vivarium-public-health 3.0.1__tar.gz → 3.0.3__tar.gz

{vivarium_public_health-3.0.1 → vivarium_public_health-3.0.3}/.github/workflows/build.yml

@@ -41,21 +41,21 @@ jobs:
         run: |
           pip install .[dev]
           git checkout ${branch_name}
-      - name: check for upstream branch
+      - name: check for dependency branches and install if needed
         run: |
-          sh get_upstream_branch.sh ${branch_name}
+          cd ..
+          git clone https://github.com/ihmeuw/vivarium_build_utils.git
+          cd vivarium_public_health
+          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 layered_config_tree ${branch_name}
+          sh ../vivarium_build_utils/install_dependency_branch.sh vivarium ${branch_name}
       - name: print environment values
         run: |
           cat $GITHUB_ENV
-      - name: Retrieve vivarium branch
-        if: env.vivarium_branch_name != 'main'
-        run: |
-          echo "Cloning upstream branch: ${vivarium_branch_name}"
-          pushd ..
-          git clone --branch=${vivarium_branch_name} https://github.com/ihmeuw/vivarium.git
-          pushd vivarium
-          pip install .
-          popd && popd
       - name: Lint
         run: |
           pip install black==22.3.0 isort

{vivarium_public_health-3.0.1 → vivarium_public_health-3.0.3}/CHANGELOG.rst

@@ -1,3 +1,13 @@
+**3.0.3- 08/20/24**
+
+ - Use external script to find matching dependency branches
+ - Fix bug when excluding all but one causes of disability from results
+ - Update FertilityAgeSpecificRates for new data format of age specific fertility rates
+
+**3.0.2- 08/19/24**
+
+ - Parameterize the script to find matching dependency branches
+
 **3.0.1 - 08/19/24**
 
  - Fix bug in build script when the upstream vivarium branch should be main
@@ -56,11 +66,11 @@ Other changes:
 
  - Implement CausesConfigurationParser to parse causes configuration into DiseaseModel components
  - Bugfix assign sex-location-age demographic proportions by year when only one year in dataset
- 
+
 **2.1.4 - 01/10/24**
 
  - Exclude undesirable arguments from the return of `BaseDiseaseState` `name` and `__repr__` methods
- 
+
 **2.1.3 - 01/09/24**
 
  - Update PyPI to 2FA with trusted publisher
@@ -237,7 +247,7 @@ Other changes:
 **0.10.3 - 12/13/19**
 
  - Fix regression bug in SIR_fixed_duration.
- 
+
 **0.10.2 - 11/29/19**
 
  - Fix disease observer bug that prevented it from loading its configuration.

{vivarium_public_health-3.0.1/src/vivarium_public_health.egg-info → vivarium_public_health-3.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.1
+Version: 3.0.3
 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-3.0.3/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.0.3"

{vivarium_public_health-3.0.1 → vivarium_public_health-3.0.3}/src/vivarium_public_health/population/add_new_birth_cohorts.py

@@ -204,8 +204,10 @@ class FertilityAgeSpecificRates(Component):
 
     def load_age_specific_fertility_rate_data(self, builder: Builder) -> pd.DataFrame:
         asfr_data = builder.data.load("covariate.age_specific_fertility_rate.estimate")
-        columns = ["year_start", "year_end", "age_start", "age_end", "mean_value"]
-        asfr_data = asfr_data.loc[asfr_data.sex == "Female"][columns]
+        columns = ["year_start", "year_end", "age_start", "age_end", "value"]
+        asfr_data = asfr_data.loc[
+            (asfr_data.sex == "Female") & (asfr_data.parameter == "mean_value")
+        ].reset_index()[columns]
         return asfr_data
 
     ########################

{vivarium_public_health-3.0.1 → vivarium_public_health-3.0.3}/src/vivarium_public_health/results/disability.py

@@ -158,11 +158,18 @@ class DisabilityObserver(PublicHealthObserver):
         once), and so the results here are actually wide by disability weight
         pipeline name.
         """
-
-        # Drop the unused 'value' column and rename the pipeline names to causes
-        results = results.drop(columns=["value"]).rename(
-            columns={col: col.replace(".disability_weight", "") for col in results.columns},
-        )
+        if len(self.causes_of_disability) > 1:
+            # Drop the unused 'value' column and rename the remaining pipeline names to cause names
+            results = results.rename(
+                columns={
+                    col: col.replace(".disability_weight", "") for col in results.columns
+                }
+            )[[col.state_id for col in self.causes_of_disability]]
+        else:
+            # Rename the 'value' column to the single cause of disability
+            results = results.rename(
+                columns={COLUMNS.VALUE: self.causes_of_disability[0].state_id}
+            )
         # Get desired index names prior to stacking
         idx_names = list(results.index.names) + [COLUMNS.SUB_ENTITY]
         results = pd.DataFrame(results.stack(), columns=[COLUMNS.VALUE])

