2.3.0

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)

2.2.0

New features

• Add ability to get list of tuples when indexing a DynamicTable. i.e. disable conversion to pandas.DataFrame.
  @ajtritt (#418)

Internal improvements

• Improve documentation and index out of bounds error message for DynamicTable. @rly (#419)

Bug fixes:

• Fix error when constructing DynamicTable with DataChunkIterators as columns. @ajtritt (#418)

2.1.0

New features

• Users can now use the MultiContainerInterface class to generate custom API classes that contain collections of
  containers of a specified type. @bendichter @rly (#399)
  • See the user guide
    https://hdmf.readthedocs.io/en/stable/tutorials/multicontainerinterface.html for more information.

Internal improvements

• Add ability to pass callable functions to run when adding or removing items from a LabelledDict.
  An error is now raised when using unsupported functionality in LabelledDict. @rly (#405)
• Raise a warning when building a container that is missing a required dataset. @rly (#413)

2.0.1

Internal improvements

• Add tests for writing table columns with DataIO data, e.g., chunked, compressed data. @rly (#402)
• Add CI to check for breakpoints and print statements. @rly (#403)

Bug fixes:

• Remove breakpoint. @rly (#403)
• Allow passing None for docval enum arguments with default value None. @rly (#409)
• If a file is written with an orphan container, e.g., a link to a container that is not written, then an
  OrphanContainerBuildError will be raised. This replaces the OrphanContainerWarning that was previously raised.
  @rly (#407)

2.0.0

New features

• Users can now call HDF5IO.export and HDF5IO.export_io to write data that was read from one source to a new HDF5
  file. Developers can implement the export method in classes that extend HDMFIO to customize the export
  functionality. See https://hdmf.readthedocs.io/en/latest/export.html for more details. @rly (#388)
• Users can use the new export functionality to read data from one source, modify the data in-memory, and then write the
  modified data to a new file. Modifications can include additions and removals. To facilitate removals,
  AbstractContainer contains a new _remove_child method and BuildManager contains a new purge_outdated method.
  @rly (#388)
• Users can now call Container.generate_new_id to generate new object IDs for the container and all of its children.
  @rly (#401)
• Use hdmf-common-schema 1.2.0. @ajtritt @rly (#397)
  • VectorIndex now extends VectorData instead of Index. This change allows VectorIndex to index other VectorIndex types.
  • The Index data type is now unused and has been removed.
  • Fix missing dtype for VectorIndex.
  • Add new VocabData data type.

Breaking changes

• Builder objects no longer have the written field which was used by HDF5IO to mark the object as written. This
  is replaced by HDF5IO.get_written. @rly (#381)
• HDMFIO.write and HDMFIO.write_builder no longer have the keyword argument exhaust_dcis. This remains present in
  HDF5IO.write and HDF5IO.write_builder. @rly (#388)
• The class method HDF5IO.copy_file is no longer supported and may be removed in a future version. Please use the
  HDF5IO.export method or h5py.File.copy method instead. @rly (#388)

1.6.4

Internal improvements

• Add ability to close open links. @rly (#383)

Bug fixes:

• Fix validation of empty arrays and scalar attributes. @rly (#377)
• Fix issue with constructing DynamicTable with empty array colnames. @rly (#379)
• Fix TestCase.assertContainerEqual passing wrong arguments. @rly (#385)
• Fix 'link_data' argument not being used when writing non-root level datasets. @rly (#384)
• Fix handling of ASCII numpy array. @rly (#387)
• Fix error when optional attribute reference is missing. @rly (#392)
• Improve testing for get_data_shape and fix issue with sets. @rly (#394)
• Fix inability to write references to HDF5 when the root builder is not named "root". @rly (#395)

1.6.3

Internal improvements

• Improve documentation of DynamicTable. @rly (#371)
• Add user guide / tutorial for DynamicTable. @rly (#372)
• Improve logging of build and write processes. @rly (#373)

Bug fixes:

• Fix adding of optional predefined columns to DynamicTable. @rly (#371)
• Use dtype from dataset data_type definition when extended spec lacks dtype. @rly (#364)

1.6.2

Internal improvements:

• Update MacOS in CI. @rly (#310)
• Raise more informative error when adding column to DynamicTable w/ used name. @rly (#307)
• Refactor _init_class_columns for use by DynamicTable subclasses. @rly (#323)
• Add/fix docstrings for DynamicTable. @oruebel, @rly (#304, #353)
• Make docval-decorated functions more debuggable in pdb. @rly (#308)
• Change dtype conversion warning to include path to type. @rly (#311)
• Refactor DynamicTable.add_column to raise error when name is an optional column. @rly (#305)
• Improve unsupported filter error message. @bendichter (#329)
• Add functionality to validate a yaml file against a json schema file. @bendichter (#332)
• Update requirements-min.txt for yaml validator. @bendichter (#333)
• Add allowed value / enum validation in docval. @rly (#335)
• Add logging of build and hdf5 write process. @rly (#336, #349)
• Allow loading namespaces from h5py.File object not backed by file. @rly (#348)
• Add CHANGELOG.md. @rly (#352)
• Fix codecov reports. @rly (#362)
• Make getargs raise an error if the argument name is not found. @rly (#365)
• Improve get_class and docval support for uint. @rly (#361)

Bug fixes:

• Register new child types before new parent type for dynamic class generation. @rly (#322)
• Raise warning not error when adding column with existing attr name. @rly (#324)
• Add __version__. @rly (#345)
• Only write a specific namespace version if it does not exist. @ajtritt (#346)
• Fix documentation formatting for DynamicTable. @rly (#353)

1.6.1

Minor enhancements:

• Allow docval to warn about use of positional arguments. @rly (#293)
• Improve efficiency of writing chunks with DataChunkIterator and HDF5. @d-sot, @oruebel (#295)

Bug fixes:

• Flake8 style fixes. @oruebel (#291)
• Handle missing namespace version. @rly (#292)
• Do not raise error when a numeric type with a higher precision is provided for a spec with a lower precision and different base type. Raise a warning when the base type of a given value is converted to the specified base type, regardless of precision level. Add missing support for boolean conversions. @rly (#298, #299)
• Add forgotten validation of links. @t-b, @ajtritt (#286)
• Improve msg for "can't change contianer_source" error. @rly (#302)
• Fix setup.py development status. @rly (#303)
• Refactor missing namespace version handling. @rly, @ajtritt (#297)
• Add print function for DynamicTableRegion. @oruebel, @rly (#290)
• Fix writing of refined RefSpec attribute. @oruebel, @rly (#301)

1.6.0

Minor enhancements:

• Allow extending/overwriting attributes on dataset builders. @rly, @ajtritt (#279)
• Allow ASCII data where UTF8 is specified. @rly (#282)
• Add function to convert DynamicTableRegion to a pandas dataframe. @oruebel (#239)
• Add "mode" property to HDF5IO. @t-b (#280)

Bug fixes:

• Fix readthedocs config to include all submodules. @rly (#277)
• Fix test runner double printing in non-verbose mode. @rly (#278)