vivarium-public-health 3.0.9__tar.gz → 3.0.11__tar.gz

vivarium_public_health-3.0.11/.github/workflows/build.yml

@@ -0,0 +1,25 @@
+# -----------------------------------------------------------------------------
+#   - invoked on push, pull_request, manual trigger, or schedule
+#   - test under at least 3 versions of python
+# -----------------------------------------------------------------------------
+name: build
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 8 * * *"
+  
+jobs:
+  build:
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+    uses: 
+      ihmeuw/vivarium_build_utils/.github/workflows/build.yml@main
+    with:
+      dependencies: "layered_config_tree,vivarium"
+      skip_mypy: true
+    secrets:
+      NOTIFY_EMAIL: ${{ secrets.NOTIFY_EMAIL }}
+      NOTIFY_PASSWORD: ${{ secrets.NOTIFY_PASSWORD }}

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/CHANGELOG.rst

@@ -1,3 +1,11 @@
+**3.0.11 - 11/07/24**
+
+ - Add ScaledPopulation component to population package
+
+**3.0.10 - 10/29/24**
+
+ - Import subpackage classes to top-level namespace
+
 **3.0.9 - 09/12/24**
 
  - Fix broken import in scale_up module

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/Jenkinsfile

@@ -1,3 +1,15 @@
+def githubUsernameToSlackName(github_author) {
+  // Add team members as necessary
+  def mapping = [
+    "Jim Albright": "albrja",
+    "Steve Bachmeier": "sbachmei",
+    "Hussain Jafari": "hjafari",
+    "Patrick Nast": "pnast",
+    "Rajan Mudambi": "rmudambi",
+  ]
+  return mapping.get(github_author, "channel")
+}
+
 pipeline_name="vivarium_public_health"
 conda_env_name="${pipeline_name}-${BUILD_NUMBER}"
 conda_env_path="/tmp/${conda_env_name}"
@@ -190,40 +202,54 @@ pipeline {
             } // build and deploy stage
         } // stages bracket within Python matrix
         post {
-            always {
-              sh "${ACTIVATE} && make clean"
-              sh "rm -rf ${CONDA_ENV_PATH}"
-              // Delete the workspace directory.
-              deleteDir()
-            }
-            failure {
-              script {
-                if (env.BRANCH == "main") {
-                  channelName = "simsci-ci-status"
-                } else {
-                  channelName = "simsci-ci-status-test"
-                }
+          always {
+            sh "${ACTIVATE} && make clean"
+            sh "rm -rf ${CONDA_ENV_PATH}"
+            // Generate a message to send to Slack.
+            script {
+              if (env.BRANCH == "main") {
+                channelName = "simsci-ci-status"
+              } else {
+                channelName = "simsci-ci-status-test"
               }
-              // TODO: DM the developer instead of the slack channel
-              echo "This build failed on ${GIT_BRANCH}. Sending a failure message to Slack."
-              slackSend channel: "#${channelName}",
-                          message: ":x: JOB FAILURE: $JOB_NAME - $BUILD_ID\n\n${BUILD_URL}console\n\n<!channel>",
+              // Run git command to get the author of the last commit
+              developerID = sh(
+                script: "git log -1 --pretty=format:'%an'",
+                returnStdout: true
+              ).trim()
+              slackID = githubUsernameToSlackName(developerID)
+              slackMessage = """
+                Job: *${env.JOB_NAME}*
+                Build number: #${env.BUILD_NUMBER}
+                Build status: *${currentBuild.result}*
+                Author: @${slackID}
+                Build details: <${env.BUILD_URL}/console|See in web console>
+            """.stripIndent()
+            }
+
+            // Delete the workspace directory.
+            deleteDir()
+          }
+          failure {
+            echo "This build triggered by ${developerID} failed on ${GIT_BRANCH}. Sending a failure message to Slack."
+            slackSend channel: "#${channelName}",
+                        message: slackMessage,
+                        teamDomain: "ihme",
+                        tokenCredentialId: "slack"
+          }
+          success {
+            script {
+              if (params.DEBUG) {
+                echo 'Debug is enabled. Sending a success message to Slack.'
+                slackSend channel: "#${channelName}",
+                          message: slackMessage,
                           teamDomain: "ihme",
                           tokenCredentialId: "slack"
-            }
-            success {
-              script {
-                if (params.DEBUG) {
-                  echo 'Debug is enabled. Sending a success message to Slack.'
-                  slackSend channel: "#${params.SLACK_TO}",
-                            message: ":white_check_mark: (debugging) JOB SUCCESS: $JOB_NAME - $BUILD_ID\n\n${BUILD_URL}console",
-                            teamDomain: "ihme",
-                            tokenCredentialId: "slack"
-                } else {
-                  echo 'Debug is not enabled. No success message will be sent to Slack.'
-                }
+              } else {
+                echo 'Debug is not enabled. No success message will be sent to Slack.'
               }
             }
+          }
         } // post bracket
       } // Python matrix bracket
     } // Python matrix stage bracket

