vivarium-public-health 2.2.0__py3-none-any.whl → 2.2.2__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "2.2.0"
+__version__ = "2.2.2"

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/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.dist-info → vivarium_public_health-2.2.2.dist-info}/METADATA

@@ -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.dist-info → vivarium_public_health-2.2.2.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=DKk-1b-rZsJFxFi1JoJ7TmEvIEQ0rf-C9HAZWwvjuM0,22
+vivarium_public_health/_version.py,sha256=toAYzE_ok1SiBE0AqAVdW0O8YCXCwcx0w4JATYQuJOg,22
 vivarium_public_health/utilities.py,sha256=_X9sZQ7flsi2sVWQ9zrf8GJw8QwZsPZm3NUjx1gu7bM,2555
 vivarium_public_health/disease/__init__.py,sha256=RuuiRcvAJfX9WQGt_WZZjxN7Cu3E5rMTmuaRS-UaFPM,419
 vivarium_public_health/disease/model.py,sha256=7xFGo6JqPjQjm2VUZ3u3ThXWSzmitTOCZ8N9PTTL6MU,8253
@@ -26,7 +26,7 @@ vivarium_public_health/plugins/parser.py,sha256=uhBw5t-Lmb8YDN2GvVG93l50ZuCIsg4V
 vivarium_public_health/population/__init__.py,sha256=17rtbcNVK5LtCCxAex7P7Q_vYpwbeTepyf3nazS90Yc,225
 vivarium_public_health/population/add_new_birth_cohorts.py,sha256=qNsZjvaJ7Et8_Kw7JNyRshHHRA3pEQMM4TSqCp48Gr4,9092
 vivarium_public_health/population/base_population.py,sha256=U9FibBoPuYWvUqPFCUIVwjBxQVuhTb58cUy-2EJSzio,15345
-vivarium_public_health/population/data_transformations.py,sha256=3MNDrfaZMMGM3crNzucGfYWZOTGHoavIcu8wxq1xIU8,21838
+vivarium_public_health/population/data_transformations.py,sha256=PsvE1-S-Q_K4viBgF2Ss0DaaoH0WyhRX26ZJYwJ0O84,22322
 vivarium_public_health/population/mortality.py,sha256=w1Oxb958LjUkNwxJ0vdA3TZndpeNiaH3d7RukLas_oQ,10085
 vivarium_public_health/risks/__init__.py,sha256=XvX12RgD0iF5PBoc2StsOhxJmK1FP-RaAYrjIT9MfDs,232
 vivarium_public_health/risks/base_risk.py,sha256=6D7YlxQOdQm-Kw5_vjpQmFqU7spF-lTy14WEEefRQlA,6494
@@ -40,10 +40,10 @@ vivarium_public_health/testing/mock_artifact.py,sha256=T6Fw0rSEGfDr7Lqq-YxcJBmZt
 vivarium_public_health/testing/utils.py,sha256=bbAEGw5kRzVB_80uc5u5mp47NMj2xD6Nw7vlEsT_-Wg,2199
 vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
 vivarium_public_health/treatment/magic_wand.py,sha256=iPKFN3VjfiMy_XvN94UqM-FUrGuI0ULwmOdAGdOepYQ,1979
-vivarium_public_health/treatment/scale_up.py,sha256=7QKBgAII4dwkds9gdbQ5d6oDaD02iwcQCVcYRN-B4Mg,7573
+vivarium_public_health/treatment/scale_up.py,sha256=EkuEAmKaW7AvPWDqDa9WJ2Iy_yiKFytsJu8HVli5Lrg,7078
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=VwZ7t90zzfGoBusduIvcE4lDe5zTvzmHiUNB3u2I52Y,2339
-vivarium_public_health-2.2.0.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-2.2.0.dist-info/METADATA,sha256=AyFXCJ4aiPYreEVtAkAFpOODBMkUCIs0pXiTp5W-dy8,3531
-vivarium_public_health-2.2.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-vivarium_public_health-2.2.0.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-2.2.0.dist-info/RECORD,,
+vivarium_public_health-2.2.2.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-2.2.2.dist-info/METADATA,sha256=df-s-fZYuzBiLipOvirDKpAXcGzljkDaWgcDxHxIzBc,3531
+vivarium_public_health-2.2.2.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+vivarium_public_health-2.2.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-2.2.2.dist-info/RECORD,,