBitbucket()
-              }
             }
             failure {
-              slackSend channel: "#${params.SLACK_TO}",
-                        message: ":x: JOB FAILURE: $JOB_NAME - $BUILD_ID\n\n${BUILD_URL}console\n\n<!channel>",
-                        teamDomain: "ihme",
-                        tokenCredentialId: "slack"
+              script {
+                if (env.BRANCH == "main") {
+                  channelName = "simsci-ci-status"
+                } else {
+                  channelName = "simsci-ci-status-test"
+                }
+              }
+              // TODO: DM the developer instead of the slack channel
+              echo "This build failed on ${GIT_BRANCH}. Sending a failure message to Slack."
+              slackSend channel: "#${channelName}",
+                          message: ":x: JOB FAILURE: $JOB_NAME - $BUILD_ID\n\n${BUILD_URL}console\n\n<!channel>",
+                          teamDomain: "ihme",
+                          tokenCredentialId: "slack"
             }
             success {
               script {

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/Makefile

@@ -57,11 +57,22 @@ build-env: # Make a new conda environment
 install: # Install setuptools, install this package in editable mode
 	pip install --upgrade pip setuptools
 	pip install -e .[DEV]
-	@echo "Checking if the vivarium repository has the branch $(GIT_BRANCH)..."
-	@$(eval BRANCH_EXISTS=$(shell curl -s https://api.github.com/repos/ihmeuw/vivarium/branches | grep -q '"name": "$(GIT_BRANCH)"' && echo "yes" || echo "no"))
-	@if [ "$(BRANCH_EXISTS)" = "yes" ]; then \
-		pip install git+https://github.com/ihmeuw/vivarium@${GIT_BRANCH}; \
+	@cd ..
+	@echo "----------------------------------------"
+	@if [ ! -d "vivarium_build_utils" ]; then \
+		# Clone the build utils repo if it doesn't exist. \
+		git clone https://github.com/ihmeuw/vivarium_build_utils.git; \
+	else \
+		echo "vivarium_build_utils already exists. Skipping clone."; \
 	fi
+	@echo "Contents of install_dependency_branch.sh"
+	@echo "----------------------------------------"
+	@cat vivarium_build_utils/install_dependency_branch.sh
+	@echo ""
+	@echo "----------------------------------------"
+	@sh vivarium_build_utils/install_dependency_branch.sh vivarium ${GIT_BRANCH} jenkins
+	@sh vivarium_build_utils/install_dependency_branch.sh layered_config_tree ${GIT_BRANCH} jenkins
+	@sh vivarium_build_utils/install_dependency_branch.sh risk_distributions ${GIT_BRANCH} jenkins
 
 format: setup.py pyproject.toml $(MAKE_SOURCES) # Run the code formatter and import sorter
 	black $(LOCATIONS)

{vivarium_public_health-3.0.3/src/vivarium_public_health.egg-info → vivarium_public_health-3.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.3
+Version: 3.0.5
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers

vivarium_public_health-3.0.5/docs/source/api_reference/results/simple_cause.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.results.simple_cause

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/docs/source/tutorials/risk_exposure.rst

@@ -2,13 +2,16 @@
 Non-standard Risk Exposure and Effect Models
 ============================================
 
-:mod:`vivarium_public_health` provides two components for modeling the impact
+:mod:`vivarium_public_health` provides three components for modeling the impact
 of some health attributes on others:
 
 - :class:`~vivarium_public_health.risks.base_risk.Risk`: Model of the
   underlying exposure based on a continuous or categorical distribution.
 - :class:`~vivarium_public_health.risks.effect.RiskEffect`: Model of the
   impact of different exposure levels on another health attribute.
+- :class:`~vivarium_public_health.risks.effect.NonLogLinearRiskEffect`: 
+  Special-case risk effect model where the risk factors are parameterized
+  by exposure levels.
 
 The standard model is to think of exposure to environmental, metabolic, and
 behavioral risk factors and their impact on disease incidence rates. However,
@@ -16,10 +19,11 @@ we've found many situations to extend this model to other attributes, such as
 interventions and their impacts on other risks, diseases, or mortality itself.
 
 In order to support these extended models, we've made the
-:class:`~vivarium_public_health.risks.base_risk.Risk` and
-:class:`~vivarium_public_health.risks.effect.RiskEffect` components
+:class:`~vivarium_public_health.risks.base_risk.Risk`, 
+:class:`~vivarium_public_health.risks.effect.RiskEffect`, and
+:class:`~vivarium_public_health.risks.effect.NonLogLinearRiskEffect` components
 configurable. This tutorial explains the various configuration options you can
-use with these two components.
+use with these components.
 
