Migrate to Zarr 3

Pre-work to #6

This MR has the following:

1. Migration to Zarr 3 API while removing the deprecated yet still supported Zarr 2 API usage.
2. Essential fixes for the main-branch resulting from the learnings out of the global-hackathon exploits (The non-essential ones will be fixed in a seperate branch).

apps/hiopy/configure/create_dataset.py

@@ -36,18 +36,14 @@ def add_coordinates(
 
     lat_list, lon_list = zip(*coordinates)
 
-    lon = dataset.create_array(
-        name=coord_names[0], dtype=np.float32, shape=(len(coordinates),)
-    )
+    lon = dataset.create_array(name=coord_names[0], dtype=np.float32, shape=(len(coordinates),))
     lon[:] = np.array(lon_list)
     lon.attrs["_ARRAY_DIMENSIONS"] = [coord_names[0]]
     lon.attrs["long_name"] = "longitude"
     lon.attrs["units"] = "degree"
     lon.attrs["standard_name"] = "grid_longitude"
 
-    lat = dataset.create_array(
-        name=coord_names[1], dtype=np.float32, shape=(len(coordinates),)
-    )
+    lat = dataset.create_array(name=coord_names[1], dtype=np.float32, shape=(len(coordinates),))
     lat[:] = np.array(lat_list)
     lat.attrs["_ARRAY_DIMENSIONS"] = [coord_names[1]]
     lat.attrs["long_name"] = "latitude"