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Update dependency scikit-image to ^0.24.0 #28

Merged
merged 1 commit into from
Aug 23, 2024
Merged

Update dependency scikit-image to ^0.24.0 #28

merged 1 commit into from
Aug 23, 2024

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@renovate renovate bot commented Apr 13, 2024 •
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This PR contains the following updates:

Package Change Age Adoption Passing Confidence
scikit-image (source) ^0.22.0 -> ^0.24.0 age adoption passing confidence

Release Notes

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

v0.24.0

Compare Source

scikit-image 0.24.0

We're happy to announce the release of scikit-image 0.24.0!

Highlights
  • Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#​7040).
New Features
  • Add new class skimage.transform.ThinPlateSplineTransform, which can estimate and model non-linear transforms with thin-plate splines and allows image warping with skimage.transform.warp (#​7040).
  • Add skimage.morphology.remove_objects_by_distance, which removes labeled objects, ordered by size (default), until the remaining objects are a given distance apart (#​4165).
Performance
  • In skimage.feature.corner_fast, test four directions earlier, which should more than half the computation time for most cases (#​7394).
Documentation
  • Remove obsolete instruction about documenting changes (#​7321).
  • Clarify description of data_range parameter in skimage.metrics.structural_similarity (#​7345).
  • Update release process notes (#​7402).
  • Fix typo in docstring of skimage.measure.regionprops (#​7405).
  • Fix typos in skimage.measure.find_contours (#​7411).
  • Add algorithmic complexity description + suggested alternatives to skimage.restoration.rolling_ball docstring (#​7424).
  • Remove ineffective PR contribution clause (#​7429).
  • Clarify objection period for lazy consensus in SKIP 1 (#​7020).
  • Add a new gallery example "Use thin-plate splines for image warping" (#​7040).
  • Add a new gallery example on "Removing objects" based on their size or distance (#​4165).
Infrastructure
  • Escape user-controlled variables in GA workflow (#​7415).
  • Add generation of GitHub artifact attestations to built sdist and wheels before upload to PyPI (#​7427).
  • For publishing actions use the full length commit SHA (#​7433).
  • Be mindful of resources by canceling in-progress workflows (#​7436).
  • Add out-of-tree Pyodide builds in CI for scikit-image (#​7350).
Maintenance
  • Replace deprecated nose style setup/teardown with autouse fixtures (#​7343).
  • Temporarily pin macos-12 runner in CI (#​7408).
  • Fix NumPy2 dtype promotion issues in pywt dependent code (#​7414).
  • In skimage.util.compare_images, deprecate the parameter image2. Instead use image0, image1 to pass the compared images. Furthermore, all other parameters will be turned into keyword-only parameters once the deprecation is complete (#​7322).
  • Add support back for Python 3.9 to enhance compatibility with Numpy 2 (#​7412).
  • Disable ruff/pyupgrade rule UP038 (#​7430).
  • Stop verifying wheel attestations temporarily (#​7444).
Contributors

13 authors added to this release (alphabetically):

15 reviewers added to this release (alphabetically):

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

v0.23.2

Compare Source

scikit-image 0.23.2

We're happy to announce the release of scikit-image 0.23.2!

Bug Fixes
  • Make sure skimage.util.img_as_ubyte supports the edge case where dtype('uint64').type of the provided image is np.ulonglong instead of np.uint64 (#​7392).
Documentation
  • Add date to 0.23.1 release notes (#​7384).
  • Fix docstring of connectivity parameter in skimage.segmentation.watershed (#​7360).
Infrastructure
  • Ignore Sphinx warning about unpickable cache (#​7400).
  • Simplify instructions on changelist in PR template (#​7401).
Maintenance
  • Use numpy.inf instead of deprecated numpy.infty (#​7386).
  • Update Ruff config (#​7387).
  • Update matrix and names of Azure pipelines configuration (#​7390).
  • Use upload- and download-artifact v4 (#​7389).
  • Ignore arch specific cast warnings originating from astype in tests (#​7393).
  • Update link to numpydoc example.py (#​7395).
Contributors

4 authors added to this release (alphabetically):

4 reviewers added to this release (alphabetically):

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

v0.23.1

Compare Source

scikit-image 0.23.1

We're happy to announce the release of scikit-image 0.23.1!

[!NOTE]
Due to an issue with the CI system scikit-image 0.23.0 was never released.
This release is identical to what 0.23.0 would have been other than the CI fix and the version number.

