vivarium-public-health 2.1.1__tar.gz → 2.1.3__tar.gz

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/.github/workflows/build.yml

@@ -63,7 +63,7 @@ jobs:
           isort . --check --verbose --only-modified --diff
       - name: Test
         run: |
-          if github.event_name == 'schedule'; then
+          if "${{ github.event_name == 'schedule' }}"; then
             pytest --runslow ./tests
           else
             pytest ./tests
@@ -74,3 +74,22 @@ jobs:
       - name: Doctest
         run: |
           make doctest -C docs/
+      - name: Send mail
+        # Notify when cron job fails
+        if: (github.event_name == 'schedule' && failure())
+        uses: dawidd6/action-send-mail@v2
+        with:
+          # mail server settings
+          server_address: smtp.gmail.com
+          server_port: 465
+          # user credentials
+          username: ${{ secrets.NOTIFY_EMAIL }}
+          password: ${{ secrets.NOTIFY_PASSWORD }}
+          # email subject
+          subject: ${{ github.job }} job of ${{ github.repository }} has ${{ job.status }}
+          # email body as text
+          body: ${{ github.job }} job in worflow ${{ github.workflow }} of ${{ github.repository }} has ${{ job.status }}
+          # comma-separated string, send email to
+          to: uw_ihme_simulationscience@uw.edu
+          # from email name
+          from: Vivarium Notifications

vivarium_public_health-2.1.3/.github/workflows/deploy.yml

@@ -0,0 +1,49 @@
+name: deploy
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python --version
+          python -m pip install --upgrade pip
+          pip install setuptools wheel build
+      - name: Test
+        run: |
+          pip install .[test]
+          pytest --runslow ./tests
+      - name: Build
+        run: python -m build
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1
+      - name: Send mail
+        # Notify when cron job fails
+        if: failure()
+        uses: dawidd6/action-send-mail@v2
+        with:
+          # mail server settings
+          server_address: smtp.gmail.com
+          server_port: 465
+          # user credentials
+          username: ${{ secrets.NOTIFY_EMAIL }}
+          password: ${{ secrets.NOTIFY_PASSWORD }}
+          # email subject
+          subject: ${{ github.job }} job of ${{ github.repository }} has ${{ job.status }}
+          # email body as text
+          body: ${{ github.job }} job in worflow ${{ github.workflow }} of ${{ github.repository }} has ${{ job.status }}
+          # comma-separated string, send email to
+          to: uw_ihme_simulationscience@uw.edu
+          # from email name
+          from: Vivarium Notifications

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**2.1.3 - 01/09/24**
+
+ - Update PyPI to 2FA with trusted publisher
+
+**2.1.2 - 12/21/23**
+
+ - Fix tests failing due to Vivarium 2.3.0 release
+
 **2.1.1 - 10/13/23**
 
  - Perform actions in DiseaseState setup using class methods rather than hardcoding to allow for cleaner subclassing

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 2.1.1
+Version: 2.1.3
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -25,10 +25,32 @@ Classifier: Topic :: Scientific/Engineering :: Mathematics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
+License-File: LICENSE.txt
+Requires-Dist: vivarium>=2.0.0
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: tables
+Requires-Dist: risk_distributions>=2.0.11
 Provides-Extra: docs
+Requires-Dist: sphinx<7.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: IPython; extra == "docs"
+Requires-Dist: matplotlib; extra == "docs"
 Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: hypothesis; extra == "test"
 Provides-Extra: dev
-License-File: LICENSE.txt
+Requires-Dist: sphinx<7.0; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: sphinx-click; extra == "dev"
+Requires-Dist: IPython; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
+Requires-Dist: hypothesis; extra == "dev"
 
 Vivarium Public Health
 ======================

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/docs/nitpick-exceptions

@@ -16,4 +16,6 @@ py:class Logger
 # TODO: Need to revisit this. Nitpicking here to avoid failing everywhere
 py:class Builder
 py:class SimulantData
-py:class Event
+py:class Event
+py:class LookupTable
+py:class Pipeline

vivarium_public_health-2.1.3/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "2.1.3"

