Update for zarr 2.18.0 and zarr 2.18.1 (#195)

CHANGELOG.md

@@ -1,5 +1,9 @@
 # HDMF-ZARR Changelog
 
+## 0.7.0 (May 2, 2024)
+### Bug Fixes
+* Fixed bug on how we access scalar arrays. Added warning filter for Zarr deprecation of NestedDirectoryStore. Fixed bug on how we write a dataset of references. @mavaylon1 [#195](https://github.com/hdmf-dev/hdmf-zarr/pull/195)
+
 ## 0.7.0 (May 2, 2024)
 ### Enhancements
 * Added support for python 3.12. @mavaylon1 [#172](https://github.com/hdmf-dev/hdmf-zarr/pull/172)

src/hdmf_zarr/backend.py

@@ -1096,7 +1096,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
             self._written_builders.set_written(builder)  # record that the builder has been written
             dset.attrs['zarr_dtype'] = type_str
             if hasattr(refs, '__len__'):
-                dset[:] = refs
+                dset[:] = np.array(refs)
             else:
                 dset[0] = refs
         # write a 'regular' dataset without DatasetIO info
@@ -1287,7 +1287,8 @@ def __list_fill__(self, parent, name, data, options=None):  # noqa: C901
         # standard write
         else:
             try:
-                dset[:] = data  # If data is an h5py.Dataset then this will copy the data
+                dset[:] = np.array(data)
+            # If data is an h5py.Dataset then this will copy the data
             # For compound data types containing strings Zarr sometimes does not like writing multiple values
             # try to write them one-at-a-time instead then
             except ValueError:
@@ -1451,8 +1452,7 @@ def __read_dataset(self, zarr_obj, name):
 
         # Read scalar dataset
         if dtype == 'scalar':
-            data = zarr_obj[0]
-
+            data = zarr_obj[()]
         if isinstance(dtype, list):
             # Check compound dataset where one of the subsets contains references
             has_reference = False

test_gallery.py

@@ -77,6 +77,10 @@ def _import_from_file(script):
     r"datetime.datetime.utcfromtimestamp() *"
 )
 
+_deprecation_warning_zarr_store = (
+    r"The NestedDirectoryStore is deprecated *"
+)
+
 def run_gallery_tests():
     global TOTAL, FAILURES, ERRORS
     logging.info("Testing execution of Sphinx Gallery files")
@@ -142,6 +146,9 @@ def run_gallery_tests():
                     # this is triggered from datetime
                     "ignore", message=_deprecation_warning_datetime, category=DeprecationWarning
                 )
+                warnings.filterwarnings(
+                    "ignore", message=_deprecation_warning_zarr_store, category=FutureWarning
+                )
                 _import_from_file(script_abs)
         except Exception:
             print(traceback.format_exc())