Simp vax

.dev_scripts/create_auth_token_args.py

@@ -0,0 +1,39 @@
+import argparse
+from COMPS import Client
+from COMPS.CredentialPrompt import CredentialPrompt
+
+__comps_client_version = 10
+
+
+class StaticCredentialPrompt(CredentialPrompt):
+    def __init__(self, comps_url, username, password):
+        if (comps_url is None) or (username is None) or (password is None):
+            print("Usage: python create_auth_token_args.py --comps_url url --username username --password pwd")
+            print("\n")
+            raise RuntimeError('Missing comps_url, or username or password')
+        self._times_prompted = 0
+        self.comps_url = comps_url
+        self.username = username
+        self.password = password
+
+    def prompt(self):
+        print("logging in with user/pw")
+        self._times_prompted = self._times_prompted + 1
+        if self._times_prompted > 3:
+            raise RuntimeError('Failure authenticating')
+        return {'Username': self.username, 'Password': self.password}
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('-c', '--comps_url', default='https://comps2.idmod.org', help='comps url')
+    parser.add_argument('-u', '--username', help='enter username')
+    parser.add_argument('-p', '--password', help='enter password')
+
+    args = parser.parse_args()
+
+    compshost = args.comps_url
+
+    Client.login(compshost, StaticCredentialPrompt(comps_url=args.comps_url, username=args.username,
+                                                   password=args.password))

.github/workflows/run_test.yml

@@ -0,0 +1,61 @@
+name: run all tests
+on:
+  workflow_dispatch:
+
+jobs:
+  run-all-test-dev-install:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ 3.9 ]
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v2
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Config github user
+        run: |
+          git config --global user.email "[email protected]"
+          git config --global user.name "BambooUser-IDM"
+      - uses: actions/setup-python@master
+        with:
+          python-version: ${{ matrix.python-version }}
+          architecture: x64
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements_2018.txt --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple
+      - name: Install from source
+        run: |
+          pip install -e .
+      - name: install test dependencies
+        run: |
+          pip3 install unittest-xml-reporting pytest
+#      - name: Install idm-test package
+#        run: |
+#          pip install idm-test>=0.0.13 --extra-index-url https://packages.idmod.org/api/pypi/pypi-production/simple
+      - name: Login to comps2
+        run: |
+          python ./.dev_scripts/create_auth_token_args.py --username "${{ secrets.COMPS_USER }}" --password "${{ secrets.COMPS_PASSWORD }}"
+      - name: run unittests
+        run: |
+          cd tests/unittests
+          py.test -sv --junitxml=reports/test_results.xml
+      - name: Upload unittest result to artifactory
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: unittest_results
+          path: |
+            **/test_results.xml
+      - name: run workflow tests
+        run: |
+          cd tests/workflow_tests
+          py.test -sv --junitxml=reports/test_results.xml
+      - name: Upload workflow tests results to artifactory
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: unittest_results
+          path: |
+            **/test_results.xml

