Coverage to 90%

src/hdmf/__init__.py

@@ -1,32 +1,10 @@
 from . import query
-from .backends.hdf5.h5_utils import H5Dataset, H5RegionSlicer
+from .backends.hdf5.h5_utils import H5Dataset
 from .container import Container, Data, DataRegion, HERDManager
-from .region import ListSlicer
 from .utils import docval, getargs
 from .term_set import TermSet, TermSetWrapper, TypeConfigurator
 
 
-@docval(
-    {"name": "dataset", "type": None, "doc": "the HDF5 dataset to slice"},
-    {"name": "region", "type": None, "doc": "the region reference to use to slice"},
-    is_method=False,
-)
-def get_region_slicer(**kwargs):
-    import warnings  # noqa: E402
-
-    warnings.warn(
-        "get_region_slicer is deprecated and will be removed in HDMF 3.0.",
-        DeprecationWarning,
-    )
-
-    dataset, region = getargs("dataset", "region", kwargs)
-    if isinstance(dataset, (list, tuple, Data)):
-        return ListSlicer(dataset, region)
-    elif isinstance(dataset, H5Dataset):
-        return H5RegionSlicer(dataset, region)
-    return None
-
-
 try:
     # see https://effigies.gitlab.io/posts/python-packaging-2023/
     from ._version import __version__

src/hdmf/backends/hdf5/__init__.py

@@ -1,3 +1,3 @@
 from . import h5_utils, h5tools
-from .h5_utils import H5RegionSlicer, H5DataIO
+from .h5_utils import H5DataIO
 from .h5tools import HDF5IO, H5SpecWriter, H5SpecReader

src/hdmf/backends/hdf5/h5_utils.py

@@ -16,10 +16,8 @@
 import os
 import logging
 
-from ...array import Array
 from ...data_utils import DataIO, AbstractDataChunkIterator, append_data
 from ...query import HDMFDataset, ReferenceResolver, ContainerResolver, BuilderResolver
-from ...region import RegionSlicer
 from ...spec import SpecWriter, SpecReader
 from ...utils import docval, getargs, popargs, get_docval, get_data_shape
 
@@ -85,7 +83,7 @@ def append(self, dataset, data):
 
 
 class H5Dataset(HDMFDataset):
-    @docval({'name': 'dataset', 'type': (Dataset, Array), 'doc': 'the HDF5 file lazily evaluate'},
+    @docval({'name': 'dataset', 'type': (Dataset), 'doc': 'the HDF5 file lazily evaluate'},
             {'name': 'io', 'type': 'hdmf.backends.hdf5.h5tools.HDF5IO',
              'doc': 'the IO object that was used to read the underlying dataset'})
     def __init__(self, **kwargs):
@@ -189,7 +187,7 @@ def get_object(self, h5obj):
 
 class AbstractH5TableDataset(DatasetOfReferences):
 
-    @docval({'name': 'dataset', 'type': (Dataset, Array), 'doc': 'the HDF5 file lazily evaluate'},
+    @docval({'name': 'dataset', 'type': (Dataset), 'doc': 'the HDF5 file lazily evaluate'},
             {'name': 'io', 'type': 'hdmf.backends.hdf5.h5tools.HDF5IO',
              'doc': 'the IO object that was used to read the underlying dataset'},
             {'name': 'types', 'type': (list, tuple),
@@ -420,28 +418,6 @@ def read_namespace(self, ns_path):
         return ret
 
 
-class H5RegionSlicer(RegionSlicer):
-
-    @docval({'name': 'dataset', 'type': (Dataset, H5Dataset), 'doc': 'the HDF5 dataset to slice'},
-            {'name': 'region', 'type': RegionReference, 'doc': 'the region reference to use to slice'})
-    def __init__(self, **kwargs):
-        self.__dataset = getargs('dataset', kwargs)
-        self.__regref = getargs('region', kwargs)
-        self.__len = self.__dataset.regionref.selection(self.__regref)[0]
-        self.__region = None
-
-    def __read_region(self):
-        if self.__region is None:
-            self.__region = self.__dataset[self.__regref]
-
-    def __getitem__(self, idx):
-        self.__read_region()
-        return self.__region[idx]
-
-    def __len__(self):
-        return self.__len
-
-
 class H5DataIO(DataIO):
     """
     Wrap data arrays for write via HDF5IO to customize I/O behavior, such as compression and chunking