Resource file path from simulation

src/scripts/enhanced_lifestyle_analyses/enhanced_lifestyle_analyses.py

@@ -510,20 +510,20 @@ def run():
     end_date = Date(2050, 1, 1)
     pop_size = 20000
 
+    # Path to the resource files used by the disease and intervention methods
+    resourcefilepath = './resources'
+
     # This creates the Simulation instance for this run. Because we"ve passed the `seed` and
     # `log_config` arguments, these will override the default behaviour.
-    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config)
-
-    # Path to the resource files used by the disease and intervention methods
-    resources = "./resources"
+    sim = Simulation(start_date=start_date, seed=seed, log_config=log_config, resourcefilepath=resourcefilepath)
 
     # We register all modules in a single call to the register method, calling once with multiple
     # objects. This is preferred to registering each module in multiple calls because we will be
     # able to handle dependencies if modules are registered together
     sim.register(
-        demography.Demography(resourcefilepath=resources),
-        enhanced_lifestyle.Lifestyle(resourcefilepath=resources),
-        simplified_births.SimplifiedBirths(resourcefilepath=resources)
+        demography.Demography(),
+        enhanced_lifestyle.Lifestyle(),
+        simplified_births.SimplifiedBirths()
 
     )
 

src/scripts/simplified_births_analyses/analysis_simplified_births_calibrations.py

@@ -30,12 +30,12 @@ def run():
     end_date = Date(2099, 12, 31)
     pop_size = 20_000
 
-    sim = Simulation(start_date=start_date, log_config=log_config)
+    sim = Simulation(start_date=start_date, log_config=log_config, resourcefilepath=resourcefilepath)
 
     # Registering all required modules
     sim.register(
-        demography.Demography(resourcefilepath=resourcefilepath),
-        simplified_births.SimplifiedBirths(resourcefilepath=resourcefilepath)
+        demography.Demography(),
+        simplified_births.SimplifiedBirths()
     )
 
     sim.make_initial_population(n=pop_size)

src/tlo/methods/demography.py

@@ -73,9 +73,8 @@ class Demography(Module):
     The core demography module.
     """
 
-    def __init__(self, name=None, resourcefilepath=None, equal_allocation_by_district: bool = False):
+    def __init__(self, name=None, equal_allocation_by_district: bool = False):
         super().__init__(name)
-        self.resourcefilepath = resourcefilepath
         self.equal_allocation_by_district = equal_allocation_by_district
         self.initial_model_to_data_popsize_ratio = None  # will store scaling factor
         self.popsize_by_year = dict()  # will store total population size each year
@@ -154,17 +153,17 @@ def __init__(self, name=None, resourcefilepath=None, equal_allocation_by_distric
         'age_days': Property(Types.INT, 'The age of the individual in whole days'),
     }
 
-    def read_parameters(self, data_folder):
+    def read_parameters(self, resourcefilepath = None):
         """Load the parameters from `ResourceFile_Demography_parameters.csv` and data from other `ResourceFiles`."""
 
         # General parameters
         self.load_parameters_from_dataframe(pd.read_csv(
-            Path(self.resourcefilepath) / 'demography' / 'ResourceFile_Demography_parameters.csv')
+            Path(resourcefilepath) / 'demography' / 'ResourceFile_Demography_parameters.csv')
         )
 
         # Initial population size:
         self.parameters['pop_2010'] = pd.read_csv(
-            Path(self.resourcefilepath) / 'demography' / 'ResourceFile_Population_2010.csv'
+            Path(resourcefilepath) / 'demography' / 'ResourceFile_Population_2010.csv'
         )
 
         # Lookup dicts to map from district_num_of_residence (in the df) and District name and Region name
@@ -186,17 +185,17 @@ def read_parameters(self, data_folder):
 
         # Fraction of babies that are male
         self.parameters['fraction_of_births_male'] = pd.read_csv(
-            Path(self.resourcefilepath) / 'demography' / 'ResourceFile_Pop_Frac_Births_Male.csv'
+            Path(resourcefilepath) / 'demography' / 'ResourceFile_Pop_Frac_Births_Male.csv'
         ).set_index('Year')['frac_births_male']
 
         # All-Cause Mortality schedule:
         self.parameters['all_cause_mortality_schedule'] = pd.read_csv(
-            Path(self.resourcefilepath) / 'demography' / 'ResourceFile_Pop_DeathRates_Expanded_WPP.csv'
+            Path(resourcefilepath) / 'demography' / 'ResourceFile_Pop_DeathRates_Expanded_WPP.csv'
         )
 
