[Neuroimaging] ANN: NiBabel 3.1.0 and 2.5.2

Christopher Markiewicz markiewicz at stanford.edu
Mon Apr 20 09:25:08 EDT 2020

Hi all,

NiBabel 3.1.0 is out. This release completes a conversion from nose to pytest, ensuring Python 3.9 compatibility when that comes out later this year. Additionally, we added some conformation tools as both a Python function and a new nib-conform command-line interface.

NiBabel 2.5.2 was released about two weeks ago, an update in the 2.5.x series that retains support for Python 2.7 and 3.4. A couple fixes for SyntaxWarnings were back-ported, but the main change was setting maximum compatible versions for numpy and scipy to 1.16.x and 1.2.x, which are respectively the final series with Python 2 support in those projects. Python 3 users who want to use newer features of numpy and scipy are encouraged to upgrade to NiBabel 3.

Particular thanks to the team that sprinted on tests in February (Dorota Jarecka, Roberto Guidotti, Anibal Solon, and Or Duek). And thanks as usual to everyone who's contributed, submitted bug reports or fixes.

Please cite NiBabel 2.5.2 using the Zenodo archive: https://doi.org/10.5281/zenodo.3745545
Please cite NiBabel 3.1.0 using the Zenodo archive: https://doi.org/10.5281/zenodo.3757992

I hope everybody is staying well.

Full changelog follows.


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, Stephan Gerhard and Ross Markello (RM).

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

3.1.0 (Monday 20 April 2020)

New feature release in the 3.1.x series.

New features
* Conformation function (``processing.conform``) and CLI tool
  (``nib-conform``) to apply shape, orientation and zooms (pr/853) (Jakub
  Kaczmarzyk, reviewed by CM, YOH)
* Affine rescaling function (``affines.rescale_affine``) to update
  dimensions and voxel sizes (pr/853) (CM, reviewed by Jakub Kaczmarzyk)

Bug fixes
* Delay import of h5py until neded (pr/889) (YOH, reviewed by CM)

* Fix typo in documentation (pr/893) (Zvi Baratz, reviewed by CM)
* Tests converted from nose to pytest (pr/865 + many sub-PRs)
  (Dorota Jarecka, Krzyzstof Gorgolewski, Roberto Guidotti, Anibal Solon,
  Or Duek, CM)

API changes and deprecations
* ``kw_only_meth``/``kw_only_func`` decorators are deprecated (pr/848)
  (RM, reviewed by CM)

2.5.2 (Wednesday 8 April 2020)

Bug-fix release in the 2.5.x series. This is an extended-support series,
providing bug fixes for Python 2.7 and 3.4.

This and all future releases in the 2.5.x series will be incompatible with
Python 3.9. The last compatible series of numpy and scipy are 1.16.x and
1.2.x, respectively.

If you are able to upgrade to Python 3, it is recommended to upgrade to
NiBabel 3.

Bug fixes
* Change strings with invalid escapes to raw strings (pr/827) (EL, reviewed
  by CM)
* Re-import externals/netcdf.py from scipy to resolve numpy deprecation
  (pr/821) (CM)

* Set maximum numpy to 1.16.x, maximum scipy to 1.2.x (pr/901) (CM)


Chris Markiewicz

Center for Reproducible Neuroscience

Stanford University
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