Resource file path from simulation

docs/tlo_parameters.py

@@ -302,10 +302,11 @@ def write_parameters_file(
     )
     args = parser.parse_args()
     simulation = Simulation(
-        start_date=Date(2010, 1, 1), seed=1234, log_config={"suppress_stdout": True}
+        start_date=Date(2010, 1, 1), seed=1234, log_config={"suppress_stdout": True},
+        resourcefilepath=args.resource_file_path
     )
     status_quo_parameters = get_parameters_for_status_quo()
-    simulation.register(*fullmodel.fullmodel(args.resource_file_path))
+    simulation.register(*fullmodel.fullmodel())
     internal_link_formatter = _formatters[args.output_file_path.suffix]["internal_link"]
     character_escaper = _formatters[args.output_file_path.suffix]["character_escaper"]
     module_parameter_tables, module_structured_parameters = get_parameter_tables(

src/scripts/Alri_analyses/alri_calibration_plots/GBD_comparison_plots.py

@@ -55,19 +55,19 @@
     seed = random.randint(0, 50000)
 
     # Establish the simulation object
-    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config, show_progress_bar=True)
+    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config,
+                     show_progress_bar=True, resourcefilepath=resourcefilepath)
 
     # run the simulation
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-        symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-        healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath),
-        healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-        healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                  service_availability=['*']),
-        alri.Alri(resourcefilepath=resourcefilepath),
+        demography.Demography(),
+        enhanced_lifestyle.Lifestyle(),
+        symptommanager.SymptomManager(),
+        healthseekingbehaviour.HealthSeekingBehaviour(),
+        healthburden.HealthBurden(),
+        simplified_births.SimplifiedBirths(),
+        healthsystem.HealthSystem(service_availability=['*']),
+        alri.Alri(),
         alri.AlriPropertiesOfOtherModules()
     )
 

src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_default_params.py

@@ -51,18 +51,19 @@
 }
 
 # Establish the simulation object
-sim = Simulation(start_date=start_date, log_config=log_config, show_progress_bar=True)
+sim = Simulation(start_date=start_date, log_config=log_config,
+                 show_progress_bar=True, resourcefilepath=resourcefilepath)
 
 # run the simulation
 sim.register(
-    demography.Demography(resourcefilepath=resourcefilepath),
-    enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-    symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-    healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath),
-    healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-    simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-    healthsystem.HealthSystem(resourcefilepath=resourcefilepath, disable=True),
-    alri.Alri(resourcefilepath=resourcefilepath),
+    demography.Demography(),
+    enhanced_lifestyle.Lifestyle(),
+    symptommanager.SymptomManager(),
+    healthseekingbehaviour.HealthSeekingBehaviour(),
+    healthburden.HealthBurden(),
+    simplified_births.SimplifiedBirths(),
+    healthsystem.HealthSystem(disable=True),
+    alri.Alri(),
     alri.AlriPropertiesOfOtherModules()
 )
 

src/scripts/Alri_analyses/alri_calibration_plots/analysis_Alri_with_and_without_treatment.py

@@ -61,21 +61,18 @@
         _disable_and_reject_all = False
 
     # add file handler for the purpose of logging
-    sim = Simulation(start_date=start_date, log_config=log_config, show_progress_bar=True)
+    sim = Simulation(start_date=start_date, log_config=log_config,
+                     show_progress_bar=True, resourcefilepath=resourcefilepath)
 
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-        symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-        healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath,
-                                                      force_any_symptom_to_lead_to_healthcareseeking=True),
-        healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-        healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                  disable=_disable,
-                                  disable_and_reject_all=_disable_and_reject_all),
-
-        alri.Alri(resourcefilepath=resourcefilepath),
+        demography.Demography(),
+        enhanced_lifestyle.Lifestyle(),
+        simplified_births.SimplifiedBirths(),
+        symptommanager.SymptomManager(),
+        healthseekingbehaviour.HealthSeekingBehaviour(force_any_symptom_to_lead_to_healthcareseeking=True),
+        healthburden.HealthBurden(),
+        healthsystem.HealthSystem(disable=_disable,  disable_and_reject_all=_disable_and_reject_all),
+        alri.Alri(),
         alri.AlriPropertiesOfOtherModules()
     )
 

