idmtools-test 0.0.0.dev0__py3-none-any.whl → 0.0.3__py3-none-any.whl

idmtools_test/inputs/custom/emodules_map.json

@@ -0,0 +1,9 @@
+{
+   "disease_plugins": [],
+   "interventions": [],
+   "reporter_plugins": [
+      "Assets\\reporter_plugins\\libReportMalariaFiltered.dll",
+      "Assets\\reporter_plugins\\libreporteventcounter.dll",
+      "Assets\\reporter_plugins\\libSpatialReportMalariaFiltered.dll"
+   ]
+}

idmtools_test/inputs/emod_files/campaign.json

@@ -0,0 +1,21 @@
+{
+  "Campaign_Name": "Initial Seeding",
+  "Events": [
+    {
+      "Event_Coordinator_Config": {
+        "Demographic_Coverage": 0.0005,
+        "Intervention_Config": {
+          "Outbreak_Source": "PrevalenceIncrease",
+          "class": "OutbreakIndividual"
+        },
+        "class": "StandardInterventionDistributionEventCoordinator"
+      },
+      "Event_Name": "Outbreak",
+      "Nodeset_Config": {
+        "class": "NodeSetAll"
+      },
+      "class": "CampaignEvent"
+    }
+  ],
+  "Use_Defaults": 1
+}

