search

PennLINC / aslprep

Preprocessing of arterial spin labeling (ASL) data
https://aslprep.readthedocs.io
Other
41 stars 15 forks source link

Update nibabel requirement from <=5.2.1 to <=5.3.1 #450

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.

5.3.1

DOI

Release notes

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. (#1378) (CM, reviewed by Basile Pinsard)
  • Remove test order dependency in test_api_validators (#1377) (CM)
Changelog

Sourced from nibabel's changelog.

5.3.1 (Tuesday 15 October 2024)

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)

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)

... (truncated)

Commits
  • 96c8320 REL: 5.3.1
  • 6260442 Merge pull request #1378 from effigies/fix/legacy_nifti_extension_content
  • e97f572 FIX: Restore access to private attr Nifti1Extension._content
  • 1712cb0 TEST: Do not depend on test order in test_api_validators (#1377)
  • 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
  • Additional commits viewable in compare view


Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
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 (a98a281) to head (efd3164).

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #450 +/- ## ======================================= Coverage 84.34% 84.34% ======================================= Files 37 37 Lines 3986 3986 ======================================= Hits 3362 3362 Misses 624 624 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.