Update config for brazil run

Author: albrja

src/vivarium_csu_alzheimers/components/treatment.py

@@ -198,14 +198,11 @@ def on_initialize_simulants(self, pop_data: SimulantData) -> None:
                 COLUMNS.TREATMENT_STATE,
                 COLUMNS.WAITING_FOR_TREATMENT_EVENT_TIME,
                 COLUMNS.WAITING_FOR_TREATMENT_EVENT_COUNT,
-                COLUMNS.TREATMENT_DURATION,
             ],
-        ] = [
-            TREATMENT_DISEASE_MODEL.WAITING_FOR_TREATMENT_STATE,
-            event_time,
-            1,
-            self.get_treatment_duration(start_treatment_idx),
-        ]
+        ] = [TREATMENT_DISEASE_MODEL.WAITING_FOR_TREATMENT_STATE, event_time, 1]
+        update.loc[
+            start_treatment_idx, COLUMNS.TREATMENT_DURATION
+        ] = self.get_treatment_duration(start_treatment_idx)
 
         update.loc[
             decline_treatment_idx,

src/vivarium_csu_alzheimers/model_specifications/branches/scenarios.yaml

@@ -7,11 +7,11 @@ branches:
         - baseline
         # - bbbm_testing
         - bbbm_testing_and_treatment
-    input_data:
-      artifact_path:
+    # input_data:
+    #   artifact_path:
         # - '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/united_states_of_america.hdf'
         # - '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/china.hdf'
-        - '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/brazil.hdf'
+        # - '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/brazil.hdf'
         # - '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/germany.hdf'
         # - '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/israel.hdf'
         # - '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/japan.hdf'

src/vivarium_csu_alzheimers/model_specifications/model_spec.yaml

@@ -24,8 +24,7 @@ components:
 configuration:
     input_data:
         input_draw_number: 0
-        artifact_path: /home/albrja/scratch/artifacts/united_states_of_america.hdf
-        # artifact_path: '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/united_states_of_america.hdf'
+        artifact_path: '/mnt/team/simulation_science/pub/models/vivarium_csu_alzheimers/artifacts/model8.3/brazil.hdf'
     interpolation:
         order: 0
         extrapolate: True
@@ -38,7 +37,7 @@ configuration:
             month: 1
             day: 1
         end:
-            year: 2500
+            year: 2100
             month: 12
             day: 31
         step_size: 182  # days 365/2 = 182.5. 182 days guarantees 2 events per year for the 
@@ -65,4 +64,4 @@ configuration:
                 - bbbm_test_results
 
     intervention:
-        scenario: bbbm_testing_and_treatment  # can be 'baseline', 'bbbm_testing', or 'bbbm_testing_and_treatment'
+        scenario: baseline  # can be 'baseline', 'bbbm_testing', or 'bbbm_testing_and_treatment'