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/_zarr_utils.py

@@ -4,7 +4,10 @@ import zarr
 def get_var_group(v):
     store = zarr.open(v.store)
     parent_group_path = "/".join(v.path.split("/")[:-1])
-    return store[parent_group_path]
+    if parent_group_path == "":
+        return store
+    else:
+        return store[parent_group_path]
 
 
 def get_time_axis(v):
@@ -18,3 +21,9 @@ def get_time_axis(v):
         return time_axis
     else:
         return None
+
+def get_var_parent_group(v):
+    var_group = get_var_group(v)
+    parent_var_path = var_group.attrs["hiopy::parent"]
+    parent_group = zarr.open(v.store)[parent_var_path]
+    return parent_group