Hdmf

Bug fix
- 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)

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)

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)

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
- Update CI. rly (432)
- Added driver option for ros3. bendichter (506)

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)

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)

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)