From 42249754f921206d7e219f033e51015acc317e58 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Wed, 13 Sep 2023 20:36:16 -0700 Subject: [PATCH 01/28] Cache latest working example with 2-D sweep. --- .../from_files/config_comps_ref.json | 10 +++--- .../blantyre_noHINT/from_files/example.py | 35 ++++++++++++++----- 2 files changed, 32 insertions(+), 13 deletions(-) diff --git a/examples/blantyre_noHINT/from_files/config_comps_ref.json b/examples/blantyre_noHINT/from_files/config_comps_ref.json index 9482ced..bf9f654 100644 --- a/examples/blantyre_noHINT/from_files/config_comps_ref.json +++ b/examples/blantyre_noHINT/from_files/config_comps_ref.json @@ -13,14 +13,14 @@ "Acquisition_Blocking_Immunity_Decay_Rate": 0.1, "Acquisition_Blocking_Immunity_Duration_Before_Decay": 60, - "Age_Initialization_Distribution_Type": "DISTRIBUTION_COMPLEX", + "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE", "Air_Temperature_Filename": "", "Air_Temperature_Offset": 0, "Air_Temperature_Variance": 2, "Animal_Reservoir_Type": "NO_ZOONOSIS", "Base_Air_Temperature": 30, "Base_Incubation_Period": 3000000, - "Base_Individual_Sample_Rate": 0.25, + "Base_Individual_Sample_Rate": 0.1, "Base_Infectious_Period": 70000000, "Base_Infectivity": 0.3, "Base_Land_Temperature": 30, @@ -38,11 +38,11 @@ "Climate_Model": "CLIMATE_OFF", "Climate_Update_Resolution": "CLIMATE_UPDATE_DAY", "Config_Name": "149_Typhoid", - "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER", + "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER", "Default_Geography_Initial_Node_Population": 1000, "Default_Geography_Torus_Size": 10, "Demographics_Filenames": [ - "TestDemographics_Mystery_Fert.json" + "demographics.json" ], "Enable_Absolute_Time": "NO", "Enable_Aging": 1, @@ -142,9 +142,9 @@ "Typhoid_Carrier_Removal_Year": 2500, "Typhoid_Chronic_Relative_Infectiousness": 0.5, "Typhoid_Contact_Exposure_Rate": 0.44535910269531453, - "Environmental_Cutoff_Days": 1, "Typhoid_Environmental_Exposure_Rate": 0.24619971394455994, "__Typhoid_Environmental_Exposure_Rate": 0.024619971394455994, + "Environmental_Cutoff_Days": 1, "Environmental_Peak_Start": 287.2811494864098, "Environmental_Ramp_Down_Duration": 1, "Environmental_Ramp_Up_Duration": 1, diff --git a/examples/blantyre_noHINT/from_files/example.py b/examples/blantyre_noHINT/from_files/example.py index 0ad9471..c0f40b6 100755 --- a/examples/blantyre_noHINT/from_files/example.py +++ b/examples/blantyre_noHINT/from_files/example.py @@ -18,15 +18,33 @@ import manifest +sim_idx = 0 def update_sim_random_seed(simulation, value): - return {"Run_Number": value} + global sim_idx + sim_idx += 1 + simulation.task.config["Run_Number"] = value + return {"Run_Number": value, "idx": sim_idx } + +def update_sim_param(simulation, value): + simulation.task.config["Typhoid_Acute_Infectiousness"] = 13435+value + return {"Typhoid_Acute_Infectiousness": 13435+value} def run(): # Create a platform # Show how to dynamically set priority and node_group platform = Platform("SLURM", node_group="idm_48cores", priority="Highest") - task = EMODTask.from_files(config_path="config_comps_ref.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_comps_ref.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_comps_ref.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["demographics.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_py.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["demographics.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["demographics.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_literal_5mods.json", eradication_path=manifest.eradication_path, campaign_path="campaign_baseline.json", demographics_paths=["TestDemographics_Blantyre.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_june242019.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_june242019_plus_to_params.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_june242019_seasonal.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) + #task = EMODTask.from_files(config_path="config_june242019_seasonal_to.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) + task = EMODTask.from_files(config_path="config_feb162019.json", eradication_path=manifest.eradication_path, campaign_path="campaign_feb162019.json", demographics_paths=["TestDemographics_Blantyre.json"], ep4_path=None) + print("Adding asset dir...") task.common_assets.add_directory(assets_directory=manifest.reporters, relative_path="reporter_plugins") @@ -35,21 +53,22 @@ def run(): # Create simulation sweep with builder builder = SimulationBuilder() - builder.add_sweep_definition( update_sim_random_seed, range(1) ) + builder.add_sweep_definition( update_sim_random_seed, range(4) ) + builder.add_sweep_definition( update_sim_param, range(4) ) # create experiment from builder - experiment = Experiment.from_builder(builder, task, name="Typhoid Blantyre emodpy") + experiment = Experiment.from_builder(builder, task, name="Typhoid Blantyre NoHINT emodpy from_files") # The last step is to call run() on the ExperimentManager to run the simulations. experiment.run(wait_until_done=True, platform=platform) task.handle_experiment_completion( experiment ) # download and plot some stuff. - EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json", "SpatialOutput_Prevalence.bin" ] ) + EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json" ] ) task.cache_experiment_metadata_in_sql( experiment.uid ) - import emod_api.channelreports.plot_icj_means as plotter - chan_data = plotter.collect( str( experiment.uid ), "Infected" ) - plotter.display( chan_data, False, "Infected", str( experiment.uid ) ) + #import emod_api.channelreports.plot_icj_means as plotter + #chan_data = plotter.collect( "Typhoid Blantyre NoHINT emodpy from_files".replace( " ", "_" ), "Infected" ) + #plotter.display( chan_data, False, "Infected", str( experiment.uid ) ) if __name__ == "__main__": From 897b58612c64092d555bd05c110c698f71e6be5c Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 14 Sep 2023 16:25:26 -0700 Subject: [PATCH 02/28] Making versions of emod-typhoid and emodpy really specific for now in this branch. --- requirements.txt | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/requirements.txt b/requirements.txt index 25bfa20..c1a1fdf 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,2 +1,3 @@ -emodpy~=1.16 -emod-typhoid +emod-typhoid==0.0.2.dev0 +emodpy==1.22.0.dev2 + From c65b0a8ced180f30600e6542d89c52fe37760acc Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 14 Sep 2023 16:36:03 -0700 Subject: [PATCH 03/28] Adding Feb162019 config and campaign files. --- .../from_files/TestDemographics_Blantyre.json | 1850 +++++++++++++++++ .../from_files/campaign_feb162019.json | 30 + .../from_files/config_feb162019.json | 176 ++ .../from_files/dtk_centos_2018.id | 1 + 4 files changed, 2057 insertions(+) create mode 100644 examples/blantyre_noHINT/from_files/TestDemographics_Blantyre.json create mode 100644 examples/blantyre_noHINT/from_files/campaign_feb162019.json create mode 100644 examples/blantyre_noHINT/from_files/config_feb162019.json create mode 100644 examples/blantyre_noHINT/from_files/dtk_centos_2018.id diff --git a/examples/blantyre_noHINT/from_files/TestDemographics_Blantyre.json b/examples/blantyre_noHINT/from_files/TestDemographics_Blantyre.json new file mode 100644 index 0000000..b4207e3 --- /dev/null +++ b/examples/blantyre_noHINT/from_files/TestDemographics_Blantyre.json @@ -0,0 +1,1850 @@ +{ + "Metadata": { + "DateCreated": "Sun Sep 25 23:19:55 2011", + "Tool": "convertdemog.py", + "Author": "jsteinkraus", + "IdReference": "Gridded world grump2.5arcmin", + "NodeCount": 1 + }, + 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"Transmission_Blocking_Immunity_Decay_Rate": 0.1, + "Transmission_Blocking_Immunity_Duration_Before_Decay": 60, + "Typhoid_3year_Susceptible_Fraction": 0, + "Typhoid_6month_Susceptible_Fraction": 0, + "Typhoid_6year_Susceptible_Fraction": 0, + "Typhoid_Acute_Infectiousness": 13435, + "Typhoid_Carrier_Probability": 0.108, + "Typhoid_Carrier_Removal_Year": 2500, + "Typhoid_Chronic_Relative_Infectiousness": 0.241, + "Typhoid_Contact_Exposure_Rate": 0.06918859049226553, + "Typhoid_Environmental_Exposure_Rate": 0.06169346985005757, + + "Typhoid_Environmental_Cutoff_Days": 157.20690133538764, + "Typhoid_Environmental_Peak_Start": 355.0579483941714, + "Typhoid_Environmental_Ramp_Down_Duration": 112.30224910440123, + "Typhoid_Environmental_Ramp_Up_Duration": 39.540475369174146, + "Environmental_Cutoff_Days": 157.20690133538764, + "Environmental_Peak_Start": 355.0579483941714, + "Environmental_Ramp_Down_Duration": 112.30224910440123, + "Environmental_Ramp_Up_Duration": 39.540475369174146, + "Typhoid_Exposure_Lambda": 7.0, + "Typhoid_Prepatent_Relative_Infectiousness": 0.5, + "Typhoid_Protection_Per_Infection": 0.98, + "Typhoid_Subclinical_Relative_Infectiousness": 1, + "Typhoid_Symptomatic_Fraction": 0.07, + "__sample_index__": 416, + "logLevel_default": "WARNING", + "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 + } +} diff --git a/examples/blantyre_noHINT/from_files/dtk_centos_2018.id b/examples/blantyre_noHINT/from_files/dtk_centos_2018.id new file mode 100644 index 0000000..f31211e --- /dev/null +++ b/examples/blantyre_noHINT/from_files/dtk_centos_2018.id @@ -0,0 +1 @@ +79791913-ee50-ee11-aa0a-b88303911bc1::Asset Collection \ No newline at end of file From b89024b3ffa76b13776ad49baf410ea71e5d4331 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 14 Sep 2023 16:36:43 -0700 Subject: [PATCH 04/28] Point manifest to 2018 files. --- examples/blantyre_noHINT/from_files/manifest.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/examples/blantyre_noHINT/from_files/manifest.py b/examples/blantyre_noHINT/from_files/manifest.py index 7821ad8..361640b 100644 --- a/examples/blantyre_noHINT/from_files/manifest.py +++ b/examples/blantyre_noHINT/from_files/manifest.py @@ -1,10 +1,12 @@ import os requirements = "./requirements.txt" #model_dl_dir = "stash" -model_dl_dir = "model-from-to" +#model_dl_dir = "model-from-to" +model_dl_dir = "model_2018" schema_file=os.path.join(model_dl_dir, "schema.json") eradication_path=os.path.join(model_dl_dir, "Eradication") assets_input_dir="Assets" reporters=model_dl_dir -sif="dtk_centos.id" +#sif="dtk_centos.id" +sif="dtk_centos_2018.id" world_bank_dataset="../world_bank_dataset.csv" From 728c96b889cf71d54cedd69af207522b4d03f5e1 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 14 Sep 2023 16:37:54 -0700 Subject: [PATCH 05/28] example.py uses new path param in cache_experiment_metadata_in_sql function. --- examples/blantyre_noHINT/from_files/example.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/examples/blantyre_noHINT/from_files/example.py b/examples/blantyre_noHINT/from_files/example.py index c0f40b6..3c32392 100755 --- a/examples/blantyre_noHINT/from_files/example.py +++ b/examples/blantyre_noHINT/from_files/example.py @@ -56,8 +56,9 @@ def run(): builder.add_sweep_definition( update_sim_random_seed, range(4) ) builder.add_sweep_definition( update_sim_param, range(4) ) + exp_name = "Typhoid Blantyre NoHINT emodpy from_files" # create experiment from builder - experiment = Experiment.from_builder(builder, task, name="Typhoid Blantyre NoHINT emodpy from_files") + experiment = Experiment.from_builder(builder, task, name=exp_name ) # The last step is to call run() on the ExperimentManager to run the simulations. experiment.run(wait_until_done=True, platform=platform) @@ -65,11 +66,14 @@ def run(): # download and plot some stuff. EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json" ] ) - task.cache_experiment_metadata_in_sql( experiment.uid ) + task.cache_experiment_metadata_in_sql( experiment.uid, path=exp_name ) #import emod_api.channelreports.plot_icj_means as plotter #chan_data = plotter.collect( "Typhoid Blantyre NoHINT emodpy from_files".replace( " ", "_" ), "Infected" ) #plotter.display( chan_data, False, "Infected", str( experiment.uid ) ) if __name__ == "__main__": + # Uncomment these two lines just for when you run first time after installing a new emod-typhoid module. + #import emod_typhoid.bootstrap as dtk + #dtk.setup( manifest.model_dl_dir ) run() From 79585fa8989611ad53da9a0c218dc8291fc854dd Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Tue, 19 Sep 2023 21:17:03 -0700 Subject: [PATCH 06/28] Populate PrevalenceDistributionXXX keys in demographics since older binaries look for that unconditionally. --- emodpy_typhoid/demographics/TyphoidDemographics.