revert some files back to master

Author: tdm32

src/scripts/bladder_cancer_analyses/bladder_cancer_analyses_single_run.py

@@ -9,13 +9,17 @@
 from tlo.analysis.utils import parse_log_file
 from tlo.methods import (
     bladder_cancer,
+    care_of_women_during_pregnancy,
+    contraception,
     demography,
     enhanced_lifestyle,
     healthburden,
     healthseekingbehaviour,
     healthsystem,
-    schisto,
-    simplified_births,
+    labour,
+    newborn_outcomes,
+    postnatal_supervisor,
+    pregnancy_supervisor,
     symptommanager,
 )
 
@@ -34,30 +38,39 @@
 
 start_date = Date(2010, 1, 1)
 end_date = Date(2013,  1, 1)
-popsize = 5000
+popsize = 19000
 
 # Establish the simulation object
 log_config = {
     'filename': 'LogFile',
     'directory': outputpath,
     'custom_levels': {
-        "*": logging.WARNING,
-        'tlo.methods.bladder_cancer': logging.INFO,
-        'tlo.methods.schisto': logging.INFO,
+        'tlo.methods.demography': logging.CRITICAL,
+        'tlo.methods.contraception': logging.CRITICAL,
+        'tlo.methods.healthsystem': logging.CRITICAL,
+        'tlo.methods.labour': logging.CRITICAL,
+        'tlo.methods.healthburden': logging.CRITICAL,
+        'tlo.methods.symptommanager': logging.CRITICAL,
+        'tlo.methods.healthseekingbehaviour': logging.CRITICAL,
+        'tlo.methods.pregnancy_supervisor': logging.CRITICAL
     }
 }
 sim = Simulation(start_date=start_date, seed=4, log_config=log_config)
 
 # 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),
-             simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath),
-             bladder_cancer.BladderCancer(resourcefilepath=resourcefilepath),
-             schisto.Schisto(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)
              )
 
 # Run the simulation and flush the logger

src/scripts/calibration_analyses/analysis_scripts/analysis_cause_of_death_and_disability_calibrations.py

@@ -474,9 +474,3 @@ def get_total_num_dalys_by_wealth_and_label(_df):
         output_folder=args.results_folder,
         resourcefilepath=Path('./resources')
     )
-
-    # apply(
-    #     results_folder=Path("outputs/long_run_all_diseases-2024-03-05T114732Z"),
-    #     output_folder=Path("outputs/long_run_all_diseases-2024-03-05T114732Z"),
-    #     resourcefilepath=Path('./resources')
-    # )

src/scripts/calibration_analyses/scenarios/long_run_all_diseases.py

@@ -24,7 +24,7 @@ def __init__(self):
         self.end_date = Date(2031, 1, 1)  # The simulation will stop before reaching this date.
         self.pop_size = 20_000
         self.number_of_draws = 1
-        self.runs_per_draw = 1
+        self.runs_per_draw = 10
 
     def log_configuration(self):
         return {