vivarium-public-health 4.3.4__tar.gz → 4.3.6__tar.gz

{vivarium_public_health-4.3.4 → vivarium_public_health-4.3.6}/.gitignore

@@ -114,4 +114,8 @@ src/vivarium_public_health/_version.py
 tests/proportion_test_diagnostics.csv
 
 # macOS
-*.DS_Store
+*.DS_Store
+
+# Visual Studio Code project settings
+.vscode/
+

{vivarium_public_health-4.3.4 → vivarium_public_health-4.3.6}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**4.3.6 - 08/28/25**
+
+  - Feature: ScaledPopulation can handle multiple year data inputs.
+
+**4.3.5 - 08/01/25**
+
+  - Use vivarium_dependencies for common setup constraints
+
 **4.3.4 - 07/31/25**
 
   - Modify futurewarning fix from v4.2.6 to not require pandas>=2.2.0
@@ -22,7 +30,7 @@
   - Add Intervention and InterventionEffect classes
   - Refactor to pass Exposure component to RiskExposureDistribution classes
   - Update exposure category names for DichotomousDistribution
-  
+
 **4.2.6 - 07/25/25**
 
   - Feature: Support new environment creation via 'make build-env'

{vivarium_public_health-4.3.4/src/vivarium_public_health.egg-info → vivarium_public_health-4.3.6}/PKG-INFO

@@ -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 → vivarium_public_health-4.3.6}/setup.py

@@ -42,42 +42,27 @@ if __name__ == "__main__":
         long_description = f.read()
 
     install_requirements = [
+        "vivarium_dependencies[pandas,numpy_lt_2,scipy,tables,loguru,pyarrow]",
         "vivarium_build_utils>=2.0.1,<3.0.0",
         "vivarium>=3.4.3",
-        "layered_config_tree>=3.2.0",
-        "loguru",
-        "numpy<2.0.0",
-        "pandas",
-        "scipy",
-        "tables",
+        "layered_config_tree",
         "risk_distributions>=2.0.11",
-        "pyarrow",
     ]
 
     setup_requires = ["setuptools_scm"]
 
     test_requirements = [
+        "vivarium_dependencies[pytest]",
         "vivarium_testing_utils",
-        "pytest",
-        "pytest-cov",
-        "pytest-mock",
         "hypothesis",
         "pyyaml",
     ]
 
-    doc_requirements = [
-        "sphinx<7.0",
-        "sphinx-rtd-theme",
-        "sphinx-click",
-        "sphinx-autodoc-typehints",
-        "IPython",
-        "matplotlib",
-    ]
+    doc_requirements = ["vivarium_dependencies[sphinx,sphinx-click,ipython,matplotlib]"]
 
-    lint_requirements = [
-        "black==22.3.0",
-        "isort==5.13.2",
-    ]
+    interactive_requirements = ["vivarium_dependencies[interactive]"]
+
+    lint_requirements = ["vivarium_dependencies[lint]"]
 
     setup(
         name=about["__title__"],
@@ -115,8 +100,12 @@ if __name__ == "__main__":
         tests_require=test_requirements,
         extras_require={
             "docs": doc_requirements,
+            "interactive": interactive_requirements,
             "test": test_requirements,
-            "dev": doc_requirements + test_requirements + lint_requirements,
+            "dev": doc_requirements
+            + interactive_requirements
+            + test_requirements
+            + lint_requirements,
         },
         zip_safe=False,
         use_scm_version={

vivarium_public_health-4.3.6/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.3.6"

{vivarium_public_health-4.3.4 → vivarium_public_health-4.3.6}/src/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 → vivarium_public_health-4.3.6/src/vivarium_public_health.egg-info}/PKG-INFO

@@ -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-4.3.6/src/vivarium_public_health.egg-info/requires.txt

@@ -0,0 +1,26 @@
+vivarium_dependencies[loguru,numpy_lt_2,pandas,pyarrow,scipy,tables]
+vivarium_build_utils<3.0.0,>=2.0.1
+vivarium>=3.4.3
+layered_config_tree
+risk_distributions>=2.0.11
+
+[dev]
+vivarium_dependencies[ipython,matplotlib,sphinx,sphinx-click]
+vivarium_dependencies[interactive]
+vivarium_dependencies[pytest]
+vivarium_testing_utils
+hypothesis
+pyyaml
+vivarium_dependencies[lint]
+
+[docs]
+vivarium_dependencies[ipython,matplotlib,sphinx,sphinx-click]
+
+[interactive]
+vivarium_dependencies[interactive]
+
+[test]
+vivarium_dependencies[pytest]
+vivarium_testing_utils
+hypothesis
+pyyaml

{vivarium_public_health-4.3.4 → vivarium_public_health-4.3.6}/tests/population/test_base_population.py

@@ -1,8 +1,10 @@
 import math
+from itertools import product
 
 import numpy as np
 import pandas as pd
 import pytest
+from layered_config_tree import LayeredConfigTree
 from vivarium import InteractiveContext
 from vivarium.testing_utilities import get_randomness
 from vivarium_testing_utils import FuzzyChecker
@@ -349,6 +351,125 @@ def test_scaled_population(
         )
 
