vivarium-public-health 3.0.4__py3-none-any.whl → 3.0.5__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "3.0.4"
+__version__ = "3.0.5"

vivarium_public_health/results/disability.py

@@ -1,7 +1,7 @@
 """
-===================
-Disability Observer
-===================
+====================
+Disability Observers
+====================
 
 This module contains tools for observing years lived with disability (YLDs)
 in the simulation.
@@ -102,7 +102,7 @@ class DisabilityObserver(PublicHealthObserver):
         )
         # Convert to SimpleCause instances and add on all_causes
         causes_of_disability = [
-            SimpleCause.create_from_disease_state(cause) for cause in causes_of_disability
+            SimpleCause.create_from_specific_cause(cause) for cause in causes_of_disability
         ] + [SimpleCause("all_causes", "all_causes", "cause")]
 
         excluded_causes = (

vivarium_public_health/results/disease.py

@@ -1,7 +1,7 @@
 """
-================
-Disease Observer
-================
+=================
+Disease Observers
+=================
 
 This module contains tools for observing disease incidence and prevalence
 in the simulation.

vivarium_public_health/results/mortality.py

@@ -1,7 +1,7 @@
 """
-==================
-Mortality Observer
-==================
+===================
+Mortality Observers
+===================
 
 This module contains tools for observing cause-specific and
 excess mortality in the simulation, including "other causes".
@@ -130,7 +130,7 @@ class MortalityObserver(PublicHealthObserver):
 
         # Convert to SimpleCauses and add on other_causes and not_dead
         self.causes_of_death = [
-            SimpleCause.create_from_disease_state(cause) for cause in causes_of_death
+            SimpleCause.create_from_specific_cause(cause) for cause in causes_of_death
         ] + [
             SimpleCause("not_dead", "not_dead", "cause"),
             SimpleCause("other_causes", "other_causes", "cause"),

vivarium_public_health/results/observer.py

@@ -1,3 +1,13 @@
+"""
+===============
+Basic Observers
+===============
+
+This module contains convenience classes for building concrete observers in
+public health models.
+
+"""
+
 from typing import Callable, List, Optional, Union
 
 import pandas as pd

vivarium_public_health/results/simple_cause.py

@@ -1,12 +1,21 @@
+"""
+============
+Simple Cause
+============
+
+This module contains tools for creating a minimal representation of a cause
+as required by observers.
+
+"""
+
 from dataclasses import dataclass
 
 
 @dataclass
 class SimpleCause:
-    """A simple dataclass to represent the bare minimum information needed
-    for observers, e.g. 'all_causes' as a cause of disability.
+    """A simple dataclass to represent the bare minimum information needed by observers.
 
-    It also includes a class method to convert a provided disease state into a
+    It also includes a class method to convert a provided cause into a
     ``SimpleCause`` instance.
 
     """
@@ -19,6 +28,16 @@ class SimpleCause:
     """The cause type of the cause."""
 
     @classmethod
-    def create_from_disease_state(cls, disease_state: type) -> "SimpleCause":
-        """Create a SimpleCause instance from a"""
-        return cls(disease_state.state_id, disease_state.model, disease_state.cause_type)
+    def create_from_specific_cause(cls, cause: type) -> "SimpleCause":
+        """Create a SimpleCause instance from a more specific cause.
+
+        Parameters
+        ----------
+        cause
+            The cause to be converted into a SimpleCause instance.
+
+        Returns
+        -------
+            A SimpleCause instance.
+        """
+        return cls(cause.state_id, cause.model, cause.cause_type)

{vivarium_public_health-3.0.4.dist-info → vivarium_public_health-3.0.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.4
+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-3.0.4.dist-info → vivarium_public_health-3.0.5.dist-info}/RECORD