Jenkinsfile

@@ -12,108 +12,95 @@ podTemplate(
   ]) {
   node(POD_LABEL) {
     container('dtk-rpm-builder'){
-		def build_ok = true
+        def build_ok = true
 		stage('Cleanup Workspace') {
 			cleanWs()
 			echo "Cleaned Up Workspace For Project"
 			echo "${params.BRANCH}"
 		}
+		stage('Prepare') {
+			sh 'python --version'
+			sh 'python3 --version'
+			sh 'pip3 --version'
+
+			sh 'python3 -m pip install --upgrade pip'
+			sh 'pip3 install wheel unittest-xml-reporting pytest'
+			sh 'python3 -m pip install --upgrade setuptools'
+			sh 'pip3 freeze'
+		}
 		stage('Code Checkout') {
 			if (env.CHANGE_ID) {
 				echo "I execute on the pull request ${env.CHANGE_ID}"
 				checkout([$class: 'GitSCM',
-							branches: [[name: "pr/${env.CHANGE_ID}/head"]],
-							doGenerateSubmoduleConfigurations: false,
-							extensions: [],
-							gitTool: 'Default',
-							submoduleCfg: [],
-							userRemoteConfigs: [[refspec: '+refs/pull/*:refs/remotes/origin/pr/*', credentialsId: '704061ca-54ca-4aec-b5ce-ddc7e9eab0f2', url: '[email protected]:InstituteforDiseaseModeling/emodpy-typhoid.git']]])
+				branches: [[name: "pr/${env.CHANGE_ID}/head"]],
+				doGenerateSubmoduleConfigurations: false,
+				extensions: [],
+				gitTool: 'Default',
+				submoduleCfg: [],
+				userRemoteConfigs: [[refspec: '+refs/pull/*:refs/remotes/origin/pr/*', credentialsId: '704061ca-54ca-4aec-b5ce-ddc7e9eab0f2', url: '[email protected]:InstituteforDiseaseModeling/emod-typhoid.git']]])
 			} else {
 				echo "I execute on the ${env.BRANCH_NAME} branch"
 				git branch: "${env.BRANCH_NAME}",
 				credentialsId: '704061ca-54ca-4aec-b5ce-ddc7e9eab0f2',
-				url: '[email protected]:InstituteforDiseaseModeling/emodpy-typhoid.git'
-			}
-		}
-		stage('Prepare') {
-			sh 'python3 -m pip install --upgrade pip'
-			sh "pip3 install wheel"
-			sh 'python3 -m pip install --upgrade setuptools'
-			sh 'pip3 freeze'
-		}
-		stage('Build') {
-			sh 'pwd'
-			sh 'ls -a'
-			sh 'python3 package_setup.py bdist_wheel'
-
-		}
+				url: '[email protected]:InstituteforDiseaseModeling/emod-typhoid.git'
+            }
+        }
 		stage('Install') {
 			def curDate = sh(returnStdout: true, script: "date").trim()
 			echo "The current date is ${curDate}"
-
-			echo "I am installing emodpy-typhoid from wheel file built from code"
-			def wheelFile = sh(returnStdout: true, script: "find ./dist -name '*.whl'").toString().trim()
-			//def wheelFile = sh(returnStdout: true, script: "python3 ./.github/scripts/get_wheel_filename.py --package-file package_setup.py").toString().trim()
-			echo "This is the package file: ${wheelFile}"
-			sh "pip3 install $wheelFile --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple"
-
-			sh "pip3 install dataclasses"
-			sh 'pip3 install keyrings.alt'
-			sh "pip3 freeze"
+			echo "I am installing emodpy-typhoid from github source code"
+			sh "pip3 install -r requirements_2018.txt --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple"
+			sh "pip3 list"
+			sh "pip3 install -e ."
+			sh "pip3 list"
 		}
 		stage('Login') {
-				withCredentials([string(credentialsId: 'Comps_emodpy_user', variable: 'user'), string(credentialsId: 'Comps_emodpy_password', variable: 'password'),
-								 string(credentialsId: 'Bamboo_id', variable: 'bamboo_user'), string(credentialsId: 'Bamboo', variable: 'bamboo_password')]) {
-					sh 'python3 .dev_scripts/create_auth_token_args.py --comps_url https://comps2.idmod.org --username $user --password $password'
-					sh 'python3 .dev_scripts/create_auth_token_args.py --comps_url https://comps.idmod.org --username yechen --password $password'
-					dir('tests/workflow_testing') {
-						sh 'python3 bamboo_login_with_arguments.py -u $bamboo_user -p $bamboo_password'
-					}
-				}
+			withCredentials([usernamePassword(credentialsId: 'comps_jenkins_user', usernameVariable: 'COMPS_USERNAME', passwordVariable: 'COMPS_PASSWORD'),
+					         usernamePassword(credentialsId: 'comps2_jenkins_user', usernameVariable: 'COMPS2_USERNAME', passwordVariable: 'COMPS2_PASSWORD')])
+			{
+				sh 'python3 .dev_scripts/create_auth_token_args.py --comps_url https://comps2.idmod.org --username $COMPS2_USERNAME --password $COMPS2_PASSWORD'
+				sh 'python3 .dev_scripts/create_auth_token_args.py --comps_url https://comps.idmod.org --username $COMPS_USERNAME --password $COMPS_PASSWORD'
 			}
-
+		}
+
 		try{
 			stage('Unit Test') {
 				echo "Running Unit test Tests"
 				dir('tests/unittests') {
-					sh "pip3 install unittest-xml-reporting"
-					sh 'python3 -m xmlrunner discover'
-					junit '*.xml'
+					sh 'py.test -sv --junitxml=reports/test_results.xml'
+					junit 'reports/*.xml'
 				}
 			}
 		} catch(e) {
 			build_ok = false
-			echo e.toString()  
+			echo e.toString()
 		}
-		
+
 		try{
-			stage('Workflow Tests') {
+			stage('Workflow Test') {
 				echo "Running Workflow Tests"
-				dir('tests/workflow_testing') {
-					sh 'python3 -m xmlrunner discover'
-					junit '*.xml'
+				dir('tests/workflow_tests') {
+				    sh 'py.test -sv --junitxml=reports/test_results.xml'
+				    junit 'reports/*.xml'
 				}
 			}
 		} catch(e) {
 			build_ok = false
-			echo e.toString()  
-		}
-
-		stage('Run Examples') {		    
-			echo "Running examples"
-			//sh 'yum -y remove mpich'
-			//sh 'yum -y install mpich-3.2'
-			//sh 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpich/lib'
-            sh 'pip3 install snakemake'
-			dir('examples') {
-				sh 'snakemake --cores=4 --config python_version=python3'
-			}
-			}
-		if(build_ok) {
-			currentBuild.result = "SUCCESS"
-		} else {
-			currentBuild.result = "FAILURE"
+			echo e.toString()
 		}
+
+    // 	stage('Run Examples') {
+    // 		echo "Running examples"
+    // 			dir('examples') {
+				// sh 'pip3 install snakemake'
+    //               		sh 'snakemake --cores=4 --config python_version=python3'
+    // 			}
+    // 		}
+        if(build_ok) {
+    		currentBuild.result = "SUCCESS"
+    	} else {
+    		currentBuild.result = "FAILURE"
+    	}
 	}
  }
 }

