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Update dependency scikit-image to ^0.25.0#123

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Update dependency scikit-image to ^0.25.0#123
renovate[bot] wants to merge 1 commit intomainfrom
renovate/scikit-image-0.x

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@renovate renovate bot commented Dec 16, 2024 •
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This PR contains the following updates:

Package Change Age Adoption Passing Confidence
scikit-image ^0.24.0 -> ^0.25.0 age adoption passing confidence

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Release Notes

scikit-image/scikit-image (scikit-image)

v0.25.0

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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).
  • Use correct spin test --coverage in contribution guide (#​7515).
  • Tweak advice to new developers; remove AI warning (#​7522).
  • Rework installation instructions (#​7434).
  • Improve the description of the image parameter in skimage.restoration.richardson_lucy (#​7477).
  • Account for empty arrays when counting segments per contour level in gallery example "Segment human cells (in mitosis)" (#​7551).
  • Fix typo in morphology doc (#​7606).
  • Change type description of parameter radius in skimage.morphology.ball from int to float (#​7627).

Infrastructure

  • Fix CI tests with minimal dependencies and make dependency resolution more robust (#​7462).
  • Add CI to test scikit-image against free-threaded Python 3.13 (#​7463).
  • Address autosummary.import_cycle warning (#​7486).
  • Temporarily exclude Dask 2024.8.0 to fix CI (#​7493).
  • Uncomment currentmodule directive again (#​7492).
  • Add CI to release nightly free-threaded wheels (#​7481).
  • Update deprecated configuration (#​7501).
  • Bump spin version to 0.11 (#​7507).
  • Ensure only a single type: label is present in PRs (#​7512).
  • Update pydata-sphinx-theme (#​7511).
  • Fix OpenBLAS s_cmp unresolved symbol error, update Emscripten CI testing (#​7525).
  • Render paragraphs in dormant message (#​7549).
  • Build sphinx documentation with parallel jobs (#​7579).
  • Don't check test coverage in CI (#​7594).
  • Explicitly setup conda on macos for wheel building (#​7608).

Maintenance

  • Verify all artifacts that have been attested by looping over them in CI (#​7447).
  • Update circleci-artifacts-redirector-action that moved to the Scientific Python org (#​7446).
  • Use NumPy 2.0 stable to build packages (#​7451).
  • FIX Use python3 in Meson version script shebang (#​7482).
  • Refactored tests for skeletonize (#​7459).
  • Remove unused and deprecated dependency pytest-runner (#​7495).
  • Exclude imageio 2.35.0 that forces numpy downgrade (#​7502).
  • Don't test thresholding funcs for Dask compatibility (#​7509).
  • Fix build dependency (#​7510).
  • Add sdist check to spin sdist (#​7438).
  • Reorder items in TODO list (#​7519).
  • Use Rotation.from_euler to compute 3D rotation matrix (#​7503).
  • Update spin (0.12) (#​7532).
  • Import lazy_loader as private symbol in top-level namespaces (#​7540).
  • Set -DNPY_NO_DEPRECATED_API=NPY_1_23_API_VERSION on build (#​7538).
  • Update up/download artifact version (#​7545).
  • Don't use deprecated io.show and io.imshow (#​7556).
  • Hide traceback inside assert_stacklevel (#​7558).
  • Update pre-commit versions (#​7560).
  • Drop Python 3.9 support (#​7561).
  • Update minimum dependencies (SPEC 0) (#​7562).
  • Remove unused PYX files in io/_plugins (#​7557).
  • Support Python 3.13 (#​7565).
  • During deprecation cycles, preserve the value of deprecated parameters that don't have a new parameter as a replacement (#​7552).
  • Fix missing minigalleries by using full names in directives (#​7567).
  • Build Python 3.13 wheels (#​7571).
  • Update TODO (#​7573).
  • Remove deprecated gaussian output parameter (#​7574).
  • Test Py3.13 on windows (#​7578).
  • Update ruff linter / formatter (#​7580).
  • Fix formatting issues (#​7581).
  • CI: bump macos image pin from 12 to 13 (#​7582).
  • Update build dependencies (#​7587).
  • Update minimum supported pyamg (#​7586).
  • Update documentation dependencies (#​7590).
  • Bump changelist to v0.5 (#​7601).
  • Pin kaleido to 0.2.1 (#​7612).
  • Update upload-nightly-action (#​7609).
  • Update pillow (#​7615).
  • Remove Python 2.7 cruft (#​7616).
  • Use intersphinx_registry package in conf.py to keep intersphinx urls up to date. This means that building docs now requires the intersphinx-registry package (#​7611).
  • Update build dependencies (#​7614).
  • Update file extension and reformat Markdown file (#​7617).
  • Add forgotten TODO about deprecated square, cube & rectangle (#​7624).
  • Upgrade to spin 0.13 (#​7622).
  • Lazy load legacy imports in skimage top module (#​6892).
  • CI pre-commit fix (#​7631).

Contributors

30 authors added to this release (alphabetically):

25 reviewers added to this release (alphabetically):

These lists are automatically generated, and may not be complete or may contain duplicates.

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