Added script to attach latest alert levels to geopackage

tier_info.py

+"""Adds Tier info to geopackage"""
+
+import os
+import yaml
+import h5py
+import numpy as np
+import geopandas as gp
+from covid.cli_arg_parse import cli_args
+import model_spec
+
+DTYPE = model_spec.DTYPE
+
+GIS_TEMPLATE = "data/UK2019mod_pop.gpkg"
+
+if __name__ == "__main__":
+
+    args = cli_args()
+
+    # Get general config
+    with open(args.config, "r") as f:
+        config = yaml.load(f, Loader=yaml.FullLoader)
+
+    # Load covariate data
+    covar_data = model_spec.read_covariates(config)
+
+    # Load geopackage
+    geo = gp.read_file(
+        os.path.join(
+            config["output"]["results_dir"], config["output"]["geopackage"]
+        )
+    )
+    geo = geo[geo["lad19cd"].str.startswith("E")]  # England only, for now.
+    geo = geo.sort_values("lad19cd")
+
+    tiers = covar_data["L"][-1].to_dataframe()[["value"]]
+    tiers = tiers[tiers["value"] == 1.0].reset_index()
+    geo["current_alert_level"] = tiers["alert_level"]
+    geo.to_file(
+        os.path.join(
+            config["output"]["results_dir"], config["output"]["geopackage"]
+        ),
+        driver="GPKG",
+    )