4.0.0

HDMF 4.0.0 (January 22, 2025)

Breaking changes

• The following classes have been deprecated and removed: Array, AbstractSortedArray, SortedArray, LinSpace, Query, RegionSlicer, ListSlicer, H5RegionSlicer, DataRegion, RegionBuilder. 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 development for region references. @mavaylon1, @rly #1998, #1212
• Importing from hdmf.build.map is no longer supported. Import from hdmf.build instead. @rly #1221
• Python 3.8 has reached end of life. Dropped support for Python 3.8 and add support for Python 3.13. @mavaylon1 #1209
• Support for Zarr is limited to versions < 3. @rly #1229
• Scipy is no longer a required dependency. Users using the CSRMatrix data type should install scipy separately or with pip install "hdmf[sparse]". @rly #1140

Changed

• Added checks to ensure that group and dataset spec names and default names do not contain slashes. @bendichter #1219
• Updated copyright dates. @rly #1230
• Created optional dependency groups in pyproject.toml and update GitHub Actions workflows to use those instead of requirements files. @rly #1230
• Stopped using pinned dependencies in the docs and testing. These are not necessary for library testing, confuse new users and developers, and add maintenance burden. Current dependencies are stable enough that they need not be pinned and users can report the libraries they use. @rly #1230
• Stopped redundant testing using a conda environment. @rly #1230
• Adopted changelog format conventions: https://keepachangelog.com/en/1.1.0/ . @rly #1230

Added

• Added script to check Python version support for HDMF dependencies. @rly #1230

Fixed

• Fixed issue with DynamicTable.add_column not allowing subclasses of DynamicTableRegion or EnumData. @rly #1091