Update CI dependencies (master) (minor) #2568

renovate · 2025-01-01T18:36:31Z

This PR contains the following updates:

Package	Change	Type	Update
prospector-profile-duplicated	`1.8.1` -> `1.10.0`		minor
renovatebot/pre-commit-hooks	`39.42.4` -> `39.86.3`	repository	minor
scikit-image	`==0.24.0` -> `==0.25.0`		minor

Note: The pre-commit manager in Renovate is not supported by the pre-commit maintainers or community. Please do not report any problems there, instead create a Discussion in the Renovate repository if you have any questions.

Release Notes

sbrunner/prospector-profile-duplicated (prospector-profile-duplicated)

`v1.10.0`

Compare Source

1.10.0 (2024-12-30)

New feature

#103 Add more codestyle ignore with Black (@sbrunner)

`v1.9.0`

Compare Source

1.9.0 (2024-12-03)

New feature

61fec84 Use Ruff instead of multiple tools (@sbrunner)

renovatebot/pre-commit-hooks (renovatebot/pre-commit-hooks)

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

`v0.25.0`

Compare Source

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):

@aeisenbarth
@FedericoWZhaw
@jakirkham
@michaelbratsch
Adeyemi Biola (@decorouz)
Aditi Juneja (@Schefflera-Arboricola)
Agriya Khetarpal (@agriyakhetarpal)
Brigitta Sipőcz (@bsipocz)
Dan Schult (@dschult)
Edgar Andrés Margffoy Tuay (@andfoy)
Egor Panfilov (@soupault)
Erik Welch (@eriknw)
Gianluca (@geeanlooca)
Gregory Lee (@grlee77)
Hayato Ikoma (@hayatoikoma)
Henrik Finsberg (@finsberg)
Jarrod Millman (@jarrodmillman)
Jordão Bragantini (@JoOkuma)
João Seródio (@SerodioJ)
Kushaan Gupta (@kushaangupta)
Lars Grüter (@lagru)
Loïc Estève (@lesteve)
M Bussonnier (@Carreau)
Marianne Corvellec (@mkcor)
Mark Harfouche (@hmaarrfk)
Matthew Feickert (@matthewfeickert)
Paritosh Dahiya (@hnhparitosh)
Piyush Amitabh (@pamitabh)
Ricky Walsh (@rickymwalsh)
Stefan van der Walt (@stefanv)

25 reviewers added to this release (alphabetically):

@aeisenbarth
@FedericoWZhaw
@jakirkham
@michaelbratsch
Agriya Khetarpal (@agriyakhetarpal)
Brigitta Sipőcz (@bsipocz)
Dan Schult (@dschult)
Edgar Andrés Margffoy Tuay (@andfoy)
Egor Panfilov (@soupault)
Gianluca (@geeanlooca)
Gregory Lee (@grlee77)
Hayato Ikoma (@hayatoikoma)
Jarrod Millman (@jarrodmillman)
Jordão Bragantini (@JoOkuma)
João Seródio (@SerodioJ)
Juan Nunez-Iglesias (@jni)
Kushaan Gupta (@kushaangupta)
Lars Grüter (@lagru)
Marianne Corvellec (@mkcor)
Mark Harfouche (@hmaarrfk)
Matthew Feickert (@matthewfeickert)
Nathan Goldbaum (@ngoldbaum)
Piyush Amitabh (@pamitabh)
Ralf Gommers (@rgommers)
Stefan van der Walt (@stefanv)

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

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Update CI dependencies

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renovate bot added the dependencies Update the dependencies label Jan 1, 2025

renovate bot enabled auto-merge (squash) January 1, 2025 18:36

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Update CI dependencies (master) (minor) #2568

Update CI dependencies (master) (minor) #2568

renovate bot commented Jan 1, 2025

Update CI dependencies (master) (minor) #2568

Update CI dependencies (master) (minor) #2568

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Release Notes

1.10.0 (2024-12-30)

New feature

1.9.0 (2024-12-03)

New feature

scikit-image 0.25.0

New Features

API Changes

Enhancements

Performance

Bug Fixes

Documentation

Infrastructure

Maintenance

Contributors

Configuration