vivarium-public-health 3.2.1__tar.gz → 4.0.0__tar.gz

{vivarium_public_health-3.2.1 → vivarium_public_health-4.0.0}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**4.0.0 - 03/17/25**
+
+ - Feature: Use birth exposure artifact key for LBWSG components
+
+**3.2.2 - 2/21/25**
+
+ - Bugfix: Use relative risk data to get age intervals for LBWSGRiskEffect
+
 **3.2.1 - 1/30/25**
 
  - Get python versions from python_versions.json

{vivarium_public_health-3.2.1 → vivarium_public_health-4.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.2.1
+Version: 4.0.0
 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-4.0.0/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.0.0"

{vivarium_public_health-3.2.1 → vivarium_public_health-4.0.0}/src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -202,6 +202,9 @@ class LBWSGRisk(Risk):
     @property
     def configuration_defaults(self) -> dict[str, Any]:
         configuration_defaults = super().configuration_defaults
+        configuration_defaults[self.name]["data_sources"][
+            "exposure"
+        ] = f"{self.risk}.birth_exposure"
         configuration_defaults[self.name]["distribution_type"] = "lbwsg"
         return configuration_defaults
 
@@ -371,11 +374,9 @@ class LBWSGRiskEffect(RiskEffect):
 
     def get_age_intervals(self, builder: Builder) -> dict[str, pd.Interval]:
         age_bins = builder.data.load("population.age_bins").set_index("age_start")
-        exposure = builder.data.load(f"{self.risk}.exposure")
-        exposure = exposure[exposure["age_end"] > 0]
-
+        relative_risks = builder.data.load(f"{self.risk}.relative_risk")
         exposed_age_group_starts = (
-            exposure.groupby("age_start")["value"].any().reset_index()["age_start"]
+            relative_risks.groupby("age_start")["value"].any().reset_index()["age_start"]
         )
 
         return {

{vivarium_public_health-3.2.1 → vivarium_public_health-4.0.0}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.2.1
+Version: 4.0.0
 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-3.2.1 → vivarium_public_health-4.0.0}/src/vivarium_public_health.egg-info/SOURCES.txt

@@ -19,7 +19,6 @@ setup.py
 tox.ini
 .github/CODEOWNERS
 .github/pull_request_template.md
-.github/workflows/build.yml
 .github/workflows/deploy.yml
 docs/Makefile
 docs/nitpick-exceptions

{vivarium_public_health-3.2.1 → vivarium_public_health-4.0.0}/tests/risks/test_low_birth_weight_and_short_gestation.py

@@ -41,9 +41,7 @@ def test_parsing_lbwsg_descriptions(description, expected_weight_values, expecte
     assert age_interval.right == expected_age_values[1]
 
 
-def test_lbwsg_risk_effect_rr_pipeline(
-    base_config, base_plugins, mocker, mock_rr_interpolators
-):
+def test_lbwsg_risk_effect_rr_pipeline(base_config, base_plugins, mock_rr_interpolators):
 
     risk = LBWSGRisk()
     lbwsg_effect = LBWSGRiskEffect("cause.test_cause.cause_specific_mortality_rate")
@@ -56,11 +54,15 @@ def test_lbwsg_risk_effect_rr_pipeline(
     # Create exposure with matching demograph index as age_bins
     age_bins = make_age_bins()
     agees = age_bins.drop(columns="age_group_name")
-    exposure_data = make_categorical_exposure_data(agees)
+    # Have to match age bins and rr data to make age intervals
+    rr_data = make_categorical_data(agees)
+    # Exposure data used for risk component
+    exposure = make_categorical_data(agees)
 
     # Add data dict to add to artifact
     data = {
-        f"{risk.name}.exposure": exposure_data,
+        f"{risk.name}.birth_exposure": exposure,
+        f"{risk.name}.relative_risk": rr_data,
         f"{risk.name}.population_attributable_fraction": 0,
         f"{risk.name}.categories": categories,
         f"{risk.name}.relative_risk_interpolator": mock_rr_interpolators,
@@ -118,9 +120,62 @@ def test_lbwsg_risk_effect_rr_pipeline(
                 assert (actual_rr == 1.0).all()
 