{vivarium_public_health-3.0.9/src/vivarium_public_health.egg-info → vivarium_public_health-3.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.9
+Version: 3.0.11
 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-3.0.11/src/vivarium_public_health/__init__.py

@@ -0,0 +1,60 @@
+from vivarium_public_health.__about__ import (
+    __author__,
+    __copyright__,
+    __email__,
+    __license__,
+    __summary__,
+    __title__,
+    __uri__,
+)
+from vivarium_public_health._version import __version__
+from vivarium_public_health.disease import (
+    SI,
+    SIR,
+    SIS,
+    DiseaseModel,
+    DiseaseState,
+    NeonatalSWC_with_incidence,
+    NeonatalSWC_without_incidence,
+    RecoveredState,
+    RiskAttributableDisease,
+    SIR_fixed_duration,
+    SIS_fixed_duration,
+    SusceptibleState,
+    TransientDiseaseState,
+)
+from vivarium_public_health.plugins import CausesConfigurationParser
+from vivarium_public_health.population import (
+    BasePopulation,
+    FertilityAgeSpecificRates,
+    FertilityCrudeBirthRate,
+    FertilityDeterministic,
+    Mortality,
+    ScaledPopulation,
+)
+from vivarium_public_health.results import (
+    CategoricalRiskObserver,
+    DisabilityObserver,
+    DiseaseObserver,
+    MortalityObserver,
+    ResultsStratifier,
+)
+from vivarium_public_health.risks import (
+    LBWSGRisk,
+    LBWSGRiskEffect,
+    NonLogLinearRiskEffect,
+    Risk,
+    RiskEffect,
+)
+from vivarium_public_health.treatment import AbsoluteShift, LinearScaleUp, TherapeuticInertia
+
+__all__ = [
+    __author__,
+    __copyright__,
+    __email__,
+    __license__,
+    __summary__,
+    __title__,
+    __uri__,
+    __version__,
+]

vivarium_public_health-3.0.11/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.0.11"

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/src/vivarium_public_health/disease/__init__.py

@@ -5,6 +5,7 @@ from .models import (
     SIS,
     NeonatalSWC_with_incidence,
     NeonatalSWC_without_incidence,
+    SIR_fixed_duration,
     SIS_fixed_duration,
 )
 from .special_disease import RiskAttributableDisease

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/src/vivarium_public_health/population/__init__.py

@@ -3,5 +3,5 @@ from .add_new_birth_cohorts import (
     FertilityCrudeBirthRate,
     FertilityDeterministic,
 )
-from .base_population import BasePopulation, generate_population
+from .base_population import BasePopulation, ScaledPopulation, generate_population
 from .mortality import Mortality

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/src/vivarium_public_health/population/base_population.py

@@ -8,6 +8,8 @@ characteristics to simulants.
 
 """
 
+from __future__ import annotations
+
 from typing import Callable, Dict, Iterable, List
 
 import numpy as np
@@ -76,12 +78,11 @@ class BasePopulation(Component):
         # Validate configuration for deprecated keys
         self._validate_config_for_deprecated_keys()
 
-        source_population_structure = load_population_structure(builder)
+        source_population_structure = self._load_population_structure(builder)
         self.demographic_proportions = assign_demographic_proportions(
             source_population_structure,
             include_sex=self.config.include_sex,
         )
-
         self.randomness = self.get_randomness_streams(builder)
         self.register_simulants = builder.randomness.register_simulants
 
@@ -138,7 +139,6 @@ class BasePopulation(Component):
         demographic_proportions = self.get_demographic_proportions_for_creation_time(
             self.demographic_proportions, pop_data.creation_time.year
         )
-
         self.population_view.update(
             generate_population(
                 simulant_ids=pop_data.index,
@@ -202,6 +202,50 @@ class BasePopulation(Component):
                 f"Public Health. Use the new key '{mapper[key]}' instead."
             )
 
