Merge remote-tracking branch 'origin/main'

# Conflicts:
#	emodpy_typhoid/interventions/typhoid_vaccine.py
#	examples/future_campaign/multi_sweep.py
#	examples/future_campaign/requirements.txt
#	examples/vax_efficacy_sweep/requirements.txt

.bump_version.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-__version__ = '0.0.4'
+__version__ = '0.1.0'
 commit = True
 tag = False
 

.github/workflows/run_test.yml

@@ -31,9 +31,9 @@ jobs:
       - 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: Install idm-test package
+        run: |
+          pip install idm-test>=0.1.2 --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 }}"
@@ -56,6 +56,17 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@v3
         with:
-          name: unittest_results
+          name: workflow_results
+          path: |
+            **/test_results.xml
+      - name: run sft tests
+        run: |
+          cd tests/sft_tests
+          python run_all_sft_tests.py
+      - name: Upload workflow tests results to artifactory
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: sft_results
           path: |
             **/test_results.xml

Jenkinsfile

@@ -88,6 +88,19 @@ podTemplate(
 			build_ok = false
 			echo e.toString()
 		}
+		try{
+			stage('SFT Test') {
+				echo "Running SFT Tests"
+				dir('tests/sft_tests') {
+				    sh 'pip3 install idm-test>=0.1.2 --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple'
+				    sh 'python3 run_all_sft_tests.py'
+				    junit '**/test_results.xml'
+				}
+			}
+		} catch(e) {
+			build_ok = false
+			echo e.toString()
+		}
 
     // 	stage('Run Examples') {
     // 		echo "Running examples"

docs/conf.py

@@ -291,7 +291,7 @@
     search_project = os.environ["READTHEDOCS_PROJECT"]
     search_version = os.environ["READTHEDOCS_VERSION"]
 
-    rtd_sphinx_search_default_filter = f"subprojects:{search_project_parent}/{search_version}"
+    rtd_sphinx_search_default_filter = f"subprojects:{search_project}/{search_version}"
 
     rtd_sphinx_search_filters = {
         "Search this project": f"project:{search_project}/{search_version}",

emodpy_typhoid/interventions/typhoid_vaccine.py

@@ -26,7 +26,6 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, d
          decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0.
          expected_expiration (float, optional): The mean duration before efficacy becomes 0. If this is set to non-zero value, the constant_period and decay_constant are ignored. These are two different modes of waning.
 
-
      Returns:
          TyphoidVaccine: A fully configured instance of the TyphoidVaccine intervention with the specified parameters.
      """
@@ -36,9 +35,10 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, d
     intervention.Mode = mode
     intervention.Changing_Effect = _get_waning( constant_period=constant_period, decay_constant=decay_constant, expected_expiration=expected_expiration ) 
     intervention.Changing_Effect.Initial_Effect = efficacy
+
     return intervention
 
-def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_constant=0, expected_expiration=0 ):
+def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_constant=0, expected_expiration=0, deduplication_policy="replace"  ):
     """
      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.
 
@@ -49,6 +49,7 @@ def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_c
          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.
          expected_expiration (float, optional): The mean duration before efficacy becomes 0. If this is set to non-zero value, the constant_period and decay_constant are ignored. These are two different modes of waning.
+         deduplication_policy (string): "replace" (default) or "combine". If giving vax to someone who already has one, based on Intervention_Name which defaults to intervention classname ("SimpleVaccine"), "replace" will purge the existing one, and "combine" will add the new one without replacement, and rely on code and configuration to calculate the combinatorix. If using "combine", make sure you _know_ the combinatorix.
 