         # GBD Dataset for Causes of Death
         self.parameters['gbd_causes_of_death_data'] = pd.read_csv(
-            Path(self.resourcefilepath) / 'gbd' / 'ResourceFile_CausesOfDeath_GBD2019.csv'
+            Path(resourcefilepath) / 'gbd' / 'ResourceFile_CausesOfDeath_GBD2019.csv'
         ).set_index(['Sex', 'Age_Grp'])
 
     def pre_initialise_population(self):

src/tlo/methods/enhanced_lifestyle.py

@@ -24,9 +24,8 @@ class Lifestyle(Module):
     by urban/rural, wealth, tobacco usage etc.
     """
 
-    def __init__(self, name=None, resourcefilepath=None):
+    def __init__(self, name=None):
         super().__init__(name)
-        self.resourcefilepath: Path = resourcefilepath
 
         # a pointer to the linear models class
         self.models = None
@@ -340,10 +339,10 @@ def __init__(self, name=None, resourcefilepath=None):
         "li_is_circ": Property(Types.BOOL, "Is the person circumcised if they are male (False for all females)"),
     }
 
-    def read_parameters(self, data_folder):
+    def read_parameters(self, resourcefilepath = None):
         p = self.parameters
         dataframes = pd.read_excel(
-            Path(self.resourcefilepath) / 'ResourceFile_Lifestyle_Enhanced.xlsx',
+            Path(resourcefilepath) / 'ResourceFile_Lifestyle_Enhanced.xlsx',
             sheet_name=["parameter_values", "urban_rural_by_district"],
         )
         self.load_parameters_from_dataframe(dataframes["parameter_values"])

src/tlo/methods/simplified_births.py

@@ -84,9 +84,8 @@ class SimplifiedBirths(Module):
                                             categories=['none', 'non_exclusive', 'exclusive']),
     }
 
-    def __init__(self, name=None, resourcefilepath=None):
+    def __init__(self, name=None):
         super().__init__(name)
-        self.resourcefilepath = resourcefilepath
         self.asfr = dict()
 
         # Define defaults for properties:
@@ -102,16 +101,16 @@ def __init__(self, name=None, resourcefilepath=None):
             'nb_breastfeeding_status': 'none',
         }
 
-    def read_parameters(self, data_folder):
+    def read_parameters(self, resourcefilepath = None):
         """Load parameters for probability of pregnancy/birth and breastfeeding status for newborns"""
 
         self.parameters['age_specific_fertility_rates'] = \
-            pd.read_csv(Path(self.resourcefilepath) / 'demography' / 'ResourceFile_ASFR_WPP.csv')
+            pd.read_csv(Path(resourcefilepath) / 'demography' / 'ResourceFile_ASFR_WPP.csv')
 
         self.parameters['months_between_pregnancy_and_delivery'] = 9
 
         # Breastfeeding status for newborns (importing from the Newborn resourcefile)
-        rf = pd.read_excel(Path(self.resourcefilepath) / 'ResourceFile_NewbornOutcomes.xlsx')
+        rf = pd.read_excel(Path(resourcefilepath) / 'ResourceFile_NewbornOutcomes.xlsx')
         param_as_string = rf.loc[rf.parameter_name == 'prob_breastfeeding_type']['value'].iloc[0]
         parameter = json.loads(param_as_string)[0]
         self.parameters['prob_breastfeeding_type'] = parameter

src/tlo/simulation.py

@@ -44,7 +44,7 @@ class Simulation:
     """
 
     def __init__(self, *, start_date: Date, seed: int = None, log_config: dict = None,
-                 show_progress_bar=False):
+                 show_progress_bar=False, resourcefilepath = None):
         """Create a new simulation.
 
         :param start_date: the date the simulation begins; must be given as
@@ -53,6 +53,7 @@ def __init__(self, *, start_date: Date, seed: int = None, log_config: dict = Non
         :param log_config: sets up the logging configuration for this simulation
         :param show_progress_bar: whether to show a progress bar instead of the logger
             output during the simulation
+        :param resourcefilepath: path to the resources folder
         """
         # simulation
         self.date = self.start_date = start_date
@@ -80,6 +81,7 @@ def __init__(self, *, start_date: Date, seed: int = None, log_config: dict = Non
             data=f'Simulation RNG {seed_from} entropy = {self._seed_seq.entropy}'
         )
         self.rng = np.random.RandomState(np.random.MT19937(self._seed_seq))
+        self.resourcefilepath = resourcefilepath
 
     def _configure_logging(self, filename: str = None, directory: Union[Path, str] = "./outputs",
                            custom_levels: Dict[str, int] = None, suppress_stdout: bool = False):
@@ -165,7 +167,7 @@ def register(self, *modules, sort_modules=True, check_all_dependencies=True):
 
             self.modules[module.name] = module
             module.sim = self
-            module.read_parameters('')
+            module.read_parameters(self.resourcefilepath)
 
         if self._custom_log_levels:
             logging.set_logging_levels(self._custom_log_levels)
@@ -313,7 +315,6 @@ def find_events_for_person(self, person_id: int):
 
         return person_events
 
-
 class EventQueue:
     """A simple priority queue for events.