emodpy_typhoid/config.py

@@ -8,5 +8,4 @@ def cleanup_for_2018_mode( config ):
     config.parameters.Infectious_Period_Distribution = "FIXED_DURATION" # hack
     config.parameters.Base_Incubation_Period = 1
     config.parameters.Base_Infectious_Period = 1
-    config.parameters["Listed_Events"] = []
 

emodpy_typhoid/interventions/outbreak.py

@@ -0,0 +1,31 @@
+from emod_api import schema_to_class as s2c
+from emod_api.interventions import utils
+from emod_api.interventions import common
+import json
+
+def add_outbreak_individual(start_day: int = 1,
+                            demographic_coverage: float = 1.0,
+                            node_ids: list = None,
+                            repetitions: int = 1,
+                            timesteps_between_repetitions: int = 365,
+                            ind_property_restrictions: list = None):
+    import emod_api.campaign as campaign
+    import emod_api.interventions.outbreak as ob
+    from emod_api.interventions.common import ScheduledCampaignEvent
+
+    outbreak = ob.seed_by_coverage(
+        timestep=start_day,
+        campaign_builder=campaign,
+        coverage=demographic_coverage,
+        intervention_only=True
+    )
+
+    outbreak_event = ScheduledCampaignEvent(camp=campaign,
+                                            Start_Day=start_day,
+                                            Node_Ids=node_ids,
+                                            Number_Repetitions=repetitions,
+                                            Timesteps_Between_Repetitions=timesteps_between_repetitions,
+                                            Property_Restrictions=ind_property_restrictions,
+                                            Intervention_List=[outbreak],
+                                            Demographic_Coverage=demographic_coverage)
+    return outbreak_event

emodpy_typhoid/interventions/typhoid_vaccine.py

@@ -27,6 +27,37 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, d
     intervention.Changing_Effect.Decay_Time_Constant = decay_constant
     return intervention
 