idmtools_test/inputs/emod_files/config.json

@@ -0,0 +1,125 @@
+{
+  "parameters": {
+    "Acquisition_Blocking_Immunity_Decay_Rate": 0.1,
+    "Acquisition_Blocking_Immunity_Duration_Before_Decay": 60,
+    "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE",
+    "Animal_Reservoir_Type": "NO_ZOONOSIS",
+    "Base_Incubation_Period": 0,
+    "Base_Individual_Sample_Rate": 1,
+    "Base_Infectious_Period": 4,
+    "Base_Infectivity": 3.5,
+    "Base_Mortality": 0,
+    "Base_Population_Scale_Factor": 1,
+    "Birth_Rate_Dependence": "POPULATION_DEP_RATE",
+    "Birth_Rate_Time_Dependence": "NONE",
+    "Burnin_Cache_Mode": "none",
+    "Burnin_Cache_Period": 0,
+    "Burnin_Name": "",
+    "Campaign_Filename": "campaign.json",
+    "Climate_Model": "CLIMATE_OFF",
+    "Config_Name": "01_SIR",
+    "Custom_Coordinator_Events": [],
+    "Custom_Individual_Events": [],
+    "Custom_Node_Events": [],
+    "Custom_Reports_Filename": "NoCustomReports",
+    "Default_Geography_Initial_Node_Population": 1000,
+    "Default_Geography_Torus_Size": 10,
+    "Demographics_Filenames": [
+      "demographics.json"
+    ],
+    "Enable_Air_Migration": 0,
+    "Enable_Default_Reporting": 1,
+    "Enable_Default_Shedding_Function": 1,
+    "Enable_Demographics_Birth": 0,
+    "Enable_Demographics_Builtin": 0,
+    "Enable_Demographics_Gender": 1,
+    "Enable_Demographics_Other": 0,
+    "Enable_Demographics_Reporting": 1,
+    "Enable_Disease_Mortality": 0,
+    "Enable_Family_Migration": 0,
+    "Enable_Heterogeneous_Intranode_Transmission": 0,
+    "Enable_Immune_Decay": 0,
+    "Enable_Immunity": 0,
+    "Enable_Infectivity_Reservoir": 0,
+    "Enable_Initial_Prevalence": 0,
+    "Enable_Initial_Susceptibility_Distribution": 0,
+    "Enable_Interventions": 1,
+    "Enable_Local_Migration": 0,
+    "Enable_Maternal_Transmission": 0,
+    "Enable_Property_Output": 0,
+    "Enable_Regional_Migration": 0,
+    "Enable_Sea_Migration": 0,
+    "Enable_Skipping": 0,
+    "Enable_Spatial_Output": 0,
+    "Enable_Strain_Tracking": 0,
+    "Enable_Superinfection": 0,
+    "Enable_Susceptibility_Scaling": 0,
+    "Enable_Termination_On_Zero_Total_Infectivity": 0,
+    "Enable_Vital_Dynamics": 0,
+    "Geography": "SamplesInput",
+    "Immunity_Acquisition_Factor": 0,
+    "Immunity_Initialization_Distribution_Type": "DISTRIBUTION_OFF",
+    "Immunity_Mortality_Factor": 0,
+    "Immunity_Transmission_Factor": 0,
+    "Incubation_Period_Constant": 0,
+    "Incubation_Period_Distribution": "CONSTANT_DISTRIBUTION",
+    "Individual_Sampling_Type": "TRACK_ALL",
+    "Infection_Updates_Per_Timestep": 1,
+    "Infectious_Period_Distribution": "EXPONENTIAL_DISTRIBUTION",
+    "Infectious_Period_Exponential": 4,
+    "Infectivity_Scale_Type": "CONSTANT_INFECTIVITY",
+    "Job_Node_Groups": "Chassis08",
+    "Job_Priority": "BELOWNORMAL",
+    "Listed_Events": [],
+    "Load_Balance_Filename": "",
+    "Local_Simulation": 0,
+    "Maternal_Transmission_Probability": 0,
+    "Max_Individual_Infections": 1,
+    "Max_Node_Population_Samples": 40,
+    "Migration_Model": "NO_MIGRATION",
+    "Minimum_Adult_Age_Years": 15,
+    "Mortality_Blocking_Immunity_Decay_Rate": 0.001,
+    "Mortality_Blocking_Immunity_Duration_Before_Decay": 60,
+    "Mortality_Time_Course": "DAILY_MORTALITY",
+    "Node_Grid_Size": 0.042,
+    "Num_Cores": 1,
+    "Number_Basestrains": 1,
+    "Number_Substrains": 1,
+    "PKPD_Model": "FIXED_DURATION_CONSTANT_EFFECT",
+    "Population_Density_C50": 30,
+    "Population_Density_Infectivity_Correction": "CONSTANT_INFECTIVITY",
+    "Population_Scale_Type": "USE_INPUT_FILE",
+    "Post_Infection_Acquisition_Multiplier": 0,
+    "Post_Infection_Mortality_Multiplier": 0,
+    "Post_Infection_Transmission_Multiplier": 0,
+    "Report_Coordinator_Event_Recorder": 0,
+    "Report_Event_Recorder": 0,
+    "Report_Node_Event_Recorder": 0,
+    "Report_Surveillance_Event_Recorder": 0,
+    "Run_Number": 1,
+    "Sample_Rate_0_18mo": 1,
+    "Sample_Rate_10_14": 1,
+    "Sample_Rate_15_19": 1,
+    "Sample_Rate_18mo_4yr": 1,
+    "Sample_Rate_20_Plus": 1,
+    "Sample_Rate_5_9": 1,
+    "Sample_Rate_Birth": 1,
+    "Serialization_Type": "NONE",
+    "Simulation_Duration": 90,
+    "Simulation_Timestep": 1,
+    "Simulation_Type": "GENERIC_SIM",
+    "Start_Time": 0,
+    "Susceptibility_Scale_Type": "CONSTANT_SUSCEPTIBILITY",
+    "Symptomatic_Infectious_Offset": 0,
+    "Transmission_Blocking_Immunity_Decay_Rate": 0.1,
+    "Transmission_Blocking_Immunity_Duration_Before_Decay": 60,
+    "x_Air_Migration": 1,
+    "x_Birth": 1,
+    "x_Local_Migration": 1,
+    "x_Other_Mortality": 1,
+    "x_Population_Immunity": 1,
+    "x_Regional_Migration": 1,
+    "x_Sea_Migration": 1,
+    "x_Temporary_Larval_Habitat": 1
+  }
+}

