vivarium-public-health 2.1.3__tar.gz → 2.2.0__tar.gz

vivarium_public_health-2.2.0/.github/CODEOWNERS

@@ -0,0 +1,2 @@
+# default owners
+* @albrja @collijk @hussain-jafari @patricktnast @rmudambi @stevebachmeier

{vivarium_public_health-2.1.3 → vivarium_public_health-2.2.0}/CHANGELOG.rst

@@ -1,3 +1,12 @@
+**2.2.0 - 02/14/24**
+
+ - Implement CausesConfigurationParser to parse causes configuration into DiseaseModel components
+ - Bugfix assign sex-location-age demographic proportions by year when only one year in dataset
+ 
+**2.1.4 - 01/10/24**
+
+ - Exclude undesirable arguments from the return of `BaseDiseaseState` `name` and `__repr__` methods
+ 
 **2.1.3 - 01/09/24**
 
  - Update PyPI to 2FA with trusted publisher

{vivarium_public_health-2.1.3 → vivarium_public_health-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 2.1.3
+Version: 2.2.0
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -27,6 +27,7 @@ Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
 Requires-Dist: vivarium>=2.0.0
+Requires-Dist: loguru
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: scipy
@@ -42,6 +43,7 @@ Provides-Extra: test
 Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-mock; extra == "test"
 Requires-Dist: hypothesis; extra == "test"
+Requires-Dist: pyyaml; extra == "test"
 Provides-Extra: dev
 Requires-Dist: sphinx<7.0; extra == "dev"
 Requires-Dist: sphinx-rtd-theme; extra == "dev"
@@ -51,6 +53,7 @@ Requires-Dist: matplotlib; extra == "dev"
 Requires-Dist: pytest; extra == "dev"
 Requires-Dist: pytest-mock; extra == "dev"
 Requires-Dist: hypothesis; extra == "dev"
+Requires-Dist: pyyaml; extra == "dev"
 
 Vivarium Public Health
 ======================

vivarium_public_health-2.2.0/docs/source/api_reference/plugins/index.rst

@@ -0,0 +1,11 @@
+===============
+Manager Plugins
+===============
+
+.. automodule:: vivarium_public_health.plugins
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *

vivarium_public_health-2.2.0/docs/source/api_reference/plugins/parser.rst

@@ -0,0 +1 @@
+.. automodule:: vivarium_public_health.plugins.parser

{vivarium_public_health-2.1.3 → vivarium_public_health-2.2.0}/setup.py

@@ -16,6 +16,7 @@ if __name__ == "__main__":
 
     install_requirements = [
         "vivarium>=2.0.0",
+        "loguru",
         "numpy",
         "pandas",
         "scipy",
@@ -29,6 +30,7 @@ if __name__ == "__main__":
         "pytest",
         "pytest-mock",
         "hypothesis",
+        "pyyaml",
     ]
 
     doc_requirements = [

vivarium_public_health-2.2.0/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "2.2.0"

{vivarium_public_health-2.1.3 → vivarium_public_health-2.2.0}/src/vivarium_public_health/disease/state.py

@@ -6,7 +6,7 @@ Disease States
 This module contains tools to manage standard disease states.
 
 """
-from typing import Callable, Dict, List, Optional
+from typing import Any, Callable, Dict, List, Optional
 
 import numpy as np
 import pandas as pd
@@ -82,6 +82,13 @@ class BaseDiseaseState(State):
     # Helper methods #
     ##################
 
+    def get_initialization_parameters(self) -> Dict[str, Any]:
+        """Exclude side effect function and cause type from name and __repr__."""
+        initialization_parameters = super().get_initialization_parameters()
+        del initialization_parameters["side_effect_function"]
+        del initialization_parameters["cause_type"]
+        return initialization_parameters
+
     def get_initial_event_times(self, pop_data: SimulantData) -> pd.DataFrame:
         return pd.DataFrame(
             {self.event_time_column: pd.NaT, self.event_count_column: 0}, index=pop_data.index

vivarium_public_health-2.2.0/src/vivarium_public_health/plugins/__init__.py

@@ -0,0 +1 @@
+from vivarium_public_health.plugins.parser import CausesConfigurationParser