vivarium-public-health 4.2.4__tar.gz → 4.2.6__tar.gz

{vivarium_public_health-4.2.4 → vivarium_public_health-4.2.6}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**4.2.6 - 07/25/25**
+
+  - Feature: Support new environment creation via 'make build-env'
+
+**4.2.5 - 07/18/25**
+
+  - Hush FutureWarnings: add include_groups=False to apply call in StratifiedObservation
+
 **4.2.4 - 07/16/25**
 
   - Support pinning of vivarium_build_utils; pin vivarium_build_utils>=1.1.0,<2.0.0

vivarium_public_health-4.2.6/Makefile

@@ -0,0 +1,69 @@
+# Check if we're running in Jenkins
+ifdef JENKINS_URL
+# 	Files are already in workspace from shared library
+	MAKE_INCLUDES := .
+else
+# 	For local dev, use the installed vivarium_build_utils package if it exists
+# 	First, check if we can import vivarium_build_utils and assign 'yes' or 'no'.
+# 	We do this by importing the package in python and redirecting stderr to the null device.
+# 	If the import is successful (&&), it will print 'yes', otherwise (||) it will print 'no'.
+	VIVARIUM_BUILD_UTILS_AVAILABLE := $(shell python -c "import vivarium_build_utils" 2>/dev/null && echo "yes" || echo "no")
+# 	If vivarium_build_utils is available, get the makefiles path or else set it to empty
+	ifeq ($(VIVARIUM_BUILD_UTILS_AVAILABLE),yes)
+		MAKE_INCLUDES := $(shell python -c "from vivarium_build_utils.resources import get_makefiles_path; print(get_makefiles_path())")
+	else
+		MAKE_INCLUDES :=
+	endif
+endif
+
+# Set the package name as the last part of this file's parent directory path
+PACKAGE_NAME = $(notdir $(CURDIR))
+
+ifneq ($(MAKE_INCLUDES),) # not empty
+# Include makefiles from vivarium_build_utils
+include $(MAKE_INCLUDES)/base.mk
+include $(MAKE_INCLUDES)/test.mk
+else # empty
+# Use this help message (since the vivarium_build_utils version is not available)
+help:
+	@echo
+	@echo "For Make's standard help, run 'make --help'."
+	@echo
+	@echo "Most of our Makefile targets are provided by the vivarium_build_utils"
+	@echo "package. To access them, you need to create a development environment first."
+	@echo
+	@echo "make build-env"
+	@echo
+	@echo "USAGE:"
+	@echo "  make build-env name=<environment_name> [py=<python_version>]"
+	@echo
+	@echo "ARGUMENTS:"
+	@echo "  name  [required]  Name of the conda environment to create"
+	@echo "  py    [optional]  Python version (defaults to latest supported)"
+	@echo
+	@echo "EXAMPLE:"
+	@echo "  make build-env name=vivarium_dev"
+	@echo "  make build-env name=vivarium_dev py=3.9"
+	@echo
+	@echo "After creating the environment:"
+	@echo "  1. Activate it: 'conda activate <environment_name>'"
+	@echo "  2. Run 'make help' again to see all newly available targets"
+	@echo
+endif
+
+build-env: # Create a new environment with installed packages
+ifndef name
+	@echo "Error: name is required and must be passed in as a keyword argument."
+	@echo "Usage: make build-env name=<ENV_NAME> py=<PYTHON_VERSION>"
+	@exit 1
+endif
+#	Check if py is set, otherwise use the latest supported version
+	@$(eval py ?= $(shell python -c "import json; versions = json.load(open('python_versions.json')); print(max(versions, key=lambda x: tuple(map(int, x.split('.')))))"))
+	conda create -n $(name) python=$(py) --yes
+# 	Bootstrap vivarium_build_utils into the new environment
+	conda run -n $(name) pip install vivarium_build_utils
+	conda run -n $(name) make install
+	@echo
+	@echo "Environment built ($(name))"
+	@echo "Don't forget to activate it with: 'conda activate $(name)'"
+	@echo

{vivarium_public_health-4.2.4 → vivarium_public_health-4.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.2.4
+Version: 4.2.6
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,12 +26,12 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
-Requires-Dist: vivarium_build_utils<2.0.0,>=1.1.0
+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: pandas>=2.2.0
 Requires-Dist: scipy
 Requires-Dist: tables
 Requires-Dist: risk_distributions>=2.0.11

{vivarium_public_health-4.2.4 → vivarium_public_health-4.2.6}/setup.py

@@ -42,12 +42,12 @@ if __name__ == "__main__":
         long_description = f.read()
 
     install_requirements = [
-        "vivarium_build_utils>=1.1.0,<2.0.0",
+        "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",
+        "pandas>=2.2.0",
         "scipy",
         "tables",
         "risk_distributions>=2.0.11",

vivarium_public_health-4.2.6/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.2.6"

{vivarium_public_health-4.2.4 → vivarium_public_health-4.2.6}/src/vivarium_public_health/population/data_transformations.py

@@ -54,21 +54,27 @@ def assign_demographic_proportions(
 
     population_data["P(sex, location, age| year)"] = (
         population_data.groupby("year_start", as_index=False)
-        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
+        .apply(
+            lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum(), include_groups=False
+        )
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )
 
     population_data["P(sex, location | age, year)"] = (
         population_data.groupby(["age", "year_start"], as_index=False)
-        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
+        .apply(
+            lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum(), include_groups=False
+        )
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )
 
     population_data["P(age | year, sex, location)"] = (
         population_data.groupby(["year_start", "sex", "location"], as_index=False)
-        .apply(lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum())
+        .apply(
+            lambda sub_pop: sub_pop[["value"]] / sub_pop["value"].sum(), include_groups=False
+        )
         .reset_index(level=0)["value"]
         .fillna(0.0)
     )

{vivarium_public_health-4.2.4 → vivarium_public_health-4.2.6}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.2.4
+Version: 4.2.6
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,12 +26,12 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Classifier: Topic :: Scientific/Engineering :: Physics
 Classifier: Topic :: Software Development :: Libraries
 License-File: LICENSE.txt
-Requires-Dist: vivarium_build_utils<2.0.0,>=1.1.0
+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: pandas>=2.2.0
 Requires-Dist: scipy
 Requires-Dist: tables
 Requires-Dist: risk_distributions>=2.0.11

{vivarium_public_health-4.2.4 → vivarium_public_health-4.2.6}/src/vivarium_public_health.egg-info/requires.txt

@@ -1,9 +1,9 @@
-vivarium_build_utils<2.0.0,>=1.1.0
+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
+pandas>=2.2.0
 scipy
 tables
 risk_distributions>=2.0.11

vivarium_public_health-4.2.4/Makefile

@@ -1,14 +0,0 @@
-# Check if we're running in Jenkins
-ifdef JENKINS_URL
-	# Files are already in workspace from shared library
-	MAKE_INCLUDES := .
-else
-	# For local dev, use the installed vivarium_build_utils package
-	MAKE_INCLUDES := $(shell python -c "from vivarium_build_utils.resources import get_makefiles_path; print(get_makefiles_path())")
-endif
-
-PACKAGE_NAME = vivarium_public_health
-
-# Include makefiles from vivarium_build_utils
-include $(MAKE_INCLUDES)/base.mk
-include $(MAKE_INCLUDES)/test.mk

vivarium_public_health-4.2.4/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.2.4"