readding dependencies for test files

src/scripts/hiv/projections_jan2023/calibration_script.py

@@ -0,0 +1,125 @@
+"""
+This file defines a batch run through which the hiv and tb modules are run across a set of parameter values
+
+check the batch configuration gets generated without error:
+tlo scenario-run --draw-only src/scripts/hiv/deviance_for_calibration/calibration_script.py
+
+Test the scenario starts running without problems:
+tlo scenario-run src/scripts/hiv/deviance_for_calibration/calibration_script.py
+
+or execute a single run:
+tlo scenario-run src/scripts/hiv/deviance_for_calibration/calibration_script.py --draw 1 0
+
+Run on the batch system using:
+tlo batch-submit src/scripts/hiv/deviance_for_calibration/calibration_script.py
+
+weds 16th feb runs:
+Job ID: calibration_script-2022-02-16T202042Z
+
+this ^^ is the large calibration run (100 jobs, pop=760k)
+
+
+Display information about a job:
+tlo batch-job tlo_q1_demo-123 --tasks
+
+Download result files for a completed job:
+tlo batch-download calibration_script-2022-04-12T190518Z
+
+12th Apr 2022
+Job ID: calibration_script-2022-04-12T190518Z
+
+
+"""
+
+import os
+import random
+
+import pandas as pd
+
+from tlo import Date, logging
+from tlo.methods import (
+    demography,
+    enhanced_lifestyle,
+    epi,
+    healthburden,
+    healthseekingbehaviour,
+    healthsystem,
+    hiv,
+    hiv_tb_calibration,
+    simplified_births,
+    symptommanager,
+    tb,
+)
+from tlo.scenario import BaseScenario
+
+number_of_draws = 1
+runs_per_draw = 5
+
+
+class TestScenario(BaseScenario):
+    # this imports the resource filepath automatically
+
+    def __init__(self):
+        super().__init__()
+        self.seed = random.randint(0, 50000)
+        self.start_date = Date(2010, 1, 1)
+        self.end_date = Date(2020, 1, 1)
+        self.pop_size = 500000
+        self.number_of_draws = number_of_draws
+        self.runs_per_draw = runs_per_draw
+
+        self.sampled_parameters = pd.read_excel(
+            os.path.join(self.resources, "../../../../resources/ResourceFile_HIV.xlsx"),
+            sheet_name="LHC_samples",
+        )
+
+    def log_configuration(self):
+        return {
+            'filename': 'deviance_runs',
+            'directory': './outputs',
+            'custom_levels': {
+                '*': logging.WARNING,
+                "tlo.methods.deviance_measure": logging.INFO,
+            }
+        }
+
+    def modules(self):
+        return [
+            demography.Demography(resourcefilepath=self.resources),
+            simplified_births.SimplifiedBirths(resourcefilepath=self.resources),
+            enhanced_lifestyle.Lifestyle(resourcefilepath=self.resources),
+            healthsystem.HealthSystem(
+                resourcefilepath=self.resources,
+                service_availability=["*"],  # all treatment allowed
+                mode_appt_constraints=0,  # mode of constraints to do with officer numbers and time
+                cons_availability="all",  # mode for consumable constraints (if ignored, all consumables available)
+                ignore_priority=True,  # do not use the priority information in HSI event to schedule
+                capabilities_coefficient=1.0,  # multiplier for the capabilities of health officers
+                disable=False,  # disables the healthsystem (no constraints and no logging) and every HSI runs
+                disable_and_reject_all=False,  # disable healthsystem and no HSI runs
+                store_hsi_events_that_have_run=False,  # convenience function for debugging
+            ),
+            symptommanager.SymptomManager(resourcefilepath=self.resources),
+            healthseekingbehaviour.HealthSeekingBehaviour(resourcefilepath=self.resources),
+            healthburden.HealthBurden(resourcefilepath=self.resources),
+            epi.Epi(resourcefilepath=self.resources),
+            hiv.Hiv(resourcefilepath=self.resources),
+            tb.Tb(resourcefilepath=self.resources),
+            hiv_tb_calibration.Deviance(resourcefilepath=self.resources),
+        ]
+
+    def draw_parameters(self, draw_number, rng):
+
+        return {
+            'Hiv': {
+                'beta': self.sampled_parameters.hiv[draw_number],
+            },
+            'Tb': {
+                'transmission_rate': self.sampled_parameters.tb[draw_number],
+            },
+        }
+
+
+if __name__ == '__main__':
+    from tlo.cli import scenario_run
+    scenario_run([__file__])