src/scripts/Alri_analyses/alri_calibration_plots/analysis_effect_of_treatment.py

@@ -39,22 +39,19 @@ def get_sim(popsize):
     """Return a simulation (composed of only <5 years old) that has run for 0 days."""
     resourcefilepath = Path('./resources')
     start_date = Date(2010, 1, 1)
-    sim = Simulation(start_date=start_date, seed=0)
+    sim = Simulation(start_date=start_date, seed=0, resourcefilepath=resourcefilepath)
 
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-        symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
+        demography.Demography(),
+        simplified_births.SimplifiedBirths(),
+        enhanced_lifestyle.Lifestyle(),
+        symptommanager.SymptomManager(),
         healthseekingbehaviour.HealthSeekingBehaviour(
-            resourcefilepath=resourcefilepath,
             force_any_symptom_to_lead_to_healthcareseeking=True,
         ),
-        healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-        healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                  cons_availability='all',
-                                  ),
-        alri.Alri(resourcefilepath=resourcefilepath),
+        healthburden.HealthBurden(),
+        healthsystem.HealthSystem(cons_availability='all'),
+        alri.Alri(),
         AlriPropertiesOfOtherModules(),
     )
     sim.modules['Demography'].parameters['max_age_initial'] = 5

src/scripts/Alri_analyses/alri_calibration_plots/analysis_pulse_oximeter_vs_none.py

@@ -44,21 +44,19 @@ def run_scenario(**kwargs):
         }
     }
 
-    sim = Simulation(start_date=start_date, log_config=log_config, show_progress_bar=True)
+    sim = Simulation(start_date=start_date, log_config=log_config,
+                     show_progress_bar=True, resourcefilepath=resourcefilepath)
 
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-        symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-        healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath,
+        demography.Demography(),
+        enhanced_lifestyle.Lifestyle(),
+        simplified_births.SimplifiedBirths(),
+        symptommanager.SymptomManager(),
+        healthseekingbehaviour.HealthSeekingBehaviour(
                                                       force_any_symptom_to_lead_to_healthcareseeking=True),
-        healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-        healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                  disable=True,
-                                  cons_availability='all',
-                                  ),
-        alri.Alri(resourcefilepath=resourcefilepath),
+        healthburden.HealthBurden(),
+        healthsystem.HealthSystem(disable=True, cons_availability='all'),
+        alri.Alri(),
         alri.AlriPropertiesOfOtherModules()
     )
 

src/scripts/Alri_analyses/alri_calibration_plots/baseline_outputs.py

@@ -55,19 +55,19 @@
     seed = random.randint(0, 50000)
 
     # Establish the simulation object
-    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config, show_progress_bar=True)
+    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config,
+                     show_progress_bar=True, resourcefilepath=resourcefilepath)
 
     # run the simulation
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-        symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-        healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath),
-        healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-        healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                  service_availability=['*']),
-        alri.Alri(resourcefilepath=resourcefilepath),
+        demography.Demography(),
+        enhanced_lifestyle.Lifestyle(),
+        symptommanager.SymptomManager(),
+        healthseekingbehaviour.HealthSeekingBehaviour(),
+        healthburden.HealthBurden(),
+        simplified_births.SimplifiedBirths(),
+        healthsystem.HealthSystem(service_availability=['*']),
+        alri.Alri(),
         alri.AlriPropertiesOfOtherModules()
     )
 

src/scripts/Alri_analyses/other_scripts/analysis_alri_classification.py

@@ -53,23 +53,21 @@
     seed = random.randint(0, 50000)
 
     # Establish the simulation object
-    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config, show_progress_bar=True)
+    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config,
+                     show_progress_bar=True, resourcefilepath=resourcefilepath)
 