+    def _load_population_structure(self, builder: Builder) -> pd.DataFrame:
+        return load_population_structure(builder)
+
+
+class ScaledPopulation(BasePopulation):
+    """This component is to be used in place of BasePopulation when all simulants are
+    a subset of the total population and need to be rescaled. The base population
+    structure is multiplied by a provided scaling factor. This scaling factor
+    can be a dataframe passed in or a string that corresponds to an artifact key.
+    If providing an artifact key, users can specify that in the configuration file.
+    For example:
+
+    .. code-block:: yaml
+
+    components:
+        vivarium_public_health:
+            population:
+                - ScaledPopulation("some.artifact.key")
+
+
+    """
+
+    def __init__(self, scaling_factor: str | pd.DataFrame):
+        super().__init__()
+        self.scaling_factor = scaling_factor
+        """Set a multiplicative scaling factor for the population structure."""
+
+    def _load_population_structure(self, builder: Builder) -> pd.DataFrame:
+        scaling_factor = self.get_data(builder, self.scaling_factor)
+        population_structure = load_population_structure(builder)
+        if not isinstance(scaling_factor, pd.DataFrame):
+            raise ValueError(
+                f"Scaling factor must be a pandas DataFrame. Provided value: {scaling_factor}"
+            )
+        scaling_factor = scaling_factor.set_index(
+            [col for col in scaling_factor.columns if col != "value"]
+        )
+        population_structure = population_structure.set_index(
+            [col for col in population_structure.columns if col != "value"]
+        )
+        scaled_population_structure = (population_structure * scaling_factor).reset_index()
+
+        return scaled_population_structure
+
 
 class AgeOutSimulants(Component):
     """Component for handling aged-out simulants"""

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/src/vivarium_public_health/population/data_transformations.py

@@ -13,6 +13,7 @@ from typing import Tuple, Union
 
 import numpy as np
 import pandas as pd
+from vivarium.framework.engine import Builder
 from vivarium.framework.randomness import RandomnessStream
 
 _SORT_ORDER = ["location", "year_start", "sex", "age_start"]
@@ -493,11 +494,12 @@ def get_cause_deleted_mortality_rate(all_cause_mortality_rate, list_of_csmrs):
     )
 
 
-def load_population_structure(builder):
+def load_population_structure(builder: Builder) -> pd.DataFrame:
     data = builder.data.load("population.structure")
     # create an age column which is the midpoint of the age group
     data["age"] = data.apply(lambda row: (row["age_start"] + row["age_end"]) / 2, axis=1)
     data["location"] = builder.data.load("population.location")
+
     return data
 
 

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/src/vivarium_public_health/results/__init__.py

@@ -4,4 +4,5 @@ from .disease import DiseaseObserver
 from .mortality import MortalityObserver
 from .observer import PublicHealthObserver
 from .risk import CategoricalRiskObserver
+from .simple_cause import SimpleCause
 from .stratification import ResultsStratifier

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11/src/vivarium_public_health.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.9
+Version: 3.0.11
 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-3.0.9 → vivarium_public_health-3.0.11}/tests/population/test_add_new_birth_cohort.py

@@ -130,7 +130,7 @@ def test_FertilityCrudeBirthRate_extrapolate(base_config, base_plugins):
         }
     )
     pop_size = base_config.population.population_size
-    true_pop_size = 50000  # What's available in the mock artifact
+    true_pop_size = 25000  # What's available in the mock artifact
     live_births_by_sex = 500
     components = [TestPopulation(), FertilityCrudeBirthRate()]
 

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/tests/population/test_base_population.py

@@ -1,15 +1,16 @@
 import math
-from pathlib import Path
 
 import numpy as np
 import pandas as pd
 import pytest
 from vivarium import InteractiveContext
 from vivarium.testing_utilities import get_randomness
+from vivarium_testing_utils import FuzzyChecker
 
 import vivarium_public_health.population.base_population as bp
 import vivarium_public_health.population.data_transformations as dt
-from tests.test_utilities import make_uniform_pop_data
+from tests.mock_artifact import MockArtifact
+from tests.test_utilities import make_uniform_pop_data, simple_pop_structure
 from vivarium_public_health import utilities
 
