vivarium-public-health 2.2.0__tar.gz → 2.2.2__tar.gz

{vivarium_public_health-2.2.0 → vivarium_public_health-2.2.2}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**2.2.2 - 2/28/24**
+
+ - Fix bug in rescale_binned_proportions to update midpoitn for new age bins
+
+**2.2.1 - 2/26/24**
+
+ - Update LinearScaleUp configuration defaults
+
 **2.2.0 - 02/14/24**
 
  - Implement CausesConfigurationParser to parse causes configuration into DiseaseModel components

{vivarium_public_health-2.2.0 → vivarium_public_health-2.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 2.2.0
+Version: 2.2.2
 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-2.2.2/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "2.2.2"

{vivarium_public_health-2.2.0 → vivarium_public_health-2.2.2}/src/vivarium_public_health/population/data_transformations.py

@@ -138,7 +138,21 @@ def rescale_binned_proportions(
         pop_data.loc[padding_bin.index, columns_to_scale] += remainder
 
         pop_data.loc[min_bin.index, "age_start"] = age_start
+        pop_data.loc[min_bin.index, "age"] = float(
+            (
+                pop_data.loc[min_bin.index, "age_start"].iloc[0]
+                + pop_data.loc[min_bin.index, "age_end"].iloc[0]
+            )
+            / 2
+        )
         pop_data.loc[padding_bin.index, "age_end"] = age_start
+        pop_data.loc[padding_bin.index, "age"] = float(
+            (
+                pop_data.loc[padding_bin.index, "age_start"].iloc[0]
+                + pop_data.loc[padding_bin.index, "age_end"].iloc[0]
+            )
+            / 2
+        )
 
         max_bin = sub_pop[(sub_pop["age_end"] > age_end) & (age_end >= sub_pop["age_start"])]
         padding_bin = sub_pop[sub_pop["age_start"] == float(max_bin["age_end"].iloc[0])]

{vivarium_public_health-2.2.0 → vivarium_public_health-2.2.2}/src/vivarium_public_health/treatment/scale_up.py

@@ -6,14 +6,13 @@ Linear Scale-Up Model
 This module contains tools for applying a linear scale-up to an intervention
 
 """
-from datetime import datetime
 from typing import Any, Callable, Dict, Tuple
 
 import pandas as pd
 from vivarium import Component
 from vivarium.framework.engine import Builder
 from vivarium.framework.lookup import LookupTable
-from vivarium.framework.time import Time, get_time_stamp
+from vivarium.framework.time import Time
 from vivarium.framework.values import Pipeline
 
 from vivarium_public_health.utilities import EntityString
@@ -36,16 +35,10 @@ class LinearScaleUp(Component):
         configuration:
             treatment_scale_up:
                 start:
-                    date:
-                        year: 2020
-                        month: 1
-                        day: 1
+                    date: "2020-01-01"
                     value: 0.0
                 end:
-                    date:
-                        year: 2020
-                        month: 12
-                        day: 31
+                    date: "2020-12-31"
                     value: 0.9
 
     """
@@ -53,8 +46,8 @@ class LinearScaleUp(Component):
     CONFIGURATION_DEFAULTS = {
         "treatment": {
             "date": {
-                "start": "start",
-                "end": "end",
+                "start": "2020-01-01",
+                "end": "2020-12-31",
             },
             "value": {
                 "start": "data",
@@ -114,17 +107,9 @@ class LinearScaleUp(Component):
         return builder.time.clock()
 
     # noinspection PyMethodMayBeStatic
-    def get_scale_up_dates(self, builder: Builder) -> Tuple[datetime, datetime]:
+    def get_scale_up_dates(self, builder: Builder) -> Tuple[pd.Timestamp, pd.Timestamp]:
         scale_up_config = builder.configuration[self.configuration_key]["date"]
-
-        def get_endpoint(endpoint_type: str) -> datetime:
-            if scale_up_config[endpoint_type] == endpoint_type:
-                endpoint = get_time_stamp(builder.configuration.time[endpoint_type])
-            else:
-                endpoint = get_time_stamp(scale_up_config[endpoint_type])
-            return endpoint
-
-        return get_endpoint("start"), get_endpoint("end")
+        return pd.Timestamp(scale_up_config["start"]), pd.Timestamp(scale_up_config["end"])
 
     def get_scale_up_values(self, builder: Builder) -> Tuple[LookupTable, LookupTable]:
         """

{vivarium_public_health-2.2.0 → vivarium_public_health-2.2.2}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 2.2.0
+Version: 2.2.2
 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-2.2.0/src/vivarium_public_health/_version.py

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