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/src/vivarium_public_health/disease/state.py

@@ -373,6 +373,20 @@ class DiseaseState(BaseDiseaseState):
     def get_prevalence(
         self, builder: Builder, prevalence_data: LookupTableData
     ) -> LookupTable:
+        """Builds a LookupTable for the prevalence of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        prevalence_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the prevalence of this state.
+        """
         return builder.lookup.build_table(
             prevalence_data, key_columns=["sex"], parameter_columns=["age", "year"]
         )
@@ -386,6 +400,21 @@ class DiseaseState(BaseDiseaseState):
     def get_birth_prevalence(
         self, builder: Builder, birth_prevalence_data: LookupTableData
     ) -> LookupTable:
+        """
+        Builds a LookupTable for the birth prevalence of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        birth_prevalence_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the birth prevalence of this state.
+        """
         return builder.lookup.build_table(
             birth_prevalence_data, key_columns=["sex"], parameter_columns=["year"]
         )
@@ -434,6 +463,21 @@ class DiseaseState(BaseDiseaseState):
     def get_base_disability_weight(
         self, builder: Builder, disability_weight_data: LookupTableData
     ) -> LookupTable:
+        """
+        Builds a LookupTable for the base disability weight of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        disability_weight_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the disability weight of this state.
+        """
         return builder.lookup.build_table(
             disability_weight_data, key_columns=["sex"], parameter_columns=["age", "year"]
         )
@@ -458,6 +502,21 @@ class DiseaseState(BaseDiseaseState):
     def get_base_excess_mortality_rate(
         self, builder: Builder, excess_mortality_data: LookupTableData
     ) -> LookupTable:
+        """
+        Builds a LookupTable for the base excess mortality rate of this state.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        excess_mortality_data
+            The data to use to build the LookupTable.
+
+        Returns
+        -------
+        LookupTable
+            The LookupTable for the base excess mortality rate of this state.
+        """
         return builder.lookup.build_table(
             excess_mortality_data, key_columns=["sex"], parameter_columns=["age", "year"]
         )

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/src/vivarium_public_health/population/mortality.py

@@ -128,6 +128,19 @@ class Mortality(Component):
 
     # noinspection PyMethodMayBeStatic
     def get_all_cause_mortality_rate(self, builder: Builder) -> Union[LookupTable, Pipeline]:
+        """
+        Load all cause mortality rate data and build a lookup table or pipeline.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        Union[LookupTable, Pipeline]
+            A lookup table or pipeline returning the all cause mortality rate.
+        """
         acmr_data = builder.data.load("cause.all_causes.cause_specific_mortality_rate")
         return builder.lookup.build_table(
             acmr_data, key_columns=["sex"], parameter_columns=["age", "year"]
@@ -135,6 +148,19 @@ class Mortality(Component):
 
     # noinspection PyMethodMayBeStatic
     def get_life_expectancy(self, builder: Builder) -> Union[LookupTable, Pipeline]:
+        """
+        Load life expectancy data and build a lookup table or pipeline.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        Union[LookupTable, Pipeline]
+            A lookup table or pipeline returning the life expectancy.
+        """
         life_expectancy_data = builder.data.load(
             "population.theoretical_minimum_risk_life_expectancy"
         )
@@ -142,6 +168,20 @@ class Mortality(Component):
 
     # noinspection PyMethodMayBeStatic
     def get_raw_unmodeled_csmr(self, builder: Builder) -> Union[LookupTable, Pipeline]:
+        """
+        Load unmodeled cause specific mortality rate data and build a lookup
+        table or pipeline.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        Union[LookupTable, Pipeline]
+            A lookup table or pipeline returning the unmodeled csmr.
+        """
         unmodeled_causes = builder.configuration.unmodeled_causes
         raw_csmr = 0.0
         for idx, cause in enumerate(unmodeled_causes):

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/src/vivarium_public_health/risks/effect.py