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/emodpy_typhoid/demographics/TyphoidDemographics.py b/emodpy_typhoid/demographics/TyphoidDemographics.py index e39f7b8..0434a7c 100644 --- a/emodpy_typhoid/demographics/TyphoidDemographics.py +++ b/emodpy_typhoid/demographics/TyphoidDemographics.py @@ -9,6 +9,9 @@ class TyphoidDemographics(Demographics): """ def __init__(self, nodes, idref="Gridded world grump2.5arcmin", base_file=None): super().__init__( nodes, idref, base_file ) + self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistributionFlag"] = 0 + self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistribution1"] = 0 + self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistribution2"] = 0 #super().SetDefaultProperties() def fromBasicNode(lat=0, lon=0, pop=1e6, name=1, forced_id=1): From 37a28ace458066173c46e5d07f58a4cffb42807f Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Tue, 19 Sep 2023 21:22:57 -0700 Subject: [PATCH 07/28] All-important __init__.py might have been missing still. --- emodpy_typhoid/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 emodpy_typhoid/__init__.py diff --git a/emodpy_typhoid/__init__.py b/emodpy_typhoid/__init__.py new file mode 100644 index 0000000..e69de29 From 6fe9c48959084b6c8e215f0e7a67e5e67e0e030f Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Tue, 19 Sep 2023 22:34:37 -0700 Subject: [PATCH 08/28] Added requirements.txt for 2018 model. --- emodpy_typhoid/config.py | 12 ++++++++++++ requirements_2018.txt | 3 +++ 2 files changed, 15 insertions(+) create mode 100644 emodpy_typhoid/config.py create mode 100644 requirements_2018.txt diff --git a/emodpy_typhoid/config.py b/emodpy_typhoid/config.py new file mode 100644 index 0000000..28245c6 --- /dev/null +++ b/emodpy_typhoid/config.py @@ -0,0 +1,12 @@ +def cleanup_for_2018_mode( config ): + # when using 2018 binary + config.parameters.pop( "Serialized_Population_Filenames" ) + config.parameters.pop( "Serialization_Time_Steps" ) + config.parameters.pop( "Demographics_Filename" ) + + config.parameters.Incubation_Period_Distribution = "FIXED_DURATION" # hack + config.parameters.Infectious_Period_Distribution = "FIXED_DURATION" # hack + config.parameters.Base_Incubation_Period = 1 + config.parameters.Base_Infectious_Period = 1 + config.parameters["Listed_Events"] = [] + diff --git a/requirements_2018.txt b/requirements_2018.txt new file mode 100644 index 0000000..7932181 --- /dev/null +++ b/requirements_2018.txt @@ -0,0 +1,3 @@ +emodpy==1.22.0.dev3 +emod-api==1.30.0.dev3 +emod-typhoid==0.0.2.dev1 From 1b3859b1ba83a334bd35018b347afd2645acda27 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Tue, 19 Sep 2023 22:35:04 -0700 Subject: [PATCH 09/28] Bump to 0.0.3 --- version.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/version.py b/version.py index 392c239..c060c7d 100644 --- a/version.py +++ b/version.py @@ -1,3 +1 @@ -__version__='0.0.2' - - +__version__='0.0.3' From ec2d7a6c501047a365b725b03d61cecddd2c7f40 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Tue, 19 Sep 2023 22:35:47 -0700 Subject: [PATCH 10/28] Update start_here to work natively with 2018 model. --- examples/start_here/example.py | 23 ++++++++++++++--------- examples/start_here/manifest.py | 2 +- 2 files changed, 15 insertions(+), 10 deletions(-) diff --git a/examples/start_here/example.py b/examples/start_here/example.py index e3eb2c8..7c5eb1b 100755 --- a/examples/start_here/example.py +++ b/examples/start_here/example.py @@ -31,13 +31,17 @@ def set_param_fn( config ): config.parameters.Simulation_Type = "TYPHOID_SIM" config.parameters.Simulation_Duration = 365.0 config.parameters.Base_Individual_Sample_Rate = 0.25 - #config.parameters.Enable_Birth = 0 # temporary - config.parameters.Minimum_End_Time = 90 + #config.parameters.Minimum_End_Time = 90 # cover up for default bugs in schema - config.parameters.Inset_Chart_Reporting_Start_Year = 1850 + config.parameters.Inset_Chart_Reporting_Start_Year = 1900 config.parameters.Inset_Chart_Reporting_Stop_Year = 2050 config.parameters.Enable_Demographics_Reporting = 0 + config.parameters.Node_Contagion_Decay_Rate = 0.33 + + # when using 2018 binary + import emodpy_typhoid.config as config_utils + config_utils.cleanup_for_2018_mode( config ) return config @@ -92,15 +96,16 @@ def run_test(): task.handle_experiment_completion( experiment ) # download and plot some stuff. - EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json" ] ) - task.cache_experiment_metadata_in_sql( experiment.uid ) - import emod_api.channelreports.plot_icj_means as plotter - chan_data = plotter.collect( str( experiment.uid ), "Infected" ) - plotter.display( chan_data, False, "Infected", str( experiment.uid ) ) + if experiment.succeeded: + EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json", "ReportTyphoidByAgeAndGender.csv" ] ) + task.cache_experiment_metadata_in_sql( experiment.uid ) + import emod_api.channelreports.plot_icj_means as plotter + chan_data = plotter.collect( str( experiment.uid ), "Infected" ) + plotter.display( chan_data, False, "Infected", str( experiment.uid ) ) if __name__ == "__main__": import emod_typhoid.bootstrap as dtk - dtk.setup( manifest.model_dl_dir ) + #dtk.setup( manifest.model_dl_dir ) run_test() diff --git a/examples/start_here/manifest.py b/examples/start_here/manifest.py index 5648b1d..17f8239 100644 --- a/examples/start_here/manifest.py +++ b/examples/start_here/manifest.py @@ -5,5 +5,5 @@ eradication_path=os.path.join(model_dl_dir, "Eradication") assets_input_dir="Assets" reporters=model_dl_dir -sif="dtk_centos.id" +sif="dtk_centos_2018.id" world_bank_dataset="../world_bank_dataset.csv" From cad0a8cccb926d3371f8f4c6f4d611150664ce0c Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Tue, 19 Sep 2023 23:09:06 -0700 Subject: [PATCH 11/28] Show how to grab csv report. --- examples/start_here/example.