vivarium-public-health 2.3.0__py3-none-any.whl → 2.3.2__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "2.3.0"
+__version__ = "2.3.2"

vivarium_public_health/disease/state.py

@@ -85,8 +85,9 @@ class BaseDiseaseState(State):
     def get_initialization_parameters(self) -> Dict[str, Any]:
         """Exclude side effect function and cause type from name and __repr__."""
         initialization_parameters = super().get_initialization_parameters()
-        del initialization_parameters["side_effect_function"]
-        del initialization_parameters["cause_type"]
+        for key in ["side_effect_function", "cause_type"]:
+            if key in initialization_parameters.keys():
+                del initialization_parameters[key]
         return initialization_parameters
 
     def get_initial_event_times(self, pop_data: SimulantData) -> pd.DataFrame:

vivarium_public_health/metrics/mortality.py

@@ -54,6 +54,17 @@ class MortalityObserver(Component):
         }
     }
 
+    def __init__(self):
+        super().__init__()
+        self.causes_of_death = ["other_causes"]
+        self.required_death_columns = ["alive", "exit_time"]
+        self.required_yll_columns = [
+            "alive",
+            "cause_of_death",
+            "exit_time",
+            "years_of_life_lost",
+        ]
+
     ##############
     # Properties #
     ##############
@@ -75,17 +86,14 @@ class MortalityObserver(Component):
     def setup(self, builder: Builder) -> None:
         self.clock = builder.time.clock()
         self.config = builder.configuration.stratification.mortality
-        self._cause_components = builder.components.get_components_by_type(
+        cause_components = builder.components.get_components_by_type(
             (DiseaseState, RiskAttributableDisease)
         )
-
+        self.causes_of_death += [
+            cause.state_id for cause in cause_components if cause.has_excess_mortality
+        ]
         if not self.config.aggregate:
-            causes_of_death = ["other_causes"] + [
-                cause.state_id
-                for cause in self._cause_components
-                if cause.has_excess_mortality
-            ]
-            for cause_of_death in causes_of_death:
+            for cause_of_death in self.causes_of_death:
                 self._register_mortality_observations(
                     builder, cause_of_death, f'cause_of_death == "{cause_of_death}"'
                 )
@@ -100,15 +108,15 @@ class MortalityObserver(Component):
         self, builder: Builder, cause: str, additional_pop_filter: str = ""
     ) -> None:
         pop_filter = (
-            'alive == "dead"'
+            'alive == "dead" and tracked == True'
             if additional_pop_filter == ""
-            else f'alive == "dead" and {additional_pop_filter}'
+            else f'alive == "dead" and tracked == True and {additional_pop_filter}'
         )
         builder.results.register_observation(
             name=f"death_due_to_{cause}",
             pop_filter=pop_filter,
             aggregator=self.count_deaths,
-            requires_columns=["alive", "exit_time"],
+            requires_columns=self.required_death_columns,
             additional_stratifications=self.config.include,
             excluded_stratifications=self.config.exclude,
             when="collect_metrics",
@@ -117,12 +125,7 @@ class MortalityObserver(Component):
             name=f"ylls_due_to_{cause}",
             pop_filter=pop_filter,
             aggregator=self.calculate_ylls,
-            requires_columns=[
-                "alive",
-                "cause_of_death",
-                "exit_time",
-                "years_of_life_lost",
-            ],
+            requires_columns=self.required_yll_columns,
             additional_stratifications=self.config.include,
             excluded_stratifications=self.config.exclude,
             when="collect_metrics",

{vivarium_public_health-2.3.0.dist-info → vivarium_public_health-2.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 2.3.0
+Version: 2.3.2
 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-2.3.0.dist-info → vivarium_public_health-2.3.2.dist-info}/RECORD

@@ -1,17 +1,17 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
-vivarium_public_health/_version.py,sha256=CpK8IH_dCUAwg9tqv7zm9FxbBFkxCnED1JUiRe7cftU,22
+vivarium_public_health/_version.py,sha256=J4CRnpR3v72FGOMp8gqSua_XWZpAfXuqgVWiQFB-gTY,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=9Ru3mg3UUp3h1W0y-1xkWjQBgxqSq-LXM0ByiEcNmGA,8332
 vivarium_public_health/disease/models.py,sha256=uiB2qUlxBsPPPmHJ8Cgot_T1ItZ8RYSNVOBtxtn93Y0,3478
 vivarium_public_health/disease/special_disease.py,sha256=gl8aK0z6afCxiCZxgJafLe4xmbR91zk3079hsi2pUAw,14751
-vivarium_public_health/disease/state.py,sha256=83GRVyioDofeN396tJ3a5_XVH6X57OccZqLdaWKWiHY,24785
+vivarium_public_health/disease/state.py,sha256=wTSiWKXgJ4k9kr0p8oC3gAHil0-zQPOifNoBftHnTRw,24837
 vivarium_public_health/disease/transition.py,sha256=Or5nucRzeGG-UuE_CGkPZ9qE35-Ed9I9LWHj4rjknCc,5334
 vivarium_public_health/metrics/__init__.py,sha256=bWAvvdCm_7RPIazo12qFohA2x5-_EV6ceV8IhKS37sk,209
 vivarium_public_health/metrics/disability.py,sha256=zm0vAG00wj44CHjYGdT2_pebgARa3XXIerrR06t80rc,3984
 vivarium_public_health/metrics/disease.py,sha256=_WQYjd6FRrxRs1Oj8NR9ZmcbXVvsHqX_hods10hwHzU,4546
-vivarium_public_health/metrics/mortality.py,sha256=Um29BnDPojr2K-9Zy5mrGxmX6RPnLncmvkrbaxz3b64,4643
+vivarium_public_health/metrics/mortality.py,sha256=B1AX-N4aO1Jd2NEJ_yMC1NHaDr4pEXmQxNm5kXoLz8w,4826
 vivarium_public_health/metrics/risk.py,sha256=ANwgwpasX-5t0OHMQysV8p_cM86NL2bV6za1FM0JR88,3201
 vivarium_public_health/metrics/stratification.py,sha256=_ChQy8yeP09wFKne4UPPiUEfCKDM6UGfHl4moKCjoNQ,4612
 vivarium_public_health/mslt/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -42,8 +42,8 @@ vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfV
 vivarium_public_health/treatment/magic_wand.py,sha256=iPKFN3VjfiMy_XvN94UqM-FUrGuI0ULwmOdAGdOepYQ,1979
 vivarium_public_health/treatment/scale_up.py,sha256=EkuEAmKaW7AvPWDqDa9WJ2Iy_yiKFytsJu8HVli5Lrg,7078
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=VwZ7t90zzfGoBusduIvcE4lDe5zTvzmHiUNB3u2I52Y,2339
-vivarium_public_health-2.3.0.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-2.3.0.dist-info/METADATA,sha256=cenPaCk9zKdjvDxbdF3eC2N877KFTelGRVLLjQUcSdY,3590
-vivarium_public_health-2.3.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-vivarium_public_health-2.3.0.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-2.3.0.dist-info/RECORD,,
+vivarium_public_health-2.3.2.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-2.3.2.dist-info/METADATA,sha256=UWxOYZMSTZHmUbO4DQhLZ4maatsr-kGX_1Paks8518Q,3590
+vivarium_public_health-2.3.2.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+vivarium_public_health-2.3.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-2.3.2.dist-info/RECORD,,

{vivarium_public_health-2.3.0.dist-info → vivarium_public_health-2.3.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any