+def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_constant=6935.0 ):
+    """
+     Create a new 'SimpleVaccine' intervention with specified parameters. If you use this function directly, you'll need to distribute the intervention with a function like ScheduledCampaignEvent or TriggeredCampaignEvent from emod_api.interventions.common.
+
+     Args:
+         camp (Camp): The camp to which the intervention is applied.
+         efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82.
+         mode (str, optional): The mode of the intervention. Default is "Acquisition" Can also be "Transmission" or "All".
+         constant_period (float, optional): The constant period of the waning effect in days. Default is 0.
+         decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0.
+
+     Returns:
+         SimpleVaccine: A fully configured instance of the SimpleVaccine intervention with the specified parameters.
+     """
+
+    intervention = s2c.get_class_with_defaults( "SimpleVaccine", camp.schema_path )
+    if mode == "Acquisition":
+        intervention.Vaccine_Type = "AcquisitionBlocking"
+    elif mode == "Transmission":
+        intervention.Vaccine_Type = "TransmissionBlocking"
+    elif mode == "All":
+        intervention.Vaccine_Type = "General"
+    else:
+        raise ValueError( f"mode {mode} not recognized. Options are: 'Acquisition', 'Transmission', or 'All'." )
+
+    intervention.Waning_Config = s2c.get_class_with_defaults( "WaningEffectBoxExponential" )
+    intervention.Waning_Config.Initial_Effect = efficacy
+    intervention.Waning_Config.Box_Duration = constant_period
+    intervention.Waning_Config.Decay_Time_Constant = decay_constant
+    return intervention
+
 def new_triggered_intervention( 
         camp, 
         efficacy=0.82,
@@ -65,6 +96,49 @@ def new_triggered_intervention(
 
     return event
 
+def new_routine_immunization( 
+        camp, 
+        efficacy=0.82,
+        mode="Acquisition",
+        constant_period=0,
+        decay_constant=6935.0,
+        start_day=1, 
+        child_age=9*30,
+        coverage=1.0, 
+        node_ids=None,
+        property_restrictions_list=[],
+        co_event=None # expansion slot
+    ):
+    """
+    Create a new delayed, birth-triggered SimpleVaccine intervention based on specified parameters. Does not add to campaign.
+
+    Args:
+         camp (Camp): The camp to which the intervention is applied.
+         efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82.
+         mode (str, optional): The mode of the intervention. Default is "Shedding".
+         constant_period (float, optional): The constant period of the waning effect in days. Default is 0.
+         decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0.
+         start_day (int, optional): The day on which the intervention starts. Default is 1.
+         child_age (int, optional): The age of the person when they get the vaccine. Defaults to 9 months. Vaccines are actually distribute +/- 7 days.
+         coverage (float, optional): Demographic coverage of the intervention. Default is 1.0.
+         node_ids (list, optional): List of node IDs where the intervention is applied. Default is None.
+         property_restrictions_list (list, optional): List of property restrictions for the intervention. Default is an empty list.
+         co_event (None, optional): Expansion slot for future use.
+
+     Returns:
+         TriggeredCampaignEvent: An instance of a triggered campaign event with the TyphoidVaccine intervention.
+    """
+    iv = new_vax( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant )
+    age_min = max(0,child_age-7)
+    delay = {
+            "Delay_Period_Min": age_min,
+            "Delay_Period_Max": child_age+7
+            }
+
+    event = common.triggered_campaign_delay_event( camp, start_day=start_day, trigger="Births", delay=delay, intervention=iv, ip_targeting=property_restrictions_list, coverage=coverage )
+
+    return event
+
 def new_scheduled_intervention( 
         camp, 
         efficacy=0.82,