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Releases: hdmf-dev/hdmf

2.5.8

16 Jun 22:21
2.5.8
929ec93
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Minor improvements

  • Improve Sphinx documentation. @rly (#627)

Bug fix

  • Fix error with representing an indexed table column when the VectorIndex dtype precision is upgraded more
    than one step, e.g., uint8 to uint32. This can happen when, for example, a single add_row call is used to
    add more than 65535 elements to an empty indexed column. @rly (#631)

2.5.7

05 Jun 06:11
2.5.7
1b084d5
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Bug fix

  • Fix generation of extension classes that extend MultiContainerInterface and use a custom _fieldsname. @rly (#626)

2.5.6

24 May 18:16
2.5.6
f983e80
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Bug fix

  • Raise minimum version of pandas from 0.23 to 1.0.5 to be compatible with numpy 1.20. @rly (#618)
  • Update documentation and update structure of requirements files. @rly (#619)

2.5.5

18 May 00:14
2.5.5
db51148
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Bug fix

  • Fix incompatibility issue with downstream github-release tool used to deploy releases to GitHub. @rly (#614)

2.5.4

18 May 00:16
@rly rly
2.5.4
b5974dd
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Bug fix

  • Fix incompatibility issue with downstream github-release tool used to deploy releases to GitHub. @rly (#607)
  • Fix issue where dependencies of included types were not being loaded in namespaces / extensions. @rly (#613)

2.5.3

12 May 23:02
2.5.3
6be6692
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Bug fix

  • Fix issue where tables with multi-indexed columns defined using __columns__ did not have attributes properly set.
    @rly (#605)

2.5.2

11 May 18:22
2.5.2
8493f96
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Bug fixes

  • Add explicit setuptools requirement. @hrnciar (#596)
  • Fix issue with generated custom classes that use a custom fields name (e.g., PyNWB uses __nwbfields__ instead
    of __fields__). @rly (#598)
  • Fix issue with Sphinx Gallery. @rly (#601)

2.5.1

23 Apr 16:20
2.5.1
73d9336
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Bug fix

  • Revert breaking change in TypeMap.get_container_cls. While this function is returned to its original behavior,
    it will be modified at the next major release. Please use the new TypeMap.get_dt_container_cls instead. @rly (#590)

2.5.0

22 Apr 22:01
2.5.0
1365149
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New features

  • DynamicTable can be automatically generated using get_class. Now the HDMF API can read files with extensions
    that contain a DynamicTable without needing to import the extension first. @rly and @bendichter (#536)
  • Add HDF5IO.get_namespaces(path=path, file=file) method which returns a dict of namespace name mapped to the
    namespace version (the largest one if there are multiple) for each namespace cached in the given HDF5 file.
    @rly (#527)
  • Use HDMF common schema 1.5.0.
    • Add experimental namespace to HDMF common schema. New data types should go in the experimental namespace
      (hdmf-experimental) prior to being added to the core (hdmf-common) namespace. The purpose of this is to provide
      a place to test new data types that may break backward compatibility as they are refined. @ajtritt (#545)
    • ExternalResources was changed to support storing both names and URIs for resources. @mavaylon (#517, #548)
    • The VocabData data type was replaced by EnumData to provide more flexible support for data from a set of
      fixed values.
    • Added AlignedDynamicTable, which defines a DynamicTable that supports storing a collection of sub-tables.
      Each sub-table is itself a DynamicTable that is aligned with the main table by row index. Each sub-table
      defines a sub-category in the main table effectively creating a table with sub-headings to organize columns.
    • See https://hdmf-common-schema.readthedocs.io/en/latest/format_release_notes.html#april-19-2021 for more
      details.
  • Add EnumData type for storing data that comes from a fixed set of values. This replaces VocabData i.e.
    VocabData has been removed. VocabData stored vocabulary elements in an attribute, which has a size limit.
    EnumData now stores elements in a separate dataset, referenced by an attribute stored on the EnumData dataset.
    @ajtritt (#537)
  • Add AlignedDynamicTable type which defines a DynamicTable that supports storing a collection of subtables.
    Each sub-table is itself a DynamicTable that is aligned with the main table by row index. Each subtable
    defines a sub-category in the main table effectively creating a table with sub-headings to organize columns.
    @oruebel (#551)
  • Add tutoral for new AlignedDynamicTable type. @oruebel (#571)
  • Equality check for DynamicTable now also checks that the name and description of the table are the same. @rly (#566)

Internal improvements

  • Update CI and copyright year. @rly (#523, #524)
  • Refactor class generation code. @rly (#533, #535)
  • Equality check for DynamicTable returns False if the other object is a DynamicTable instead of raising an error.
    @rly (#566)
  • Update ruamel.yaml usage to new API. @rly (#587)
  • Remove use of ColoredTestRunner for more readable verbose test output. @rly (#588)

Bug fixes

  • Fix CI testing on Python 3.9. @rly (#523)
  • Fix certain edge cases where GroupValidator would not validate all of the child groups or datasets
    attached to a GroupBuilder. @dsleiter (#526)
  • Fix bug for generating classes from link specs and ignored 'help' fields. @rly (#535)
  • Various fixes for dynamic class generation. @rly (#561)
  • Fix generation of classes that extends both MultiContainerInterface and another class that extends
    MultiContainerInterface. @rly (#567)
  • Fix make clean command for docs to clean up sphinx-gallery tutorial files. @oruebel (#571)
  • Make sure we cannot set AlignedDynamicTable as a category on an AlignedDynamicTable. @oruebel (#571)
  • Fix included data type resolution between HDMF and custom classes that customize the data_type_inc key. @rly (#503)
  • Fix classification of attributes as new/overridden. @rly (#503)

2.4.0

23 Feb 17:25
2.4.0
aff2e1d
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HDMF 2.4.0 (February 23, 2021)

New features

  • GroupValidator now checks if child groups, datasets, and links have the correct quantity of elements and returns
    an IncorrectQuantityError for each mismatch. @dsleiter (#500)

Internal improvements

Bug fixes

  • Allow np.bool_ as a valid bool dtype when validating. @dsleiter (#505)
  • Fix building of Data objects where the spec has no dtype and the Data object value is a DataIO wrapping an
    AbstractDataChunkIterator. @rly (#512)
  • Fix TypeError when validating a group with an illegally-linked child.
    @dsleiter (#515)
  • Fix DynamicTable.get for compound type columns. @rly (#518)
  • Fix and removed error "Field 'x' cannot be defined in y." when opening files with some extensions. @rly
    (#519)