Latest (updated on 2025-11-25 01:11 UTC)

[pre-commit.ci] pre-commit autoupdate (#1344)

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4.1.2

Fixed

• Fixed bug when converting string datasets that are Zarr arrays. @oruebel @rly #1171
• Fixed unclear shape validation error message. @bendichter @rly #787
• Fixed testing of sphinx gallery examples with optional dependencies. @rly #1343

4.1.1

Fixed

• Fixed copying of TypeMap and TypeConfigurator. Previously, the same global TypeConfigurator instance was used in all copies of a TypeMap. @rly #1302
• Fixed get_data_shape to use Data.data.shape instead of Data.shape, which may be overridden by subclasses. @rly #1311
• Fixed HTML representation of datasets when reading from LINDI. @bendichter #1335
• Fixed bug where compound datatypes were disregarding custom data I/O options with the zarr backend. @pauladkisson #1297

Added

• Added a check for a compound datatype that is not defined in the schema or spec. This is currently not supported. @mavaylon1 #1276
• Added checks when loading a namespace for link specification conflicts between extension and core schemas. @stephprince #1309
• Added GitHub Actions workflow that tests compatibility with NWB extensions from the NWB extensions catalog. @rly #1319
• Added unit tests for hdmf.common module to improve code coverage. @stephprince #1330

Changed

• Changed error for attempting to overwrite an existing specification into a warning that any specification redefinitions will be ignored. @stephprince #1309
• Deprecated the experimental HERDManager.link_resources and HERDManager.link_external_resources and added the property HERDManager.external_resources to support downstream API function overloading. @mavaylon1, @rly #1292

4.1.0

hdmf 4.1.0

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

3.14.6

HDMF 3.14.6 (December 20, 2024)

Enhancements

• Added support for expandable datasets of references for untyped and compound data types. @stephprince #1188
• Improved html representation of data in Container objects. @h-mayorquin #1100
• Added error when using colon for Container name. A colon cannot be used as a group name when writing to Zarr on Windows. @stephprince #1202
• Adjusted testing for hdmf-zarr. @rly #1222

Bug fixes

• Fixed inaccurate error message when validating reference data types. @stephprince #1199
• Fixed incorrect dtype conversion of a StrDataset. @stephprince #1205

3.14.5

Enhancements

• Added support for overriding backend configurations of h5py.Dataset objects in Container.set_data_io. @pauladkisson #1172

Bug fixes

• Fixed bug in writing of string arrays to an HDF5 file that were read from an HDF5 file that was introduced in 3.14.4. @rly @stephprince
  #1189
• Fixed export of scalar datasets with a compound data type. @stephprince #1185
• Fixed mamba-related error in conda-based GitHub Actions. @rly #1194

3.14.4

hdmf 3.14.4

3.14.3

hdmf 3.14.3

3.14.2

hdmf 3.14.2