     # run the simulation
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-        symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-        healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath),
-        healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-        healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                  service_availability=['*'],
-                                  mode_appt_constraints=0,
-                                  ignore_priority=True,
+        demography.Demography(),
+        enhanced_lifestyle.Lifestyle(),
+        symptommanager.SymptomManager(),
+        healthseekingbehaviour.HealthSeekingBehaviour(),
+        healthburden.HealthBurden(),
+        simplified_births.SimplifiedBirths(),
+        healthsystem.HealthSystem(service_availability=['*'], mode_appt_constraints=0, ignore_priority=True,
                                   capabilities_coefficient=1.0,
                                   disable=True),
-        alri.Alri(resourcefilepath=resourcefilepath),
+        alri.Alri(),
         alri.AlriPropertiesOfOtherModules()
     )
 

src/scripts/Alri_analyses/other_scripts/create_new_logfile.py

@@ -53,23 +53,23 @@
     seed = random.randint(0, 50000)
 
     # Establish the simulation object
-    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config, show_progress_bar=True)
+    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config,
+                     show_progress_bar=True, resourcefilepath=resourcefilepath)
 
     # run the simulation
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-        symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-        healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath),
-        healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-        healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                  service_availability=['*']),
+        demography.Demography(),
+        enhanced_lifestyle.Lifestyle(),
+        symptommanager.SymptomManager(),
+        healthseekingbehaviour.HealthSeekingBehaviour(),
+        healthburden.HealthBurden(),
+        simplified_births.SimplifiedBirths(),
+        healthsystem.HealthSystem(service_availability=['*']),
         # mode_appt_constraints=0,
         # ignore_priority=True,
         # capabilities_coefficient=1.0,
         # disable=True),
-        alri.Alri(resourcefilepath=resourcefilepath),
+        alri.Alri(),
         alri.AlriPropertiesOfOtherModules()
     )
 

src/scripts/bladder_cancer_analyses/bladder_cancer_analyses.py

@@ -46,22 +46,21 @@
 def run_sim(service_availability):
     # Establish the simulation object and set the seed
     # seed is not set - each simulation run gets a random seed
-    sim = Simulation(start_date=start_date, log_config={"filename": "LogFile"})
+    sim = Simulation(start_date=start_date, log_config={"filename": "LogFile"}, resourcefilepath=resourcefilepath)
     # Register the appropriate modules
-    sim.register(demography.Demography(resourcefilepath=resourcefilepath),
-                 contraception.Contraception(resourcefilepath=resourcefilepath),
-                 enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-                 healthsystem.HealthSystem(resourcefilepath=resourcefilepath,
-                                           service_availability=service_availability),
-                 symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-                 healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath),
-                 healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-                 labour.Labour(resourcefilepath=resourcefilepath),
-                 pregnancy_supervisor.PregnancySupervisor(resourcefilepath=resourcefilepath),
-                 bladder_cancer.BladderCancer(resourcefilepath=resourcefilepath),
-                 care_of_women_during_pregnancy.CareOfWomenDuringPregnancy(resourcefilepath=resourcefilepath),
-                 newborn_outcomes.NewbornOutcomes(resourcefilepath=resourcefilepath),
-                 postnatal_supervisor.PostnatalSupervisor(resourcefilepath=resourcefilepath)
+    sim.register(demography.Demography(),
+                 contraception.Contraception(),
+                 enhanced_lifestyle.Lifestyle(),
+                 healthsystem.HealthSystem(service_availability=service_availability),
+                 symptommanager.SymptomManager(),
+                 healthseekingbehaviour.HealthSeekingBehaviour(),
+                 healthburden.HealthBurden(),
+                 labour.Labour(),
+                 pregnancy_supervisor.PregnancySupervisor(),
+                 bladder_cancer.BladderCancer(),
+                 care_of_women_during_pregnancy.CareOfWomenDuringPregnancy(),
+                 newborn_outcomes.NewbornOutcomes(),
+                 postnatal_supervisor.PostnatalSupervisor()
                  )
     # Run the simulation
     sim.make_initial_population(n=popsize)
@@ -99,7 +98,7 @@ def get_cols_excl_none(allcols, stub):
     dalys = dalys.sort_index()
     # 4) DEATHS wrt age (total over whole simulation)
     deaths = output['tlo.methods.demography']['death']
-    deaths['age_group'] = deaths['age'].map(demography.Demography(resourcefilepath=resourcefilepath).AGE_RANGE_LOOKUP)
+    deaths['age_group'] = deaths['age'].map(demography.Demography().AGE_RANGE_LOOKUP)
     x = deaths.loc[deaths.cause == 'BladderCancer'].copy()
     x['age_group'] = x['age_group'].astype(make_age_grp_types())
     bladder_cancer_deaths = x.groupby(by=['age_group']).size()
@@ -162,7 +161,7 @@ def get_cols_excl_none(allcols, stub):
 deaths = results_no_healthsystem['bladder_cancer_deaths']
 deaths.index = deaths.index.astype(make_age_grp_types())
 # # make a series with the right categories and zero so formats nicely in the grapsh:
-agegrps = demography.Demography(resourcefilepath=resourcefilepath).AGE_RANGE_CATEGORIES
+agegrps = demography.Demography().AGE_RANGE_CATEGORIES
 totdeaths = pd.Series(index=agegrps, data=np.nan)
 totdeaths.index = totdeaths.index.astype(make_age_grp_types())
 totdeaths = totdeaths.combine_first(deaths).fillna(0.0)

