Skip to content

3.0.0
Compare
Choose a tag to compare
@rly rly released this 07 Jul 17:05
· 309 commits to dev since this release
3.0.0
This tag was signed with the committer’s verified signature.
rly Ryan Ly
GPG key ID: F7D49F824A175808
Learn about vigilant mode.
0953ab0
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Learn about vigilant mode.

New features

  • Add support for Python 3.9, drop support for Python 3.6. @rly (#620)
  • Add support for h5py 3. @ajtritt (#480)
    • h5py 3 introduced [breaking changes regarding how strings are handled]
      (https://docs.h5py.org/en/latest/whatsnew/3.0.html#breaking-changes-deprecations), specifically that
      variable-length UTF-8 strings in datasets are now read as bytes objects instead of str by default.
      To reduce the impact of this change on HDMF users, when HDMF reads a variable-length UTF-8 string
      dataset, instead of returning an h5py.Dataset that is read as bytes objects, HDMF will return a
      hdmf.utils.StrDataset object that extends h5py.Dataset and is read as str objects, which preserves
      previous behavior. For example, under HDMF 2.x, an HDF5 dataset d with data ['a', 'b'] is read as a
      h5py.Dataset object, and d[:] returns str objects. Under HDMF 3.x, the same dataset d is read
      as a hdmf.utils.StrDataset object and d[:] still returns str objects.
  • Add RRID to docs. @oruebel (#633)
  • Allow passing index=True to DynamicTable.to_dataframe() to support returning DynamicTableRegion columns
    as indices or Pandas DataFrame. @rly (#579)
  • Improve DynamicTable documentation. @rly (#639)
  • Updated external resources tutorial. @mavaylon (#611)

Breaking changes and deprecations

  • Previously, when using DynamicTable.__getitem__ or DynamicTable.get to access a selection of a
    DynamicTable containing a DynamicTableRegion, new columns with mangled names for the table data referred to
    by the DynamicTableRegion were added to the returned DataFrame. This did not work properly for ragged
    DynamicTableRegion, multiple levels of nesting, or multiple rows returned.
    Now, these methods will by default return columns of indices of the DynamicTableRegion. If index=False is
    passed to DynamicTable.get, then nested DataFrames will be returned, one DataFrame per row of the original
    resulting DataFrame. @rly (#579)

Minor improvements

  • Updated requirements and tests. @rly (#640)

Bug fixes

  • Update the validator to allow extensions to data types which only define data_type_inc. @dsleiter (#609)
  • Fix error when validating lazy-loaded datasets containing references. @dsleiter (#609)
  • Fix error when using DynamicTable.__getitem__ or DynamicTable.get when table has a ragged
    DynamicTableRegion. @rly (#579)
Assets 2
Loading