idmtools_test/inputs/emod_files/demographics.json

@@ -0,0 +1,81 @@
+{
+  "Metadata": {
+    "DateCreated": "Sun Sep 25 23:19:55 2011",
+    "Tool": "convertdemog.py",
+    "Author": "jsteinkraus",
+    "IdReference": "0",
+    "NodeCount": 1,
+    "Resolution": 150
+  },
+  "Defaults": {},
+  "Nodes": [
+    {
+      "NodeID": 1,
+      "NodeAttributes": {
+        "Latitude": 0,
+        "Longitude": 0,
+        "Altitude": 0,
+        "Airport": 0,
+        "Region": 1,
+        "Seaport": 0,
+        "InitialPopulation": 10000,
+        "BirthRate": 0.0000548
+      },
+      "IndividualAttributes": {
+        "AgeDistributionFlag": 3,
+        "AgeDistribution1": 0.000118,
+        "AgeDistribution2": 0,
+        "PrevalenceDistributionFlag": 0,
+        "PrevalenceDistribution1": 0,
+        "PrevalenceDistribution2": 0,
+        "SusceptibilityDistributionFlag": 0,
+        "SusceptibilityDistribution1": 1,
+        "SusceptibilityDistribution2": 0,
+        "RiskDistributionFlag": 0,
+        "RiskDistribution1": 1,
+        "RiskDistribution2": 0,
+        "MigrationHeterogeneityDistributionFlag": 0,
+        "MigrationHeterogeneityDistribution1": 1,
+        "MigrationHeterogeneityDistribution2": 0,
+        "MortalityDistribution": {
+          "NumDistributionAxes": 2,
+          "AxisNames": [
+            "gender",
+            "age"
+          ],
+          "AxisUnits": [
+            "male=0,female=1",
+            "years"
+          ],
+          "AxisScaleFactors": [
+            1,
+            365
+          ],
+          "NumPopulationGroups": [
+            2,
+            1
+          ],
+          "PopulationGroups": [
+            [
+              0,
+              1
+            ],
+            [
+              0
+            ]
+          ],
+          "ResultUnits": "deaths per day",
+          "ResultScaleFactor": 1,
+          "ResultValues": [
+            [
+              0.0000548
+            ],
+            [
+              0.0000548
+            ]
+          ]
+        }
+      }
+    }
+  ]
+}

idmtools_test/inputs/files/campaign.json

@@ -0,0 +1,21 @@
+{
+  "Campaign_Name": "Initial Seeding",
+  "Events": [
+    {
+      "Event_Coordinator_Config": {
+        "Demographic_Coverage": 0.0005,
+        "Intervention_Config": {
+          "Outbreak_Source": "PrevalenceIncrease",
+          "class": "OutbreakIndividual"
+        },
+        "class": "StandardInterventionDistributionEventCoordinator"
+      },
+      "Event_Name": "Outbreak",
+      "Nodeset_Config": {
+        "class": "NodeSetAll"
+      },
+      "class": "CampaignEvent"
+    }
+  ],
+  "Use_Defaults": 1
+}

