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scikit-image 0.22.0 (2023-11-03)

doc/source/release_notes/release_0.22.rst

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scikit-image 0.22.0 (2023-11-03)

We're happy to announce the release of scikit-image 0.22.0!

Highlights

  • Add new image sequence skimage.data.palisades_of_vogt showing in-vivo tissue of the palisades of Vogt (#6858 <https://github.com/scikit-image/scikit-image/pull/6858>_).
  • Add inpainting example to gallery (#6853 <https://github.com/scikit-image/scikit-image/pull/6853>_).

New Features

  • Add new image sequence skimage.data.palisades_of_vogt showing in-vivo tissue of the palisades of Vogt (#6858 <https://github.com/scikit-image/scikit-image/pull/6858>_).

API Changes

  • Update minimal required NumPy version to 1.22 (#7005 <https://github.com/scikit-image/scikit-image/pull/7005>_).
  • Update minimal required lazy_loader version to 0.3 (#7043 <https://github.com/scikit-image/scikit-image/pull/7043>_).
  • Make PyWavelets an optional dependency which is only required for skimage.restoration.denoise_wavelet and skimage.restoration.estimate_sigma (#7156 <https://github.com/scikit-image/scikit-image/pull/7156>_).
  • Remove deprecated skimage.filters.inverse. Use skimage.filters.filter_inverse instead (#7161 <https://github.com/scikit-image/scikit-image/pull/7161>_).
  • Remove deprecated function skimage.filters.ridges.compute_hessian_eigenvalues. Use skimage.feature.hessian_matrix_eigvals on the results of skimage.feature.hessian_matrix instead (#7162 <https://github.com/scikit-image/scikit-image/pull/7162>_).
  • Remove deprecated automatic detection of the color channel in skimage.filters.gaussian. channel_axis=None now indicates a grayscale image. Set the color channel with channel_axis=-1 explicitly (#7164 <https://github.com/scikit-image/scikit-image/pull/7164>_).
  • Change number of returned arguments in skimage.registration.phase_cross_correlation. The function now always returns the 3 arguments shift, error, and phasediff (#7166 <https://github.com/scikit-image/scikit-image/pull/7166>_).
  • Deprecate return_error in skimage.registration.phase_cross_correlation (#7174 <https://github.com/scikit-image/scikit-image/pull/7174>_).

Performance

  • Add lazy loading to the skimage.feature submodule (#6983 <https://github.com/scikit-image/scikit-image/pull/6983>_).
  • Add lazy loading to the skimage.graph submodule (#6985 <https://github.com/scikit-image/scikit-image/pull/6985>_).
  • Add lazy loading to the skimage.measure submodule (#6999 <https://github.com/scikit-image/scikit-image/pull/6999>_).
  • Add lazy loading to the skimage.transform submodule (#7009 <https://github.com/scikit-image/scikit-image/pull/7009>_).
  • Add lazy loading to the skimage.restoration submodule (#7021 <https://github.com/scikit-image/scikit-image/pull/7021>_).
  • Add lazy loading to the skimage.registration submodule (#7032 <https://github.com/scikit-image/scikit-image/pull/7032>_).
  • Avoid unnecessary padding in skimage.measure.block_resize (#7092 <https://github.com/scikit-image/scikit-image/pull/7092>_).

Bug Fixes

  • Add missing properties num_pixels and coords_scaled to skimage.measure.regionprops_table (#7039 <https://github.com/scikit-image/scikit-image/pull/7039>_).
  • Fix too many values to unpack error with imageio 2.31.1 in video.rst (#7076 <https://github.com/scikit-image/scikit-image/pull/7076>_).
  • Address error in skimage.filters.threshold_triangle when images with a uniform intensity are passed. In these cases the uniform intensity is returned as the threshold (#7098 <https://github.com/scikit-image/scikit-image/pull/7098>_).
  • Fix error in skimage.color.lab2rgb for 1D input (#7116 <https://github.com/scikit-image/scikit-image/pull/7116>_).
  • Make skimage.registration.phase_cross_correlation consistently return an array even if disambiguate=True (#7112 <https://github.com/scikit-image/scikit-image/pull/7112>_).
  • Allow extra_properties of non-equal lengths to be passed correctly to skimage.measure.regionprops_table (#7136 <https://github.com/scikit-image/scikit-image/pull/7136>_).

