vivarium-public-health 3.1.4__tar.gz → 3.1.5__tar.gz

{vivarium_public_health-3.1.4 → vivarium_public_health-3.1.5}/CHANGELOG.rst

@@ -1,3 +1,7 @@
+**3.1.5 - 01/14/25**
+
+ - Bugfix: Vivarium InteractiveContext no longer returns int
+
 **3.1.4 - 11/22/24**
 
  - Feature: Enable initializing a population of all newborns

vivarium_public_health-3.1.5/Jenkinsfile

@@ -0,0 +1,2 @@
+@Library("vivarium_build_utils") _
+reusable_pipeline(scheduled_branches: ["main"], test_types: ["integration"], python_versions: ["3.10", "3.11"])

{vivarium_public_health-3.1.4 → vivarium_public_health-3.1.5}/Makefile

@@ -101,4 +101,4 @@ build-package: $(MAKE_SOURCES) # Build the package as a pip wheel
 clean: # Delete build artifacts and do any custom cleanup such as spinning down services
 	@rm -rf format lint build-doc build-package integration .pytest_cache
 	@rm -rf dist output
-	$(shell find . -type f -name '*py[co]' -delete -o -type d -name __pycache__ -delete)
+	$(shell find . -type f -name '*py[co]' -delete -o -type d -name __pycache__ -delete)

{vivarium_public_health-3.1.4 → vivarium_public_health-3.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.1.4
+Version: 3.1.5
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -64,6 +64,15 @@ Requires-Dist: hypothesis; extra == "dev"
 Requires-Dist: pyyaml; extra == "dev"
 Requires-Dist: black==22.3.0; extra == "dev"
 Requires-Dist: isort; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 Vivarium Public Health
 ======================

vivarium_public_health-3.1.5/src/vivarium_public_health/_version.py

@@ -0,0 +1 @@
+__version__ = "3.1.5"

{vivarium_public_health-3.1.4 → vivarium_public_health-3.1.5}/src/vivarium_public_health.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: vivarium_public_health
-Version: 3.1.4
+Version: 3.1.5
 Summary: Components for modelling diseases, risks, and interventions with ``vivarium``
 Home-page: https://github.com/ihmeuw/vivarium_public_health
 Author: The vivarium developers
@@ -64,6 +64,15 @@ Requires-Dist: hypothesis; extra == "dev"
 Requires-Dist: pyyaml; extra == "dev"
 Requires-Dist: black==22.3.0; extra == "dev"
 Requires-Dist: isort; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: summary
 
 Vivarium Public Health
 ======================

{vivarium_public_health-3.1.4 → vivarium_public_health-3.1.5}/tests/population/test_add_new_birth_cohort.py

@@ -48,7 +48,6 @@ def crude_birth_rate_data(live_births=500):
 def test_FertilityDeterministic(config):
     pop_size = config.population.population_size
     annual_new_simulants = 1000
-    step_size = config.time.step_size
     num_days = 100
 
     config.update(
@@ -58,10 +57,12 @@ def test_FertilityDeterministic(config):
 
     components = [TestPopulation(), FertilityDeterministic()]
     simulation = InteractiveContext(components=components, configuration=config)
-    num_steps = simulation.run_for(duration=pd.Timedelta(days=num_days))
+    start_time = simulation.current_time
+    simulation.run_for(duration=pd.Timedelta(days=num_days))
+    end_time = simulation.current_time
     pop = simulation.get_population()
 
-    assert num_steps == num_days // step_size
+    assert (end_time - start_time) / pd.Timedelta(days=1) == num_days
     assert np.all(pop.alive == "alive")
     assert (
         int(num_days * annual_new_simulants / utilities.DAYS_PER_YEAR)