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/examples/start_here/example.py b/examples/start_here/example.py index 7c5eb1b..1f79a10 100755 --- a/examples/start_here/example.py +++ b/examples/start_here/example.py @@ -97,11 +97,11 @@ def run_test(): # download and plot some stuff. if experiment.succeeded: - EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json", "ReportTyphoidByAgeAndGender.csv" ] ) + EMODTask.get_file_from_comps( experiment.uid, [ "InsetChart.json", "ReportTyphoidByAgeAndGender.csv" ], group=True ) task.cache_experiment_metadata_in_sql( experiment.uid ) - import emod_api.channelreports.plot_icj_means as plotter - chan_data = plotter.collect( str( experiment.uid ), "Infected" ) - plotter.display( chan_data, False, "Infected", str( experiment.uid ) ) + #import emod_api.channelreports.plot_icj_means as plotter + #chan_data = plotter.collect( str( experiment.uid ), "Infected" ) + #plotter.display( chan_data, False, "Infected", str( experiment.uid ) ) if __name__ == "__main__": From 3399ed8856f9f0b2ed32a3da75bf00a090eec7f6 Mon Sep 17 00:00:00 2001 From: AKraay-IDM <140118269+AKraay-IDM@users.noreply.github.com> Date: Thu, 21 Sep 2023 12:35:18 -0700 Subject: [PATCH 12/28] add pakistan demographics --- .../from_files/TestDemographics_Pakistan.json | 9504 +++++++++++++++++ 1 file changed, 9504 insertions(+) create mode 100644 examples/blantyre_noHINT/from_files/TestDemographics_Pakistan.json diff --git a/examples/blantyre_noHINT/from_files/TestDemographics_Pakistan.json b/examples/blantyre_noHINT/from_files/TestDemographics_Pakistan.json new file mode 100644 index 0000000..f57a32a --- /dev/null +++ b/examples/blantyre_noHINT/from_files/TestDemographics_Pakistan.json @@ -0,0 +1,9504 @@ +{ + "Metadata": { + "DateCreated": "Sun Sep 25 23:19:55 2011", + "Tool": "convertdemog.py", + "Author": "jsteinkraus", + "IdReference": "Gridded world grump2.5arcmin", + "NodeCount": 1 + }, + "Nodes": [ + { + "NodeID": 340461476, + "NodeAttributes": { + "Latitude": 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+ 174.64, + 218.35, + 218.35, + 160.87, + 160.87, + 77.7, + 77.7, + 27.46, + 27.46, + 8.71, + 8.71, + 0.74, + 0.74, + 0.66, + 0.66, + 43.21, + 43.21, + 174.64, + 174.64, + 218.35, + 218.35, + 160.87, + 160.87, + 77.7, + 77.7, + 27.46, + 27.46, + 8.71, + 8.71, + 0.74, + 0.74, + 0.61, + 0.61, + 42.27, + 42.27, + 172.24, + 172.24, + 213.99, + 213.99, + 155.84, + 155.84, + 75.35, + 75.35, + 26.17, + 26.17, + 8.19, + 8.19, + 0.7, + 0.7, + 0.61, + 0.61, + 42.27, + 42.27, + 172.24, + 172.24, + 213.99, + 213.99, + 155.84, + 155.84, + 75.35, + 75.35, + 26.17, + 26.17, + 8.19, + 8.19, + 0.7, + 0.7 + ] + } + } + } + ] +} + From 3a2a0ca8f56590bec9efcda3bca40ce3d4e4b957 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Mon, 25 Sep 2023 10:08:11 -0700 Subject: [PATCH 13/28] Rev'd emod-api and emod-typhoid to enable use of scheduled typhoid vaccine interventions with 2018 branch model. --- requirements_2018.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/requirements_2018.txt b/requirements_2018.txt index 7932181..456a266 100644 --- a/requirements_2018.txt +++ b/requirements_2018.txt @@ -1,3 +1,3 @@ emodpy==1.22.0.dev3 -emod-api==1.30.0.dev3 -emod-typhoid==0.0.2.dev1 +emod-api==1.30.0.dev4 +emod-typhoid==0.0.2.dev2 From 1c7156d1658e5f6df104209032dbcdf23a0e663e Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Mon, 25 Sep 2023 15:38:29 -0700 Subject: [PATCH 14/28] Make vaccine efficacy profile functional. --- emodpy_typhoid/interventions/typhoid_vaccine.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py index e3cc410..c0000b6 100644 --- a/emodpy_typhoid/interventions/typhoid_vaccine.py +++ b/emodpy_typhoid/interventions/typhoid_vaccine.py @@ -3,7 +3,7 @@ from emod_api.interventions import common import json -def new_intervention( camp, efficacy=1.0, mode="Shedding" ): +def new_intervention( camp, efficacy=0.82, mode="Shedding" ): """ TyphoidVaccine intervention wrapper. Just the intervention. No configuration yet. """ @@ -11,10 +11,15 @@ def new_intervention( camp, efficacy=1.0, mode="Shedding" ): intervention.Effect = efficacy intervention.Mode = mode # WaningEffect is TBD. + intervention.Changing_Effect = s2c.get_class_with_defaults( "WaningEffectExponential" ) + intervention.Changing_Effect.Initial_Effect = efficacy + intervention.Changing_Effect.Decay_Time_Constant = 6935.0 return intervention def new_triggered_intervention( camp, + efficacy=0.82, + mode="Shedding", start_day=1, triggers=[ "Births" ], coverage=1.0, @@ -26,7 +31,7 @@ def new_triggered_intervention( Distribute TyphoidVaccine when something happens as determined by a signal published from the model or another campaign event. """ - iv = new_intervention( camp ) + iv = new_intervention( camp, efficacy, mode ) #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.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" ) @@ -35,6 +40,8 @@ def new_triggered_intervention( def new_scheduled_intervention( camp, + efficacy=0.82, + mode="Shedding", start_day=1, coverage=1.0, node_ids=None, @@ -45,7 +52,7 @@ def new_scheduled_intervention( Distribute TyphoidVaccine when something happens as determined by a signal published from the model or another campaign event. """ - iv = new_intervention( camp ) + iv = new_intervention( camp, efficacy, mode ) #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 ) From 7c526171747690216fd697e290935743ab8e1cf6 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Mon, 25 Sep 2023 15:47:32 -0700 Subject: [PATCH 15/28] Make vaccine efficacy profile functional. --- emodpy_typhoid/interventions/typhoid_vaccine.