 
@@ -283,6 +284,71 @@ def test__assign_demography_with_age_bounds_error(base_simulants, include_sex):
         )
 
 
+@pytest.mark.parametrize("constructor_type", ["string", "data"])
+def test_scaled_population(
+    constructor_type, config, base_plugins, mocker, fuzzy_checker: FuzzyChecker
+):
+    config.update(
+        {
+            "population": {
+                "population_size": 1_000_000,
+                "include_sex": "Both",
+            },
+            "time": {"step_size": 1},
+        },
+        layer="override",
+    )
+
+    # Simple pop data
+    pop_structure = simple_pop_structure()
+    # Simple scalar data to pass to ScaledPopulation
+    scalar_data = simple_pop_structure().drop(columns=["location"])
+    scalar_values = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0]
+    scalar_data["value"] = scalar_values
+
+    # Add data to artifact and mock return for plugin
+    mock_art = MockArtifact()
+    mock_art.write("population.structure", pop_structure)
+    mocker.patch(
+        "tests.mock_artifact.MockArtifactManager._load_artifact",
+    ).return_value = mock_art
+
+    if constructor_type == "string":
+        mock_art.write("population.scalar", scalar_data)
+        scaling_factor = "population.scalar"
+    else:
+        scaling_factor = scalar_data
+    scaled_pop = bp.ScaledPopulation(scaling_factor)
+    sim = InteractiveContext(
+        components=[scaled_pop], configuration=config, plugin_configuration=base_plugins
+    )
+    pop = sim.get_population()
+    # Use FuzzyChecker to compare population structure to demographic proportion by
+    # iterating through each age_group/sex combination
+    scaled_structure = pop_structure.copy()
+    scaled_structure["value"] = scaled_structure["value"] * scalar_data["value"]
+
+    for row in range(len(scaled_structure)):
+        row_data = scaled_structure.iloc[row]
+        age_start = row_data["age_start"]
+        sex = row_data["sex"]
+        # Get proportion of each age group
+        target_proportion = row_data["value"] / scaled_structure["value"].sum()
+        number_of_sims = len(
+            pop.loc[
+                (pop["age"] >= age_start)
+                & (pop["age"] <= row_data["age_end"])
+                & (pop["sex"] == sex)
+            ]
+        )
+        fuzzy_checker.fuzzy_assert_proportion(
+            observed_numerator=number_of_sims,
+            observed_denominator=len(pop),
+            target_proportion=target_proportion,
+            name=f"scaled_pop_proportion_check_{sex}_{age_start}",
+        )
+
+
 def _check_population(simulants, initial_age, step_size, include_sex):
     assert len(simulants) == len(simulants.age.unique())
     assert simulants.age.min() > initial_age

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/tests/population/test_data_transformations.py

@@ -127,7 +127,7 @@ def test_smooth_ages(pop_data, include_sex):
             "sex": (
                 ["Male", "Female"] * 10000 if include_sex == "Both" else [include_sex] * 20000
             ),
-            "location": [1, 2] * 10000,
+            "location": [1] * 20000,
         }
     )
     randomness = get_randomness()

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.11}/tests/test_utilities.py

@@ -64,7 +64,7 @@ def make_uniform_pop_data(age_bin_midpoint=False):
     age_bins = [(b.age_start, b.age_end) for b in make_age_bins().itertuples()]
     sexes = ("Male", "Female")
     years = zip(range(1990, 2018), range(1991, 2019))
-    locations = (1, 2)
+    locations = list(range(1, 2))
 
