Merge branch 'dev' into link_error

CHANGELOG.md

@@ -7,6 +7,7 @@
 * Added support for Pathlib paths. @mavaylon1 [#212](https://github.com/hdmf-dev/hdmf-zarr/pull/212)
 * Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly [#214](https://github.com/hdmf-dev/hdmf-zarr/pull/214)
 * Add `force_overwite` parameter for `ZarrIO.__init__` to allow overwriting an existing file or directory. @oruebel [#229](https://github.com/hdmf-dev/hdmf-zarr/pull/229)
+* Remove allowance of `hdmf.Array` in `__init__` of `AbstractZarrTableDataset` and `ZarrDataset` to be compatible with HDMF 4.0. @rly [#236](https://github.com/hdmf-dev/hdmf-zarr/pull/236)
 
 ### Bug Fixes
 * Fix reading of cached specs and caching of specs during export. @rly [#232](https://github.com/hdmf-dev/hdmf-zarr/pull/232)

requirements.txt

@@ -1,6 +1,7 @@
 # pinned dependencies to reproduce an entire development environment to use HDMF-ZARR
 hdmf==3.14.5
-zarr==2.18.3
+zarr==2.18.3; python_version >= "3.10"  # zarr 2.18.3 dropped support for python 3.9
+zarr==2.18.2; python_version < "3.10"
 pynwb==2.8.2
 numpy==2.1.3
 numcodecs==0.13.1

src/hdmf_zarr/backend.py

@@ -731,7 +731,7 @@ def __is_ref(self, dtype):
         elif isinstance(dtype, np.dtype):
             return False
         else:
-            return dtype == DatasetBuilder.OBJECT_REF_TYPE or dtype == DatasetBuilder.REGION_REF_TYPE
+            return dtype == DatasetBuilder.OBJECT_REF_TYPE
 
     def resolve_ref(self, zarr_ref):
         """
@@ -790,7 +790,7 @@ def _create_ref(self, ref_object, ref_link_source=None):
         elif isinstance(ref_object, ReferenceBuilder):
             builder = ref_object.builder
 
-        path = self.__get_path(builder) # This is the internal path in the store to the item.
+        path = self.__get_path(builder)  # This is the internal path in the store to the item.
 
         # get the object id if available
         object_id = builder.get('object_id', None)
@@ -1074,12 +1074,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
                 # and will be refactored/removed.
                 if self.__is_ref(dts['dtype']):
                     refs.append(i)
-                    ref_tmp = self._create_ref(data[0][i], ref_link_source=self.path)
-                    if isinstance(ref_tmp, ZarrReference):
-                        dts_str = 'object'
-                    else:
-                        dts_str = 'region'
-                    type_str.append({'name': dts['name'], 'dtype': dts_str})
+                    type_str.append({'name': dts['name'], 'dtype': 'object'})
                 else:
                     i = list([dts, ])
                     t = self.__resolve_dtype_helper__(i)
@@ -1208,7 +1203,6 @@ def write_dataset(self, **kwargs):  # noqa: C901
         "ref": ZarrReference,
         "reference": ZarrReference,
         "object": ZarrReference,
-        "region": ZarrReference,
     }
 
     @classmethod
@@ -1535,20 +1529,15 @@ def __read_dataset(self, zarr_obj, name):
             # Check compound dataset where one of the subsets contains references
             has_reference = False
             for i, dts in enumerate(dtype):
-                if dts['dtype'] in ['object', 'region']:  # check items for object reference
+                if dts['dtype'] == 'object':  # check items for object reference
                     has_reference = True
                     break
             retrieved_dtypes = [dtype_dict['dtype'] for dtype_dict in dtype]
             if has_reference:
-                # TODO:  BuilderZarrTableDataset does not yet support region reference
                 data = BuilderZarrTableDataset(zarr_obj, self, retrieved_dtypes)
         elif self.__is_ref(dtype):
             # Array of references
-            if dtype == 'object':
-                data = BuilderZarrReferenceDataset(data, self)
-            # TODO: Resolution of Region reference not yet supported by BuilderZarrRegionDataset
-            # elif dtype == 'region':
-            #     data = BuilderZarrRegionDataset(data, self)
+            data = BuilderZarrReferenceDataset(data, self)
 