Highlights
  • Ensure skimage.morphology.closing and skimage.morphology.opening are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#​6695).
  • Add parameter mode to binary_erosion, binary_dilation, binary_opening and binary_closing in skimage.morphology. These new parameters determine how array borders are handled (#​6695).
  • Add parameters mode and cval to erosion, dilation, opening, closing, white_tophat, and black_tophat in skimage.morphology. These new parameters determine how array borders are handled (#​6695).
  • Speedup skimage.util.map_array by parallelization with Cython's prange (#​7266).
New Features
  • Add new intensity_std property to skimage.measure.regionprops which computes the standard deviation of the intensity in a region (#​6712).
  • Add parameter mode to binary_erosion, binary_dilation, binary_opening and binary_closing in skimage.morphology. These new parameters determine how array borders are handled (#​6695).
  • Add functions mirror_footprint and pad_footprint to skimage.morphology (#​6695).
  • Add parameters mode and cval to erosion, dilation, opening, closing, white_tophat, and black_tophat in skimage.morphology. These new parameters determine how array borders are handled (#​6695).
  • Add new parameter spacing to segmentation.expand_labels to support anisotropic images (#​7080).
API Changes
  • Drop support for Python 3.9 (#​7217).
  • Parameters shift_x and shift_y in skimage.morphology.erosion and skimage.morphology.dilation are deprecated. Use pad_footprint or modify the footprint manually instead (#​6695).
  • Remove unexpected value scaling in skimage.morphology.skeletonize_3d for non-binary input images. skeletonize_3d now always returns a binary array like similar functions (#​7095).
  • Deprecate function skimage.feature.plot_matches in favor of skimage.feature.plot_matched_features (#​7255).
  • Deprecate skimage.morphology.skeletonize_3d in favor of just skimage.morphology.skeletonize (#​7094).
  • Deprecate parameter output in skimage.filters.gaussian; use out instead (#​7225).
  • Change the default value of the parameters shift_x, shift_y and shift_z from False to 0 in the skimage.filters.rank functions. This has not impact on the results. Warn in case boolean shifts are provided from now on (#​7320).
Performance
  • Add lazy loading to skimage.metrics module (#​7211).
  • Speedup skimage.util.map_array by parallelization with Cython's prange (#​7266).
Bug Fixes
  • Add exception to avoid surprising result when image is too small for the given parameters in skimage.feature.hog (#​7153).
  • Ensure skimage.morphology.closing and skimage.morphology.opening are extensive and anti-extensive, respectively, if the footprint is not mirror symmetric (#​6695).
  • Avoid a TypeError in skimage.registration.phase_cross_correlation when the real-time shift cannot be determined (disambiguate=True). Display a warning instead (#​7259).
  • Fix logic in skimage.graph.pixel_graph which raised a TypeError when the parameter edge_function was provided without a mask (#​7310).
  • Ensure cache stays empty when cache=False is passed to skimage.measure.regionprops (#​7333).
Documentation
  • Update instructions for updating dev environment (#​7160).
  • Make titles in RAG gallery examples more explicit (#​7202).
  • Add docstring to skimage.graph module (#​7192).
  • Use consistent notation for array dimensions in the docstrings (#​3031).
  • Specify default markers in watershed docstring (#​7154).
  • Stop HTML documentation from intercepting left and right-arrow keys to improve keyboard accessibility (#​7226).
  • Fix reference formatting for nitpicky sphinx (#​7228).
  • Document how to deal with other array-likes such as xarray.DataArray and pandas.DataFrame in the crash course on NumPy for images (#​7159).
  • Fix broken function calls and syntax issues in user guide (#​7234).
  • Use correct default mode in docstring of skimage.transform.swirl (#​7241).
  • Add missing documentation about spacing parameter in moments_normalized (#​7248).
  • Update docstring & example in the hough_ellipse transform (#​6893).
  • Point binder tag/branch to commit corresponding to docs/release (#​7252).
  • Add example to FundamentalMatrixTransform class (#​6863).
  • Adds explanation of what the optional dependency on Matplotlib offers to the install instructions (#​7286).
  • Use correct symbol θ for tightness in the docstring of skimage.registration.optical_flow_tvl1 (#​7314).
  • The description of the parameter cval is modified in "int or float". cval is a numerical value not a string (#​7319).
  • Remove obsolete instruction about documenting changes (#​7321).
  • Added comment to clarify that dt corresponds to tau, i.e. the time step. Changed gray scale in grayscale in the entire registration module (#​7324).
  • Create SECURITY.md (#​7230).
  • Remove deprecated parameter coordinates from docstring example of skimage.segmentation.active_contour (#​7329).
  • Include dates in release note headings (#​7269).
  • Update description of how to document pull requests for inclusion in the release notes (#​7267).
  • Clarify description of data_range parameter in skimage.metrics.structural_similarity (#​7345).
  • Use object-oriented Matplotlib style in longer gallery examples and demonstrations (doc/examples/applications) (#​7346).
  • In the gallery example on segmenting human cells (in mitosis), include the border when generating basin markers for watershed (#​7362).
  • Add missing minus sign in docstring of skimage.transform.EuclideanTransform (#​7097).
Infrastructure
  • Update wording on the stale bot to assume the core team dropped the ball (#​7196).
  • Update Azure job name following the drop of Python 3.9 (#​7218).
  • Schedule nightly wheel builds at uncommon time (#​7254).
  • Build nightly wheels with nightly NumPy 2.0 (#​7251).
  • Use pytest-doctestplus instead of classic pytest-doctest (#​7289).
  • Update the scientific-python/upload-nightly-action to v0.5.0 for dependency stability and to take advantage of Anaconda Cloud upload bug fixes (#​7325).
  • Add assert_stacklevel helper to check stacklevel of captured warnings (#​7294).
  • Exclude pre-commit[bot] from changelist's contributor list (#​7358).
Maintenance
  • Remove outdated & duplicate "preferred" field in version_switcher.json (#​7184).
  • Upgrade to spin 0.7 (#​7168).
  • Do not compare types, use isinstance (#​7186).
  • [pre-commit.ci] pre-commit autoupdate (#​7181).
  • Increase tolerance for moments test for 32 bit floats (#​7188).
  • Temporarily pin Cython to <3.0.3 until CI is fixed (#​7189).
  • Remove obsolete meson instructions (#​7193).
  • Temporarily pin Cython to <3.0.3 until CI is fixed, take 2 (#​7201).
  • Fix chocolatey (#​7200).
  • Pin Pillow to <10.1.0 until incompatibility with imageio is fixed (#​7208).
  • Use Black (#​7197).
  • Apply black to _hog.py after previous merge lacking black (#​7215).
  • Unpin Cython after release of Cython 3.0.4 (#​7214).
  • [pre-commit.ci] pre-commit autoupdate (#​7236).
  • Cleanup for Python 3.12 (#​7173).
  • Make Python 3.12 default CI Python (#​7244).
  • Add explicit noexcept to address Cython 3.0 warnings (#​7250).
  • Update imageio to fix Pillow incompatibility (#​7245).
  • Upgrade docker/setup-qemu-action to v3 (#​7134).
  • Fix warningfilter for deprecation in SciPy 1.12.0rc1 (#​7275).
  • Update to numpy>=1.23 and matplotlib>=3.6 according to SPEC 0 (#​7284).
  • Add new deprecate_parameter helper (#​7256).
  • Update meson and Cython (#​7283).
  • Handle floating point warning for empty images in skimage.registration.phase_cross_correlation (#​7287).
  • Update spin (0.8) (#​7285).
  • Complete deprecations that were scheduled for our 0.23 release. Remove now unused deprecate_kwarg and remove_arg; they are entirely succeeded by deprecate_parameter (#​7290).
  • For security best practices, use the scientific-python/upload-nightly-action GitHub Action from known commit shas that correspond to tagged releases. These can be updated automatically via Dependabot (#​7306).
  • Update pre-commits repos (#​7303).
  • The test suite can now be run without numpydoc installed (#​7307).
  • Deal with parallel write warning from Pydata theme (#​7311).
  • Test nightly wheel build with NumPy 2.0 (#​7288).
  • Make it clear that funcs in _optical_flow_utils are private (#​7328).
  • Update dependencies (spec 0) (#​7335).
  • Follow-up cleaning & fixes for compatibility with NumPy 1 & 2 (#​7326).
  • Replace ignored teardown with autouse fixture in test_fits.py (#​7340).
  • Address new copy semantics & broadcasting in np.solve in NumPy 2 (#​7341).
  • Ignore table of execution times by Sphinx gallery (#​7327).
  • Allow a very small floating point tolerance for pearson test (#​7356).
  • Update numpydoc to version 1.7 (#​7355).
  • [pre-commit.ci] pre-commit autoupdate (#​7365).
  • Simplify warning filters in test suite (#​7349).
  • Build against NumPy >=2.0.0rc1 (#​7367).
  • Remove ensure_python_version function (#​7370).
  • Update GitHub actions to setup-python@v5, cache@v4, upload-artifact@v4, and download-artifact@v4 (#​7368).
  • Update lazyloader to v0.4 (#​7373).
Contributors