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py index c0000b6..c76f98b 100644 --- a/emodpy_typhoid/interventions/typhoid_vaccine.py +++ b/emodpy_typhoid/interventions/typhoid_vaccine.py @@ -3,23 +3,25 @@ from emod_api.interventions import common import json -def new_intervention( camp, efficacy=0.82, mode="Shedding" ): +def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, decay_constant=6935.0 ): """ TyphoidVaccine intervention wrapper. Just the intervention. No configuration yet. """ intervention = s2c.get_class_with_defaults( "TyphoidVaccine", camp.schema_path ) intervention.Effect = efficacy intervention.Mode = mode - # WaningEffect is TBD. - intervention.Changing_Effect = s2c.get_class_with_defaults( "WaningEffectExponential" ) + intervention.Changing_Effect = s2c.get_class_with_defaults( "WaningEffectBoxExponential" ) intervention.Changing_Effect.Initial_Effect = efficacy - intervention.Changing_Effect.Decay_Time_Constant = 6935.0 + intervention.Changing_Effect.Box_Duration = constant_period + intervention.Changing_Effect.Decay_Time_Constant = decay_constant return intervention def new_triggered_intervention( camp, efficacy=0.82, mode="Shedding", + constant_period=0, + decay_constant=6935.0, start_day=1, triggers=[ "Births" ], coverage=1.0, @@ -42,6 +44,8 @@ def new_scheduled_intervention( camp, efficacy=0.82, mode="Shedding", + constant_period=0, + decay_constant=6935.0, start_day=1, coverage=1.0, node_ids=None, From de10aa8c482de180e4b6f90e7b34aec0eae0b521 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Wed, 27 Sep 2023 16:40:54 -0700 Subject: [PATCH 16/28] Pass through waning/duration params. --- emodpy_typhoid/interventions/typhoid_vaccine.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py index c76f98b..5dbcbf5 100644 --- a/emodpy_typhoid/interventions/typhoid_vaccine.py +++ b/emodpy_typhoid/interventions/typhoid_vaccine.py @@ -33,9 +33,8 @@ def new_triggered_intervention( Distribute TyphoidVaccine when something happens as determined by a signal published from the model or another campaign event. """ - iv = new_intervention( camp, efficacy, mode ) + 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.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 @@ -56,7 +55,7 @@ def new_scheduled_intervention( Distribute TyphoidVaccine when something happens as determined by a signal published from the model or another campaign event. """ - iv = new_intervention( camp, efficacy, mode ) + 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 ) From aa60096d7298d01a693b18a389a99ac9cae7397f Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Wed, 27 Sep 2023 17:16:48 -0700 Subject: [PATCH 17/28] Don't want that file in version control. --- .../from_files/config_comps_ref.json | 169 ------------------ 1 file changed, 169 deletions(-) delete mode 100644 examples/blantyre_noHINT/from_files/config_comps_ref.json diff --git a/examples/blantyre_noHINT/from_files/config_comps_ref.json b/examples/blantyre_noHINT/from_files/config_comps_ref.json deleted file mode 100644 index bf9f654..0000000 --- a/examples/blantyre_noHINT/from_files/config_comps_ref.json +++ /dev/null @@ -1,169 +0,0 @@ -{ - "parameters": { - "Custom_Coordinator_Events": [], - "Custom_Individual_Events": [], - "Custom_Node_Events": [], - "Enable_Abort_Zero_Infectivity": 0, - "Enable_Maternal_Protection": 0, - "Enable_Natural_Mortality": 1, - "Enable_Susceptibility_Scaling": 0, - "Report_Coordinator_Event_Recorder": 0, - "Report_Node_Event_Recorder": 0, - "Report_Surveillance_Event_Recorder": 0, - - "Acquisition_Blocking_Immunity_Decay_Rate": 0.1, - "Acquisition_Blocking_Immunity_Duration_Before_Decay": 60, - "Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE", - "Air_Temperature_Filename": "", - "Air_Temperature_Offset": 0, - "Air_Temperature_Variance": 2, - "Animal_Reservoir_Type": "NO_ZOONOSIS", - "Base_Air_Temperature": 30, - "Base_Incubation_Period": 3000000, - "Base_Individual_Sample_Rate": 0.1, - "Base_Infectious_Period": 70000000, - "Base_Infectivity": 0.3, - "Base_Land_Temperature": 30, - "Base_Mortality": 0, - "Base_Population_Scale_Factor": 1.64, - "Base_Rainfall": 100, - "Base_Relative_Humidity": 0.5, - "Base_Year": 1917, - "Birth_Rate_Dependence": "INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR", - "Birth_Rate_Time_Dependence": "NONE", - "Burnin_Cache_Mode": "none", - "Burnin_Cache_Period": 0, - "Burnin_Name": "", - "Campaign_Filename": "campaign_routine_exp.json", - "Climate_Model": "CLIMATE_OFF", - "Climate_Update_Resolution": "CLIMATE_UPDATE_DAY", - "Config_Name": "149_Typhoid", - "Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_YEAR_AND_AGE_FOR_EACH_GENDER", - "Default_Geography_Initial_Node_Population": 1000, - "Default_Geography_Torus_Size": 10, - "Demographics_Filenames": [ - "demographics.json" - ], - "Enable_Absolute_Time": "NO", - "Enable_Aging": 1, - "Enable_Birth": 1, - "Enable_Climate_Stochasticity": 1, - "Enable_Default_Reporting": 1, - "Enable_Default_Shedding_Function": 1, - "Enable_Demographics_Birth": 0, - "Enable_Demographics_Builtin": 0, - "Enable_Demographics_Gender": 1, - "Enable_Demographics_Initial": 1, - "Enable_Demographics_Other": 0, - "Enable_Demographics_Reporting": 0, - "Enable_Disease_Mortality": 0, - "Enable_Heterogeneous_Intranode_Transmission": 0, - "Enable_Immune_Decay": 0, - "Enable_Immunity": 0, - "Enable_Immunity_Initialization_Distribution": 0, - "Enable_Interventions": 1, - "Enable_Maternal_Transmission": 0, - "Enable_Property_Output": 0, - "Enable_Rainfall_Stochasticity": 1, - "_Enable_Skipping": 1, - "Enable_Skipping": 0, - "Enable_Spatial_Output": 0, - "Enable_Superinfection": 0, - "Enable_Vital_Dynamics": 1, - "Environmental_Incubation_Period": 1, - "Geography": "", - "Immunity_Acquisition_Factor": 0, - "Immunity_Initialization_Distribution_Type": "DISTRIBUTION_OFF", - "Immunity_Mortality_Factor": 0, - "Immunity_Transmission_Factor": 0, - "Incubation_Period_Distribution": "FIXED_DURATION", - "Individual_Sampling_Type": "FIXED_SAMPLING", - "Infection_Updates_Per_Timestep": 1, - "Infectious_Period_Distribution": "EXPONENTIAL_DURATION", - "Infectivity_Scale_Type": "CONSTANT_INFECTIVITY", - "Inset_Chart_Reporting_Start_Year": 1917, - "Inset_Chart_Reporting_Stop_Year": 2100, - "Job_Node_Groups": "Chassis08", - "Job_Priority": "BELOWNORMAL", - "Land_Temperature_Filename": "", - "Land_Temperature_Offset": 0, - "Land_Temperature_Variance": 2, - "Listed_Events": [], - "Load_Balance_Filename": "", - "Load_Balance_Scheme": "STATIC", - "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_Contagion_Decay_Rate": 0.056278, - "Node_Grid_Size": 0.009, - "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": "FIXED_SCALING", - "Python_Script_Path": "\\\\idmppfil01\\idm\\home\\jgauld\\input\\Python_Scripts\\", - "Rainfall_Filename": "", - "Rainfall_Scale_Factor": 