     age_bins, sexes, years, locations = zip(*product(age_bins, sexes, years, locations))
     mins, maxes = zip(*age_bins)
@@ -116,3 +116,39 @@ def make_age_bins():
         names=["age_start", "age_end", "age_group_name"],
     )
     return pd.DataFrame(index=idx).reset_index()
+
+
+def simple_pop_structure() -> pd.DataFrame:
+    # Create simple population structure
+    age_idx = pd.MultiIndex.from_tuples(
+        [
+            (0.0, 25.0, "Young People"),
+            (25.0, 50.0, "Old People"),
+            (50.0, 75.0, "Ancient People"),
+            (75.0, 100.0, "People Who Beat the Odds"),
+        ],
+        names=["age_start", "age_end", "age_group_name"],
+    )
+    age_df = pd.DataFrame(index=age_idx).reset_index()
+    age_bins = [(group.age_start, group.age_end) for group in age_df.itertuples()]
+    sexes = ("Male", "Female")
+    location = ["Kenya"]
+    years = zip(range(2021, 2022), range(2022, 2023))
+
+    age_bins, sexes, years, location = zip(*product(age_bins, sexes, years, location))
+    mins, maxes = zip(*age_bins)
+    year_starts, year_ends = zip(*years)
+
+    pop_structure = pd.DataFrame(
+        {
+            "age_start": mins,
+            "age_end": maxes,
+            "sex": sexes,
+            "year_start": year_starts,
+            "year_end": year_ends,
+            "location": location,
+            # We have 8 demographic groups (4 age groups * 2 sexes)
+            "value": [1.0, 1.0, 2.0, 2.0, 3.0, 3.0, 4.0, 4.0],
+        }
+    )
+    return pop_structure

vivarium_public_health-3.0.9/.github/workflows/build.yml

@@ -1,96 +0,0 @@
-# -----------------------------------------------------------------------------
-#   - invoked on push, pull_request, manual trigger, or schedule
-#   - test under at least 3 versions of python
-# -----------------------------------------------------------------------------
-name: build
-on:
-  push:
-  pull_request:
-  workflow_dispatch:
-  schedule:
-    - cron: "0 8 * * *"
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: ["3.9", "3.10", "3.11"]
-    defaults:
-      run:
-        shell: bash -le {0}
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: get upstream branch name
-        run: |
-          if "${{ github.event_name == 'pull_request' }}" ; then
-            echo "branch_name=${GITHUB_HEAD_REF}" >> $GITHUB_ENV
-          else
-            echo "branch_name=${GITHUB_REF_NAME}" >> $GITHUB_ENV
-          fi
-      - name: Update pip
-        run: |
-          python -m pip install --upgrade pip
-      - name: Install dependencies
-        run: |
-          pip install .[dev]
-          git checkout ${branch_name}
-      - name: check for dependency branches and install if needed
-        run: |
-          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} github
-          sh ../vivarium_build_utils/install_dependency_branch.sh vivarium ${branch_name} github
-          sh ../vivarium_build_utils/install_dependency_branch.sh risk_distributions ${branch_name} github
-      - name: print environment values
-        run: |
-          cat $GITHUB_ENV
-      - name: Lint
-        run: |
-          pip install black==22.3.0 isort
-          isort . --check --verbose --only-modified --diff
-          black . --check --diff
-      - name: Test
-        run: |
-          if "${{ github.event_name == 'schedule' }}"; then
-            pytest --runslow ./tests
-          else
-            pytest ./tests
-          fi
-      - name: Doc build
-        run: |
-          make html -C docs/ SPHINXOPTS="-W --keep-going -n"
-      - name: Doctest
-        run: |
-          make doctest -C docs/
-      - name: Send mail
-        # Notify when cron job fails
-        if: (github.event_name == 'schedule' && failure())
-        uses: dawidd6/action-send-mail@v2
-        with:
-          # mail server settings
-          server_address: smtp.gmail.com
-          server_port: 465
-          # user credentials
-          username: ${{ secrets.NOTIFY_EMAIL }}
-          password: ${{ secrets.NOTIFY_PASSWORD }}
-          # email subject
-          subject: ${{ github.job }} job of ${{ github.repository }} has ${{ job.status }}
-          # email body as text
-          body: ${{ github.job }} job in worflow ${{ github.workflow }} of ${{ github.repository }} has ${{ job.status }}
-          # comma-separated string, send email to
-          to: uw_ihme_simulationscience@uw.edu
-          # from email name
-          from: Vivarium Notifications

vivarium_public_health-3.0.9/src/vivarium_public_health/__init__.py

@@ -1,21 +0,0 @@
-from vivarium_public_health.__about__ import (
-    __author__,
-    __copyright__,
-    __email__,
-    __license__,
-    __summary__,
-    __title__,
-    __uri__,
-)
-from vivarium_public_health._version import __version__
-
-__all__ = [
-    __author__,
-    __copyright__,
-    __email__,
-    __license__,
-    __summary__,
-    __title__,
-    __uri__,
-    __version__,
-]

vivarium_public_health-3.0.9/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "3.0.9"