adapt to zarr 2.11

Author: TonioF

test/cli/test_prune.py

@@ -1,7 +1,6 @@
 import os.path
 import sys
 
-import numpy as np
 import xarray as xr
 
 from test.cli.helpers import CliTest
@@ -25,12 +24,24 @@ class PruneDataTest(CliTest):
     def setUp(self) -> None:
         rimraf(self.TEST_CUBE)
         cube = new_cube(time_periods=3,
-                        variables=dict(precipitation=np.nan,
-                                       temperature=np.nan)) \
+                        variables=dict(precipitation=1.0,
+                                       temperature=1.0)) \
             .chunk(dict(time=1, lat=90, lon=90))
 
         write_cube(cube, self.TEST_CUBE, "zarr", cube_asserted=True)
 
+        # we need to manually edit the fill values, otherwise, as of zarr 2.11,
+        # empty chunks are not written
+        import json
+        with open(f'{self.TEST_CUBE}/.zmetadata') as metadata:
+            metadata_dict = json.load(metadata)
+            metadata_dict['metadata']['precipitation/.zarray']['fill_value'] \
+                = 1.0
+            metadata_dict['metadata']['temperature/.zarray']['fill_value'] \
+                = 1.0
+        with open(f'{self.TEST_CUBE}/.zmetadata', 'w') as metadata:
+            json.dump(metadata_dict, metadata)
+
     def tearDown(self) -> None:
         rimraf(self.TEST_CUBE)