Update dependency nibabel to v5.3.0

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
nibabel	==5.2.1 -> ==5.3.0

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Release Notes

nipy/nibabel (nibabel)

v5.3.0

Compare Source

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This release primarily adds support for Python 3.13 and Numpy 2.0.

NiBabel 6.0 will drop support for Numpy 1.x.

New features

• Update NIfTI extension protocol to include .content : bytes, .text : str and .json : dict
  properties for accessing extension contents. Exceptions will be raised on .text and .json if
  conversion fails. (pr/1336) (CM)

Enhancements

• Ability to read data from many multiframe DICOM files that previously generated errors (pr/1340)
  (Brendan Moloney, reviewed by CM)
• nib-nifti-dx now supports NIfTI-2 files with a --nifti2 flag (pr/1323) (CM)
• Update :mod:nibabel.streamlines.tractogram to support ragged arrays. (pr/1291)
  (Serge Koudoro, reviewed by CM)
• Filter numpy UserWarning on np.finfo(np.longdouble). This can occur on
  Windows systems, but it's done in the context of checking for the problem that
  is being warned against, so there's no need to be noisy. (pr/1310)
  (Joshua Newton, reviewed by CM)
• Improve error message for for dicomwrapper errors in shape calculation (pr/1302)
  (YOH, reviewed by CM)
• Support "flat" ASCII-encoded GIFTI DataArrays (pr/1298) (PM, reviewed by CM)

Bug fixes

• Fix location initialization/update in OrthoSlicer3D for permuted axes (pr/1319, pr/1350)
  (Guillaume Becq, reviewed by CM)
• Fix DICOM scaling, making frame filtering explicit (pr/1342) (Brendan Moloney, reviewed by CM)
• Fixed multiframe DICOM issue where data could be flipped along slice dimension relative to the
  affine (pr/1340) (Brendan Moloney, reviewed by CM)
• Fixed multiframe DICOM issue where image_position and the translation component in the
  affine could be incorrect (pr/1340) (Brendan Moloney, reviewed by CM)

Maintenance

• Numpy 2.0 compatibility and addressing deprecations in numpy API
  (pr/1304, pr/1330, pr/1331, pr/1334, pr/1337) (Jon Haitz Legarreta Gorroño, CM)
• Python 3.13 compatibility (pr/1315) (Sandro from the Fedora Project, reviewed by CM)
• Testing on Python 3.13 with free-threading (pr/1339) (CM)
• Testing on ARM64 Mac OS runners (pr/1320) (CM)
• Proactively address deprecations in coming Python versions (pr/1329, pr/1332, pr/1333)
  (Jon Haitz Legarreta Gorroño, reviewed by CM)
• Replace nose-era setup() and teardown() functions with pytest equivalents
  (pr/1325) (Sandro from the Fedora Project, reviewed by Étienne Mollier and CM)
• Transitioned from blue/isort/flake8 to ruff <https://docs.astral.sh/ruff/>__. (pr/1289)
  (Dimitri Papadopoulos, reviewed by CM)
• Vetted and added various rules to the ruff configuration for auto-formatting and style
  guide enforcement. (pr/1321, pr/1351, pr/1352, pr/1353, pr/1354, pr/1355, pr/1357, pr/1358,
  pr/1359, pr/1360, pr/1361, pr/1362, pr/1363, pr/1364, pr/1368, pr/1369)
  (Dimitri Papadopoulos, reviewed by CM)
• Fixing typos when found. (pr/1313, pr/1370) (MB, Dimitri Papadopoulos)
• Applied Repo-Review suggestions (Dimitri Papadopoulos, reviewed by CM)

API changes and deprecations

• Raise :class:~nibabel.spatialimages.HeaderDataError from
  :func:~nibabel.nifti1.Nifti1Header.set_qform if the affine fails to decompose.
  This would previously result in :class:numpy.linalg.LinAlgError. (pr/1227) (CM)
• The :func:nibabel.onetime.auto_attr module can be replaced by :func:functools.cached_property
  in all supported versions of Python. This alias may be removed in future versions. (pr/1341) (CM)
• Removed the deprecated nisext (setuptools extensions) package. (pr/1290) (CM, reviewed by MB)

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