vivarium-public-health 3.2.0__tar.gz → 3.2.2__tar.gz

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/.readthedocs.yml

@@ -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

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**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
+
 **3.2.0 - 1/15/25**
 
  - Bugfix: Fix bug in LBWSGRiskEffect where relative risk pipeline was not properly created

vivarium_public_health-3.2.2/Jenkinsfile

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

vivarium_public_health-3.2.2/Makefile

@@ -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

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.2.0
+Version: 3.2.2
 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

vivarium_public_health-3.2.2/python_versions.json

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

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/setup.py

@@ -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(

vivarium_public_health-3.2.2/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.2.2"

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/src/vivarium_public_health/risks/implementations/low_birth_weight_and_short_gestation.py

@@ -371,11 +371,9 @@ 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-3.2.0 → vivarium_public_health-3.2.2}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.2.0
+Version: 3.2.2
 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

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/src/vivarium_public_health.egg-info/SOURCES.txt

@@ -14,6 +14,7 @@ MANIFEST.in
 Makefile
 README.rst
 pyproject.toml
+python_versions.json
 setup.py
 tox.ini
 .github/CODEOWNERS

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/src/vivarium_public_health.egg-info/requires.txt

@@ -22,7 +22,7 @@ pytest-mock
 hypothesis
 pyyaml
 black==22.3.0
-isort
+isort==5.13.2
 
 [docs]
 sphinx<7.0

{vivarium_public_health-3.2.0 → vivarium_public_health-3.2.2}/tests/risks/test_low_birth_weight_and_short_gestation.py

@@ -56,11 +56,15 @@ 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}.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 +122,9 @@ def test_lbwsg_risk_effect_rr_pipeline(
                 assert (actual_rr == 1.0).all()
 
 
-def make_categorical_exposure_data(data: pd.DataFrame) -> pd.DataFrame:
+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 +141,6 @@ 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-3.2.0/Jenkinsfile

@@ -1,2 +0,0 @@
-@Library("vivarium_build_utils") _
-reusable_pipeline(scheduled_branches: ["main"], test_types: ["integration"], python_versions: ["3.10", "3.11"])

