PyPI - vivarium-public-health - Versions diffs - 3.1.5__tar.gz → 3.2.1__tar.gz - Mend

@@ -361,18 +361,11 @@ class LBWSGRiskEffect(RiskEffect):
         paf_data = builder.data.load(paf_key)
         return paf_data, builder.data.value_columns()(paf_key)
-    def get_target_modifier(
-        self, builder: Builder
-    ) -> Callable[[pd.Index, pd.Series], pd.Series]:
-        def adjust_target(index: pd.Index, target: pd.Series) -> pd.Series:
-            return target * self.relative_risk(index)
-        return adjust_target
     def register_target_modifier(self, builder: Builder) -> None:
         builder.value.register_value_modifier(
             self.target_pipeline_name,
-            modifier=self.target_modifier,
+            modifier=self.adjust_target,
+            component=self,
             requires_values=[self.relative_risk_pipeline_name],
         )
@@ -392,11 +385,12 @@ class LBWSGRiskEffect(RiskEffect):
             for age_start in exposed_age_group_starts
         }
-    def get_relative_risk(self, builder: Builder) -> Pipeline:
+    def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
         return builder.value.register_value_producer(
             self.relative_risk_pipeline_name,
-            source=self.get_relative_risk_source,
-            requires_columns=["age"] + self.rr_column_names,
+            source=self._relative_risk_source,
+            component=self,
+            required_resources=["age"] + self.rr_column_names,
         )
     def get_interpolator(self, builder: Builder) -> pd.Series:
@@ -469,7 +463,7 @@ class LBWSGRiskEffect(RiskEffect):
     # Pipeline sources and modifiers #
     ##################################
-    def get_relative_risk_source(self, index: pd.Index) -> pd.Series:
+    def _get_relative_risk(self, index: pd.Index) -> pd.Series:
         pop = self.population_view.get(index)
         relative_risk = pd.Series(1.0, index=index, name=self.relative_risk_pipeline_name)
@@ -479,3 +473,6 @@ class LBWSGRiskEffect(RiskEffect):
                 age_group_mask, self.relative_risk_column_name(age_group)
             ]
         return relative_risk
+    def get_relative_risk_source(self, builder: Builder) -> Callable[[pd.Index], pd.Series]:
+        return self._get_relative_risk

@@ -1,6 +1,10 @@
 # This is the version for the readthedocs configuration. Version 2 ignores
 # web-based configuration and uses everything from this file.
 version: 2
+# Doc builds will fail if there are any warnings
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: true
 # Configure the python version and environment construction run before
 # docs are built.
@@ -15,7 +19,3 @@ python:
       path: .
       extra_requirements:
         - docs
-# Doc builds will fail if there are any warnings
-sphinx:
-  fail_on_warning: true

@@ -1,3 +1,11 @@
+**3.2.1 - 1/30/25**
+ - Get python versions from python_versions.json
+**3.2.0 - 1/15/25**
+ - Bugfix: Fix bug in LBWSGRiskEffect where relative risk pipeline was not properly created
 **3.1.5 - 01/14/25**
  - Bugfix: Vivarium InteractiveContext no longer returns int

@@ -0,0 +1,4 @@
+@Library("vivarium_build_utils") _
+reusable_pipeline(scheduled_branches: ["main"],
+                  upstream_repos: ["vivarium", "layered_config_tree", "risk_distributions"],
+                 )

@@ -0,0 +1,13 @@
+# Check if we're running in Jenkins
+ifdef JENKINS_URL
+	# Files are already in workspace from shared library
+	MAKE_INCLUDES := .
+else
+	# For local dev, search in parent directory
+	MAKE_INCLUDES := ../vivarium_build_utils/resources/makefiles
+endif
+PACKAGE_NAME = vivarium_public_health
+include $(MAKE_INCLUDES)/base.mk
+include $(MAKE_INCLUDES)/test.mk

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.1.5
+Version: 3.2.1
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -63,7 +63,7 @@ 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; extra == "dev"
+Requires-Dist: isort==5.13.2; extra == "dev"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

@@ -1,8 +1,35 @@
 #!/usr/bin/env python
+import json
 import os
+import sys
+from packaging.version import parse
 from setuptools import find_packages, setup
+with open("python_versions.json", "r") as f:
+    supported_python_versions = json.load(f)
+python_versions = [parse(v) for v in supported_python_versions]
+min_version = min(python_versions)
+max_version = max(python_versions)
+if not (
+    min_version <= parse(".".join([str(v) for v in sys.version_info[:2]])) <= max_version
+):
+    py_version = ".".join([str(v) for v in sys.version_info[:3]])
+    # NOTE: Python 3.5 does not support f-strings
+    error = (
+        "\n--------------------------------------------\n"
+        "Error: Vivarium Public Health runs under python {min_version}-{max_version}.\n"
+        "You are running python {py_version}.\n".format(
+            min_version=min_version.base_version,
+            max_version=max_version.base_version,
+            py_version=py_version,
+        )
+        + "--------------------------------------------\n"
+    )
+    print(error, file=sys.stderr)
+    sys.exit(1)
 if __name__ == "__main__":
     base_dir = os.path.dirname(__file__)
     src_dir = os.path.join(base_dir, "src")
@@ -48,7 +75,7 @@ if __name__ == "__main__":
     lint_requirements = [
         "black==22.3.0",
-        "isort",
+        "isort==5.13.2",
     ]
     setup(

@@ -114,7 +114,7 @@ class RiskEffect(Component):
         self.exposure = self.get_risk_exposure(builder)
         self._relative_risk_source = self.get_relative_risk_source(builder)
-        self.relative_risk = self.get_relative_risk(builder)
+        self.relative_risk = self.get_relative_risk_pipeline(builder)
         self.register_target_modifier(builder)
         self.register_paf_modifier(builder)
@@ -297,7 +297,7 @@ class RiskEffect(Component):
         return generate_relative_risk
-    def get_relative_risk(self, builder: Builder) -> Pipeline:
+    def get_relative_risk_pipeline(self, builder: Builder) -> Pipeline:
         return builder.value.register_value_producer(
             f"{self.risk.name}_on_{self.target.name}.relative_risk",
             self._relative_risk_source,

@@ -14,6 +14,7 @@ MANIFEST.in
 Makefile
 README.rst
 pyproject.toml
+python_versions.json
 setup.py
 tox.ini
 .github/CODEOWNERS
@@ -124,6 +125,7 @@ tests/__init__.py
 tests/conftest.py
 tests/mock_artifact.py
 tests/test_utilities.py
+tests/data/rr_interpolator.csv
 tests/disease/__init__.py
 tests/disease/test_disease.py
 tests/disease/test_special_disease.py

	@@ -0,0 +1 @@
1	+ ["3.10", "3.11"]

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

vivarium-public-health 3.1.5__tar.gz → 3.2.1__tar.gz

vivarium-public-health 3.1.5tar.gz → 3.2.1tar.gz