      Returns:
          SimpleVaccine: A fully configured instance of the SimpleVaccine intervention with the specified parameters.
@@ -64,6 +65,16 @@ def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_c
     else:
         raise ValueError( f"mode {mode} not recognized. Options are: 'Acquisition', 'Transmission', or 'All'." )
 
+    # combine: DAD=0
+    # replace: DAD=1, EIR=1
+    # abort: DAD=1, EIR=0  -- not supported
+    if deduplication_policy == "replace":
+        intervention.Enable_Intervention_Replacement = 1 # D_A_D should be set implicitly
+    elif deduplication_policy == "combine":
+        intervention.Dont_Allow_Duplicates = 0
+    else:
+        raise ValueError( f"deduplication_policy needs to be 'replace' or 'combine', not '{deduplication_policy}'." )
+
     intervention.Waning_Config = _get_waning( constant_period=constant_period, decay_constant=decay_constant, expected_expiration=expected_expiration ) 
     intervention.Waning_Config.Initial_Effect = efficacy
     return intervention
@@ -95,14 +106,18 @@ def new_triggered_intervention(
          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.
+         co_event (None, optional): The name of the event to be broadcast. This event name can be set in the Report_Event_Recorder_Events configuration parameter. It will be collected in ReportEventRecorder.csv with default event "VaccineDistributed".
 
      Returns:
          TriggeredCampaignEvent: An instance of a triggered campaign event with the TyphoidVaccine intervention.
     """
     iv = new_intervention( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant )
-
-    event = common.TriggeredCampaignEvent( camp, Start_Day=start_day, Triggers=triggers, Demographic_Coverage=coverage, Intervention_List=[ iv ], Node_Ids=node_ids, Property_Restrictions=property_restrictions_list, Event_Name="Triggered Typhoid Vax" )
+    if co_event:
+        signal = common.BroadcastEvent(camp, co_event)
+        iv = [iv, signal]
+    else:
+        iv = [iv]
+    event = common.TriggeredCampaignEvent( camp, Start_Day=start_day, Triggers=triggers, Demographic_Coverage=coverage, Intervention_List=iv, Node_Ids=node_ids, Property_Restrictions=property_restrictions_list, Event_Name="Triggered Typhoid Vax" )
 
     return event
 
@@ -135,11 +150,12 @@ def new_routine_immunization(
          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.
+         co_event (str, optional): The name of the event to be broadcast. This event name can be set in the Report_Event_Recorder_Events configuration parameter. It will be collected in ReportEventRecorder.csv with default event "VaccineDistributed" if not set with other name.
 
      Returns:
          TriggeredCampaignEvent: An instance of a triggered campaign event with the TyphoidVaccine intervention.
     """
+    # routine_immunization will always be a first vax (unless something is really whack) so mode doesn't matter.
     iv = new_vax( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant, expected_expiration=expected_expiration )
     if co_event:
         signal = common.BroadcastEvent( camp, co_event )
@@ -185,17 +201,19 @@ def new_scheduled_intervention(
          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.
+         co_event (None, optional): The name of the event to be broadcast. This event name can be set in the Report_Event_Recorder_Events configuration parameter. It will be collected in ReportEventRecorder.csv if set not None or "".
 
      Returns:
          ScheduledCampaignEvent: An instance of a scheduled campaign event with the TyphoidVaccine intervention.
     
     """
     iv = new_intervention( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant )
-
-    #event = common.ScheduledCampaignEvent( camp, Start_Day=start_day, Demographic_Coverage=coverage, Intervention_List=[ act_intervention, bcast_intervention ], Node_Ids=nodeIDs, Property_Restrictions=property_restrictions_list )
-    event = common.ScheduledCampaignEvent( camp, Start_Day=start_day, Demographic_Coverage=coverage, Intervention_List=[ iv ], Node_Ids=node_ids, Property_Restrictions=property_restrictions_list )
-
+    if co_event:
+        signal = common.BroadcastEvent(camp, co_event)
+        iv = [iv, signal]
+    else:
+        iv = [iv]
+    event = common.ScheduledCampaignEvent( camp, Start_Day=start_day, Demographic_Coverage=coverage, Intervention_List=iv, Node_Ids=node_ids, Property_Restrictions=property_restrictions_list )
     return event
 
 def new_intervention_as_file( camp, start_day, filename=None ):

examples/HINTy/requirements.txt

@@ -1,4 +1,4 @@
-emodpy-typhoid==0.0.5.dev2
+emodpy-typhoid==0.0.5
 emodpy==1.22.0.dev3
 emod-api==1.31.0.dev0
 emod-typhoid==0.0.4.dev2

examples/future_campaign/multi_sweep.py

@@ -22,8 +22,8 @@
 from emodpy_typhoid.utility.sweeping import ItvFn, CfgFn, set_param, sweep_functions
 