Documentation

  • Use a more descriptive title for current inpainting example (#6989 <https://github.com/scikit-image/scikit-image/pull/6989>_).
  • Fix URLs to the install page (#6998 <https://github.com/scikit-image/scikit-image/pull/6998>_).
  • Fix equation for Wiener filter in restoration.wiener's docstring (#6987 <https://github.com/scikit-image/scikit-image/pull/6987>_).
  • Fix missing links in INSTALL.rst and simplify language (#6984 <https://github.com/scikit-image/scikit-image/pull/6984>_).
  • Edit installation and contributor guidelines (#6991 <https://github.com/scikit-image/scikit-image/pull/6991>_).
  • Fix URLs that lead to 404 page (#7008 <https://github.com/scikit-image/scikit-image/pull/7008>_).
  • Replace with correct reference to eigenvalues in ridge detection docstrings (#7034 <https://github.com/scikit-image/scikit-image/pull/7034>_).
  • Add inpainting example to gallery (#6853 <https://github.com/scikit-image/scikit-image/pull/6853>_).
  • Fix grammar in SKIP 1 (#7081 <https://github.com/scikit-image/scikit-image/pull/7081>_).
  • Add missing minus in SimilarityTransform docstring (#6840 <https://github.com/scikit-image/scikit-image/pull/6840>_).
  • Add one-line docstring to skimage.segmentation (#6843 <https://github.com/scikit-image/scikit-image/pull/6843>_).
  • Add a short docstring to skimage.util (#6831 <https://github.com/scikit-image/scikit-image/pull/6831>_).
  • Enable version warning banners for docs (#7139 <https://github.com/scikit-image/scikit-image/pull/7139>_).
  • Clarify order of dimensions in skimage.transform.EuclideanTransform (#7103 <https://github.com/scikit-image/scikit-image/pull/7103>_).
  • Add docstring to the morphology module (#6814 <https://github.com/scikit-image/scikit-image/pull/6814>_).
  • Include Plausible analytics from Scientific Python in our HTML docs (#7145 <https://github.com/scikit-image/scikit-image/pull/7145>_).
  • Specify coordinate convention in skimage.draw.polygon2mask (#7131 <https://github.com/scikit-image/scikit-image/pull/7131>_).
  • Update 0.22.0 release notes (#7182 <https://github.com/scikit-image/scikit-image/pull/7182>_).

Infrastructure

  • Pin milestone labeler to v0.1.0 SHA (#6982 <https://github.com/scikit-image/scikit-image/pull/6982>_).
  • Ensure existing target directory for random.js (#7015 <https://github.com/scikit-image/scikit-image/pull/7015>_).
  • Assign next milestone only for PRs targeting main branch (#7018 <https://github.com/scikit-image/scikit-image/pull/7018>_).
  • Add missing directories to spin docs --clean command (#7019 <https://github.com/scikit-image/scikit-image/pull/7019>_).
  • Rework generate_release_notes.py and add PR summary parsing (#6961 <https://github.com/scikit-image/scikit-image/pull/6961>_).
  • Use packaged version of generate_release_notes.py (changelist) (#7049 <https://github.com/scikit-image/scikit-image/pull/7049>_).
  • Generate requirements files from pyproject.toml (#7085 <https://github.com/scikit-image/scikit-image/pull/7085>_).
  • Update spin to v0.5 (#7093 <https://github.com/scikit-image/scikit-image/pull/7093>_).
  • Update to LLVM 16 with choco temporarily (#7109 <https://github.com/scikit-image/scikit-image/pull/7109>_).
  • Update pytest config in pyproject.toml with repo-review recommendations (#7063 <https://github.com/scikit-image/scikit-image/pull/7063>_).
  • Use checkout action version 4 (#7180 <https://github.com/scikit-image/scikit-image/pull/7180>_).