29 authors added to this release (alphabetically):

21 reviewers added to this release (alphabetically):

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

v0.23.0

Compare Source

[!WARNING]
Due to an issue with the CI system scikit-image 0.23.0 was never released.
This release is identical to 0.23.1 other than the CI fix and the version number.

Configuration

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🚦 Automerge: Disabled by config. Please merge this manually once you are satisfied.

♻ Rebasing: Whenever PR becomes conflicted, or you tick the rebase/retry checkbox.

🔕 Ignore: Close this PR and you won't be reminded about this update again.

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This PR was generated by Mend Renovate. View the repository job log.

@renovate renovate bot force-pushed the renovate/scikit-image-0.x branch from 1ac74bd to 56ad941 Compare June 19, 2024 17:55
@renovate renovate bot changed the title Update dependency scikit-image to ^0.23.0 Update dependency scikit-image to ^0.24.0 Jun 19, 2024
@renovate renovate bot force-pushed the renovate/scikit-image-0.x branch 4 times, most recently from b74ba3f to 0dff64d Compare August 23, 2024 03:10
@renovate renovate bot force-pushed the renovate/scikit-image-0.x branch from 0dff64d to ea26a8c Compare August 23, 2024 04:15
@anarkiwi anarkiwi merged commit 48985c1 into main Aug 23, 2024
2 checks passed
@anarkiwi anarkiwi deleted the renovate/scikit-image-0.x branch August 23, 2024 04:18
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