 
-BASE_YEAR = 2005
-SIMULATION_DURATION_IN_YEARS = 25
+BASE_YEAR = 1990
+SIMULATION_DURATION_IN_YEARS = 40
 CAMP_START_YEAR = 2015
 FWD_CAMP_START_YEAR = 2024.25
 
@@ -40,14 +40,13 @@ def set_param_fn(config):
     config.parameters.Inset_Chart_Reporting_Start_Year = BASE_YEAR
     config.parameters.Inset_Chart_Reporting_Stop_Year = 2030
     config.parameters.Enable_Demographics_Reporting = 0
-    #config.parameters.Enable_Property_Output = 1  # crash
-    #config.parameters.Report_Event_Recorder_Events = ["VaccineDistributed", "PropertyChange", "NewInfectionEvent" ]
+    config.parameters.Enable_Property_Output = 0
     config.parameters.Report_Event_Recorder_Events = ["NewInfectionEvent" ]
     config.parameters["Listed_Events"] = ["VaccineDistributed"]  # old school
 
     config.parameters.Report_Typhoid_ByAgeAndGender_Start_Year = 2010
     config.parameters.Report_Typhoid_ByAgeAndGender_Stop_Year = 2030
-    config.parameters.Age_Initialization_Distribution_Type = "DISTRIBUTION_COMPLEX"
+    #config.parameters.Age_Initialization_Distribution_Type = "DISTRIBUTION_COMPLEX" # move to after
     config.parameters.Typhoid_3year_Susceptible_Fraction = 0
     config.parameters.Typhoid_6month_Susceptible_Fraction = 0
     config.parameters.Typhoid_6year_Susceptible_Fraction = 0
@@ -95,14 +94,14 @@ def add_historical_vax( camp, ria_coverage=0.75, camp_coverage=0.75, efficacy=0.
         ria = tv.new_routine_immunization(camp,
                                           efficacy=efficacy,
                                           constant_period=0,
-                                          expected_expiration=expiration,
-                                          #decay_constant=values['decay_constant'],
+                                          #expected_expiration=expiration,
+                                          decay_constant=expiration,
                                           start_day=year_to_days(CAMP_START_YEAR),
                                           coverage=ria_coverage)
         tv_iv = tv.new_vax(camp,
                            efficacy=efficacy,
-                           expected_expiration=expiration,
-                           #decay_constant=values['decay_constant'],
+                           #expected_expiration=expiration,
+                           decay_constant=expiration,
                            constant_period=0)
 
         notification_iv = comm.BroadcastEvent(camp, "VaccineDistributed")
@@ -114,7 +113,7 @@ def add_historical_vax( camp, ria_coverage=0.75, camp_coverage=0.75, efficacy=0.
                                                         Demographic_Coverage=camp_coverage,
                                                         Target_Age_Min=0.75,
                                                         Target_Age_Max=15
-                                                        )
+                                                       )
         camp.add(one_time_campaign)
 
     #add_historical_vax( camp )
@@ -151,7 +150,10 @@ def add_vax_intervention(campaign, values, min_age=0.75, max_age=15, binary_immu
     import emodpy_typhoid.interventions.typhoid_vaccine as tv
     print(f"Telling emod-api to use {manifest.schema_file} as schema.")
     campaign.set_schema(manifest.schema_file)
-    camp_coverage = values['coverage_camp']
+    for key in values.keys():
+        if 'coverage' in key:
+            camp_coverage = values[key]
+            break
 
     if binary_immunity:
         tv_iv = tv.new_vax(campaign,
@@ -165,6 +167,12 @@ def add_vax_intervention(campaign, values, min_age=0.75, max_age=15, binary_immu
                        constant_period=0)
 
