vivarium-public-health 4.2.3__tar.gz → 4.2.5__tar.gz

{vivarium_public_health-4.2.3 → vivarium_public_health-4.2.5}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**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
+
 **4.2.3 - 07/11/25**
 
   - Bugfix: Update FertilityCrudeBirthRate to properly check deprecated age_end configuration key

vivarium_public_health-4.2.5/Jenkinsfile

@@ -0,0 +1,34 @@
+/* This Jenkinsfile simply loads the `reusable_pipeline` pipeline from the
+vivariu_build_utils repository (https://github.com/ihmeuw/vivarium_build_utils).
+
+vivarium_build_utils is loaded as a Jenkins shared library 
+(https://www.jenkins.io/doc/book/pipeline/shared-libraries/).
+Jenkins shared library convention dictates that importable modules must be stored
+in the 'vars' folder.
+
+Jenkins shared libraries can be configured in the Jenkins UI:
+* Manage Jenkins
+  * Configure System
+    * Global Pipeline Libraries section
+      * Library subsection
+        * Name: The Name for the lib
+        * Version: The branch you want to use. Throws an error
+                   for nonexistent branches.
+        * Project Repository: Url to the shared lib
+        * Credentials: SSH key to access the repo
+
+Note that updating the shared repo will take affect on the next pipeline invocation.
+*/ 
+
+// Load the get_vbu_version function from vivarium_build_utils/bootstrap/
+// (the directory to load from is defined in the Jenkins shared library configuration)
+@Library("get_vbu_version@main") _
+
+// Load the full vivarium_build_utils library at the expected version
+library("vivarium_build_utils@${get_vbu_version()}")
+
+reusable_pipeline(
+    scheduled_branches: ["main"], 
+    upstream_repos: ["vivarium", "layered_config_tree", "risk_distributions"],
+    run_mypy: false,
+)

{vivarium_public_health-4.2.3 → vivarium_public_health-4.2.5}/Makefile

@@ -3,11 +3,12 @@ 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
+	# 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-4.2.3 → vivarium_public_health-4.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.2.3
+Version: 4.2.5
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,11 +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>=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-4.2.3 → vivarium_public_health-4.2.5}/setup.py

@@ -42,11 +42,12 @@ if __name__ == "__main__":
         long_description = f.read()
 
     install_requirements = [
+        "vivarium_build_utils>=1.1.0,<2.0.0",
         "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-4.2.5/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "4.2.5"

{vivarium_public_health-4.2.3 → vivarium_public_health-4.2.5}/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-4.2.3 → vivarium_public_health-4.2.5}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vivarium_public_health
-Version: 4.2.3
+Version: 4.2.5
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -26,11 +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>=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-4.2.3 → vivarium_public_health-4.2.5}/src/vivarium_public_health.egg-info/requires.txt

@@ -1,8 +1,9 @@
+vivarium_build_utils<2.0.0,>=1.1.0
 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-4.2.3/Jenkinsfile

@@ -1,6 +0,0 @@
-@Library("vivarium_build_utils") _
-reusable_pipeline(
-    scheduled_branches: ["main"], 
-    upstream_repos: ["vivarium", "layered_config_tree", "risk_distributions"],
-    run_mypy: false,
-)

vivarium_public_health-4.2.3/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "4.2.3"