Merge branch 'dev' into another_html_fix

CHANGELOG.md

@@ -1,6 +1,9 @@
 # HDMF Changelog
 
-## HDMF 3.14.6 (Upcoming)
+## HDMF 4.0.0 (Upcoming)
+
+### Deprecations
+- The following classes have been deprecated and removed: Array, AbstractSortedArray, SortedArray, LinSpace, Query, RegionSlicer, ListSlicer, H5RegionSlicer, DataRegion. The following methods have been deprecated and removed: fmt_docval_args, call_docval_func, get_container_cls, add_child, set_dataio (now refactored as set_data_io). We have also removed all early evelopment for region references. @mavaylon1 [#1998](https://github.com/hdmf-dev/hdmf/pull/1198)
 
 ### Enhancements
 - Added support for expandable datasets of references for untyped and compound data types. @stephprince [#1188](https://github.com/hdmf-dev/hdmf/pull/1188)

src/hdmf/__init__.py

@@ -1,32 +1,10 @@
 from . import query
-from .backends.hdf5.h5_utils import H5Dataset, H5RegionSlicer
-from .container import Container, Data, DataRegion, HERDManager
-from .region import ListSlicer
+from .backends.hdf5.h5_utils import H5Dataset
+from .container import Container, Data, HERDManager
 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