{vivarium_public_health-3.0.1 → vivarium_public_health-3.0.3/src/vivarium_public_health.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.1
+Version: 3.0.3
 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-3.0.1 → vivarium_public_health-3.0.3}/src/vivarium_public_health.egg-info/SOURCES.txt

@@ -13,7 +13,6 @@ LICENSE.txt
 MANIFEST.in
 Makefile
 README.rst
-get_upstream_branch.sh
 pyproject.toml
 setup.py
 tox.ini

{vivarium_public_health-3.0.1 → vivarium_public_health-3.0.3}/tests/population/test_add_new_birth_cohort.py

@@ -180,7 +180,13 @@ def test_fertility_module(base_config, base_plugins):
         setup=False,
     )
 
-    asfr_data = build_table_with_age(0.05).rename(columns={"value": "mean_value"})
+    asfr_data = build_table_with_age(
+        0.05,
+        key_columns={
+            "sex": ("Female", "Male"),
+            "parameter": ("lower_value", "mean_value", "upper_value"),
+        },
+    )
     simulation._data.write("covariate.age_specific_fertility_rate.estimate", asfr_data)
 
     simulation.setup()

{vivarium_public_health-3.0.1 → vivarium_public_health-3.0.3}/tests/results/test_disability_observer.py

@@ -278,17 +278,20 @@ def test_set_causes_of_disability_raises(mocker):
         observer.setup_component(builder)
 
 
-# FIXME: error when excluding all but one disability
-@pytest.mark.parametrize("exclusions", [[], ["all_causes"], ["all_causes", "sick_cause_0"]])
+@pytest.mark.parametrize(
+    "exclusions",
+    [
+        [],
+        ["all_causes"],
+        ["all_causes", "sick_cause_0"],
+    ],
+)
 def test_category_exclusions(
     base_config,
     base_plugins,
     exclusions,
 ):
     """Integration test for the disability observer and the Results Management system."""
-
-    if len(exclusions) == 2:
-        pytest.skip(reason="FIXME: error when excluding all but one disability")
     year_start = base_config.time.start.year
     year_end = base_config.time.end.year
 

vivarium_public_health-3.0.1/get_upstream_branch.sh

@@ -1,40 +0,0 @@
-#!/bin/bash
-
-# Define variables
-branch_name=$1
-
-vivarium_branch_name='main'
-branch_name_to_check=${branch_name}
-iterations=0
-
-while [ "$branch_name_to_check" != "$vivarium_branch_name" ] && [ $iterations -lt 20 ]
-do
-  echo "Checking for vivarium branch: '${branch_name_to_check}'"
-  if
-    git ls-remote --exit-code \
-    --heads https://github.com/ihmeuw/vivarium.git ${branch_name_to_check} == "0"
-  then
-    vivarium_branch_name=${branch_name_to_check}
-    echo "Found matching branch: ${vivarium_branch_name}"
-  else
-    echo "Could not find upstream branch '${branch_name_to_check}'. Finding parent branch."
-    branch_name_to_check="$( \
-      git show-branch -a \
-      | grep '\*' \
-      | grep -v `git rev-parse --abbrev-ref HEAD` \
-      | head -n1 \
-      | sed 's/[^\[]*//' \
-      | awk 'match($0, /\[[a-zA-Z0-9\/.-]+\]/) { print substr( $0, RSTART+1, RLENGTH-2 )}' \
-      | sed 's/^origin\///' \
-    )"
-    if [ -z "$branch_name_to_check" ]; then
-      echo "Could not find upstream branch. Will use released version."
-      branch_name_to_check="main"
-    fi
-    echo "Checking out branch: ${branch_name_to_check}"
-    git checkout ${branch_name_to_check}
-    iterations=$((iterations+1))
-  fi
-  done
-  echo "vivarium_branch_name=${vivarium_branch_name}" >> $GITHUB_ENV
-  git checkout ${branch_name}

vivarium_public_health-3.0.1/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "3.0.1"