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Update dependency scikit-image to v0.25.2

Open renovate[bot] opened this issue 5 years ago • 0 comments

This PR contains the following updates:

Package Change Age Confidence
scikit-image ==0.17.2 -> ==0.25.2 age confidence

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Release Notes

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

v0.25.2

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scikit-image 0.25.2

We're happy to announce the release of scikit-image 0.25.2!

Bug Fixes

  • Handle random degenerate case in skimage.graph.cut_normalized gracefully (#​7675).
  • In skimage.feature.BRIEF, copy keypoints if necessary to preserve contiguity (#​7692).
  • Revert a previous fix to skimage.segmentation.watershed that unintentionally changed the algorithm's behavior for markers placed at maxima in the image. We decided that the behavior originally reported as a bug (gh-6632), is not actually one (#​7702).

Documentation

  • Improve docstring of skimage.restoration.rolling_ball (#​7682).

Infrastructure

  • Only run the job if the PR got merged (vs merely closed) (#​7679).
  • Fix typo in GH workflow (#​7681).
  • Refactor GitHub's CI config and helper scripts (#​7672).
  • Use pytest config in pyproject.toml in CI (#​7555).
  • Lower CI build verbosity (#​7688).
  • Port testing on Windows from Azure CI to GitHub's CI (#​7687).
  • CI cleanup (#​7693).
  • Simultaneously resolve all dependencies; add pip caching (#​7690).
  • Reenable graph reproducibility test (#​7694).
  • Give milestone labeler necessary permissions (#​7695).
  • Milestone labeler permission not needed (#​7696).
  • Fix 313t wheel build (#​7699).

Maintenance

  • Include a missing image in meson.build so they are included in the wheel (#​7660).
  • Add zizmor to pre-commit; address GH workflow issues raised (#​7662).

Contributors

6 authors added to this release (alphabetically):

8 reviewers added to this release (alphabetically):

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

v0.25.1

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scikit-image 0.25.1

We're happy to announce the release of scikit-image 0.25.1!

Bug Fixes

  • Include centroid in __all__ of the PYI file in skimage.measure (#​7652).
  • Improve numerical stability of blur_effect (#​7643).
  • Because under-determined fits are unreliable, skimage.measure.EllipseModel will now warn and return False (no fit) when fewer than 5 data points are provided (#​7648).
  • Explicitly upcast data with dtype float16 to float32 in skimage.segmentation.random_walker; this fixes passing float16 on NumPy 1.26 (#​7655).

Documentation

  • Don't use removed QuadContourSet.collections in gallery example (#​7638).
  • Change old import convention in the gallery examples (#​7630).

Infrastructure

  • Make apigen.py work with editable hooks (#​7647).
  • Build Linux ARM wheels natively (#​7664).

Maintenance

  • Infer floating point type for sigma parameter (#​7637).
  • In skimage.segmentation.active_contour, change the type of the default argument for w_line to indicate it is a float (#​7645).
  • Temporarily disable parallel building of gallery (#​7656).
  • [pre-commit.ci] pre-commit autoupdate (#​7649).
  • Skip flaky test on azure (#​7669).

Contributors

8 authors added to this release (alphabetically):

8 reviewers added to this release (alphabetically):

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

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.

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):

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renovate[bot] avatar Jan 07 '21 01:01 renovate[bot]