chore(deps): update dependency nibabel to v5.4.2

[renovate]

This PR contains the following updates:

Package	Change	Age	Confidence
nibabel	5.0.0 → 5.4.2

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Release Notes

nipy/nibabel (nibabel)

v5.4.2

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===============================

Bug-fix release in the 5.4.x series.

This release fixes an issue with automated deployment to PyPI.

v5.4.0

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===========================

New feature release in the 5.4.x series.

This release requires a minimum Python of 3.10 and NumPy 1.25, and has been
tested up to Python 3.14 and NumPy 2.4.

New features

• Add mode parameter to :func:nibabel.processing.conform (pr/1396) (Clorindo Notte,
  reviewed by CM)

Enhancements

• Label image axes consistently in cases of extreme obliquity (pr/1450) (Leonardo Ayala,
  reviewed by CM)
• Use :mod:compression.zstd or backports.zstd in preference to pyzstd
  (pr/1444) (PM, reviewed by CM)
• Support PAR/REC files generated by Philips R11 consoles (pr/1430)
  (Alex Daniel, reviewed by CM)
• Add stub file for top-level nibabel module, improving support in code analyzers
  (pr/1436) (Jon Cluce, reviewed by CM)
• Use informative error message for missing file attribute in
  :class:~nibabel.streamlines.tck.TCKFile header (pr/1422)
  (Jon Haitz Legarreta Gorroño, reviewed by CM)
• Support ushort datatypes in MGH/MGZ files (pr/1415) (Benjamin Thyreau,
  reviewed by CM)
• Simplify :func:nibabel.cmdline.utils.table2string implementation (pr/1403) (CM)

Bug fixes

• Fix type-checking errors in :func:nibabel.volumeutils.rec2dict (pr/1424)
  (Jon Haitz Legarreta Gorroño, reviewed by CM)
• Adapt to functools.partial becoming a method descriptor in Python 3.14
  (pr/1391) (Benjamin Beasley, reviewed by CM)

Maintenance

• Split pre-release tests into cron job (pr/1466) (CM, reviewed by Remi Gau)
• Adapt to numpy 2.5 deprecation of setting :attr:~numpy.ndarray.shape attributes
  (pr/1452) (CM)
• Document and test support for :class:os.PathLike objects in streamlines APIs
  (pr/1435) (Jon Haitz Legarreta Gorroño, reviewed by CM)
• Drop CI tests on Intel Macs (pr/1439) (Dimitri Papadopoulos, reviewed by CM)
• Update license metadata using SPDX expression (pr/1425) (Dimitri Papadopoulos, reviewed by CM)
• Test on Python 3.14, us locking tox runners (pr/1431, pr/1447) (CM)
• Update style checker (ruff) and address new complaints (pr/1405, pr/1406, pr/1433) (CM,
  Dimitri Papadopoulos)
• Add broad testing for Python 3.13 (pr/1381) (CM)
• Build docs on PRs with ReadTheDocs to permit quick inspection. (pr/1398) (CM)

API changes and deprecations

• Drop support for Python 3.9, Numpy < 1.25 (pr/1448) (CM)

v5.3.3

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==============================

Bug-fix release in the 5.3.x series.

Bug fixes

• Fix frame order for single-frame DICOM files (pr/1387) (Brendan Moloney, reviewed by CM)
• Replace :class:dict literal with :class:set in test. (pr/1382) (CM)

v5.3.2

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=================================

Bug-fix release in the 5.3.x series.

Bug fixes

• Restore MRS extension type to Nifti1Extension to maintain backwards compatibility.
  (pr/1380) (CM)

v5.3.1

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===============================

Bug-fix release in the 5.3.x series.

Bug fixes

• Restore access to private attribute Nifti1Extension._content to unbreak subclasses
  that did not use public accessor methods. (pr/1378) (CM, reviewed by Basile Pinsard)
• Remove test order dependency in test_api_validators (pr/1377) (CM)

v5.3.0

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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/methods 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)

v5.2.1

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===============================

Bug-fix release in the 5.2.x series.

Enhancements

• Support "flat" ASCII-encoded GIFTI DataArrays (pr/1298) (PM, reviewed by CM)

Bug fixes

• Tolerate missing git when reporting version info (pr/1286) (CM, reviewed by
  Yuri Victorovich)
• Handle Siemens XA30 derived DWI DICOMs (pr/1296) (CM, reviewed by YOH and
  Mathias Goncalves)

Maintenance

• Add tool for generating GitHub-friendly release notes (pr/1284) (CM)
• Accommodate pytest 8 changes (pr/1297) (CM)

v5.2.0

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===============================

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)

v5.1.0

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===========================

New feature release in the 5.1.x series.

Enhancements

• Make :mod:nibabel.imagestats available with import nibabel (pr/1208)
  (Fabian Perez, reviewed by CM)
• Use symmetric threshold for identifying unit quaternions on qform
  calculations (pr/1182) (CM, reviewed by MB)
• Type annotations for :mod:~nibabel.loadsave (pr/1213) and
  :class:~nibabel.spatialimages.SpatialImage APIs (pr/1179),
  :mod:~nibabel.deprecated, :mod:~nibabel.deprecator,
  :mod:~nibabel.onetime and :mod:~nibabel.optpkg modules (pr/1188),
  :mod:~nibabel.volumeutils (pr/1189), :mod:~nibabel.filename_parser and
  :mod:~nibabel.openers (pr/1197) (CM, reviewed by Zvi Baratz)

Bug fixes

• Require explicit overrides to write GIFTI files that contain data arrays
  with data types not permitted by the GIFTI standard (pr/1199) (CM, reviewed
  by Alexis Thual)

Maintenance

• Move compression detection logic into a private nibabel._compression
  module, resolving unexpected errors from pyzstd. (pr/1212) (CM)
• Improved consistency of docstring formatting (pr/1200) (Zvi Baratz, reviewed
  by CM)
• Modernized README text (pr/1195) (Zvi Baratz, reviewed by CM)
• Updated README badges to include package distributions (pr/1192) (Horea
  Christian, reviewed by CM)
• Removed all dependencies on distutils and setuptools (pr/1190) (CM,
  reviewed by Zvi Baratz)
• Add a _version.pyi stub to allow mypy_ to run without building nibabel
  (pr/1210) (CM)

.. _mypy: https://mypy.readthedocs.io/

v5.0.1

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===============================

Bug-fix release in the 5.0.x series.

Bug fixes

• Support ragged voxel arrays in
  :class:~nibabel.cifti2.cifti2_axes.ParcelsAxis (pr/1194) (Michiel Cottaar,
  reviewed by CM)
• Return to cwd on exception in :class:~nibabel.tmpdirs.InTemporaryDirectory
  (pr/1184) (CM)

Maintenance

• Add py.typed to module root to enable use of types in downstream
  projects (CM, reviewed by Fernando Pérez-Garcia)
• Cache git-archive separately from Python packages in GitHub Actions
  (pr/1186) (CM, reviewed by Zvi Baratz)

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