Merge pull request #293 from ihmeuw/develop

Develop

.github/CODEOWNERS

@@ -1,2 +1,2 @@
 # default owners
-* @albrja @beatrixkh @collijk @hussain-jafari @mattkappel @rmudambi @stevebachmeier
+* @albrja @beatrixkh @collijk @hussain-jafari @mattkappel @ramittal @rmudambi @stevebachmeier

.github/pull_request_template.md

@@ -5,8 +5,9 @@
 <!-- For use in commit message, wrap at 72 chars. 72 chars is here: -->
 - *Category*: <!-- one of bugfix, feature, refactor, POC, CI/infrastructure, documentation, 
                    revert, test, release, other/misc -->
-- *JIRA issue*: <!-- [MIC-XYZ](https://jira.ihme.washington.edu/browse/MIC-XYZ) -->
+- *JIRA issue*: [MIC-XYZ](https://jira.ihme.washington.edu/browse/MIC-XYZ)
 
+### Changes and notes
 <!-- 
 Change description – why, what, anything unexplained by the above.
 Include guidance to reviewers if changes are complex.

CHANGELOG.rst

@@ -1,3 +1,8 @@
+**0.10.21 - 11/16/22**
+
+ - Fix bug in timing of disease transition observations
+ - Add logging when adding risks with a relative risk less than 1 from artifact
+
 **0.10.20 - 07/25/22**
 
  - Update Vivarium pin

src/vivarium_public_health/__about__.py

@@ -13,7 +13,7 @@
 __summary__ = "Components for modelling diseases, risks, and interventions with ``vivarium``"
 __uri__ = "https://github.com/ihmeuw/vivarium_public_health"
 
-__version__ = "0.10.20"
+__version__ = "0.10.21"
 
 __author__ = "The vivarium_public_health developers"
 __email__ = "[email protected]"

src/vivarium_public_health/metrics/disease.py

@@ -138,7 +138,7 @@ def _register_time_step_prepare_listener(self, builder: Builder) -> None:
         builder.event.register_listener("time_step__prepare", self.on_time_step_prepare)
 
     def _register_collect_metrics_listener(self, builder: Builder) -> None:
-        builder.event.register_listener("time_step", self.on_collect_metrics)
+        builder.event.register_listener("collect_metrics", self.on_collect_metrics)
 
     def _register_metrics_modifier(self, builder: Builder) -> None:
         builder.value.register_value_modifier(

src/vivarium_public_health/risks/data_transformations.py

@@ -7,10 +7,12 @@
 risk data and performing any necessary data transformations.
 
 """
+
 from typing import Union
 
 import numpy as np
 import pandas as pd
+from loguru import logger
 
 from vivarium_public_health.utilities import EntityString, TargetString
 
@@ -181,6 +183,12 @@ def get_relative_risk_data(builder, risk: EntityString, target: TargetString):
         "unordered_polytomous",
     ]:
         relative_risk_data = pivot_categorical(relative_risk_data)
+        # Check if any values for relative risk are below expected boundary of 1.0
+        category_columns = [c for c in relative_risk_data.columns if "cat" in c]
+        if not relative_risk_data[(relative_risk_data[category_columns] < 1.0).any(axis=1)].empty:
+            logger.warning(
+                f"WARNING: Some data values are below the expected boundary of 1.0 for {risk}.relative_risk"
+            )
 
     else:
         relative_risk_data = relative_risk_data.drop(columns=["parameter"])