@@ -1,6 +1,6 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
-vivarium_public_health/_version.py,sha256=gNoy6uoSQO4ZzowTZAJz3hphzq1F_Y-3X9YrQdb7ppc,22
+vivarium_public_health/_version.py,sha256=3kxZhPRWwAKER8BleEtUBQTUGwcBGPmrbjLu-HEi-hI,22
 vivarium_public_health/utilities.py,sha256=5cl9jjVkOQ1UeXT4DjDMAhaBNNjAsDo-SVJwpv6FDw0,3071
 vivarium_public_health/disease/__init__.py,sha256=RuuiRcvAJfX9WQGt_WZZjxN7Cu3E5rMTmuaRS-UaFPM,419
 vivarium_public_health/disease/model.py,sha256=0WIYDEx-hwlUJp6Zl8m8bUMoWxuVkOWsJvh_YlZiOPs,8234
@@ -24,12 +24,12 @@ vivarium_public_health/population/data_transformations.py,sha256=QVh_63Wwg9BUkaQ
 vivarium_public_health/population/mortality.py,sha256=w7b_TUssHjRcnULdXu7MXKfZBjCrlYWbB94oO3JWogI,10264
 vivarium_public_health/results/__init__.py,sha256=XKuX9HTXUur1kpHM7zuMSnkJxlg-W7eMAPmh8LP9Xp4,281
 vivarium_public_health/results/columns.py,sha256=V-L3JgTcsk51Zx9PcUwSgaE1iZjuGyfZ8aShPjynadU,495
-vivarium_public_health/results/disability.py,sha256=DqSNI1CEdhNXy-mhTtuTXom22e6XGrvFoaeQwyBdlig,9872
-vivarium_public_health/results/disease.py,sha256=q5-g495tPbcs1zfApwoCTfkionAwQbCeXn3JigBUOIk,12526
-vivarium_public_health/results/mortality.py,sha256=Bo8l8CYcBmI6BsXl8l_7mPieGLzyUp3XeFBm497mThE,9652
-vivarium_public_health/results/observer.py,sha256=-VoOYOaT-vmxVNi0bxm3It0ZFdLIq8D9Ng28xO1JuLw,7143
+vivarium_public_health/results/disability.py,sha256=JQm3Q7CoGCT2AgxaoH6MKkvnq4xF83wfFmEvEOvTmvA,9876
+vivarium_public_health/results/disease.py,sha256=OwxhPrfDsCnCZSaw8Yiq2AnibWikoqI-gM7xDdhFLcM,12529
+vivarium_public_health/results/mortality.py,sha256=imH5OGze_rb0i60hmFs-JUjE6XXoH8Gt9wWeut0sk_M,9656
+vivarium_public_health/results/observer.py,sha256=SQmKL1OCs2gDS8clIuJvZ3WiuspMkGEVDhnuNMJAvHc,7300
 vivarium_public_health/results/risk.py,sha256=GS4qJVjW3MqsDeRDDac2etFQlqIluxOxIZFMy1Ytmp8,6622
-vivarium_public_health/results/simple_cause.py,sha256=jlrllbSiEIOrf69gQvrJww29uMrR8xzK_5TApu1Mxqg,724
+vivarium_public_health/results/simple_cause.py,sha256=ibdE6KwhDfQWntCVkOEooBcmUydEoupmd3_poHSHyu8,1007
 vivarium_public_health/results/stratification.py,sha256=4I3YGHVabNAZENE7YboOtWsWU4X-8LUBJ9iwYMbpl6E,5387
 vivarium_public_health/risks/__init__.py,sha256=z8DcnZGxqNVAyFZm2WAV-IVNGvrSS4izju_0DNe2Ghw,212
 vivarium_public_health/risks/base_risk.py,sha256=WhvB0RRYIsGsPQvJEWckcBlOVSh4Rx-B-VGZDSWWb7s,10416
@@ -42,8 +42,8 @@ vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfV
 vivarium_public_health/treatment/magic_wand.py,sha256=i9N57-MEuQv5B6dQ5iVMTAdOPghYcgiRRz-dTzigf1s,1980
 vivarium_public_health/treatment/scale_up.py,sha256=aKJmZ2G6N80n7oPkJM8IpqZOhftUBkAMBn4hR4EZzhE,7015
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=8Z97s7GfcpfLu1U1ESJSqeEk4L__a3M0GbBV21MFg2s,2346
-vivarium_public_health-3.0.4.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-3.0.4.dist-info/METADATA,sha256=mVOUpc6PRXAW7lnKkJ3BRJPKHT3erLyQuS60qlMFUzU,4061
-vivarium_public_health-3.0.4.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
-vivarium_public_health-3.0.4.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-3.0.4.dist-info/RECORD,,
+vivarium_public_health-3.0.5.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-3.0.5.dist-info/METADATA,sha256=FX6CeaoApBMGJFO3USOMhAIsMpl7srL1gQIkUV8Ay54,4061
+vivarium_public_health-3.0.5.dist-info/WHEEL,sha256=UvcQYKBHoFqaQd6LKyqHw9fxEolWLQnlzP0h_LgJAfI,91
+vivarium_public_health-3.0.5.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-3.0.5.dist-info/RECORD,,