     notification_iv = comm.BroadcastEvent(campaign, "VaccineDistributed")
+    # NOTE: the order of interventions in Intervention_List matters. This is because multiple
+    # interventions are delivered using a MultiInterventionDistributor intervention and de-duplication
+    # operates on Intervention_Name, so that when we try to distribute this intervention 'package',
+    # the model looks at the name of the existing intervention, which is the vax, and the name of the
+    # 'package' here, which would be MultiInterventionDistributor. But there is code in emod_api which
+    # sets the MID name to the name of the first intervention in the list, which here will be SimpleVaccine.
     one_time_campaign = comm.ScheduledCampaignEvent(campaign,
                                                     Start_Day=year_to_days(FWD_CAMP_START_YEAR),
                                                     Intervention_List=[tv_iv, notification_iv],
@@ -219,6 +227,7 @@ def run( sweep_choice="All", age_targeted=True, binary_immunity=True ):
     task.config.parameters.Demographics_Filenames = ["demographics.json","TestDemographics_pak_updated.json"]
     task.config.parameters.Death_Rate_Dependence = "NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER"
     task.config.parameters.Birth_Rate_Dependence = "INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR"
+    task.config.parameters.Age_Initialization_Distribution_Type = "DISTRIBUTION_COMPLEX"
     # this is dumb
     task.common_assets.add_directory(assets_directory=manifest.assets_input_dir)
     task.set_sif(manifest.sif)
@@ -234,7 +243,7 @@ def get_sweep_list_from_values(start_day_offset, vax_effs, cov, decay):
     def get_sweep_list_full():
         start_day_offset = [1]
         vax_effs = np.linspace(0.1, 1.0, 10)
-        decay = [1, 365, 3650, 365000]
+        decay = [1, 365, 3650, 36500]
         cov = np.linspace(start=0.0, stop=1.0, num=5)
         return get_sweep_list_from_values(start_day_offset, vax_effs, cov, decay)
 
@@ -286,15 +295,26 @@ def get_sweep_list_duration():
             sweep_list.append({'start_day_offset': c[0], 'efficacy': c[1], 'coverage': c[2], 'decay_constant': c[3]})
         return sweep_list
 
+    def get_sweep_list_just_one():
+        start_day_offset = [1]
+        vax_effs = [1]
+        decay = [3000]
+        cov = [0.75]
+        combinations = list(itertools.product(start_day_offset, vax_effs, cov, decay))
+        sweep_list = []
+        for c in combinations:
+            sweep_list.append({'start_day_offset': c[0], 'efficacy': c[1], 'coverage_camp': c[2], 'decay_constant': c[3]})
+        return sweep_list
+
     def get_sweep_list_from_csv():
         # This is wrong. Just load rows. Code is recreating. But have to stop work for now.
         import pandas as pd
         df = pd.load_csv( manifest.sweep_config )
         raise NotImplemented( "get_sweep_list_from_csv" )
 
     def get_config_sweep_list():
-        tac = [ 13435, 15320 ]
-        tel = [ 5.0, 7.0 ]
+        tac = [ 13435 ]
+        tel = [ 7.0 ]
         combinations = list(itertools.product(tac, tel))
         sweep_list = []
         for c in combinations:
@@ -307,7 +327,8 @@ def get_config_sweep_list():
             "Coverage": get_sweep_list_coverage,
             "Coverage_RIA": get_sweep_list_coverage_ria,
             "Coverage_Camp": get_sweep_list_coverage_camp,
-            "Vax_Duration": get_sweep_list_duration
+            "Vax_Duration": get_sweep_list_duration,
+            "Just_One": get_sweep_list_just_one
             }
 
     if sweep_choice not in sweep_selections.keys():
@@ -319,10 +340,7 @@ def get_config_sweep_list():
     else:
         avi_age_coverage = partial( add_vax_intervention, min_age=0, max_age=125 )
 
-    if binary_immunity:
-        avi_decay = partial( avi_age_coverage, binary_immunity=True )
-    else:
-        avi_decay = partial( avi_age_coverage, binary_immunity=False )
+    avi_decay = partial( avi_age_coverage, binary_immunity=binary_immunity )
 
     builders = get_sweep_builders(sweep_list, get_config_sweep_list(), add_vax_fn=avi_decay)
 
@@ -344,4 +362,4 @@ def get_config_sweep_list():
     dtk.setup(manifest.model_dl_dir)
 
     import sys
-    run( sys.argv[1] if len(sys.argv)>1 else "Efficacy" )
+    run( sys.argv[1] if len(sys.argv)>1 else "Just_One", binary_immunity=False )