[Neuroimaging] [ANN] Nibabel 2.5.1

Christopher Markiewicz markiewicz at stanford.edu
Tue Sep 24 17:06:12 EDT 2019

Hi all,

Nibabel 2.5.1 was released yesterday. These fixes deal primarily with edge cases, and no critical issues that demand immediate upgrade.

As a reminder, the 2.5.x series will have extended bug-fix-only support for Python 2.7 (and probably 3.4, in passing) through the end of 2020, while Nibabel 3+ will require Python 3.5+. A Nibabel 3.0 release candidate is scheduled for November, with a 3.0 release will target December or early January.

For more details or to weigh in on our schedule, see the following issues:

 - Release schedule: https://github.com/nipy/nibabel/issues/734
 - Python 2 support: https://github.com/nipy/nibabel/issues/735

Thanks to new contributor Henry Braun, and to everybody who contributed their time with bug reports, reviews or code.

Please cite this version using the Zenodo archive: https://doi.org/10.5281/zenodo.3458246

The full changelog follows.


Bug fix release for the 2.5.x series.

Most work on NiBabel so far has been by Matthew Brett (MB), Chris Markiewicz (CM), Michael Hanke (MH), Marc-Alexandre Côté (MC), Ben Cipollini (BC), Paul McCarthy (PM), Chris Cheng (CC), Yaroslav Halchenko (YOH), Satra Ghosh (SG), Eric Larson (EL), Demian Wassermann, and Stephan Gerhard.

References like "pr/298" refer to github pull request numbers.

2.5.1 (Monday 23 September 2019)

The 2.5.x series is the last with support for either Python 2 or Python 3.4. Extended support for this series 2.5 will last through December 2020.

* Ignore endianness in ``nib-diff`` if values match (pr/799) (YOH, reviewed by CM)

Bug fixes
* Correctly handle Philips DICOMs w/ derived volume (pr/795) (Mathias Goncalves, reviewed by CM)
* Raise CSA tag limit to 1000, parametrize for future relaxing (pr/798, backported to 2.5.x in pr/800) (Henry Braun, reviewed by CM, MB)
* Coerce data types to match NIfTI intent codes when writing GIFTI data arrays (pr/806) (CM, reported by Tom Holroyd)

* Require h5py 2.10 for Windows + Python < 3.6 to resolve unexpected dtypes in Minc2 data (pr/804) (CM, reviewed by YOH)

API changes and deprecations
* Deprecate ``nicom.dicomwrappers.Wrapper.get_affine()`` in favor of ``affine`` property; final removal in nibabel 4.0 (pr/796) (YOH, reviewed by CM)


Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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