idmtools_test/inputs/files/config.json

@@ -0,0 +1,119 @@
+{
+  "parameters": {
+            "Acquisition_Blocking_Immunity_Decay_Rate": 0.1,
+            "Acquisition_Blocking_Immunity_Duration_Before_Decay": 60,
+            "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE",
+            "Animal_Reservoir_Type": "NO_ZOONOSIS",
+            "Base_Incubation_Period": 0,
+            "Base_Individual_Sample_Rate": 1,
+            "Base_Infectious_Period": 4,
+            "Base_Infectivity": 3.5,
+            "Base_Mortality": 0,
+            "Base_Population_Scale_Factor": 1,
+            "Birth_Rate_Dependence": "POPULATION_DEP_RATE",
+            "Birth_Rate_Time_Dependence": "NONE",
+            "Burnin_Cache_Mode": "none",
+            "Burnin_Cache_Period": 0,
+            "Burnin_Name": "",
+            "Campaign_Filename": "campaign.json",
+            "Climate_Model": "CLIMATE_OFF",
+            "Config_Name": "01_SIR",
+            "Custom_Coordinator_Events": [],
+            "Custom_Individual_Events": [],
+            "Custom_Node_Events": [],
+            "Custom_Reports_Filename": "NoCustomReports",
+            "Default_Geography_Initial_Node_Population": 1000,
+            "Default_Geography_Torus_Size": 10,
+            "Demographics_Filenames": [
+            ],
+            "Enable_Default_Reporting": 1,
+            "Enable_Default_Shedding_Function": 1,
+            "Enable_Demographics_Birth": 0,
+            "Enable_Demographics_Builtin": 0,
+            "Enable_Demographics_Gender": 1,
+            "Enable_Demographics_Other": 0,
+            "Enable_Demographics_Reporting": 1,
+            "Enable_Disease_Mortality": 0,
+            "Enable_Heterogeneous_Intranode_Transmission": 0,
+            "Enable_Immune_Decay": 0,
+            "Enable_Immunity": 1,
+            "Enable_Infectivity_Reservoir": 0,
+            "Enable_Initial_Prevalence": 0,
+            "Enable_Initial_Susceptibility_Distribution": 0,
+            "Enable_Interventions": 1,
+            "Enable_Maternal_Transmission": 0,
+            "Enable_Property_Output": 0,
+            "Enable_Skipping": 0,
+            "Enable_Spatial_Output": 0,
+            "Enable_Strain_Tracking": 0,
+            "Enable_Superinfection": 0,
+            "Enable_Susceptibility_Scaling": 0,
+            "Enable_Termination_On_Zero_Total_Infectivity": 0,
+            "Enable_Vital_Dynamics": 0,
+            "Geography": "SamplesInput",
+            "Immunity_Acquisition_Factor": 0,
+            "Immunity_Initialization_Distribution_Type": "DISTRIBUTION_OFF",
+            "Immunity_Mortality_Factor": 0,
+            "Immunity_Transmission_Factor": 0,
+            "Incubation_Period_Constant": 0,
+            "Incubation_Period_Distribution": "CONSTANT_DISTRIBUTION",
+            "Individual_Sampling_Type": "TRACK_ALL",
+            "Infection_Updates_Per_Timestep": 1,
+            "Infectious_Period_Exponential": 4,
+            "Infectious_Period_Distribution": "EXPONENTIAL_DISTRIBUTION",
+            "Infectivity_Scale_Type": "CONSTANT_INFECTIVITY",
+            "Job_Node_Groups": "Chassis08",
+            "Job_Priority": "BELOWNORMAL",
+            "Listed_Events": [],
+            "Load_Balance_Filename": "",
+            "Local_Simulation": 0,
+            "Maternal_Transmission_Probability": 0,
+            "Max_Individual_Infections": 1,
+            "Max_Node_Population_Samples": 40,
+            "Migration_Model": "NO_MIGRATION",
+            "Minimum_Adult_Age_Years": 15,
+            "Mortality_Blocking_Immunity_Decay_Rate": 0.001,
+            "Mortality_Blocking_Immunity_Duration_Before_Decay": 60,
+            "Mortality_Time_Course": "DAILY_MORTALITY",
+            "Node_Grid_Size": 0.042,
+            "Num_Cores": 1,
+            "Number_Basestrains": 1,
+            "Number_Substrains": 1,
+            "PKPD_Model": "FIXED_DURATION_CONSTANT_EFFECT",
+            "Population_Density_C50": 30,
+            "Population_Density_Infectivity_Correction": "CONSTANT_INFECTIVITY",
+            "Population_Scale_Type": "USE_INPUT_FILE",
+            "Post_Infection_Acquisition_Multiplier": 0,
+            "Post_Infection_Mortality_Multiplier": 0,
+            "Post_Infection_Transmission_Multiplier": 0,
+            "Report_Coordinator_Event_Recorder": 0,
+            "Report_Event_Recorder": 0,
+            "Report_Node_Event_Recorder": 0,
+            "Report_Surveillance_Event_Recorder": 0,
+            "Run_Number": 1,
+            "Sample_Rate_0_18mo": 1,
+            "Sample_Rate_10_14": 1,
+            "Sample_Rate_15_19": 1,
+            "Sample_Rate_18mo_4yr": 1,
+            "Sample_Rate_20_Plus": 1,
+            "Sample_Rate_5_9": 1,
+            "Sample_Rate_Birth": 1,
+            "Serialization_Type": "NONE",
+            "Simulation_Duration": 90,
+            "Simulation_Timestep": 1,
+            "Simulation_Type": "GENERIC_SIM",
+            "Start_Time": 0,
+            "Susceptibility_Scale_Type": "CONSTANT_SUSCEPTIBILITY",
+            "Symptomatic_Infectious_Offset": 0,
+            "Transmission_Blocking_Immunity_Decay_Rate": 0.1,
+            "Transmission_Blocking_Immunity_Duration_Before_Decay": 60,
+            "x_Air_Migration": 1,
+            "x_Birth": 1,
+            "x_Local_Migration": 1,
+            "x_Other_Mortality": 1,
+            "x_Population_Immunity": 1,
+            "x_Regional_Migration": 1,
+            "x_Sea_Migration": 1,
+            "x_Temporary_Larval_Habitat": 1
+  }
+}