 
+@pytest.mark.parametrize("test_case", ["pop_structure", "both"])
+@pytest.mark.parametrize("year", [2021, 2025])
+def test_scaled_population__format_data_inputs(
+    test_case: str,
+    year: int,
+) -> None:
+    """Test ScaledPopulation with multi-year data in population structure and/or scaling factor.
+
+    Cases:
+    1. pop_structure: Population structure has multiple years, scaling factor does not
+    2. both: Both population structure and scaling factor have multiple years
+    """
+
+    # Create multi-year population structure (2021-2024)
+    age_idx = pd.MultiIndex.from_tuples(
+        [
+            (0.0, 25.0, "Young People"),
+            (25.0, 50.0, "Old People"),
+            (50.0, 75.0, "Ancient People"),
+            (75.0, 100.0, "People Who Beat the Odds"),
+        ],
+        names=["age_start", "age_end", "age_group_name"],
+    )
+    age_df = pd.DataFrame(index=age_idx).reset_index()
+    age_bins = [(group.age_start, group.age_end) for group in age_df.itertuples()]
+    sexes = ("Male", "Female")
+    location = ["Kenya"]
+    years = [(2021, 2022), (2022, 2023), (2023, 2024)]  # Multiple years
+
+    age_bins, sexes, years, location = zip(*product(age_bins, sexes, years, location))
+    mins, maxes = zip(*age_bins)
+    year_starts, year_ends = zip(*years)
+
+    pop_structure = pd.DataFrame(
+        {
+            "location": location,
+            "sex": sexes,
+            "age_start": mins,
+            "age_end": maxes,
+            "year_start": year_starts,
+            "year_end": year_ends,
+            # Base values for each demographic group
+            "value": [1.0, 1.0, 2.0, 2.0, 3.0, 3.0, 4.0, 4.0] * 3,  # Repeated for 3 years
+        }
+    )
+
+    # Create scaling factor data based on test case
+    if test_case == "pop_structure":
+        # Scaling factor single year
+        scalar_data = pd.DataFrame(
+            {
+                "sex": ["Male", "Female"] * 4,
+                "age_start": [0.0, 0.0, 25.0, 25.0, 50.0, 50.0, 75.0, 75.0],
+                "age_end": [25.0, 25.0, 50.0, 50.0, 75.0, 75.0, 100.0, 100.0],
+                "year_start": [2021] * 8,
+                "year_end": [2022] * 8,
+                "value": [1.5, 1.2, 2.1, 1.8, 0.9, 1.1, 1.3, 1.4],
+            }
+        )
+        # Remove year_start and year end since scalar data only has one year
+        formatted_scalar_data = scalar_data.set_index(
+            ["sex", "age_start", "age_end"], drop=True
+        )[["value"]]
+    elif test_case == "both":
+        # Both have multiple years - should be able to multiply together directly
+        scalar_data = pd.DataFrame(
+            {
+                "age_start": [0.0, 0.0, 25.0, 25.0, 50.0, 50.0, 75.0, 75.0] * 3,
+                "age_end": [25.0, 25.0, 50.0, 50.0, 75.0, 75.0, 100.0, 100.0] * 3,
+                "sex": ["Male", "Female"] * 12,
+                "year_start": [2021] * 8 + [2022] * 8 + [2023] * 8,
+                "year_end": [2022] * 8 + [2023] * 8 + [2024] * 8,
+                "value": [
+                    1.0,
+                    1.0,
+                    1.0,
+                    1.0,
+                    1.0,
+                    1.0,
+                    1.0,
+                    1.0,
+                    1.5,
+                    1.2,
+                    2.1,
+                    1.8,
+                    0.9,
+                    1.1,
+                    1.3,
+                    1.4,
+                    1.8,
+                    1.4,
+                    2.3,
+                    2.0,
+                    1.2,
+                    1.6,
+                    1.7,
+                    1.9,
+                ],
+            }
+        )
+
+        # Subset to 2021 or subset to 2023 since that is latest year start to verify
+        # we are subsetting to correct year in _format_data_inputs
+        query_year = 2021 if year == 2021 else 2023
+        formatted_pop_structure = pop_structure.loc[pop_structure["year_start"] == query_year]
+        formatted_scalar_data = scalar_data.loc[scalar_data["year_start"] == query_year]
+        formatted_scalar_data = formatted_scalar_data.set_index(
+            ["sex", "age_start", "age_end", "year_start", "year_end"], drop=True
+        )
+        formatted_pop_structure = formatted_pop_structure.set_index(
+            ["location", "sex", "age_start", "age_end", "year_start", "year_end"]
+        )
+        scaled_pop = bp.ScaledPopulation("placeholder")
+        formatted = scaled_pop._format_data_inputs(pop_structure, scalar_data, year)
+        expected = (formatted[0] * formatted[1]).reset_index()
+        data = (formatted_pop_structure * formatted_scalar_data).reset_index()
+        pd.testing.assert_frame_equal(data, expected)
+
+
 def _check_population(simulants, initial_age, step_size, include_sex):
     assert len(simulants) == len(simulants.age.unique())
     assert simulants.age.min() > initial_age

vivarium_public_health-4.3.4/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.3.4"

vivarium_public_health-4.3.4/src/vivarium_public_health.egg-info/requires.txt

@@ -1,42 +0,0 @@
-vivarium_build_utils<3.0.0,>=2.0.1
-vivarium>=3.4.3
-layered_config_tree>=3.2.0
-loguru
-numpy<2.0.0
-pandas
-scipy
-tables
-risk_distributions>=2.0.11
-pyarrow
-
-[dev]
-sphinx<7.0
-sphinx-rtd-theme
-sphinx-click
-sphinx-autodoc-typehints
-IPython
-matplotlib
-vivarium_testing_utils
-pytest
-pytest-cov
-pytest-mock
-hypothesis
-pyyaml
-black==22.3.0
-isort==5.13.2
-
-[docs]
-sphinx<7.0
-sphinx-rtd-theme
-sphinx-click
-sphinx-autodoc-typehints
-IPython
-matplotlib
-
-[test]
-vivarium_testing_utils
-pytest
-pytest-cov
-pytest-mock
-hypothesis
-pyyaml