Maintenance

  • Don't test numpy prerelease on azure (#6996 <https://github.com/scikit-image/scikit-image/pull/6996>_).
  • Drop Python 3.8 support per SPEC 0 (#6990 <https://github.com/scikit-image/scikit-image/pull/6990>_).
  • Upper pin imageio (#7002 <https://github.com/scikit-image/scikit-image/pull/7002>_).
  • meson: allow proper selection of NumPy, Pythran in cross builds (#7003 <https://github.com/scikit-image/scikit-image/pull/7003>_).
  • Unpin imageio and add warningfilter (#7006 <https://github.com/scikit-image/scikit-image/pull/7006>_).
  • Update to latest attach-next-milestone action (#7014 <https://github.com/scikit-image/scikit-image/pull/7014>_).
  • Avoid deprecated auto-removal of overlapping axes in thresholding example (#7026 <https://github.com/scikit-image/scikit-image/pull/7026>_).
  • Remove conflicting setuptools upper pin (#7045 <https://github.com/scikit-image/scikit-image/pull/7045>_).
  • Remove future.graph after v0.21 release (#6899 <https://github.com/scikit-image/scikit-image/pull/6899>_).
  • Cleanup from move to pyproject.toml (#7044 <https://github.com/scikit-image/scikit-image/pull/7044>_).
  • Ignore new matplotlib warning (#7056 <https://github.com/scikit-image/scikit-image/pull/7056>_).
  • Update spin (#7054 <https://github.com/scikit-image/scikit-image/pull/7054>_).
  • Ignore SciPy 1.12.dev0 deprecation warning (#7057 <https://github.com/scikit-image/scikit-image/pull/7057>_).
  • Include expected warning for SciPy 1.12 (#7058 <https://github.com/scikit-image/scikit-image/pull/7058>_).
  • Mark NaN-related deprecation warning from np.clip as optional in tests (#7052 <https://github.com/scikit-image/scikit-image/pull/7052>_).
  • Fix abs value function warnings (#7010 <https://github.com/scikit-image/scikit-image/pull/7010>_).
  • Temporary fix for wheel recipe (#7059 <https://github.com/scikit-image/scikit-image/pull/7059>_).
  • Temporary fix for wheel building (#7060 <https://github.com/scikit-image/scikit-image/pull/7060>_).
  • Remove outdated comment (#7077 <https://github.com/scikit-image/scikit-image/pull/7077>_).
  • Include py.typed file in distribution (PEP 561) (#7073 <https://github.com/scikit-image/scikit-image/pull/7073>_).
  • Transition user guide to import skimage as ski (#7024 <https://github.com/scikit-image/scikit-image/pull/7024>_).
  • Fix for NumPy 1.25 (#6970 <https://github.com/scikit-image/scikit-image/pull/6970>_).
  • Pin sphinx until sphinx-gallery is fixed (#7100 <https://github.com/scikit-image/scikit-image/pull/7100>_).
  • Cleanup old Python 3.11 tests (#7099 <https://github.com/scikit-image/scikit-image/pull/7099>_).
  • Revert "Pin sphinx until sphinx-gallery is fixed (#7100)" (#7102 <https://github.com/scikit-image/scikit-image/pull/7102>_).
  • MNT: Remove np.float_ alias; it is removed in NumPy 2.0 (#7118 <https://github.com/scikit-image/scikit-image/pull/7118>_).
  • Fix for NumPy 1.26 (#7101 <https://github.com/scikit-image/scikit-image/pull/7101>_).
  • Update meson-python (#7120 <https://github.com/scikit-image/scikit-image/pull/7120>_).
  • We now require sklearn 1.1, as per SPEC0 (#7121 <https://github.com/scikit-image/scikit-image/pull/7121>_).
  • Update for NumPy 2 namespace cleanup (#7119 <https://github.com/scikit-image/scikit-image/pull/7119>_).
  • DOC: minor numpydoc syntax update (#7123 <https://github.com/scikit-image/scikit-image/pull/7123>_).
  • Update for NumPy 2 namespace cleanup (#7122 <https://github.com/scikit-image/scikit-image/pull/7122>_).
  • Temporary work-around for NEP 51 numpy scalar reprs + doctests (#7125 <https://github.com/scikit-image/scikit-image/pull/7125>_).
  • Update lazy loader (#7126 <https://github.com/scikit-image/scikit-image/pull/7126>_).
  • Fix PEP 8 issues (#7142 <https://github.com/scikit-image/scikit-image/pull/7142>_).
  • Remove single-threaded dask usage in face detection gallery example which fixes issues with running the example on Windows and CI (#7141 <https://github.com/scikit-image/scikit-image/pull/7141>_).
  • Update spin version to 0.6 (#7150 <https://github.com/scikit-image/scikit-image/pull/7150>_).
  • Match pep8speaks and ruff line lengths to 88 (#7148 <https://github.com/scikit-image/scikit-image/pull/7148>_).
  • Remove last reference to distutils in _build_utils/tempita.py (#7137 <https://github.com/scikit-image/scikit-image/pull/7137>_).
  • Update sphinx, sphinx-gallery & sphinx_design (#7155 <https://github.com/scikit-image/scikit-image/pull/7155>_).
  • Update minimal version of numpydoc to 1.6 (#7106 <https://github.com/scikit-image/scikit-image/pull/7106>_).
  • Build wheels for py3.12 (#7082 <https://github.com/scikit-image/scikit-image/pull/7082>_).
  • Update label and milestone workflows (#7163 <https://github.com/scikit-image/scikit-image/pull/7163>_).
  • Update TODO (see #6899) (#7165 <https://github.com/scikit-image/scikit-image/pull/7165>_).
  • Announce Python 3.12 support (#7167 <https://github.com/scikit-image/scikit-image/pull/7167>_).
  • Remove pep8speaks config (#7172 <https://github.com/scikit-image/scikit-image/pull/7172>_).
  • Filter out expected runtime warnings in registation.phase_cross_correlation when disambiguate=True (#7147 <https://github.com/scikit-image/scikit-image/pull/7147>_).
  • Use pre-commit bot (#7171 <https://github.com/scikit-image/scikit-image/pull/7171>_).
  • Fix missing warnings import in phase_cross_correlation (#7175 <https://github.com/scikit-image/scikit-image/pull/7175>_).
  • Fix release notes error (#7177 <https://github.com/scikit-image/scikit-image/pull/7177>_).
  • Use trusted publisher (#7178 <https://github.com/scikit-image/scikit-image/pull/7178>_).