1, - "Relative_Humidity_Filename": "", - "Relative_Humidity_Scale_Factor": 1, - "Relative_Humidity_Variance": 0.05, - "Report_Event_Recorder": 0, - "Report_Typhoid_ByAgeAndGender_Start_Year": 2000, - "Report_Typhoid_ByAgeAndGender_Stop_Year": 2100, - "Run_Number": 130, - "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": 2, - "Serialization_Test_Cycles": 0, - "Simulation_Duration": 44533, - "Simulation_Timestep": 1, - "Simulation_Type": "TYPHOID_SIM", - "Start_Time": 0, - "Susceptibility_Scaling_Type": "CONSTANT_SUSCEPTIBILITY", - "Transmission_Blocking_Immunity_Decay_Rate": 0.1, - "Transmission_Blocking_Immunity_Duration_Before_Decay": 60, - "Typhoid_3year_Susceptible_Fraction": 0, - "Typhoid_6month_Susceptible_Fraction": 0, - "Typhoid_6year_Susceptible_Fraction": 0, - "Typhoid_Acute_Infectiousness": 13436, - "Typhoid_Carrier_Probability": 1, - "Typhoid_Carrier_Removal_Year": 2500, - "Typhoid_Chronic_Relative_Infectiousness": 0.5, - "Typhoid_Contact_Exposure_Rate": 0.44535910269531453, - "Typhoid_Environmental_Exposure_Rate": 0.24619971394455994, - "__Typhoid_Environmental_Exposure_Rate": 0.024619971394455994, - "Environmental_Cutoff_Days": 1, - "Environmental_Peak_Start": 287.2811494864098, - "Environmental_Ramp_Down_Duration": 1, - "Environmental_Ramp_Up_Duration": 1, - "Typhoid_Exposure_Days": 3864.6481790944667, - "Typhoid_Exposure_Lambda": -0.6982908373479506, - "Typhoid_Immunity_Memory": 22750.6416223787, - "Typhoid_Prepatent_Relative_Infectiousness": 0.5, - "Typhoid_Protection_Per_Infection": 0.7932246576828436, - "Typhoid_Subclinical_Relative_Infectiousness": 0.5, - "Typhoid_Symptomatic_Fraction": 0.04594935339672988, - "__sample_index__": 0, - "logLevel_default": "ERROR", - "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 - } -} From 5670fcdbf3f14aee4d4c4177f1f1d4ac1a0d86c8 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Wed, 27 Sep 2023 17:39:26 -0700 Subject: [PATCH 18/28] Adding comments during PR review. --- emodpy_typhoid/demographics/TyphoidDemographics.py | 1 + 1 file changed, 1 insertion(+) diff --git a/emodpy_typhoid/demographics/TyphoidDemographics.py b/emodpy_typhoid/demographics/TyphoidDemographics.py index 0434a7c..ab92d8f 100644 --- a/emodpy_typhoid/demographics/TyphoidDemographics.py +++ b/emodpy_typhoid/demographics/TyphoidDemographics.py @@ -9,6 +9,7 @@ class TyphoidDemographics(Demographics): """ def __init__(self, nodes, idref="Gridded world grump2.5arcmin", base_file=None): super().__init__( nodes, idref, base_file ) + # The following is for back-compat with older versions of the model which looked for these keys unconditionally. self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistributionFlag"] = 0 self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistribution1"] = 0 self.raw["Defaults"]["IndividualAttributes"]["PrevalenceDistribution2"] = 0 From 7f05a8e9e11ac6017249a6917c2c3e7a089e7b5c Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Wed, 27 Sep 2023 17:43:58 -0700 Subject: [PATCH 19/28] Removing dead code during PR review. --- examples/blantyre_noHINT/from_files/example.py | 9 --------- 1 file changed, 9 deletions(-) diff --git a/examples/blantyre_noHINT/from_files/example.py b/examples/blantyre_noHINT/from_files/example.py index 3c32392..a568f6a 100755 --- a/examples/blantyre_noHINT/from_files/example.py +++ b/examples/blantyre_noHINT/from_files/example.py @@ -34,15 +34,6 @@ def run(): # Show how to dynamically set priority and node_group platform = Platform("SLURM", node_group="idm_48cores", priority="Highest") - #task = EMODTask.from_files(config_path="config_comps_ref.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config_comps_ref.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["demographics.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config_py.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["demographics.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config.json", eradication_path=manifest.eradication_path, campaign_path="campaign_routine_exp.json", demographics_paths=["demographics.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config_literal_5mods.json", eradication_path=manifest.eradication_path, campaign_path="campaign_baseline.json", demographics_paths=["TestDemographics_Blantyre.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config_june242019.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config_june242019_plus_to_params.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config_june242019_seasonal.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) - #task = EMODTask.from_files(config_path="config_june242019_seasonal_to.json", eradication_path=manifest.eradication_path, campaign_path="campaign_june242019.json", demographics_paths=["TestDemographics_Mystery_Fert.json"], ep4_path=None) task = EMODTask.from_files(config_path="config_feb162019.json", eradication_path=manifest.eradication_path, campaign_path="campaign_feb162019.json", demographics_paths=["TestDemographics_Blantyre.json"], ep4_path=None) From 0c0b0d624bfe94f12a98296f071daab861a09ed5 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Wed, 27 Sep 2023 17:56:41 -0700 Subject: [PATCH 20/28] Dev branch to merge, sans branch changes to keep but not merge. --- requirements.txt | 5 ++--- version.py | 4 +++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/requirements.txt b/requirements.txt index c1a1fdf..25bfa20 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,3 +1,2 @@ -emod-typhoid==0.0.2.dev0 -emodpy==1.22.0.dev2 - +emodpy~=1.16 +emod-typhoid diff --git a/version.py b/version.py index c060c7d..392c239 100644 --- a/version.py +++ b/version.py @@ -1 +1,3 @@ -__version__='0.0.3' +__version__='0.0.2' + + From e66a13a84e0061376bdd72860adec946ef998f08 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 28 Sep 2023 07:46:48 -0700 Subject: [PATCH 21/28] Added doc strings from ChatGPT for TV. --- .../interventions/typhoid_vaccine.py | 53 ++++++++++++++++--- 1 file changed, 47 insertions(+), 6 deletions(-) diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py index 5dbcbf5..08c7880 100644 --- a/emodpy_typhoid/interventions/typhoid_vaccine.py +++ b/emodpy_typhoid/interventions/typhoid_vaccine.py @@ -5,8 +5,21 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, decay_constant=6935.0 ): """ - TyphoidVaccine intervention wrapper. Just the intervention. No configuration yet. - """ + Create a new TyphoidVaccine 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 "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. + + Returns: + TyphoidVaccine: A fully configured instance of the TyphoidVaccine intervention with the specified parameters. + """ + intervention = s2c.get_class_with_defaults( "TyphoidVaccine", camp.schema_path ) intervention.Effect = efficacy intervention.Mode = mode @@ -30,8 +43,22 @@ def new_triggered_intervention( co_event=None # expansion slot ): """ - Distribute TyphoidVaccine when something happens as determined by a signal published from the - model or another campaign event. + Create a new triggered TyphoidVaccine intervention based on specified parameters. + 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. + triggers (list, optional): List of triggers for the intervention. Default is ["Births"]. + 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_intervention( camp, efficacy=efficacy, mode=mode, constant_period=constant_period, decay_constant=decay_constant ) @@ -52,8 +79,22 @@ def new_scheduled_intervention( co_event=None # expansion slot ): """ - Distribute TyphoidVaccine when something happens as determined by a signal published from the - model or another campaign event. + Create a new scheduled TyphoidVaccine intervention based on specified parameters. + 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. + 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: + 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 ) From 1e51ba21dd00621c3ba39fa4a75163993ed31c18 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 28 Sep 2023 07:57:15 -0700 Subject: [PATCH 22/28] Changed some remaining malaria references (from template) to typhiod. --- docs/conf.py | 14 +++++++------- docs/index.rst | 6 +++--- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 87daa25..bf7f837 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -29,7 +29,7 @@ else: subprocess.check_output(["make.bat", "generate-api"], cwd=os.path.dirname(os.path.abspath(__file__))) -# Rename "emodpy-malaria" to "API reference" +# Rename "emodpy-typhoid" to "API reference" filename = 'modules.rst' # This must match the Makefile with open(filename) as f: # Read existing file lines = f.readlines() @@ -310,7 +310,7 @@ # html_search_scorer = 'scorer.js' # Output file base name for HTML help builder. -htmlhelp_basename = 'emodpy-malaria' +htmlhelp_basename = 'emodpy-typhoid' # -- Options for LaTeX output --------------------------------------------- @@ -336,7 +336,7 @@ # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ - (master_doc, 'emodpy-malaria-docs.tex', u'emodpy-malaria', + (master_doc, 'emodpy-typhoid-docs.tex', u'emodpy-typhoid', u'Institute for Disease Modeling', 'manual'), ] @@ -378,7 +378,7 @@ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria', + (master_doc, 'emodpy-typhoid-docs', u'emodpy-typhoid', [author], 1) ] @@ -392,8 +392,8 @@ # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ - (master_doc, 'emodpy-malaria-docs', u'emodpy-malaria', - author, 'Institute for Disease Modeling', 'How to use emodpy for malaria simulations.', + (master_doc, 'emodpy-typhoid-docs', u'emodpy-typhoid', + author, 'Institute for Disease Modeling', 'How to use emodpy for typhoid simulations.', 'Miscellaneous'), ] @@ -420,6 +420,6 @@ 'emod_api': ('https://docs.idmod.org/projects/emod-api/en/latest/', None), 'emodpy': ('https://docs.idmod.org/projects/emodpy/en/latest/', None), 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), - 'emod-malaria': ('https://docs.idmod.org/projects/emod-malaria/en/latest/', None), + 'emod-typhoid': ('https://docs.idmod.org/projects/emod-typhoid/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) } \ No newline at end of file diff --git a/docs/index.rst b/docs/index.rst index c2faa97..677e143 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -3,13 +3,13 @@ ============================== |EMODPY_typhoid| is a collection of Python scripts and utilities created to -streamline user interactions with |EMOD_s| and |IT_s| for modeling malaria. +streamline user interactions with |EMOD_s| and |IT_s| for modeling typhoid. Much of the functionality is inherited from the :doc:`emod_api:emod_api` and :doc:`emodpy:emodpy`. Additional information about how to use |IT_s| can be found in -:doc:`idmtools:index`. Additional information about |EMOD_s| malaria -parameters can be found in :doc:`emod-malaria:parameter-overview`. +:doc:`idmtools:index`. Additional information about |EMOD_s| typhoid +parameters can be found in :doc:`emod-typhoid:parameter-overview`. See :doc:`idmtools:index` for a diagram showing how |IT_s| and each of the related packages are used in an end-to-end workflow using |EMOD_s| as the From 8578161d78d53159f53a8447778423094f921871 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 28 Sep 2023 08:07:32 -0700 Subject: [PATCH 23/28] Changed some remaining malaria references (from template) to typhiod. --- docs/_templates/breadcrumbs.html | 4 ++-- docs/_templates/footer.html | 4 ++-- docs/variables.txt | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/_templates/breadcrumbs.html b/docs/_templates/breadcrumbs.html index 391b9d0..fb68032 100644 --- a/docs/_templates/breadcrumbs.html +++ b/docs/_templates/breadcrumbs.html @@ -1,9 +1,9 @@ {% extends '!breadcrumbs.html' %} {% block breadcrumbs %}
  • IDM docs »
    • -
  • emodpy-malaria »
    • +
  • emodpy-typhoid »
    • {% for doc in parents %}
  • {{ doc.title }} »
    • {% endfor %}
  • {{ title }}
    • -{% endblock %} \ No newline at end of file +{% endblock %} diff --git a/docs/_templates/footer.html b/docs/_templates/footer.html index d93abae..ff9a591 100644 --- a/docs/_templates/footer.html +++ b/docs/_templates/footer.html @@ -1,8 +1,8 @@ {% extends '!footer.html' %} {% block extrafooter %} -

    emodpy-malaria is licensed under the Creative Commons +

    emodpy-typhoid is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.