src/scripts/bladder_cancer_analyses/bladder_cancer_analyses_single_run.py

@@ -13,14 +13,17 @@
     contraception,
     demography,
     enhanced_lifestyle,
+    epi,
     healthburden,
     healthseekingbehaviour,
     healthsystem,
+    hiv,
     labour,
     newborn_outcomes,
     postnatal_supervisor,
     pregnancy_supervisor,
     symptommanager,
+    tb,
 )
 
 # import numpy as np
@@ -55,22 +58,26 @@
         'tlo.methods.pregnancy_supervisor': logging.CRITICAL
     }
 }
-sim = Simulation(start_date=start_date, seed=4, log_config=log_config)
+sim = Simulation(start_date=start_date, seed=4, log_config=log_config, resourcefilepath=resourcefilepath)
 
 # Register the appropriate modules
-sim.register(demography.Demography(resourcefilepath=resourcefilepath),
-             care_of_women_during_pregnancy.CareOfWomenDuringPregnancy(resourcefilepath=resourcefilepath),
-             contraception.Contraception(resourcefilepath=resourcefilepath),
-             enhanced_lifestyle.Lifestyle(resourcefilepath=resourcefilepath),
-             healthsystem.HealthSystem(resourcefilepath=resourcefilepath),
-             symptommanager.SymptomManager(resourcefilepath=resourcefilepath),
-             healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=resourcefilepath),
-             healthburden.HealthBurden(resourcefilepath=resourcefilepath),
-             labour.Labour(resourcefilepath=resourcefilepath),
-             newborn_outcomes.NewbornOutcomes(resourcefilepath=resourcefilepath),
-             pregnancy_supervisor.PregnancySupervisor(resourcefilepath=resourcefilepath),
-             postnatal_supervisor.PostnatalSupervisor(resourcefilepath=resourcefilepath),
-             bladder_cancer.BladderCancer(resourcefilepath=resourcefilepath)
+sim.register(demography.Demography(),
+             care_of_women_during_pregnancy.CareOfWomenDuringPregnancy(),
+             contraception.Contraception(),
+             enhanced_lifestyle.Lifestyle(),
+             healthsystem.HealthSystem(),
+             symptommanager.SymptomManager(),
+             healthseekingbehaviour.HealthSeekingBehaviour(),
+             healthburden.HealthBurden(),
+             labour.Labour(),
+             newborn_outcomes.NewbornOutcomes(),
+             pregnancy_supervisor.PregnancySupervisor(),
+             postnatal_supervisor.PostnatalSupervisor(),
+             bladder_cancer.BladderCancer(),
+             hiv.Hiv(),
+             tb.Tb(),
+             epi.Epi()
+
              )
 
 # Run the simulation and flush the logger