Add Low Case Count Thresholds into Constants File (#73)

This update is meant to coincide with the PR in epinow2
CDCgov/cfa-epinow2-pipeline#353 to add in
pathogen-specific low case count thresholds.

This PR just adds disease-specific low case count thresholds that can be
read into the epinow2 pipeline.

Author: PatrickTCorbett

src/cfa_config_generator/utils/epinow2/constants.py

@@ -16,6 +16,8 @@
     "facility_active_proportion": 1.0,
 }
 
+low_case_count_thresholds = {"COVID-19": 10, "Influenza": 10, "RSV": 5}
+
 all_states = (
     "AK",
     "AL",

src/cfa_config_generator/utils/epinow2/functions.py

@@ -9,6 +9,7 @@
 
 from cfa_config_generator.utils.epinow2.constants import (
     all_diseases,
+    low_case_count_thresholds,
     nssp_valid_states,
     shared_params,
 )
@@ -384,6 +385,7 @@ def generate_task_configs(
                 "min_reference_date": min(reference_dates).isoformat(),
                 "max_reference_date": max(reference_dates).isoformat(),
                 "disease": d,
+                "low_case_count_thresholds": low_case_count_thresholds,
                 "geo_value": s,
                 "geo_type": "state" if s != "US" else "country",
                 "report_date": report_date.isoformat(),