    Send documentation feedback to feedback@idmod.org

    Privacy and Cookies Notice   |    Terms of Use

    -{% endblock %} \ No newline at end of file +{% endblock %} diff --git a/docs/variables.txt b/docs/variables.txt index 83678f9..49e015a 100644 --- a/docs/variables.txt +++ b/docs/variables.txt @@ -16,7 +16,7 @@ .. |IDM_l| replace:: Institute for Disease Modeling (IDM) .. |EMODPY_s| replace:: emodpy -.. |EMODPY_typhoid| replace:: typhoid +.. |EMODPY_typhoid| replace:: emodpy-typhoid .. |emod_api| replace:: emod-api .. |IDM_s| replace:: IDM .. |EMOD_l| replace:: Epidemiological MODeling software (EMOD) From 66b3208cdbc404ef1b6baecab157d5916409c0a4 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 28 Sep 2023 08:19:20 -0700 Subject: [PATCH 24/28] More whitespace for sphinx/RTD/etc. --- emodpy_typhoid/interventions/typhoid_vaccine.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py index 08c7880..73f0a5f 100644 --- a/emodpy_typhoid/interventions/typhoid_vaccine.py +++ b/emodpy_typhoid/interventions/typhoid_vaccine.py @@ -44,6 +44,7 @@ def new_triggered_intervention( ): """ Create a new triggered TyphoidVaccine intervention based on specified parameters. + Args: camp (Camp): The camp to which the intervention is applied. efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82. @@ -80,6 +81,7 @@ def new_scheduled_intervention( ): """ Create a new scheduled TyphoidVaccine intervention based on specified parameters. + Args: camp (Camp): The camp to which the intervention is applied. efficacy (float, optional): The efficacy of the Typhoid vaccine. Default is 0.82. From 84f165515c64f5727f5f38baab7a4f72e0ac55fb Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 28 Sep 2023 08:20:24 -0700 Subject: [PATCH 25/28] Less whitespace for sphinx/RTD/etc. --- emodpy_typhoid/interventions/typhoid_vaccine.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py index 73f0a5f..a2584a6 100644 --- a/emodpy_typhoid/interventions/typhoid_vaccine.py +++ b/emodpy_typhoid/interventions/typhoid_vaccine.py @@ -5,9 +5,7 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, decay_constant=6935.0 ): """ - Create a new TyphoidVaccine 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. + Create a new TyphoidVaccine 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. From 8fe80d22b2bbef4e43368c097af72cb5ca5fbafc Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Thu, 28 Sep 2023 10:24:19 -0700 Subject: [PATCH 26/28] Added html_css_files entry to conf.py for docs. --- docs/conf.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index bf7f837..8945d56 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -217,6 +217,10 @@ ] } html_js_files = ['show_block_by_os.js'] + +html_css_files = ['theme_overrides.css'] + + # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied # directly to the root of the docs. @@ -422,4 +426,4 @@ 'idmtools': ('https://docs.idmod.org/projects/idmtools/en/latest/', None), 'emod-typhoid': ('https://docs.idmod.org/projects/emod-typhoid/en/latest/', None), 'pycomps': ('https://docs.idmod.org/projects/pycomps/en/latest/', None) - } \ No newline at end of file + } From efd6edd314cda5801082e194340abe5237d00d48 Mon Sep 17 00:00:00 2001 From: Jen Schripsema Date: Thu, 28 Sep 2023 12:53:46 -0600 Subject: [PATCH 27/28] updated Sphinx config to correctly apply css, corrected typos in .gitignore and demo docstring --- .gitignore | 2 +- docs/conf.py | 32 +++++++++++++------ .../demographics/TyphoidDemographics.py | 2 +- 3 files changed, 24 insertions(+), 12 deletions(-) diff --git a/.gitignore b/.gitignore index ffdfa61..785494c 100644 --- a/.gitignore +++ b/.gitignore @@ -70,7 +70,7 @@ instance/ # Sphinx documentation docs/_build/ -docs/emodpy-typhoid*.rst +docs/emodpy_typhoid*.rst docs/modules.rst # PyBuilder diff --git a/docs/conf.py b/docs/conf.py index 8945d56..df7d08e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -59,10 +59,27 @@ 'sphinx_copybutton', 'sphinx.ext.intersphinx', 'sphinxext.remoteliteralinclude', - 'myst_parser', - 'sphinx_search.extension' + 'myst_parser', # source files written in MD or RST + 'sphinx_search.extension', # search across entire IDM docs domain + 'sphinx.ext.viewcode' # link to view source code ] +myst_enable_extensions = [ + "amsmath", + "attrs_inline", + "colon_fence", + "deflist", + "dollarmath", + "fieldlist", + "html_admonition", + "html_image", + "linkify", + "replacements", + "smartquotes", + "strikethrough", + "substitution", + "tasklist", +] plantuml = 'plantweb' autodoc_default_options = { @@ -208,18 +225,13 @@ # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] -html_context = { - 'css_files': [ - '_static/theme_overrides.css', - '_static/copy_button.css' - ] -} -html_js_files = ['show_block_by_os.js'] +html_static_path = ['_static'] html_css_files = ['theme_overrides.css'] +html_js_files = ['show_block_by_os.js'] + # Add any extra paths that contain custom files (such as robots.txt or # .htaccess) here, relative to this directory. These files are copied diff --git a/emodpy_typhoid/demographics/TyphoidDemographics.py b/emodpy_typhoid/demographics/TyphoidDemographics.py index b3789ca..89edbf2 100644 --- a/emodpy_typhoid/demographics/TyphoidDemographics.py +++ b/emodpy_typhoid/demographics/TyphoidDemographics.py @@ -81,7 +81,7 @@ def from_csv( pop_filename_in, site="No_Site", min_node_pop = 0 ): site: A string to identify the country, village, or trial site. Returns: - A :py:class:`~emodpy_malaria.demographics.MalariaDemographics` instance. + A :py:class:`~emodpy_typhoid.demographics.MalariaDemographics` instance. """ typhoid_demog = Demog.from_csv( pop_filename_in ) nodes = [] From 2b264a4e9948cc908f0b41654029c2a872d42e31 Mon Sep 17 00:00:00 2001 From: Jonathan Bloedow Date: Mon, 2 Oct 2023 07:08:55 -0700 Subject: [PATCH 28/28] Fixed bug caught by Sharon where new_intervention_as_file wasnt passing start_day by name and thus correctly. --- emodpy_typhoid/interventions/typhoid_vaccine.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/emodpy_typhoid/interventions/typhoid_vaccine.py b/emodpy_typhoid/interventions/typhoid_vaccine.py index a2584a6..8c2414a 100644 --- a/emodpy_typhoid/interventions/typhoid_vaccine.py +++ b/emodpy_typhoid/interventions/typhoid_vaccine.py @@ -105,7 +105,7 @@ def new_scheduled_intervention( def new_intervention_as_file( camp, start_day, filename=None ): import emod_api.campaign as camp - camp.add( new_triggered_intervention( camp, start_day ), first=True ) + camp.add( new_triggered_intervention( camp, start_day=start_day ), first=True ) if filename is None: filename = "TyphoidVaccine.json" camp.save( filename )