vivarium-public-health 3.0.9__tar.gz → 3.0.10__tar.gz

vivarium_public_health-3.0.10/.github/workflows/build.yml

@@ -0,0 +1,19 @@
+# -----------------------------------------------------------------------------
+#   - 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:
+  call_build:
+    uses: 
+      ihmeuw/vivarium_build_utils/.github/workflows/build.yml@main
+    with:
+      dependencies: "layered_config_tree,vivarium"
+      use_mypy: false

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.10}/CHANGELOG.rst

@@ -1,3 +1,7 @@
+**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-3.0.10}/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-3.0.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: vivarium_public_health
-Version: 3.0.9
+Version: 3.0.10
 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-3.0.10/src/vivarium_public_health/__init__.py

@@ -0,0 +1,59 @@
+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,
+)
+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-3.0.10/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.0.10"

{vivarium_public_health-3.0.9 → vivarium_public_health-3.0.10}/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-3.0.10}/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-3.0.10/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: 3.0.10
 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/.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"