Bump the actions group across 1 directory with 3 updates

[dependabot]

Bumps the actions group with 3 updates in the / directory: dask, numpy and scikit-image.

Updates dask from 2024.12.0 to 2024.12.1

Release notes

Sourced from dask's releases.

2024.12.1

Changes

• Fix map_overlap bug where rechunking and trim=False caused inconsistent chunkings @​phofl (#11605)
• Avoid reference to bound method in NestedContainer @​hendrikmakait (#11608)
• Avoid constructing NestedContainers in case of trivial inputs @​hendrikmakait (#11600)
• Avoid legacy implementation in read-csv @​phofl (#11603)
• Remove legacy DataFrame import @​phofl (#11604)
• asarray ignores dtype for array inputs @​crusaderky (#11586)
• Add back LLM chatbot to Dask docs @​dchudz (#11594)
• Avoid creating trivial DataNodes in graph conversion @​hendrikmakait (#11598)
• Don't wrap keys in TaskRef in Alias @​hendrikmakait (#11597)
• Bump JamesIves/github-pages-deploy-action from 4.6.9 to 4.7.2 @​dependabot (#11593)
• Migrate dask array creation routines to task spec @​jrbourbeau (#11582)
• Migrate most of dask array random to task spec @​jrbourbeau (#11581)
• Do not use local function in array.push @​fjetter (#11576)

See the Changelog for more information.

Commits

• 2c0ac83 Release 2024.12.1
• 076b1f4 Fix map_overlap bug where rechunking and trim=False caused inconsistent chunk...
• 0bc8c01 Avoid reference to bound method in NestedContainer (#11608)
• e95f0f2 Avoid constructing NestedContainers in case of trivial inputs (#11600)
• 24c4920 Avoid legacy implementation in read-csv (#11603)
• 44c75d0 Remove legacy DataFrame import (#11604)
• 06a7e1e asarray ignores dtype for array inputs (#11586)
• c6a5040 Add back LLM chatbot to Dask docs (#11594)
• 2eb339e Avoid creating trivial DataNodes in graph conversion (#11598)
• 07a6bd6 Don't wrap keys in TaskRef in Alias (#11597)
• Additional commits viewable in compare view

Updates numpy from 2.2.0 to 2.2.1

Release notes

Sourced from numpy's releases.

2.2.1 (DEC 21, 2024)

NumPy 2.2.1 Release Notes

NumPy 2.2.1 is a patch release following 2.2.0. It fixes bugs found after the 2.2.0 release and has several maintenance pins to work around upstream changes.

There was some breakage in downstream projects following the 2.2.0 release due to updates to NumPy typing. Because of problems due to MyPy defects, we recommend using basedpyright for type checking, it can be installed from PyPI. The Pylance extension for Visual Studio Code is also based on Pyright. Problems that persist when using basedpyright should be reported as issues on the NumPy github site.

This release supports Python 3.10-3.13.

Contributors

A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Charles Harris
• Joren Hammudoglu
• Matti Picus
• Nathan Goldbaum
• Peter Hawkins
• Simon Altrogge
• Thomas A Caswell
• Warren Weckesser
• Yang Wang +

Pull requests merged

A total of 12 pull requests were merged for this release.

• #27935: MAINT: Prepare 2.2.x for further development
• #27950: TEST: cleanups
• #27958: BUG: fix use-after-free error in npy_hashtable.cpp (#27955)
• #27959: BLD: add missing include
• #27982: BUG:fix compile error libatomic link test to meson.build
• #27990: TYP: Fix falsely rejected value types in ndarray.__setitem__
• #27991: MAINT: Don't wrap #include <Python.h> with extern "C"
• #27993: BUG: Fix segfault in stringdtype lexsort
• #28006: MAINT: random: Tweak module code in mtrand.pyx to fix a Cython...
• #28007: BUG: Cython API was missing NPY_UINTP.
• #28021: CI: pin scipy-doctest to 1.5.1
• #28044: TYP: allow None in operand sequence of nditer

Checksums

... (truncated)

Commits

• 7469245 Merge pull request #28047 from charris/prepare-2.2.1
• acb051e REL: Prepare for the NumPy 2.2.1 release [wheel build]
• 28a091a Merge pull request #28044 from charris/backport-28039
• 723605b TST: Add test for allowing None in operand sequence passed to nditer
• 554739e TYP: allow None in operand sequence of nditer
• 31bc4c8 Merge pull request #28021 from charris/backport-28020
• 32f52a3 CI: pin scipy-doctest to 1.5.1 (#28020)
• 6219aeb Merge pull request #28007 from charris/backport-28005
• eb7071c Merge pull request #28006 from charris/backport-28003
• 4f82c32 BUG: Cython API was missing NPY_UINTP.
• Additional commits viewable in compare view

Updates scikit-image from 0.24.0 to 0.25.0

Release notes

Sourced from scikit-image's releases.

v0.25.0

scikit-image 0.25.0

We're happy to announce the release of scikit-image 0.25.0!

