⬆️ Bump the production-dependencies group across 1 directory with 3 updates

[dependabot]

Bumps the production-dependencies group with 3 updates in the / directory: rich, nibabel and sphinx.

Updates rich from 13.8.1 to 13.9.2

Release notes

Sourced from rich's releases.

The Splitting segments Release

A hotfix for highlighting in the table, and a fix for Segment.split_cells

[13.9.2] - 2024-10-04

Fixed

• Fixed Table columns not highlighting when added by add_row Textualize/rich#3517
• Fixed an issue with Segment.split_cells reported in Textual Textualize/textual#5090

Hotfix for dependency issue

[13.9.1] - 2024-10-01

Fixed

• Fixed typing_extensions dependency

The so long Python 3.7 release

This version adds support for fine-grained information in tracebacks. In other words, it will highlight columns in tracebacks (for supported Python versions). Here's an example:

This version also drops support for Python 3.7, which has long since reached its EOL. If you are stuck on Python3.7 for any reason, you will not be able to upgrade to this version, but nothing should break.

See below for other changes in this release.

[13.9.0] - 2024-10-01

Changed

• Dropped support for Python3.7 Textualize/rich#3509
• Rich will display tracebacks with finely grained error locations on python 3.11+ Textualize/rich#3486

Fixed

• Fixed issue with Segment._split_cells Textualize/rich#3506
• Fix auto detection of terminal size on Windows Textualize/rich#2916
• Text.style now respected in Panel title/subtitle Textualize/rich#3509

Changelog

Sourced from rich's changelog.

[13.9.2] - 2024-10-04

Fixed

• Fixed Table columns not highlighting when added by add_row Textualize/rich#3517
• Fixed an issue with Segment.split_cells reported in Textual Textualize/textual#5090

[13.9.1] - 2024-10-01

Fixed

• Fixed typing_extensions dependency

[13.9.0] - 2024-10-01

Changed

• Dropped support for Python3.7 Textualize/rich#3509
• Rich will display tracebacks with finely grained error locations on python 3.11+ Textualize/rich#3486

Fixed

• Fixed issue with Segment._split_cells Textualize/rich#3506
• Fix auto detection of terminal size on Windows Textualize/rich#2916
• Text.style now respected in Panel title/subtitle Textualize/rich#3509

Commits

• 0f2f51b Merge pull request #3521 from Textualize/splitcells-fix
• 8b84ee9 Merge pull request #3514 from mdmintz/complete-the-3.7-drop
• 661ae8d version bump
• 834d178 tests
• babf74a more tests
• 4f40703 fix for split cells
• 6607492 Merge pull request #3518 from TomJGooding/fix-table-highlight-columns-added-b...
• e732952 Merge pull request #3519 from TomJGooding/docs-table-add-column-highlight-option
• 0176bef docs(table): add column highlight option
• 16b3830 fix(table): highlight columns added by add_row
• Additional commits viewable in compare view

Updates nibabel from 5.2.1 to 5.3.0

Release notes

Sourced from nibabel's releases.

5.3.0

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

• Raise HeaderDataError from set_qform if the affine fails to decompose. This would previously result in numpy.linalgLinAlgError. (#1227) (CM)
• The nibabel.onetime.auto_attr module can be replaced by functoolscached_property in all supported versions of Python. This alias may be removed in future versions. (#1341) (CM)
• Removed the deprecated nisext (setuptools extensions) package. (#1290) (CM, reviewed by MB)

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

Updates sphinx from 8.0.2 to 8.1.3

Release notes

Sourced from sphinx's releases.

Sphinx 8.1.3

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Bugs fixed

• #13013: Restore support for cut_lines() with no object type. Patch by Adam Turner.

Sphinx 8.1.2

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Bugs fixed

• #13012: Expose sphinx.errors.ExtensionError in sphinx.util for backwards compatibility. This will be removed in Sphinx 9, as exposing the exception in sphinx.util was never intentional. ExtensionError has been part of sphinx.errors since Sphinx 0.9. Patch by Adam Turner.

Sphinx 8.1.1

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Bugs fixed

• #13006: Use the preferred https://www.cve.org/ URL for the :cve: role. Patch by Hugo van Kemenade.
• #13007: LaTeX: Improve resiliency when the required fontawesome or fontawesome5 packages are not installed. Patch by Jean-François B.

Sphinx 8.1.0

Changelog: https://www.sphinx-doc.org/en/master/changes.html

Dependencies

• #12756: Add lower-bounds to the sphinxcontrib-* dependencies. Patch by Adam Turner.
• #12833: Update the LaTeX parskip package from 2001 to 2018. Patch by Jean-François B.

Incompatible changes

• #12763: Remove unused internal class sphinx.util.Tee. Patch by Adam Turner.
• #12822: LaTeX: for Unicode engines, the fvset default is changed to '\\fvset{fontsize=auto}' from '\\fvset{fontsize=\\small}'. Code-blocks are unchanged as FreeMono is now loaded with Scale=0.9. An adjustment to existing projects is needed only if they used a custom fontpkg configuration and did not set fvset.

... (truncated)

Changelog

Sourced from sphinx's changelog.

Release 8.1.3 (in development)

Bugs fixed

• #13013: Restore support for :func:!cut_lines with no object type. Patch by Adam Turner.

Release 8.1.2 (released Oct 12, 2024)

Bugs fixed

• #13012: Expose :exc:sphinx.errors.ExtensionError in sphinx.util for backwards compatibility. This will be removed in Sphinx 9, as exposing the exception in sphinx.util was never intentional. :exc:!ExtensionError has been part of sphinx.errors since Sphinx 0.9. Patch by Adam Turner.

Release 8.1.1 (released Oct 11, 2024)

Bugs fixed

• #13006: Use the preferred https://www.cve.org/ URL for the :rst:role::cve: <cve> role. Patch by Hugo van Kemenade.
• #13007: LaTeX: Improve resiliency when the required fontawesome or fontawesome5 packages are not installed. Patch by Jean-François B.

Release 8.1.0 (released Oct 10, 2024)

Dependencies

• #12756: Add lower-bounds to the sphinxcontrib-* dependencies. Patch by Adam Turner.
• #12833: Update the LaTeX parskip package from 2001 to 2018. Patch by Jean-François B.

Incompatible changes

• #12763: Remove unused internal class sphinx.util.Tee.

... (truncated)

Commits

• a1510de Bump to 8.1.3 final
• 62e9606 Restore support for cut_lines() with no object type (#13015)
• 5ae32ce Bump version
• a72b47b Bump to 8.1.2 final
• 39a45ad Expose ExtensionError in sphinx.util for backwards compatibility.
• 5a4859a Add docs about sphinx-autobuild (#13011)
• 05679ef Type-check the 'autodoc_intenum' example (#12827)
• 86d1d31 Prune CHANGES of unneeded sections
• b6269d3 Improve documentation for the Builder API (#13008)
• c46abc4 Improve clarity for master_doc and root_doc
• Additional commits viewable in compare view

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