vivarium-public-health 4.3.4__py3-none-any.whl → 4.3.6__py3-none-any.whl

vivarium_public_health/_version.py

@@ -1 +1 @@
-__version__ = "4.3.4"
+__version__ = "4.3.6"

vivarium_public_health/population/base_population.py

@@ -235,15 +235,50 @@ class ScaledPopulation(BasePopulation):
             raise ValueError(
                 f"Scaling factor must be a pandas DataFrame. Provided value: {scaling_factor}"
             )
-        scaling_factor = scaling_factor.set_index(
-            [col for col in scaling_factor.columns if col != "value"]
+        start_year = builder.configuration.time.start.year
+        population_structure, scaling_factor = self._format_data_inputs(
+            population_structure, scaling_factor, start_year
         )
-        population_structure = population_structure.set_index(
-            [col for col in population_structure.columns if col != "value"]
+
+        return (population_structure * scaling_factor).reset_index()
+
+    def _format_data_inputs(
+        self, pop_structure: pd.DataFrame, scalar_data: pd.DataFrame, year: int
+    ) -> tuple[pd.DataFrame, pd.DataFrame]:
+        """Data cleaning function to check whether scalar_data and population structure are compatible for scaling
+        the population structure of a simulation."""
+
+        scaling_factor = scalar_data.set_index(
+            [col for col in scalar_data.columns if col != "value"]
         )
-        scaled_population_structure = (population_structure * scaling_factor).reset_index()
+        population_structure = pop_structure.set_index(
+            [col for col in pop_structure.columns if col != "value"]
+        )
+        if "year_start" not in scaling_factor.index.names:
+            return population_structure, scaling_factor
+
+        # Subset to start year of simulation or closest year
+        pop_reference_years = sorted(
+            set(population_structure.index.get_level_values("year_start"))
+        )
+        pop_year_index = np.digitize(year, pop_reference_years).item() - 1
+        scale_reference_years = sorted(
+            set(scaling_factor.index.get_level_values("year_start"))
+        )
+        scale_year_index = np.digitize(year, scale_reference_years).item() - 1
+        # Subset to start year of simulation or earliest year. E.g. if start year = 2021 and pop
+        # structure has 2021, we will subset to 2021. If pop structure minimum year is 2025, we
+        # will subset to 2025.
+        population_structure = population_structure.loc[
+            population_structure.index.get_level_values("year_start")
+            == pop_reference_years[pop_year_index]
+        ]
+        scaling_factor = scaling_factor.loc[
+            scaling_factor.index.get_level_values("year_start")
+            == scale_reference_years[scale_year_index]
+        ]
 
-        return scaled_population_structure
+        return population_structure, scaling_factor
 
 
 class AgeOutSimulants(Component):