New Features

• Add the new Gray-Level Co-occurrence Matrix (GLCM) properties "mean", "variance", "standard deviation" and "entropy" to skimage.feature.texture.graycoprops (#7375).
• Add the new skimage.morphology.footprint_rectangle supporting generation of rectangular or hyper-rectangular footprints in one function (#7566).

API Changes

• Complete the deprecation of and remove skimage.feature.plot_matches. Use skimage.feature.plot_matched_features going forward (#7487).
• Deprecate skimage.io.imshow, skimage.io.imshow_collection and skimage.io.show. Please use matplotlib, napari, etc. to visualize images (#7508).
• Remove deprecated skimage.morphology.skeletonize_3d; use skimage.morphology.skeletonize instead (#7572).
• Deprecate skimage.io plugin infrastructure (#7353).
• Switched to using the scipy.sparse array interface. For more details, see the note about the new scipy.sparse array interface here (#7576).
• Deprecate skimage.morphology.rectangle in favor of the new function skimage.morphology.footprint_rectangle (#7566).
• Deprecate skimage.morphology.square in favor of the new function skimage.morphology.footprint_rectangle (#7566).
• Deprecate skimage.morphology.cube in favor of the new function skimage.morphology.footprint_rectangle (#7566).

Enhancements

• Improve numerical stability of skimage.morphology.local_minima for extremely small floats (#7534).
• Make sure that skimage.feature.plot_matched_features uses the same random colors, if matches_color isn't provided explicitly (#7541).
• Allow passing a sequence of colors to the parameter matches_color in skimage.feature.plot_matched_features (#7541).

Performance

• skimage.feature.peak_local_max will now skip unnecessary distance computations in the case of min_distance=1. This results in performance improvements to functions like skimage.feature.blob_dog, skimage.feature.blob_log, skimage.feature.blob_doh and skimage.feature.corner_peaks that call peak_local_max internally (#7548).
• In skimage.featurepeak_local_max, skip unnecessary check for cases where min_distance > 1 is passed (#7548).

Bug Fixes

• Ensure that skimage.morphology.remove_objects_by_distance doesn't fail if the given integer dtype cannot be safely cast to the architecture specific size of intp, e.g. on i386 architectures (#7453).
• Fix degeneracy in skimage.draw.ellipsoid_stats when all semi-axes have the same length (#7473).
• Prevent skimage.morphology.thin from accidentally modifying the input image in case it is of dtype uint8 (#7469).
• Fix numerical precision error in skimage.measure.ransac. In some cases, ransac was stopping at the first iteration (#7065).
• Fix numerical precision error in skimage.measure.ransac; very small probabilities lead to -0 number of max trials (#7496).
• Ensure that RegionProperties objects returned by skimage.measure.regionprops can be deserialized with pickle (#7569).
• Fix edge case where setting watershed_lines=True in skimage.segmentation.watershed resulted in an incorrect solution (#7071).
• Fix the behavior of skimage.segmentation.watershed when the markers don't align with local minima by making sure every marker is evaluated before successive pixels (#7071).
• Fix dtype promotion in skimage.segmentation.join_segmentations if numpy.uint is used with NumPy<2 (#7292).

Documentation

• In skimage.morphology.skeletonize, clarify the expected image dtypes and how objects of different intensities are handled (#7456).
• Fix example section in docstring of skimage.feature.graycomatrix (#7297).
• Use conda-forge consistently in instructions for setting up the development environment (#7483).
• Use new CITATION.cff instead of CITATION.bib (#7505).

... (truncated)

Changelog

Sourced from scikit-image's changelog.

How to make a new release of skimage

While following this guide, note down all the times that you need to consult a previous release manager, or that you find an instruction unclear. You will, of course, make a PR to update these notes after you are done with the release! ;-)

Before you start, make sure you have all the required write permissions (if not, you will need to ask an owner to grant you access), specifically to:

• https://pypi.org/project/scikit-image/

• https://github.com/scikit-image/skimage-web

• Check TODO.txt for any outstanding tasks.

We use a variant of "semantic versioning", where version numbers are classified as v... By default, releases are made from the main branch as part of a linear release history and, as described below, are triggered by pushing a git tag to the scikit-image repository on github. If a patch release is required, a branch can be created from the appropriate point in main and the following instructions are still apt.

Example version number

• 0.23.0rc0.dev0 # development version for 0.23.0 first release candidate
• 0.23.0rc0 # 0.23.0 first release candidate
• 0.23.0rc1.dev0 # development version for 0.23.0 second release candidate
• 0.23.0 # 0.23.0 release

Commits

• f172eba Designate 0.25.0 release
• af12cc8 Fix CI (#7631)
• 583af85 Bump version
• ee3f821 Designate 0.25.0rc2 release
• a2a80b7 Lazy load legacy imports in skimage top module (#6892)
• aa7042c Change type annotation of ball radius from int to float (#7627)
• a854ec5 Upgrade to spin 0.13 (#7622)
• 2d0c092 Add forgotten TODO about deprecated square, cube & rectangle (#7624)
• 1bd1598 Fix join_segmentations dtype error for np.uint (#7292)
• 4fb2464 Replace square, rectangle, cube with footprint_rectangle (#7566)
• Additional commits viewable in compare view

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