         kwargs['data'] = data
         if name is None:
@@ -1571,9 +1560,6 @@ def __read_attrs(self, zarr_obj):
                             ret[k] = self.__read_group(target_zarr_obj, target_name)
                         else:
                             ret[k] = self.__read_dataset(target_zarr_obj, target_name)
-                    # TODO Need to implement region references for attributes
-                    elif v['zarr_dtype'] == 'region':
-                        raise NotImplementedError("Read of region references from attributes not implemented in ZarrIO")
                     else:
                         raise NotImplementedError("Unsupported zarr_dtype for attribute " + str(v))
                 else:

src/hdmf_zarr/zarr_utils.py

@@ -7,7 +7,7 @@
 from copy import copy
 import numpy as np
 
-from zarr import Array as ZarrArray
+from zarr import Array
 
 from hdmf.build import DatasetBuilder
 from hdmf.data_utils import append_data
@@ -20,7 +20,7 @@ class ZarrDataset(HDMFDataset):
     Extension of HDMFDataset to add Zarr compatibility
     """
 
-    @docval({'name': 'dataset', 'type': (np.ndarray, ZarrArray), 'doc': 'the Zarr file lazily evaluate'},
+    @docval({'name': 'dataset', 'type': (np.ndarray, Array), 'doc': 'the Zarr file lazily evaluate'},
             {'name': 'io', 'type': 'ZarrIO', 'doc': 'the IO object that was used to read the underlying dataset'})
     def __init__(self, **kwargs):
         self.__io = popargs('io', kwargs)
@@ -129,7 +129,7 @@ class AbstractZarrTableDataset(DatasetOfReferences):
     references in compound datasets to either Builders and Containers.
     """
 
-    @docval({'name': 'dataset', 'type': (np.ndarray, ZarrArray), 'doc': 'the Zarr file lazily evaluate'},
+    @docval({'name': 'dataset', 'type': (np.ndarray, Array), 'doc': 'the Zarr file lazily evaluate'},
             {'name': 'io', 'type': 'ZarrIO', 'doc': 'the IO object that was used to read the underlying dataset'},
             {'name': 'types', 'type': (list, tuple),
              'doc': 'the list/tuple of reference types'})
@@ -138,8 +138,6 @@ def __init__(self, **kwargs):
         super().__init__(**kwargs)
         self.__refgetters = dict()
         for i, t in enumerate(types):
-            # if t is RegionReference:  # TODO: Region References not yet supported
-            #     self.__refgetters[i] = self.__get_regref
             if t == DatasetBuilder.OBJECT_REF_TYPE:
                 self.__refgetters[i] = self._get_ref
             elif t is str:
@@ -153,7 +151,6 @@ def __init__(self, **kwargs):
             sub = self.dataset.dtype[i]
             if np.issubdtype(sub, np.dtype('O')):
                 tmp.append('object')
-                # TODO: Region References are not yet supported
             if sub.metadata:
                 if 'vlen' in sub.metadata:
                     t = sub.metadata['vlen']
@@ -223,24 +220,6 @@ def dtype(self):
         return 'object'
 
 
-class AbstractZarrRegionDataset(AbstractZarrReferenceDataset):
-    """
-    Extension of DatasetOfReferences to serve as the base class for resolving Zarr
-    references in datasets to either Builders and Containers.
-
-    Note: Region References are not yet supported.
-    """
-
-    def __getitem__(self, arg):
-        obj = super().__getitem__(arg)
-        ref = self.dataset[arg]
-        return obj[ref]
-
-    @property
-    def dtype(self):
-        return 'region'
-
-
 class ContainerZarrTableDataset(ContainerResolverMixin, AbstractZarrTableDataset):
     """
     A reference-resolving dataset for resolving references inside tables
@@ -283,29 +262,3 @@ class BuilderZarrReferenceDataset(BuilderResolverMixin, AbstractZarrReferenceDat
     @classmethod
     def get_inverse_class(cls):
         return ContainerZarrReferenceDataset
-
-
-class ContainerZarrRegionDataset(ContainerResolverMixin, AbstractZarrRegionDataset):
-    """
-    A reference-resolving dataset for resolving region references that returns
-    resolved references as Containers
-
-    Note: Region References are not yet supported.
-    """
-
-    @classmethod
-    def get_inverse_class(cls):
-        return BuilderZarrRegionDataset
-
-
-class BuilderZarrRegionDataset(BuilderResolverMixin, AbstractZarrRegionDataset):
-    """
-    A reference-resolving dataset for resolving region references that returns
-    resolved references as Builders.
-
-    Note: Region References are not yet supported.
-    """
-
-    @classmethod
-    def get_inverse_class(cls):
-        return ContainerZarrRegionDataset