Contributors

24 authors added to this release (alphabetically):

  • @akonsk <https://github.com/akonsk>_
  • @patquem <https://github.com/patquem>_
  • @rraadd88 <https://github.com/rraadd88>_
  • @scott-vsi <https://github.com/scott-vsi>_
  • Adeyemi Biola (@decorouz <https://github.com/decorouz>_)
  • Amund Vedal (@vedal <https://github.com/vedal>_)
  • Ananya Srivastava (@ana42742 <https://github.com/ana42742>_)
  • Andrew J. Hesford (@ahesford <https://github.com/ahesford>_)
  • Antony Lee (@anntzer <https://github.com/anntzer>_)
  • Elena Pascal (@elena-pascal <https://github.com/elena-pascal>_)
  • Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
  • Juan Nunez-Iglesias (@jni <https://github.com/jni>_)
  • Kenfack Anafack Alex Bruno (@Br-Al <https://github.com/Br-Al>_)
  • Klaus Rettinghaus (@rettinghaus <https://github.com/rettinghaus>_)
  • Larry Bradley (@larrybradley <https://github.com/larrybradley>_)
  • Lars Grüter (@lagru <https://github.com/lagru>_)
  • Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
  • Marvin Albert (@m-albert <https://github.com/m-albert>_)
  • Matthias Bussonnier (@Carreau <https://github.com/Carreau>_)
  • Matthias Nwt (@matthiasnwt <https://github.com/matthiasnwt>_)
  • Mike Taves (@mwtoews <https://github.com/mwtoews>_)
  • Riadh Fezzani (@rfezzani <https://github.com/rfezzani>_)
  • Stefan van der Walt (@stefanv <https://github.com/stefanv>_)
  • Talley Lambert (@tlambert03 <https://github.com/tlambert03>_)

19 reviewers added to this release (alphabetically):

  • @akonsk <https://github.com/akonsk>_
  • @scott-vsi <https://github.com/scott-vsi>_
  • Adeyemi Biola (@decorouz <https://github.com/decorouz>_)
  • Ananya Srivastava (@ana42742 <https://github.com/ana42742>_)
  • Andrew J. Hesford (@ahesford <https://github.com/ahesford>_)
  • Egor Panfilov (@soupault <https://github.com/soupault>_)
  • Grzegorz Bokota (@Czaki <https://github.com/Czaki>_)
  • Jarrod Millman (@jarrodmillman <https://github.com/jarrodmillman>_)
  • Juan Nunez-Iglesias (@jni <https://github.com/jni>_)
  • Kristen Thyng (@kthyng <https://github.com/kthyng>_)
  • Larry Bradley (@larrybradley <https://github.com/larrybradley>_)
  • Lars Grüter (@lagru <https://github.com/lagru>_)
  • Marianne Corvellec (@mkcor <https://github.com/mkcor>_)
  • Mark Harfouche (@hmaarrfk <https://github.com/hmaarrfk>_)
  • Marvin Albert (@m-albert <https://github.com/m-albert>_)
  • Matthias Bussonnier (@Carreau <https://github.com/Carreau>_)
  • Maxim (@koshakOK <https://github.com/koshakOK>_)
  • Mike Taves (@mwtoews <https://github.com/mwtoews>_)
  • Stefan van der Walt (@stefanv <https://github.com/stefanv>_)

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