changes to allow use of the new field

These changes should only be merged into
main at the same time as the config generator
library gets these changse merged

Author: natemcintosh

azure/generate_configs.py

@@ -45,6 +45,17 @@ def main(
             help="Production date in ISO format. Default is today", show_default=False
         ),
     ] = date.today().isoformat(),
+    facility_active_proportion: Annotated[
+        float,
+        typer.Option(
+            help="""
+            Minimum proportion of days of a facility must be actively reporting DDI
+            counts during the modeling period. Must be a number between 0 and 1.
+            Default is 1.0, meaning all facilities must have been active every day.
+            """,
+            show_default=True,
+        ),
+    ] = 1.0,
 ):
     """
     Generate and upload config files for the epinow2 pipeline.
@@ -58,6 +69,12 @@ def main(
     if not job_id:
         raise ValueError("Job ID cannot be empty")
 
+    # Make sure facility_active_proportion is between 0 and 1.
+    if not (0 <= facility_active_proportion <= 1):
+        raise ValueError(
+            "facility_active_proportion must be between 0 and 1, inclusive."
+        )
+
     # Generate and upload to blob for all states and diseases.
     generate_config(
         state=state,
@@ -73,6 +90,7 @@ def main(
         job_id=job_id,
         as_of_date=as_of_date_str,
         output_container=output_container,
+        facility_active_proportion=facility_active_proportion,
     )
 
 

azure/generate_rerun_configs.py

@@ -50,6 +50,17 @@ def main(
             show_default=False,
         ),
     ] = None,
+    facility_active_proportion: Annotated[
+        float,
+        typer.Option(
+            help="""
+            Minimum proportion of days of a facility must be actively reporting DDI
+            counts during the modeling period. Must be a number between 0 and 1.
+            Default is 1.0, meaning all facilities must have been active every day.
+            """,
+            show_default=True,
+        ),
+    ] = 1.0,
 ):
     """
     Generate and upload config files for rerunning the epinow2 pipeline.
@@ -62,6 +73,12 @@ def main(
     if not job_id:
         raise ValueError("Job ID cannot be empty")
 
+    # Make sure facility_active_proportion is between 0 and 1.
+    if not (0 <= facility_active_proportion <= 1):
+        raise ValueError(
+            "facility_active_proportion must be between 0 and 1, inclusive."
+        )
+
     # Generate and upload to blob for all states and diseases.
     generate_rerun_config(
         state="all",
@@ -78,6 +95,7 @@ def main(
         as_of_date=now.isoformat(),
         output_container=output_container,
         data_exclusions_path=data_exclusions_path,
+        facility_active_proportion=facility_active_proportion,
     )
 
 

azure/run_container_app_job.py

@@ -98,7 +98,7 @@ def main(image_name: str, config_container: str, job_id: str):
         state_config = config_path.split("/").pop()
         job_execution_id = job_execution.id.split("/").pop()
         print(
-            f"Started Container App Job #{i+1}/{len(task_configs)} for {state_config} with execution ID: {job_execution_id}"
+            f"Started Container App Job #{i + 1}/{len(task_configs)} for {state_config} with execution ID: {job_execution_id}"
         )
 
 
@@ -118,7 +118,7 @@ def main(image_name: str, config_container: str, job_id: str):
         "--config_container",
         type=str,
         help="The name of the storage container where config files are located",
-        default="rt-epinow2-config"
+        default="rt-epinow2-config",
     )
     parser.add_argument(
         "--job_id",