idmtools_test/inputs/files/demographics.json

@@ -0,0 +1,82 @@
+{
+  "Metadata": {
+    "DateCreated": "Sun Sep 25 23:19:55 2011",
+    "Tool": "convertdemog.py",
+    "Author": "jsteinkraus",
+    "IdReference": "0",
+    "NodeCount": 1,
+    "Resolution": 150
+  },
+  "Defaults": {
+  },
+  "Nodes": [
+    {
+      "NodeID": 1,
+      "NodeAttributes": {
+        "Latitude": 0,
+        "Longitude": 0,
+        "Altitude": 0,
+        "Airport": 0,
+        "Region": 1,
+        "Seaport": 0,
+        "InitialPopulation": 10000,
+        "BirthRate": 0.0000548
+      },
+      "IndividualAttributes": {
+        "AgeDistributionFlag": 3,
+        "AgeDistribution1": 0.000118,
+        "AgeDistribution2": 0,
+        "PrevalenceDistributionFlag": 0,
+        "PrevalenceDistribution1": 0.0,
+        "PrevalenceDistribution2": 0.0,
+        "SusceptibilityDistributionFlag": 0,
+        "SusceptibilityDistribution1": 1,
+        "SusceptibilityDistribution2": 0,
+        "RiskDistributionFlag": 0,
+        "RiskDistribution1": 1,
+        "RiskDistribution2": 0,
+        "MigrationHeterogeneityDistributionFlag": 0,
+        "MigrationHeterogeneityDistribution1": 1,
+        "MigrationHeterogeneityDistribution2": 0,
+        "MortalityDistribution": {
+          "NumDistributionAxes": 2,
+          "AxisNames": [
+            "gender",
+            "age"
+          ],
+          "AxisUnits": [
+            "male=0,female=1",
+            "years"
+          ],
+          "AxisScaleFactors": [
+            1,
+            365
+          ],
+          "NumPopulationGroups": [
+            2,
+            1
+          ],
+          "PopulationGroups": [
+            [
+              0,
+              1
+            ],
+            [
+              0
+            ]
+          ],
+          "ResultUnits": "deaths per day",
+          "ResultScaleFactor": 1,
+          "ResultValues": [
+            [
+              0.0000548
+            ],
+            [
+              0.0000548
+            ]
+          ]
+        }
+      }
+    }
+  ]
+}

idmtools_test/inputs/files/hello.txt

@@ -0,0 +1 @@
+hello

idmtools_test/inputs/id_files/slurm.example_python_experiment.id

@@ -0,0 +1 @@
+73ba8f3b-8848-ee11-92fb-f0921c167864::Experiment::SlurmStage

idmtools_test/inputs/malaria_brazil_central_west_spatial/Assets/Brazil_Central_West_Brazil_Central_West_2.5arcmin_air_temperature_daily.bin.json

@@ -0,0 +1,26 @@
+{
+  "Metadata": {
+    "DateCreated": "06/05/2018",
+    "Tool": "MergeNodes.exe",
+    "Author": "Institute for Disease Modeling",
+    "WeatherSchemaVersion": "2.0",
+    "IdReference": "default",
+    "WeatherCellCount": 36,
+    "NodeCount": 36,
+    "OffsetEntryCount": 36,
+    "NumberDTKNodes": 36,
+    "DatavaluePerCell": 4380,
+    "DatavalueCount": 4380,
+    "UpdateResolution": "CLIMATE_UPDATE_DAY",
+    "OriginalDataYears": "2006-2017",
+    "StartDayOfYear": "January 1",
+    "DataProvenance": "Generated by internally-developed algorithm applied to GSOD weather-station data IDM-Brazil_Central_West",
+    "RunID": "1527897611",
+    "Resolution": "2.5arcmin",
+    "UpperLatitude": -6.99999999999997,
+    "LeftLongitude": -62.0000000000034,
+    "BottomLatitude": -24.4166666666666,
+    "RightLongitude": -45.54166666667
+  },
+  "NodeOffsets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
+}