vivarium-public-health 3.1.5__py3-none-any.whl → 3.2.1__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "3.1.5"
+__version__ = "3.2.1"

vivarium_public_health/risks/effect.py

@@ -114,7 +114,7 @@ class RiskEffect(Component):
         self.exposure = self.get_risk_exposure(builder)
 
         self._relative_risk_source = self.get_relative_risk_source(builder)
-        self.relative_risk = self.get_relative_risk(builder)
+        self.relative_risk = self.get_relative_risk_pipeline(builder)
 
         self.register_target_modifier(builder)
         self.register_paf_modifier(builder)
@@ -297,7 +297,7 @@ class RiskEffect(Component):
 
         return generate_relative_risk
 
-    def get_relative_risk(self, builder: Builder) -> Pipeline:
+    def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
         return builder.value.register_value_producer(
             f"{self.risk.name}_on_{self.target.name}.relative_risk",
             self._relative_risk_source,

vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -361,18 +361,11 @@ class LBWSGRiskEffect(RiskEffect):
         paf_data = builder.data.load(paf_key)
         return paf_data, builder.data.value_columns()(paf_key)
 
-    def get_target_modifier(
-        self, builder: Builder
-    ) -> Callable[[pd.Index, pd.Series], pd.Series]:
-        def adjust_target(index: pd.Index, target: pd.Series) -> pd.Series:
-            return target * self.relative_risk(index)
-
-        return adjust_target
-
     def register_target_modifier(self, builder: Builder) -> None:
         builder.value.register_value_modifier(
             self.target_pipeline_name,
-            modifier=self.target_modifier,
+            modifier=self.adjust_target,
+            component=self,
             requires_values=[self.relative_risk_pipeline_name],
         )
 
@@ -392,11 +385,12 @@ class LBWSGRiskEffect(RiskEffect):
             for age_start in exposed_age_group_starts
         }
 
-    def get_relative_risk(self, builder: Builder) -> Pipeline:
+    def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
         return builder.value.register_value_producer(
             self.relative_risk_pipeline_name,
-            source=self.get_relative_risk_source,
-            requires_columns=["age"] + self.rr_column_names,
+            source=self._relative_risk_source,
+            component=self,
+            required_resources=["age"] + self.rr_column_names,
         )
 
     def get_interpolator(self, builder: Builder) -> pd.Series:
@@ -469,7 +463,7 @@ class LBWSGRiskEffect(RiskEffect):
     # Pipeline sources and modifiers #
     ##################################
 
-    def get_relative_risk_source(self, index: pd.Index) -> pd.Series:
+    def _get_relative_risk(self, index: pd.Index) -> pd.Series:
         pop = self.population_view.get(index)
         relative_risk = pd.Series(1.0, index=index, name=self.relative_risk_pipeline_name)
 
@@ -479,3 +473,6 @@ class LBWSGRiskEffect(RiskEffect):
                 age_group_mask, self.relative_risk_column_name(age_group)
             ]
         return relative_risk
+
+    def get_relative_risk_source(self, builder: Builder) -> Callable[[pd.Index], pd.Series]:
+        return self._get_relative_risk

{vivarium_public_health-3.1.5.dist-info → vivarium_public_health-3.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.1.5
+Version: 3.2.1
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -63,7 +63,7 @@ Requires-Dist: pytest-mock; extra == "dev"
 Requires-Dist: hypothesis; extra == "dev"
 Requires-Dist: pyyaml; extra == "dev"
 Requires-Dist: black==22.3.0; extra == "dev"
-Requires-Dist: isort; extra == "dev"
+Requires-Dist: isort==5.13.2; extra == "dev"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{vivarium_public_health-3.1.5.dist-info → vivarium_public_health-3.2.1.dist-info}/RECORD

@@ -1,6 +1,6 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=GDeeP-7OlCBwPuv_xQoB1wNmvCaFsqfTB7qnnYApm0w,1343
-vivarium_public_health/_version.py,sha256=TWk_ugdK07uGz4H-jBQrak6YuyBu1slD1RA6eK7eSbg,22
+vivarium_public_health/_version.py,sha256=3BjxgoOdY8_gLUzv4upJn3tTpb8jX8wWqkC8k9jDva0,22
 vivarium_public_health/utilities.py,sha256=QNXQ6fhAr1HcV-GwKw7wQLz6QyuNxqNvMA-XujKjTgs,3035
 vivarium_public_health/disease/__init__.py,sha256=VUJHDLlE6ngo2qHNQUtZ8OWH5H_T7_ao-xsYKDkRmHw,443
 vivarium_public_health/disease/exceptions.py,sha256=vb30IIV82OiDf2cNZCs_E2rF6mdDDHbnZSND60no5CU,97
@@ -36,15 +36,15 @@ vivarium_public_health/risks/__init__.py,sha256=z8DcnZGxqNVAyFZm2WAV-IVNGvrSS4iz
 vivarium_public_health/risks/base_risk.py,sha256=XQ_7rYJS5gh0coEKDqcc_zYdjPDBZlj6-THsIQxL3zs,10888
 vivarium_public_health/risks/data_transformations.py,sha256=SgdPKc95BBqgMNUdlAQM8k6iaXcpxnjk5B2ySTES1Yg,9269
 vivarium_public_health/risks/distributions.py,sha256=a63-ihg2itxqgowDZbUix8soErxs_y8TRwsdtTCIUU4,18121
-vivarium_public_health/risks/effect.py,sha256=2DaBKxncS94cm8Ih-TQtbV1mGsEZhx6fEnB5V_ocIZM,21241
+vivarium_public_health/risks/effect.py,sha256=Cw-V1rMPaAPZsirbUElPzksvNuXLQc8TIIk0hgaFzvA,21259
 vivarium_public_health/risks/implementations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=Iw5e7sCrWplEu6dic1Wu6q9e0rdeem_6gQ_-N52G54E,17866
+vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py,sha256=JkS9_33AzRBPRK9BpNvtBYg70cbh7wBi3dE7hBHbSNU,17781
 vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfVhPXtTeFWSdQMgA0,222
 vivarium_public_health/treatment/magic_wand.py,sha256=zGIhrNgB9q6JD7fHlvbDQb3H5e_N_QsROO4Y0kl_JQM,1955
 vivarium_public_health/treatment/scale_up.py,sha256=hVz0ELXDqlpcExI31rKdepxqcW_hy2hZSa6qCzv6udU,7020
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=8Z97s7GfcpfLu1U1ESJSqeEk4L__a3M0GbBV21MFg2s,2346
-vivarium_public_health-3.1.5.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-3.1.5.dist-info/METADATA,sha256=OCgTn3qH2kSMuoFNe3E868FEyFggjsyWqyZdrrPDofo,4207
-vivarium_public_health-3.1.5.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-vivarium_public_health-3.1.5.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-3.1.5.dist-info/RECORD,,
+vivarium_public_health-3.2.1.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-3.2.1.dist-info/METADATA,sha256=u7H5K7zUJj2RyV59wdbkZdvvEJ9TIvqXZQ4mnUX3W7s,4215
+vivarium_public_health-3.2.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+vivarium_public_health-3.2.1.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-3.2.1.dist-info/RECORD,,