@@ -121,12 +121,40 @@ class RiskEffect(Component):
         return builder.value.get_value(self.exposure_pipeline_name)
 
     def get_relative_risk_source(self, builder: Builder) -> LookupTable:
+        """
+        Get the relative risk source for this risk effect model.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        LookupTable
+            A lookup table containing the relative risk data for this risk
+            effect model.
+        """
         relative_risk_data = get_relative_risk_data(builder, self.risk, self.target)
         return builder.lookup.build_table(
             relative_risk_data, key_columns=["sex"], parameter_columns=["age", "year"]
         )
 
     def get_population_attributable_fraction_source(self, builder: Builder) -> LookupTable:
+        """
+        Get the population attributable fraction source for this risk effect model.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        LookupTable
+            A lookup table containing the population attributable fraction data
+            for this risk effect model.
+        """
         paf_data = get_population_attributable_fraction_data(builder, self.risk, self.target)
         return builder.lookup.build_table(
             paf_data, key_columns=["sex"], parameter_columns=["age", "year"]

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/src/vivarium_public_health/treatment/scale_up.py

@@ -127,6 +127,20 @@ class LinearScaleUp(Component):
         return get_endpoint("start"), get_endpoint("end")
 
     def get_scale_up_values(self, builder: Builder) -> Tuple[LookupTable, LookupTable]:
+        """
+        Get the values at the start and end of the scale-up period.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+
+        Returns
+        -------
+        LookupTable
+            A tuple of lookup tables returning the values at the start and end
+            of the scale-up period.
+        """
         scale_up_config = builder.configuration[self.configuration_key]["value"]
 
         def get_endpoint_value(endpoint_type: str) -> LookupTable:
@@ -172,6 +186,23 @@ class LinearScaleUp(Component):
     def get_endpoint_value_from_data(
         self, builder: Builder, endpoint_type: str
     ) -> LookupTable:
+        """
+        Get the value at the start or end of the scale-up period from data.
+
+        Parameters
+        ----------
+        builder
+            Interface to access simulation managers.
+        endpoint_type
+            The type of endpoint to get the value for. Allowed values are
+            "start" and "end".
+
+        Returns
+        -------
+        LookupTable
+            A lookup table returning the value at the start or end of the
+            scale-up period.
+        """
         if endpoint_type == "start":
             endpoint_data = builder.data.load(f"{self.treatment}.exposure")
         elif endpoint_type == "end":

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
-Name: vivarium-public-health
-Version: 2.1.1
+Name: vivarium_public_health
+Version: 2.1.3
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -25,10 +25,32 @@ Classifier: Topic :: Scientific/Engineering :: Mathematics
 Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
+License-File: LICENSE.txt
+Requires-Dist: vivarium>=2.0.0
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: tables
+Requires-Dist: risk_distributions>=2.0.11
 Provides-Extra: docs
+Requires-Dist: sphinx<7.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: IPython; extra == "docs"
+Requires-Dist: matplotlib; extra == "docs"
 Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-mock; extra == "test"
+Requires-Dist: hypothesis; extra == "test"
 Provides-Extra: dev
-License-File: LICENSE.txt
+Requires-Dist: sphinx<7.0; extra == "dev"
+Requires-Dist: sphinx-rtd-theme; extra == "dev"
+Requires-Dist: sphinx-click; extra == "dev"
+Requires-Dist: IPython; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-mock; extra == "dev"
+Requires-Dist: hypothesis; extra == "dev"
 