vivarium_public_health-3.1.4/Jenkinsfile

@@ -1,257 +0,0 @@
-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/${conda_env_name}"
-// defaults for conda and pip are a local directory /svc-simsci for improved speed.
-// In the past, we used /ihme/code/* on the NFS (which is slower)
-shared_path="/svc-simsci"
-
-
-pipeline {
-  // This agent runs as svc-simsci on node simsci-slurm-sbuild-p01.
-  // It has access to standard IHME filesystems and singularity
-  agent { label "svc-simsci" }
-
-  options {
-    // Keep 100 old builds.
-    buildDiscarder logRotator(numToKeepStr: "100")
-
-    // Wait 60 seconds before starting the build.
-    // If another commit enters the build queue in this time, the first build will be discarded.
-    quietPeriod(60)
-
-    // Fail immediately if any part of a parallel stage fails
-    parallelsAlwaysFailFast()
-  }
-
-  parameters {
-    booleanParam(
-      name: "DEPLOY_OVERRIDE",
-      defaultValue: false,
-      description: "Whether to deploy despite building a non-default branch. Builds of the default branch are always deployed."
-    )
-    booleanParam(
-      name: "IS_CRON",
-      defaultValue: true,
-      description: "Indicates a recurring build. Used to skip deployment steps."
-    )
-    string(
-      name: "SLACK_TO",
-      defaultValue: "simsci-ci-status",
-      description: "The Slack channel to send messages to."
-    )
-    booleanParam(
-      name: "DEBUG",
-      defaultValue: false,
-      description: "Used as needed for debugging purposes."
-    )
-  }
-
-  stages {
-    stage("Initialization") {
-      steps {
-        script {
-          // Use the name of the branch in the build name
-          currentBuild.displayName = "#${BUILD_NUMBER} ${GIT_BRANCH}"
-        }
-      }
-    }
-
-    stage("Python version matrix") {
-      // we don't want to go to deployment if any of the matrix branches fail
-      failFast true
-      matrix {
-        // customWorkspace setting must be ran within a node
-        agent {
-          node {
-              label "svc-simsci"
-          }
-        }
-        axes {
-          axis {
-              // parallelize by python minor version
-              name 'PYTHON_VERSION'
-              values "3.10", "3.11"
-          }
-        }
-
-        environment {
-            // Get the branch being built and strip everything but the text after the last "/"
-            BRANCH = sh(script: "echo ${GIT_BRANCH} | rev | cut -d '/' -f1 | rev", returnStdout: true).trim()
-            TIMESTAMP = sh(script: 'date', returnStdout: true)
-            // Specify the path to the .condarc file via environment variable.
-            // This file configures the shared conda package cache.
-            CONDARC = "${shared_path}/miniconda3/.condarc"
-            CONDA_BIN_PATH = "${shared_path}/miniconda3/bin"
-            // Specify conda env by build number so that we don't have collisions if builds from
-            // different branches happen concurrently.
-            PYTHON_DEPLOY_VERSION = "3.11"
-            CONDA_ENV_NAME = "${conda_env_name}"
-            CONDA_ENV_PATH = "${conda_env_path}_${PYTHON_VERSION}"
-            // Set the Pip cache.
-            XDG_CACHE_HOME = "${shared_path}/pip-cache"
-            // Jenkins commands run in separate processes, so need to activate the environment every
-            // time we run pip, poetry, etc.
-            ACTIVATE = "source ${CONDA_BIN_PATH}/activate ${CONDA_ENV_PATH} &> /dev/null"
-        }
-
-        stages {
-            stage("Debug Info") {
-              steps {
-                echo "Jenkins pipeline run timestamp: ${TIMESTAMP}"
-                // Display parameters used.
-                echo """Parameters:
-                DEPLOY_OVERRIDE: ${params.DEPLOY_OVERRIDE}"""
-
-                // Display environment variables from Jenkins.
-                echo """Environment:
-                ACTIVATE:       '${ACTIVATE}'
-                BUILD_NUMBER:   '${BUILD_NUMBER}'
-                BRANCH:         '${BRANCH}'
-                CONDARC:        '${CONDARC}'
-                CONDA_BIN_PATH: '${CONDA_BIN_PATH}'
-                CONDA_ENV_NAME: '${CONDA_ENV_NAME}'
-                CONDA_ENV_PATH: '${CONDA_ENV_PATH}'
-                GIT_BRANCH:     '${GIT_BRANCH}'
-                JOB_NAME:       '${JOB_NAME}'
-                WORKSPACE:      '${WORKSPACE}'
-                XDG_CACHE_HOME: '${XDG_CACHE_HOME}'"""
-              }
-            }
-
-            stage("Build Environment") {
-              environment {
-                // Command for activating the base environment. Activating the base environment sets
-                // the correct path to the conda binary which is used to create a new conda env.
-                ACTIVATE_BASE = "source ${CONDA_BIN_PATH}/activate &> /dev/null"
-              }
-              steps {
-                // The env should have been cleaned out after the last build, but delete it again
-                // here just to be safe.
-                sh "rm -rf ${CONDA_ENV_PATH}"
-                sh "${ACTIVATE_BASE} && make build-env PYTHON_VERSION=${PYTHON_VERSION}"
-                // open permissions for test users to create file in workspace
-                sh "chmod 777 ${WORKSPACE}"
-              }
-            }
-
-            stage("Install Package") {
-              steps {
-                sh "${ACTIVATE} && make install"
-              }
-            }
-
-            // Quality Checks
-            stage("Format") {
-              steps {
-                sh "${ACTIVATE} && make format"
-              }
-            }
-
-            // stage("Lint") {
-            //   steps {
-            //     sh "${ACTIVATE} && make lint"
-            //   }
-            // }
-
-            // Tests
-            // removable, if passwords can be exported to env. securely without bash indirection
-            stage("Run Integration Tests") {
-              steps {
-                sh "${ACTIVATE} && make integration"
-                publishHTML([
-                  allowMissing: true,
-                  alwaysLinkToLastBuild: false,
-                  keepAll: true,
-                  reportDir: "output/htmlcov_integration",
-                  reportFiles: "index.html",
-                  reportName: "Coverage Report - Integration tests",
-                  reportTitles: ''
-                ])
-              }
-            }
-
-            // Build
-            stage('Build and Deploy') {
-              when {
-                expression { "${PYTHON_DEPLOY_VERSION}" == "${PYTHON_VERSION}" }
-              }
-              stages {
-                stage("Build Docs") {
-                  steps {
-                    sh "${ACTIVATE} && make build-doc"
-                  }
-                }
-                stage("Build Package") {
-                  steps {
-                    sh "${ACTIVATE} && make build-package"
-                  }
-                }
-              } // stages within build and deploy
-            } // build and deploy stage
-        } // stages bracket within Python matrix
-        post {
-          always {
-            sh "${ACTIVATE} && make clean"
-            sh "rm -rf ${CONDA_ENV_PATH}"
-            // Generate a message to send to Slack.
-            script {
-              if (env.BRANCH == "main") {
-                channelName = "simsci-ci-status"
-              } else {
-                channelName = "simsci-ci-status-test"
-              }
-              // Run git command to get the author of the last commit
-              developerID = sh(
-                script: "git log -1 --pretty=format:'%an'",
-                returnStdout: true
-              ).trim()
-              slackID = githubUsernameToSlackName(developerID)
-              slackMessage = """
-                Job: *${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"
-              } else {
-                echo 'Debug is not enabled. No success message will be sent to Slack.'
-              }
-            }
-          }
-        } // post bracket
-      } // Python matrix bracket
-    } // Python matrix stage bracket
-  } // stages bracket
-}

vivarium_public_health-3.1.4/src/vivarium_public_health/_version.py

@@ -1 +0,0 @@
-__version__ = "3.1.4"