{vivarium_public_health-4.3.4.dist-info → vivarium_public_health-4.3.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.3.4
+Version: 4.3.6
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,45 +26,28 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
+Requires-Dist: vivarium_dependencies[loguru,numpy_lt_2,pandas,pyarrow,scipy,tables]
 Requires-Dist: vivarium_build_utils<3.0.0,>=2.0.1
 Requires-Dist: vivarium>=3.4.3
-Requires-Dist: layered_config_tree>=3.2.0
-Requires-Dist: loguru
-Requires-Dist: numpy<2.0.0
-Requires-Dist: pandas
-Requires-Dist: scipy
-Requires-Dist: tables
+Requires-Dist: layered_config_tree
 Requires-Dist: risk_distributions>=2.0.11
-Requires-Dist: pyarrow
 Provides-Extra: docs
-Requires-Dist: sphinx<7.0; extra == "docs"
-Requires-Dist: sphinx-rtd-theme; extra == "docs"
-Requires-Dist: sphinx-click; extra == "docs"
-Requires-Dist: sphinx-autodoc-typehints; extra == "docs"
-Requires-Dist: IPython; extra == "docs"
-Requires-Dist: matplotlib; extra == "docs"
+Requires-Dist: vivarium_dependencies[ipython,matplotlib,sphinx,sphinx-click]; extra == "docs"
+Provides-Extra: interactive
+Requires-Dist: vivarium_dependencies[interactive]; extra == "interactive"
 Provides-Extra: test
+Requires-Dist: vivarium_dependencies[pytest]; extra == "test"
 Requires-Dist: vivarium_testing_utils; extra == "test"
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Requires-Dist: pytest-mock; extra == "test"
 Requires-Dist: hypothesis; extra == "test"
 Requires-Dist: pyyaml; extra == "test"
 Provides-Extra: dev
-Requires-Dist: sphinx<7.0; extra == "dev"
-Requires-Dist: sphinx-rtd-theme; extra == "dev"
-Requires-Dist: sphinx-click; extra == "dev"
-Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
-Requires-Dist: IPython; extra == "dev"
-Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: vivarium_dependencies[ipython,matplotlib,sphinx,sphinx-click]; extra == "dev"
+Requires-Dist: vivarium_dependencies[interactive]; extra == "dev"
+Requires-Dist: vivarium_dependencies[pytest]; extra == "dev"
 Requires-Dist: vivarium_testing_utils; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Requires-Dist: pytest-cov; extra == "dev"
-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==5.13.2; extra == "dev"
+Requires-Dist: vivarium_dependencies[lint]; extra == "dev"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{vivarium_public_health-4.3.4.dist-info → vivarium_public_health-4.3.6.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=215K0AQu12pX2_elDj3eHwDGWbBrLpNequvlrMryST8,22
+vivarium_public_health/_version.py,sha256=bXuOm7EMaj1zGwMTlGgJNLOisp5gk6scG4bpGO0RNd8,22
 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
@@ -20,7 +20,7 @@ vivarium_public_health/plugins/__init__.py,sha256=oBW_zfgG_LbwfgTDjUe0btfy9FaDvA
 vivarium_public_health/plugins/parser.py,sha256=WoUisq0d-PfJtSzKYZ6C-s-fYdQpNiRBE14vKaYE27Y,32921
 vivarium_public_health/population/__init__.py,sha256=x_9rB93q64Krw-kbBDI1-_U_JsPO1_QrL03AwiFlwXI,243
 vivarium_public_health/population/add_new_birth_cohorts.py,sha256=x6A60GE_F3I8AgLABNJ-2ziiUj52lAd66uX5yc2vIDI,9038
-vivarium_public_health/population/base_population.py,sha256=Wu797AL13KRLhXkYni_XocJBLfhfvCVgGeas08U3tCM,18898
+vivarium_public_health/population/base_population.py,sha256=XwfIfJRIcJsxphK62nVPZbrcAw0_7dhxGVuPEnGw3R0,20550
 vivarium_public_health/population/data_transformations.py,sha256=YHbwfb40EPbXsPW-Rk1s5d61rP8fqgDtMELB7OJG3mo,22662
 vivarium_public_health/population/mortality.py,sha256=Mtv45FENNY0GlPIoVd3d3pRq01aEh4cjzNXIgEe6hMo,10364
 vivarium_public_health/results/__init__.py,sha256=rKUZGlRXJgEyFY4a_WJeg3XnC0l34S5guYZ0N9JJS4E,319
@@ -43,8 +43,8 @@ vivarium_public_health/treatment/__init__.py,sha256=wONElu9aJbBYwpYIovYPYaN_GYfV
 vivarium_public_health/treatment/magic_wand.py,sha256=zg4I48G-l9fC6-qjvApbM1zNACJimZlX9ZZ9fdHKwvc,1985
 vivarium_public_health/treatment/scale_up.py,sha256=_bsf9c_yVc7-q_-yBcXimISTUfYzPps1auH0uEf7sfQ,7048
 vivarium_public_health/treatment/therapeutic_inertia.py,sha256=ZIHnpuszZwA_BkS53JbSLvpcnX_bqG2knwCUyUgkA9M,2362
-vivarium_public_health-4.3.4.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
-vivarium_public_health-4.3.4.dist-info/METADATA,sha256=nNlKCkVxNAu6ftFCGJ_-6o_4TRXBCeQ7nbGfEWgUd1E,4287
-vivarium_public_health-4.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-vivarium_public_health-4.3.4.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
-vivarium_public_health-4.3.4.dist-info/RECORD,,
+vivarium_public_health-4.3.6.dist-info/licenses/LICENSE.txt,sha256=mN4bNLUQNcN9njYRc_3jCZkfPySVpmM6MRps104FxA4,1548
+vivarium_public_health-4.3.6.dist-info/METADATA,sha256=YdB1JSLxInm6y2_uIOnjiG8tqavEJQiOBsQaxn9tqgA,3877
+vivarium_public_health-4.3.6.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+vivarium_public_health-4.3.6.dist-info/top_level.txt,sha256=VVInlpzCFD0UNNhjOq_j-a29odzjwUwYFTGfvqbi4dY,23
+vivarium_public_health-4.3.6.dist-info/RECORD,,