 Vivarium Public Health
 ======================

{vivarium_public_health-2.1.1 → vivarium_public_health-2.1.3}/tests/disease/test_disease.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pandas as pd
 import pytest
-from vivarium import InteractiveContext
+from vivarium import Component, InteractiveContext
 from vivarium.framework.state_machine import Transition
 from vivarium.framework.utilities import from_yearly
 from vivarium.testing_utilities import TestPopulation, build_table, metadata
@@ -188,7 +188,7 @@ def test_prevalence_single_state_with_migration(
     assert np.isclose(
         get_test_prevalence(simulation, "sick"), test_prevalence_level, 0.01
     ), error_message
-    simulation._clock.step_forward()
+    simulation.step()
     assert np.isclose(
         get_test_prevalence(simulation, "sick"), test_prevalence_level, 0.01
     ), error_message
@@ -199,7 +199,7 @@ def test_prevalence_single_state_with_migration(
     assert np.isclose(
         get_test_prevalence(simulation, "sick"), test_prevalence_level, 0.01
     ), error_message
-    simulation._clock.step_forward()
+    simulation.step()
     simulation.simulant_creator(
         50000,
         population_configuration={"age_start": 0, "age_end": 5, "sim_state": "time_step"},
@@ -358,11 +358,7 @@ def test_risk_deletion(base_config, base_plugins, disease):
 
     model = DiseaseModel(disease, initial_state=healthy, states=[healthy, sick])
 
-    class PafModifier:
-        @property
-        def name(self):
-            return "paf_modifier"
-
+    class PafModifier(Component):
         def setup(self, builder):
             builder.value.register_value_modifier(
                 "sick.incidence_rate.paf",
@@ -370,7 +366,7 @@ def test_risk_deletion(base_config, base_plugins, disease):
                     build_table(paf, year_start, year_end),
                     key_columns=("sex",),
                     parameter_columns=["age", "year"],
-                    value_columns=None,
+                    value_columns=(),
                 ),
             )
 
@@ -436,7 +432,7 @@ def test_prevalence_birth_prevalence_initial_assignment(base_config, base_plugin
     assert np.isclose(get_test_prevalence(simulation, "with_condition"), 1)
 
     # birth prevalence should be used for assigning initial status to newly-borns on time steps
-    simulation._clock.step_forward()
+    simulation.step()
     simulation.simulant_creator(
         pop_size,
         population_configuration={"age_start": 0, "age_end": 0, "sim_state": "time_step"},
@@ -444,7 +440,7 @@ def test_prevalence_birth_prevalence_initial_assignment(base_config, base_plugin
     assert np.isclose(get_test_prevalence(simulation, "with_condition"), 0.75, 0.01)
 
     # and prevalence should be used for ages not start = end = 0
-    simulation._clock.step_forward()
+    simulation.step()
     simulation.simulant_creator(
         pop_size,
         population_configuration={"age_start": 0, "age_end": 5, "sim_state": "time_step"},
@@ -473,7 +469,7 @@ def test_no_birth_prevalence_initial_assignment(base_config, base_plugins, disea
     assert np.isclose(get_test_prevalence(simulation, "with_condition"), 1)
 
     # with no birth prevalence provided, it should default to 0 for ages start = end = 0
-    simulation._clock.step_forward()
+    simulation.step()
     simulation.simulant_creator(
         1000,
         population_configuration={"age_start": 0, "age_end": 0, "sim_state": "time_step"},
@@ -481,7 +477,7 @@ def test_no_birth_prevalence_initial_assignment(base_config, base_plugins, disea
     assert np.isclose(get_test_prevalence(simulation, "with_condition"), 0.5, 0.01)
 
     # and default to prevalence for ages not start = end = 0
-    simulation._clock.step_forward()
+    simulation.step()
     simulation.simulant_creator(
         1000,
         population_configuration={"age_start": 0, "age_end": 5, "sim_state": "time_step"},

vivarium_public_health-2.1.1/.github/workflows/deploy.yml

@@ -1,31 +0,0 @@
-name: deploy
-
-on:
-  release:
-    types: [published]
-
-jobs:
-  deploy:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-      - name: Install dependencies
-        run: |
-          python --version
-          python -m pip install --upgrade pip
-          pip install setuptools wheel twine
-      - name: Test
-        run: |
-          pip install .[test]
-          pytest --runslow ./tests
-      - name: Build and publish
-        env:
-          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-        run: |
-          python setup.py sdist bdist_wheel
-          twine upload dist/*

vivarium_public_health-2.1.1/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "2.1.1"