vivarium_public_health-3.2.0/Makefile

@@ -1,104 +0,0 @@
-SHELL := /bin/bash
-this_makefile := $(lastword $(MAKEFILE_LIST)) # Used to automatically list targets
-.DEFAULT_GOAL := list # If someone runs "make", run "make list"
-
-# Source files to format, lint, and type check.
-LOCATIONS=src tests
-
-# Unless overridden, build conda environment using the package name.
-PACKAGE_NAME = vivarium_public_health
-SAFE_NAME = $(shell python -c "from pkg_resources import safe_name; print(safe_name(\"$(PACKAGE_NAME)\"))")
-
-setup_file   = $(shell find -name setup.py)
-version_line = $(shell grep "version = " ${setup_file})
-PACKAGE_VERSION = $(shell echo ${version_line} | cut -d "=" -f 2 | xargs)
-
-# Use this URL to pull IHME Python packages and deploy this package to PyPi.
-IHME_PYPI := https://artifactory.ihme.washington.edu/artifactory/api/pypi/pypi-shared/
-
-# If CONDA_ENV_PATH is set (from a Jenkins build), use the -p flag when making Conda env in
-# order to make env at specific path. Otherwise, make a named env at the default path using
-# the -n flag.
-PYTHON_VERSION ?= 3.11
-CONDA_ENV_NAME ?= ${PACKAGE_NAME}_py${PYTHON_VERSION}
-CONDA_ENV_CREATION_FLAG = $(if $(CONDA_ENV_PATH),-p ${CONDA_ENV_PATH},-n ${CONDA_ENV_NAME})
-
-# These are the doc and source code files in this repo.
-# When one of these files changes, it means that Make targets need to run again.
-MAKE_SOURCES := $(shell find . -type d -name "*" ! -path "./.git*" ! -path "./.vscode" ! -path "./output" ! -path "./output/*" ! -path "./archive" ! -path "./dist" ! -path "./output/htmlcov*" ! -path "**/.pytest_cache*" ! -path "**/__pycache__" ! -path "./output/docs_build*" ! -path "./.pytype*" ! -path "." ! -path "./src/${PACKAGE_NAME}/legacy*" ! -path ./.history ! -path "./.history/*" ! -path "./src/${PACKAGE_NAME}.egg-info" ! -path ./.idea ! -path "./.idea/*" )
-
-
-# Phony targets don't produce artifacts.
-.PHONY: .list-targets build-env clean debug deploy-doc deploy-package full help install list quick
-
-# List of Make targets is generated dynamically. To add description of target, use a # on the target definition.
-list help: debug .list-targets
-
-.list-targets: # Print available Make targets
-	@echo
-	@echo "Make targets:"
-	@grep -i "^[a-zA-Z][a-zA-Z0-9_ \.\-]*: .*[#].*" ${this_makefile} | sort | sed 's/:.*#/ : /g' | column -t -s:
-	@echo
-
-debug: # Print debug information (environment variables)
-	@echo "'make' invoked with these environment variables:"
-	@echo "CONDA_ENV_NAME:                   ${CONDA_ENV_NAME}"
-	@echo "IHME_PYPI:                        ${IHME_PYPI}"
-	@echo "LOCATIONS:                        ${LOCATIONS}"
-	@echo "PACKAGE_NAME:                     ${PACKAGE_NAME}"
-	@echo "PACKAGE_VERSION:                  ${PACKAGE_VERSION}"
-	@echo "PYPI_ARTIFACTORY_CREDENTIALS_USR: ${PYPI_ARTIFACTORY_CREDENTIALS_USR} "
-	@echo "Make sources:                     ${MAKE_SOURCES}"
-
-build-env: # Make a new conda environment
-	@[ "${CONDA_ENV_NAME}" ] && echo "" > /dev/null || ( echo "CONDA_ENV_NAME is not set"; exit 1 )
-	conda create ${CONDA_ENV_CREATION_FLAG} python=${PYTHON_VERSION} --yes
-
-install: # Install setuptools, install this package in editable mode
-	pip install --upgrade pip setuptools
-	pip install -e .[DEV]
-	@cd ..
-	@echo "----------------------------------------"
-	@if [ ! -d "vivarium_build_utils" ]; then \
-		# Clone the build utils repo if it doesn't exist. \
-		git clone https://github.com/ihmeuw/vivarium_build_utils.git; \
-	else \
-		echo "vivarium_build_utils already exists. Skipping clone."; \
-	fi
-	@echo "Contents of install_dependency_branch.sh"
-	@echo "----------------------------------------"
-	@cat vivarium_build_utils/install_dependency_branch.sh
-	@echo ""
-	@echo "----------------------------------------"
-	@sh vivarium_build_utils/install_dependency_branch.sh vivarium ${GIT_BRANCH} jenkins
-	@sh vivarium_build_utils/install_dependency_branch.sh layered_config_tree ${GIT_BRANCH} jenkins
-	@sh vivarium_build_utils/install_dependency_branch.sh risk_distributions ${GIT_BRANCH} jenkins
-
-format: setup.py pyproject.toml $(MAKE_SOURCES) # Run the code formatter and import sorter
-	black $(LOCATIONS)
-	isort $(LOCATIONS)
-	@echo "Ignore, Created by Makefile, `date`" > $@
-
-lint: .flake8 .bandit $(MAKE_SOURCES) # Run the code linter and package security vulnerability checker
-	-flake8 $(LOCATIONS)
-	-safety check
-	@echo "Ignore, Created by Makefile, `date`" > $@
-
-integration: $(MAKE_SOURCES) # Run the end-to-end tests
-	export COVERAGE_FILE=./output/.coverage.integration
-	pytest --runslow tests --cov --cov-report term --cov-report html:./output/htmlcov_integration
-	@echo "Ignore, Created by Makefile, `date`" > $@
-
-build-doc: $(MAKE_SOURCES) # Build the Sphinx docs
-	$(MAKE) -C docs/ html
-	@echo "Ignore, Created by Makefile, `date`" > $@
-
-build-package: $(MAKE_SOURCES) # Build the package as a pip wheel
-	pip install build
-	python -m build
-	@echo "Ignore, Created by Makefile, `date`" > $@
-
-clean: # Delete build artifacts and do any custom cleanup such as spinning down services
-	@rm -rf format lint build-doc build-package integration .pytest_cache
-	@rm -rf dist output
-	$(shell find . -type f -name '*py[co]' -delete -o -type d -name __pycache__ -delete)

vivarium_public_health-3.2.0/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "3.2.0"