 .. contents:
    :local:
@@ -29,7 +33,7 @@ Exposure Models
 ---------------
 
 We model exposure using the
-:class:`~vivarium_public_health.risks.base_risk.Risk` component.
+:class:`~vivarium_public_health.risks.base_risk.Risk` or component.
 Consider its configuration options:
 
 - ``"exposure"``: This option represents the exposure data source. It defaults
@@ -217,12 +221,22 @@ Effect Models
 -------------
 
 Non-standard effect models can **only** be used with dichotomous exposure
-models (models where someone is either exposed or not exposed. The available
+models (models where someone is either exposed or not exposed). The available
 configuration options all correspond to generating a relative risk for
 the exposed population from a set of parameters.
 
 We model exposure effects using the
-:class:`~vivarium_public_health.risks.effect.RiskEffect` component.
+:class:`~vivarium_public_health.risks.effect.RiskEffect` or
+:class:`~vivarium_public_health.risks.effect.NonLogLinearRiskEffect` components.
+
+For this tutorial, we'll focus on the ``RiskEffect`` component. The
+``NonLogLinearRiskEffect`` component is a special case of the ``RiskEffect``
+component where the risk factors are parameterized by exposure levels.
+
+.. todo::
+  
+   Add details on how to use the ``NonLogLinearRiskEffect`` component.
+
 Let's look at its configuration options:
 
 - ``"relative_risk"``: Option for specifying a relative risk value directly.

vivarium_public_health-3.0.5/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.0.5"

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/src/vivarium_public_health/disease/state.py

@@ -103,9 +103,8 @@ class BaseDiseaseState(State):
         ----------
         index
             An iterable of integer labels for the simulants.
-        event_time : pandas.Timestamp
+        event_time
             The time at which this transition occurs.
-
         """
         pop = self.population_view.get(index)
         pop[self.event_time_column] = event_time
@@ -141,13 +140,13 @@ class BaseDiseaseState(State):
             The end state after the transition.
 
         get_data_functions
-            map from transition type to the function to pull that transition's data
+            Map from transition type to the function to pull that transition's data.
         triggered
+            The trigger for the transition
 
 
         Returns
         -------
-        RateTransition
             The created transition object.
         """
         transition = RateTransition(self, output, get_data_functions, triggered)
@@ -157,7 +156,7 @@ class BaseDiseaseState(State):
     def add_proportion_transition(
         self,
         output: "BaseDiseaseState",
-        get_data_functions: Dict[str, Callable] = None,
+        get_data_functions: Optional[Dict[str, Callable]] = None,
         triggered=Trigger.NOT_TRIGGERED,
     ) -> ProportionTransition:
         """Builds a ProportionTransition from this state to the given state.
@@ -166,13 +165,13 @@ class BaseDiseaseState(State):
         ----------
         output
             The end state after the transition.
-
         get_data_functions
-            map from transition type to the function to pull that transition's data
+            Map from transition type to the function to pull that transition's data.
+        triggered
+            The trigger for the transition.
 
         Returns
         -------
-        RateTransition
             The created transition object.
         """
         if "proportion" not in get_data_functions:
@@ -302,8 +301,8 @@ class DiseaseState(BaseDiseaseState):
         allow_self_transition: bool = False,
         side_effect_function: Optional[Callable] = None,
         cause_type: str = "cause",
-        get_data_functions: Dict[str, Callable] = None,
-        cleanup_function: Callable = None,
+        get_data_functions: Optional[Dict[str, Callable]] = None,
+        cleanup_function: Optional[Callable] = None,
     ):
         """
         Parameters
@@ -312,14 +311,16 @@ class DiseaseState(BaseDiseaseState):
             The name of this state.
         allow_self_transition
             Whether this state allows simulants to remain in the state for
-            multiple time-steps
+            multiple time-steps.
         side_effect_function
             A function to be called when this state is entered.
         cause_type
             The type of cause represented by this state. Either "cause" or "sequela".
         get_data_functions
             A dictionary containing a mapping to functions to retrieve data for
-            various state attributes
+            various state attributes.
+        cleanup_function
+            The cleanup function.
         """
         super().__init__(
             state_id,
@@ -344,7 +345,7 @@ class DiseaseState(BaseDiseaseState):
 
