vivarium-public-health 1.0.0__py3-none-any.whl → 1.0.2__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.0.2"

vivarium_public_health/disease/state.py

@@ -499,10 +499,9 @@ class DiseaseState(BaseDiseaseState):
         return disability_weight
 
     def load_excess_mortality_rate_data(self, builder):
-        only_morbid = builder.data.load(f"cause.{self._model}.restrictions")["yld_only"]
         if "excess_mortality_rate" in self._get_data_functions:
             return self._get_data_functions["excess_mortality_rate"](builder, self.cause)
-        elif only_morbid:
+        elif builder.data.load(f"cause.{self._model}.restrictions")["yld_only"]:
             return 0
         else:
             return builder.data.load(f"{self.cause_type}.{self.cause}.excess_mortality_rate")

vivarium_public_health/metrics/disease.py

@@ -91,7 +91,8 @@ class DiseaseObserver:
             filter_string = (
                 f'{self.previous_state_column_name} == "{transition.from_state}" '
                 f'and {self.disease} == "{transition.to_state}" '
-                f"and tracked==True"
+                f"and tracked==True "
+                f'and alive == "alive"'
             )
             builder.results.register_observation(
                 name=f"{transition}_event_count",

{vivarium_public_health-1.0.0.dist-info → vivarium_public_health-1.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium-public-health
-Version: 1.0.0
+Version: 1.0.2
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,14 +26,14 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
-Requires-Dist: vivarium (>=1.2.1)
+Requires-Dist: vivarium >=1.2.1
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: scipy
 Requires-Dist: tables
-Requires-Dist: risk-distributions (>=2.0.11)
+Requires-Dist: risk-distributions >=2.0.11
 Provides-Extra: dev
-Requires-Dist: sphinx (>=4.0) ; extra == 'dev'
+Requires-Dist: sphinx >=4.0 ; extra == 'dev'
 Requires-Dist: sphinx-rtd-theme ; extra == 'dev'
 Requires-Dist: sphinx-click ; extra == 'dev'
 Requires-Dist: IPython ; extra == 'dev'
@@ -42,7 +42,7 @@ Requires-Dist: pytest ; extra == 'dev'
 Requires-Dist: pytest-mock ; extra == 'dev'
 Requires-Dist: hypothesis ; extra == 'dev'
 Provides-Extra: docs
-Requires-Dist: sphinx (>=4.0) ; extra == 'docs'
+Requires-Dist: sphinx >=4.0 ; extra == 'docs'
 Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
 Requires-Dist: sphinx-click ; extra == 'docs'
 Requires-Dist: IPython ; extra == 'docs'

{vivarium_public_health-1.0.0.dist-info → vivarium_public_health-1.0.2.dist-info}/RECORD

@@ -1,16 +1,16 @@
 vivarium_public_health/__about__.py,sha256=RgWycPypKZS80TpSX7o41cREnG8PfguNHDHLuLyl820,487
 vivarium_public_health/__init__.py,sha256=tomMOl3PI7O8GdxDWGBiBjT0Bwd31GpyQTYTzwIv108,361
-vivarium_public_health/_version.py,sha256=J-j-u0itpEFT6irdmWmixQqYMadNl1X91TxUmoiLHMI,22
+vivarium_public_health/_version.py,sha256=Y3LSfRioSl2xch70pq_ULlvyECXyEtN3krVaWeGyaxk,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=Kx_9WKRgKxeGAk-62vpWiyMrCw6vY3eKT3aYnHqYZ2M,7636
 vivarium_public_health/disease/models.py,sha256=MdpzLooa_HcHgJjEJ46gcUtf9TdcNDpKSCUKf26uFxo,3694
 vivarium_public_health/disease/special_disease.py,sha256=-qE7hb-WKE_wkKWtmRKYe6FgMRtIUkjtwRRjKCufwcU,14156
-vivarium_public_health/disease/state.py,sha256=itKitnTp3RTZF1lCDbRrQ6v_3QZUmcGjxkfVZrAdYLY,19772
+vivarium_public_health/disease/state.py,sha256=yOqKAAYx3KrERihm9TyfX3JS1EJu0V3Ds9eNxTFMKZc,19738
 vivarium_public_health/disease/transition.py,sha256=NO7q708Rf268VqPCKluuli6PjQL8neMAL2DLzSa0GZg,4600
 vivarium_public_health/metrics/__init__.py,sha256=bWAvvdCm_7RPIazo12qFohA2x5-_EV6ceV8IhKS37sk,209
 vivarium_public_health/metrics/disability.py,sha256=Xgve93wrq45ErSERu59qiwlR7MhWRGodFOsXxZoUfDU,3841
-vivarium_public_health/metrics/disease.py,sha256=sazSoIQb3Jt6Xj-ArK9302C7sroghvl2CGFNMbK-RA8,4500
+vivarium_public_health/metrics/disease.py,sha256=WrBYLcla3Dm4D-oAcZ3k4vDSR_O3nw_A6LtZ1ReMag4,4541
 vivarium_public_health/metrics/mortality.py,sha256=llZ_fWidi7FzCCYecLgeN2EZ873LE4X9gu4deGhj0bc,4253
 vivarium_public_health/metrics/risk.py,sha256=YN6ADadFUACJt-aZsYTxHKh53HnRlumKnJr3_kz6kF0,3795
 vivarium_public_health/metrics/stratification.py,sha256=nFZzcM3UzUSiBcka6RHXjnfgPCPh6d_bM-xuma8yDxU,4374
@@ -40,8 +40,8 @@ vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfV
 vivarium_public_health/treatment/magic_wand.py,sha256=QR4YNyUGGX7jw57uu7tuuF_zpFXhVfDAa16UgBidZYA,1594
 vivarium_public_health/treatment/scale_up.py,sha256=cK_ZERRJbHaWqnjwkVJerue4ORTOjNRmjAsWdPGMxCU,7439
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=CTvG1zZJcJ2-blKsZjrfedgkmHGyLrBjYtQ_qNpphlM,2223
-vivarium_public_health-1.0.0.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-1.0.0.dist-info/METADATA,sha256=xkjjkArufLyiUD1BUXEUU4OHUgnitT-6mG44USELrQA,3396
-vivarium_public_health-1.0.0.dist-info/WHEEL,sha256=AtBG6SXL3KF_v0NxLf0ehyVOh0cold-JbJYXNGorC6Q,92
-vivarium_public_health-1.0.0.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-1.0.0.dist-info/RECORD,,
+vivarium_public_health-1.0.2.dist-info/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-1.0.2.dist-info/METADATA,sha256=ovKe6bcz0lgha6-IDGB8yhV7vdGU8ygSYvHYuc3EQRw,3388
+vivarium_public_health-1.0.2.dist-info/WHEEL,sha256=5sUXSg9e4bi7lTLOHcm6QEYwO5TIF1TNbTSVFVjcJcc,92
+vivarium_public_health-1.0.2.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-1.0.2.dist-info/RECORD,,

{vivarium_public_health-1.0.0.dist-info → vivarium_public_health-1.0.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.0)
+Generator: bdist_wheel (0.41.1)
 Root-Is-Purelib: true
 Tag: py3-none-any