 
-def make_categorical_exposure_data(data: pd.DataFrame) -> pd.DataFrame:
+def test_use_birth_exposure(base_config, base_plugins, mock_rr_interpolators):
+    risk = LBWSGRisk()
+    lbwsg_effect = LBWSGRiskEffect("cause.test_cause.cause_specific_mortality_rate")
+
+    # Add mock data to artifact
+    categories = {
+        "cat81": "Neonatal preterm and LBWSG (estimation years) - [28, 30) wks, [2500, 3000) g",
+        "cat82": "Neonatal preterm and LBWSG (estimation years) - [28, 30) wks, [3000, 3500) g",
+    }
+    # Create exposure with matching demograph index as age_bins
+    age_bins = make_age_bins()
+    ages = age_bins.drop(columns="age_group_name")
+    # Have to match age bins and rr data to make age intervals
+    rr_data = make_categorical_data(ages)
+    # Format birth exposure data
+    exposure = pd.DataFrame(
+        {
+            "sex": ["Male", "Female", "Male", "Female"],
+            "year_start": [2021, 2021, 2021, 2021],
+            "year_end": [2022, 2022, 2022, 2022],
+            "parameter": ["cat81", "cat81", "cat82", "cat82"],
+            "value": [0.75, 0.75, 0.25, 0.25],
+        }
+    )
+
+    # Add data dict to add to artifact
+    data = {
+        f"{risk.name}.birth_exposure": exposure,
+        f"{risk.name}.relative_risk": rr_data,
+        f"{risk.name}.population_attributable_fraction": 0,
+        f"{risk.name}.categories": categories,
+        f"{risk.name}.relative_risk_interpolator": mock_rr_interpolators,
+    }
+
+    # Only have neontal age groups
+    age_start = 0.0
+    age_end = 1.0
+    base_config.update(
+        {
+            "population": {
+                "initialization_age_start": age_start,
+                "initialization_age_max": age_end,
+            }
+        }
+    )
+    sim = _setup_risk_effect_simulation(base_config, base_plugins, risk, lbwsg_effect, data)
+    pop = sim.get_population()
+
+    # Assert LBWSG birth exposure columns were created
+    assert "birth_weight_exposure" in pop.columns
+    assert "gestational_age_exposure" in pop.columns
+
+
+def make_categorical_data(data: pd.DataFrame) -> pd.DataFrame:
     # Takes age gropus and adds sex, years, categories, and values
-    exposure_dfs = []
+    dfs = []
     for year in range(1990, 2017):
         tmp = data.copy()
         tmp["year_start"] = year
@@ -137,6 +192,6 @@ def make_categorical_exposure_data(data: pd.DataFrame) -> pd.DataFrame:
         female_tmp = categories_df.copy()
         female_tmp["sex"] = "Female"
         age_sex_df = pd.concat([male_tmp, female_tmp])
-        exposure_dfs.append(age_sex_df)
+        dfs.append(age_sex_df)
 
-    return pd.concat(exposure_dfs)
+    return pd.concat(dfs)

vivarium_public_health-3.2.1/.github/workflows/build.yml

@@ -1,26 +0,0 @@
-# -----------------------------------------------------------------------------
-#   - invoked on push, pull_request, manual trigger, or schedule
-#   - test under at least 3 versions of python
-# -----------------------------------------------------------------------------
-name: build
-on:
-  push:
-  pull_request:
-  workflow_dispatch:
-  schedule:
-    - cron: "0 8 * * *"
-  
-jobs:
-  build:
-    strategy:
-      matrix:
-        python-version: ["3.10", "3.11"]
-    uses: 
-      ihmeuw/vivarium_build_utils/.github/workflows/build.yml@main
-    with:
-      dependencies: "layered_config_tree,vivarium"
-      skip_mypy: true
-      python_version: ${{ matrix.python-version }}
-    secrets:
-      NOTIFY_EMAIL: ${{ secrets.NOTIFY_EMAIL }}
-      NOTIFY_PASSWORD: ${{ secrets.NOTIFY_PASSWORD }}

vivarium_public_health-3.2.1/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "3.2.1"