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PennLINC / aslprep

Preprocessing of arterial spin labeling (ASL) data
https://aslprep.readthedocs.io
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Update nibabel requirement from <=5.2.1 to <=5.3.0 #448

Closed dependabot[bot] closed 1 month ago

dependabot[bot] commented 1 month ago

Updates the requirements on nibabel to permit the latest version.

Release notes

Sourced from nibabel's releases.

5.3.0

DOI

Release notes

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. (#1336) (CM)

Enhancements

  • Ability to read data from many multiframe DICOM files that previously generated errors (#1340) (Brendan Moloney, reviewed by CM)
  • nib-nifti-dx now supports NIfTI-2 files with a --nifti2 flag (#1323) (CM)
  • Update nibabel.streamlines.tractogram to support ragged arrays. (#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. (#1310) (Joshua Newton, reviewed by CM)
  • Improve error message for for dicomwrapper errors in shape calculation (#1302) (YOH, reviewed by CM)
  • Support "flat" ASCII-encoded GIFTI DataArrays (#1298) (PM, reviewed by CM)

Bug fixes

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

Maintenance

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

API changes and deprecations

New Contributors

... (truncated)

Changelog

Sourced from nibabel's changelog.

5.3.0 (Tuesday 8 October 2024)

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)

... (truncated)

Commits
  • 249986b MNT: Update release notes translator
  • 48dcb47 STY: ruff check --fix
  • 1d93526 MNT: Remove workarounds used for Python 3.8 support
  • fcc2957 MNT: Update support matrix for Python and numpy
  • 5a32a60 DOC: Remove end year from copyright
  • 9bdbc42 DOC: Update mailmap and contributor list
  • 607b5ca DOC: Update Zenodo contributors
  • 7a733f6 DOC: Update changelog
  • c18f542 Merge pull request #1369 from DimitriPapadopoulos/preview
  • ec15839 MNT: better way to normalize sequences to lists and flatten
  • Additional commits viewable in compare view


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codecov-commenter commented 1 month ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 84.34%. Comparing base (d484c8e) to head (02b046a).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #448 +/- ## ======================================= Coverage 84.34% 84.34% ======================================= Files 37 37 Lines 3986 3986 ======================================= Hits 3362 3362 Misses 624 624 ```

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dependabot[bot] commented 1 month ago

Superseded by #450.