Skip to content

2.3.0
Compare
Choose a tag to compare
@hdmf-bot hdmf-bot released this 09 Dec 00:54
· 414 commits to dev since this release
2.3.0
This tag was signed with the committer’s verified signature.
rly Ryan Ly
GPG key ID: F7D49F824A175808
Verified
Learn about vigilant mode.
c403feb
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

New features

  • Add methods for automatic creation of MultiContainerInterface classes. @bendichter (#420, #425)
  • Add ability to specify a custom class for new columns to a DynamicTable that are not VectorData,
    DynamicTableRegion, or VocabData using DynamicTable.__columns__ or DynamicTable.add_column(...). @rly (#436)
  • Add support for creating and specifying multi-index columns in a DynamicTable using add_column(...).
    @bendichter, @rly (#430)
  • Add capability to add a row to a column after IO. @bendichter (#426)
  • Add method AbstractContainer.get_fields_conf. @rly (#441)
  • Add functionality for storing external resource references. @ajtritt (#442)
  • Add method hdmf.utils.get_docval_macro to get a tuple of the current values for a docval_macro, e.g., 'array_data'
    and 'scalar_data'. @rly (#446)
  • Add SimpleMultiContainer, a data_type for storing a Container and Data objects together. @ajtritt (#449)
  • Support pathlib.Path paths in HDMFIO.__init__, HDF5IO.__init__, and HDF5IO.load_namespaces. @dsleiter (#450)
  • Use hdmf-common-schema 1.2.1. See https://hdmf-common-schema.readthedocs.io/en/latest/format_release_notes.html for details.
  • Block usage of h5py 3+. h5py>=2.9, <3 is supported. @rly (#461)
  • Block usage of numpy>=1.19.4 due to a known issue with numpy on some Windows 10 systems. numpy>1.16, <1.19.4 is supported.
    @rly (#461)
  • Add check for correct quantity during the build process in ObjectMapper. @rly (#463, #492)
  • Allow passing GroupSpec and DatasetSpec objects for the 'target_type' argument of LinkSpec.__init__(...).
    @rly (#468)
  • Use hdmf-common-schema 1.3.0. @rly, @ajtritt (#486)
    • Changes from hdmf-common-schema 1.2.0:
      • Add data type ExternalResources for storing ontology information / external resource references. NOTE:
        this data type is in beta testing and is subject to change in a later version.
      • Fix missing data_type_inc and use dtype uint for CSRMatrix. It now has data_type_inc: Container.
      • Add hdmf-schema-language comment at the top of each yaml file.
      • Add SimpleMultiContainer, a Container for storing other Container and Data objects together.

Internal improvements

  • Drop support for Python 3.5. @ajtritt (#459)
  • Improve warning about cached namespace when loading namespaces from file. @rly (#422)
  • Refactor HDF5IO.write_dataset to be more readable. @rly (#428)
  • Fix bug in slicing tables with DynamicTableRegions. @ajtritt (#449)
  • Add testing for Python 3.9 and using pre-release packages. @ajtritt, @rly (#459, #472)
  • Improve contributing guide. @rly (#474)
  • Update CI. @rly, @dsleiter (#481, #493, #497)
  • Add citation information to documentation and support for duecredit tool. @rly (#477, #488)
  • Add type checking and conversion in CSRMatrix. @rly (#485)
  • Clean up unreachable validator code. @rly (#483)
  • Reformat imports. @bendichter (#469)
  • Remove unused or refactored internal builder functions GroupBuilder.add_group, GroupBuilder.add_dataset,
    GroupBuilder.add_link, GroupBuilder.set_builder, BaseBuilder.deep_update, GroupBuilder.deep_update,
    DatasetBuilder.deep_update. Make BaseBuilder not instantiable and refactor builder code. @rly (#452)

Bug fixes

  • Fix development package dependency issues. @rly (#431)
  • Fix handling of empty lists against a spec with text/bytes dtype. @rly (#434)
  • Fix handling of 1-element datasets with compound dtype against a scalar spec with text/bytes dtype. @rly (#438)
  • Fix convert dtype when writing numpy array from h5py.Dataset. @rly (#427)
  • Fix inheritance when non-AbstractContainer is base class. @rly (#444)
  • Fix use of hdmf.testing.assertContainerEqual(...) for Data objects. @rly (#445)
  • Add missing support for data conversion against spec dtypes "bytes" and "short". @rly (#456)
  • Clarify the validator error message when a named data type is missing. @dsleiter (#478)
  • Update documentation on validation to indicate that the example command is not implemented @dsleiter (#482)
  • Fix generated docval for classes with a LinkSpec. @rly (#487)
  • Fix access of DynamicTableRegion of a DynamicTable with column of references. @rly (#491)
  • Fix handling of __fields__ for Data subclasses. @rly (#441)
  • Fix DynamicTableRegion having duplicate fields conf 'table'. @rly (#441)
  • Fix inefficient and sometimes inaccurate build process. @rly (#451)
  • Fix garbage collection issue in Python 3.9. @rly (#496)
Assets 4
Loading