[Neuroimaging] [ANN] NiBabel 5.2.0

[Christopher Markiewicz]

Hi all,

We've released NiBabel 5.2.0. This release is largely a collection of small quality-of-life improvements. The main new feature is a pair of pointset data structures intended to unify representations needed for resampling data and representing surface meshes. These are experimental, and we may update the API on a faster time scale than usual.

This release also has provisional support for the still-in-development NumPy 2.0, and we are testing their nightly builds. It's reasonable to expect them to continue breaking our assumptions, so please test off of our development branch if you're going to test with their nightly builds. Thanks to Mathieu Scheltienne and Eric Larson for their work in resolving the issues found so far.

The next release series will be 6.0, which I anticipate in March 2024. As usual, major releases may see DeprecationWarnings turn into ExpiredDeprecationErrors. We maintain a removal schedule in https://github.com/nipy/nibabel/blob/master/nibabel/tests/test_removalschedule.py with all deprecations and when they will be entirely removed from the package. Where Python allows, we raise ExpiredDeprecationErrors for one major version before final removal, so look at both 6.0 and 7.0 removals if you want to get ahead of this.

Many thanks to all contributors for using NiBabel, reporting bugs, updating documentation and contributing code. This release, we included commits from four new contributors: Blake Dewey, Peter Suter, Reinder Vos de Wael and Mathieu Scheltienne.

If you use NiBabel, please cite the Zenodo archive:  https://doi.org/10.5281/zenodo.10363247

The full changelog follows this message, and can also be found at the following links:

* https://nipy.org/nibabel/changelog.html#monday-11-december-2023
* https://github.com/nipy/nibabel/releases/tag/5.2.0

Best,
Chris

----

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.

5.2.0 (Monday 11 December 2023)
===============================

New feature release in the 5.2.x series.

This release requires a minimum Python of 3.8 and NumPy 1.20, and has been
tested up to Python 3.12 and NumPy 1.26.

New features
------------
* Add generic :class:`~nibabel.pointset.Pointset` and regularly spaced
  :class:`~nibabel.pointset.Grid` data structures in preparation for coordinate  
  transformation and resampling (pr/1251) (CM, reviewed by Oscar Esteban)   
  
Enhancements
------------
* Add :meth:`~nibabel.arrayproxy.ArrayProxy.copy` method to
  :class:`~nibabel.arrayproxy.ArrayProxy` (pr/1255) (CM, reviewed by Paul McCarthy)
* Permit :meth:`~nibabel.xmlutils.XmlSerializable.to_xml` methods to pass keyword
  arguments to :func:`xml.etree.ElementTree.tostring` (pr/1258)    
  (CM)
* Allow user expansion (e.g., ``~/...``) in strings passed to functions that
  accept paths (pr/1260) (Reinder Vos de Wael, reviewed by CM)              
* Expand CIFTI-2 brain structures to permit synonyms (pr/1256) (CM, reviewed
  by Mathias Goncalves)
* Annotate :class:`~nibabel.spatialimages.SpatialImage` as accepting
  ``affine=None`` argument (pr/1253) (Blake Dewey, reviewed by CM)
* Warn on invalid MINC2 spacing declarations, treat as missing (pr/1237) 
  (Peter Suter, reviewed by CM)                                           
* Refactor :func:`~nibabel.nicom.utils.find_private_section` for improved    
  readability and maintainability (pr/1228) (MB, reviewed by CM)

Bug fixes
---------
* Resolve test failure related to randomly generated invalid case (pr/1221) (CM)
  
Documentation
-------------
* Remove references to NiPy data packages from documentation (pr/1275)
  (Dimitri Papadopoulos, reviewed by CM, MB)

Maintenance
-----------
* Quality of life improvements for CI, including color output and OIDC publishing
  (pr/1282) (CM)
* Patch for NumPy 2.0 pre-release compatibility (pr/1250) (Mathieu
  Scheltienne and EL, reviewed by CM)
* Add spellchecking to tox, CI and pre-commit (pr/1266) (CM)
* Add py312-dev-x64 environment to Tox to test NumPy 2.0 pre-release
  compatibility (pr/1267) (CM, reviewed by EL)
* Resurrect tox configuration to cover development workflows and CI checks
  (pr/1262) (CM)
* Updates for Python 3.12 support (pr/1247, pr/1261, pr/1273) (CM)
* Remove uses of deprecated ``numpy.compat.py3k`` module (pr/1243) (Eric
  Larson, reviewed by CM)
* Various fixes for typos and style issues detected by Codespell, pyupgrade and
  refurb (pr/1263, pr/1269, pr/1270, pr/1271, pr/1276) (Dimitri Papadopoulos,
  reviewed by CM)
* Use stable argsorts in PARREC tests to ensure consistent behavior on systems
  with AVX512 SIMD instructions and numpy 1.25 (pr/1234) (CM)
* Resolve CodeCov submission failures (pr/1224) (CM)
* Link to logo with full URL to avoid broken links in PyPI (pr/1218) (CM,
  reviewed by Zvi Baratz)

API changes and deprecations
----------------------------
* The :mod:`nibabel.pydicom_compat` module is deprecated and will be removed
  in NiBabel 7.0. (pr/1280)
* The :func:`~nibabel.casting.int_to_float` and :func:`~nibabel.casting.as_int`
  functions are no longer needed to work around NumPy deficiencies and have been
  deprecated (pr/1272) (CM, reviewed by EL)