         Parameters
         ----------
-        builder : `engine.Builder`
+        builder
             Interface to several simulation tools.
         """
         super().setup(builder)
@@ -506,9 +507,9 @@ class DiseaseState(BaseDiseaseState):
         ----------
         index
             An iterable of integer labels for the simulants.
-        event_time:
+        event_time
             The time at which this transition occurs.
-        population_view:
+        population_view
             A view of the internal state of the simulation.
         """
         eligible_index = self._filter_for_transition_eligibility(index, event_time)
@@ -528,7 +529,6 @@ class DiseaseState(BaseDiseaseState):
 
         Returns
         -------
-        `pandas.Series`
             An iterable of disability weights indexed by the provided `index`.
         """
         disability_weight = pd.Series(0.0, index=index)
@@ -555,8 +555,12 @@ class DiseaseState(BaseDiseaseState):
         ----------
         index
             An iterable of integer labels for the simulants.
-        rates_df : `pandas.DataFrame`
+        rates_df
+            A DataFrame of mortality rates.
 
+        Returns
+        -------
+            The modified DataFrame of mortality rates.
         """
         rate = self.excess_mortality_rate(index, skip_post_processor=True)
         rates_df[self.state_id] = rate
@@ -599,17 +603,18 @@ class DiseaseState(BaseDiseaseState):
         infected_at = current_time - pd.to_timedelta(infected_at, unit="D")
         return infected_at
 
-    def _filter_for_transition_eligibility(self, index, event_time):
+    def _filter_for_transition_eligibility(self, index, event_time) -> pd.Index:
         """Filter out all simulants who haven't been in the state for the prescribed dwell time.
 
         Parameters
         ----------
         index
             An iterable of integer labels for the simulants.
+        event_time
+            The time at which this transition occurs.
 
         Returns
         -------
-        pd.Index
             A filtered index of the simulants.
         """
         population = self.population_view.get(index, query='alive == "alive"')

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/src/vivarium_public_health/mslt/delay.py

@@ -19,8 +19,7 @@ from vivarium.framework.population import SimulantData
 
 
 class DelayedRisk(Component):
-    """
-    A delayed risk represents an exposure whose impact takes time to come into
+    """A delayed risk represents an exposure whose impact takes time to come into
     effect (e.g., smoking uptake and cessation).
 
     The data required by this component are:
@@ -320,8 +319,7 @@ class DelayedRisk(Component):
     ########################
 
     def on_initialize_simulants(self, pop_data: SimulantData) -> None:
-        """
-        Define the initial distribution of the population across the bins, in
+        """Define the initial distribution of the population across the bins, in
         both the BAU and the intervention scenario.
         """
         # Set all bins to zero, in order to create the required columns.
@@ -364,7 +362,6 @@ class DelayedRisk(Component):
         - New exposures
         - Cessation of exposure
         - Increased duration of time since exposure
-
         """
         if self.clock().year == self.start_year:
             return
@@ -540,6 +537,17 @@ def pivot_load(builder: Builder, entity_key: str) -> pd.DataFrame:
     Performs a long to wide conversion if dataframe has an index column
     named 'measure'.
 
+    Parameters
+    ----------
+    builder
+        The builder object for the simulation.
+    entity_key
+        The key for the entity to be loaded.
+
+    Returns
+    -------
+    pd.DataFrame
+        The loaded data and potentially pivoted data.
     """
     data = builder.data.load(entity_key)
 

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/src/vivarium_public_health/mslt/disease.py

@@ -19,7 +19,8 @@ from vivarium.framework.population import SimulantData
 
 
 class AcuteDisease(Component):
-    """
+    """This component characterises an acute disease.
+
     An acute disease has a sufficiently short duration, relative to the
     time-step size, that it is not meaningful to talk about prevalence.
     Instead, it simply contributes an excess mortality rate, and/or a
@@ -32,10 +33,18 @@ class AcuteDisease(Component):
 
     where `<disease>` is the name as provided to the constructor.
 
-    Parameters
+    Attributes
     ----------
     disease
         The disease name (referred to as `<disease>` here).
+    excess_mortality
+        The excess mortality rate for the disease.
+    int_excess_mortality
+        The excess mortality rate for the disease in the intervention scenario.
+    disability_rate
+        The years lost due to disability (YLD) rate for the disease.
+    int_disability_rate
+        The YLD rate for the disease in the intervention scenario.
 
     """
 
@@ -77,16 +86,14 @@ class AcuteDisease(Component):
     ##################################
 
     def mortality_adjustment(self, index, mortality_rate):
-        """
-        Adjust the all-cause mortality rate in the intervention scenario, to
+        """Adjust the all-cause mortality rate in the intervention scenario, to
         account for any change in prevalence (relative to the BAU scenario).
         """
         delta = self.int_excess_mortality(index) - self.excess_mortality(index)
         return mortality_rate + delta
 
     def disability_adjustment(self, index, yld_rate):
-        """
-        Adjust the years lost due to disability (YLD) rate in the intervention
+        """Adjust the years lost due to disability (YLD) rate in the intervention
         scenario, to account for any change in prevalence (relative to the BAU
         scenario).
         """
@@ -106,10 +113,28 @@ class Disease(Component):
 
     where `<disease>` is the name as provided to the constructor.
 
-    Parameters
+    Attributes
     ----------
     disease
         The disease name (referred to as `<disease>` here).
+    clock
+        The simulation clock.
+    start_year
+        The simulation start year.
+    simplified_equations
+        Whether to use simplified equations for the disease model.
+    incidence
+        The incidence rate for the disease.
+    incidence_intervention
+        The incidence rate for the disease in the intervention scenario.
+    remission
+        The remission rate for the disease.
+    excess_mortality
+        The excess mortality rate for the disease.
+    disability_rate
+        The years lost due to disability (YLD) rate for the disease.
+    initial_prevalence
+        The initial prevalence of the disease.
 
     """
 
@@ -231,9 +256,7 @@ class Disease(Component):
         self.population_view.update(pop)
 
     def on_time_step_prepare(self, event: Event) -> None:
-        """
-        Update the disease status for both the BAU and intervention scenarios.
-        """
+        """Update the disease status for both the BAU and intervention scenarios."""
         # Do not update the disease status in the first year, the initial data
         # describe the disease state at the end of the year.
         if self.clock().year == self.start_year:
@@ -356,8 +379,7 @@ class Disease(Component):
     ##################################
 
     def mortality_adjustment(self, index, mortality_rate):
-        """
-        Adjust the all-cause mortality rate in the intervention scenario, to
+        """Adjust the all-cause mortality rate in the intervention scenario, to
         account for any change in disease prevalence (relative to the BAU
         scenario).
         """
@@ -387,8 +409,7 @@ class Disease(Component):
         return mortality_rate + delta
 
     def disability_adjustment(self, index, yld_rate):
-        """
-        Adjust the years lost due to disability (YLD) rate in the intervention
+        """Adjust the years lost due to disability (YLD) rate in the intervention
         scenario, to account for any change in disease prevalence (relative to
         the BAU scenario).
         """

{vivarium_public_health-3.0.3 → vivarium_public_health-3.0.5}/src/vivarium_public_health/mslt/intervention.py

@@ -100,9 +100,9 @@ class ModifyDiseaseRate(Component):
 
 
 class ModifyDiseaseIncidence(ModifyDiseaseRate):
-    """
-    Interventions that modify a disease incidence rate, based on a PIF lookup
+    """Interventions that modify a disease incidence rate, based on a PIF lookup
     table.
+
     """
 
     def __init__(self, intervention: str, disease: str):
@@ -110,9 +110,9 @@ class ModifyDiseaseIncidence(ModifyDiseaseRate):
 
 
 class ModifyDiseaseMortality(ModifyDiseaseRate):
-    """
-    Interventions that modify a disease fatality rate, based on a PIF lookup
+    """Interventions that modify a disease fatality rate, based on a PIF lookup
     table.
+
     """
 
     def __init__(self, intervention: str, disease: str):
@@ -120,9 +120,9 @@ class ModifyDiseaseMortality(ModifyDiseaseRate):
 
 
 class ModifyDiseaseMorbidity(ModifyDiseaseRate):
-    """
-    Interventions that modify a disease disability rate, based on a PIF lookup
+    """Interventions that modify a disease disability rate, based on a PIF lookup
     table.
+
     """
 
     def __init__(self, intervention: str, disease: str):
@@ -130,10 +130,13 @@ class ModifyDiseaseMorbidity(ModifyDiseaseRate):
 
 
 class ModifyAcuteDiseaseIncidence(Component):
-    """
-    Interventions that modify an acute disease incidence rate.
-    Note that this intervention will simply modify both the disability rate
+    """Interventions that modify an acute disease incidence rate.
+
+    Notes
+    -----
+    This intervention will simply modify both the disability rate
     and the mortality rate for the chosen acute disease.
+
     """
 
     ##############