Update all minor versions (master) (minor)

[renovate]

This PR contains the following updates:

Package	Change	Age	Adoption	Passing	Confidence
coverage	7.4.4 -> 7.5.0
prospector-profile-duplicated	1.2.0 -> 1.5.0
puppeteer (source)	22.6.5 -> 22.7.1
pytest (changelog)	8.1.2 -> 8.2.0
scikit-image (source)	0.22.0 -> 0.23.2
typing_extensions (changelog)	4.10.0 -> 4.11.0
zope.interface	6.2 -> 6.3

---

Release Notes

nedbat/coveragepy (coverage)

v7.5.0

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• Added initial support for function and class reporting in the HTML report.
  There are now three index pages which link to each other: files, functions,
  and classes. Other reports don't yet have this information, but it will be
  added in the future where it makes sense. Feedback gladly accepted!

• Other HTML report improvements:

  • There is now a "hide covered" checkbox to filter out 100% files, finishing
    issue 1384_.

  • The index page is always sorted by one of its columns, with clearer
    indications of the sorting.

  • The "previous file" shortcut key didn't work on the index page, but now it
    does, fixing issue 1765_.

• The debug output showing which configuration files were tried now shows
  absolute paths to help diagnose problems where settings aren't taking effect,
  and is renamed from "attempted_config_files" to the more logical
  "config_files_attempted."

• Python 3.13.0a6 is supported.

.. _issue 1384:https://github.com/nedbat/coveragepy/issues/13844
.. _issue 1765https://github.com/nedbat/coveragepy/issues/176565

.. _changes_7-4-4:

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

v1.5.0

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1.5.0 (2024-04-12)

New feature

• #​65 Add N803, argument name should be lowercase, with: invalid-name (@​sbrunner)

v1.4.0

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1.4.0 (2024-04-06)

New feature

• #​63 Add function name should be lowercase (@​sbrunner)

v1.3.0

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1.3.0 (2024-04-03)

New feature

• #​62 Ignore: Multi-line docstring summary should start at the first line, … (@​sbrunner)

Dependency update

• #​59 Update CI dependencies (patch) (@​renovate[bot])
• #​61 Update pre-commit hook sbrunner/hooks to v1 (@​renovate[bot])
• #​60 Update CI dependencies (minor) (@​renovate[bot])

puppeteer/puppeteer (puppeteer)

v22.7.1

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v22.7.0

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pytest-dev/pytest (pytest)

v8.2.0

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pytest 8.2.0 (2024-04-27)

Deprecations

• #​12069: A deprecation warning is now raised when implementations of one of the following hooks request a deprecated py.path.local parameter instead of the pathlib.Path parameter which replaced it:

  • pytest_ignore_collect{.interpreted-text role="hook"} - the path parameter - use collection_path instead.
  • pytest_collect_file{.interpreted-text role="hook"} - the path parameter - use file_path instead.
  • pytest_pycollect_makemodule{.interpreted-text role="hook"} - the path parameter - use module_path instead.
  • pytest_report_header{.interpreted-text role="hook"} - the startdir parameter - use start_path instead.
  • pytest_report_collectionfinish{.interpreted-text role="hook"} - the startdir parameter - use start_path instead.

  The replacement parameters are available since pytest 7.0.0.
  The old parameters will be removed in pytest 9.0.0.

  See legacy-path-hooks-deprecated{.interpreted-text role="ref"} for more details.

Features

• #​11871: Added support for reading command line arguments from a file using the prefix character @, like e.g.: pytest @​tests.txt. The file must have one argument per line.

  See Read arguments from file <args-from-file>{.interpreted-text role="ref"} for details.

Improvements

• #​11523: pytest.importorskip{.interpreted-text role="func"} will now issue a warning if the module could be found, but raised ImportError{.interpreted-text role="class"} instead of ModuleNotFoundError{.interpreted-text role="class"}.

  The warning can be suppressed by passing exc_type=ImportError to pytest.importorskip{.interpreted-text role="func"}.

  See import-or-skip-import-error{.interpreted-text role="ref"} for details.

• #​11728: For unittest-based tests, exceptions during class cleanup (as raised by functions registered with TestCase.addClassCleanup <unittest.TestCase.addClassCleanup>{.interpreted-text role="meth"}) are now reported instead of silently failing.

• #​11777: Text is no longer truncated in the short test summary info section when -vv is given.

• #​12112: Improved namespace packages detection when consider_namespace_packages{.interpreted-text role="confval"} is enabled, covering more situations (like editable installs).

• #​9502: Added PYTEST_VERSION{.interpreted-text role="envvar"} environment variable which is defined at the start of the pytest session and undefined afterwards. It contains the value of pytest.__version__, and among other things can be used to easily check if code is running from within a pytest run.

Bug Fixes

• #​12065: Fixed a regression in pytest 8.0.0 where test classes containing setup_method and tests using @staticmethod or @classmethod would crash with AttributeError: 'NoneType' object has no attribute 'setup_method'.

  Now the request.instance <pytest.FixtureRequest.instance>{.interpreted-text role="attr"} attribute of tests using @staticmethod and @classmethod is no longer None, but a fresh instance of the class, like in non-static methods.
  Previously it was None, and all fixtures of such tests would share a single self.

• #​12135: Fixed issue where fixtures adding their finalizer multiple times to fixtures they request would cause unreliable and non-intuitive teardown ordering in some instances.

• #​12194: Fixed a bug with --importmode=importlib and --doctest-modules where child modules did not appear as attributes in parent modules.

• #​1489: Fixed some instances where teardown of higher-scoped fixtures was not happening in the reverse order they were initialized in.

Trivial/Internal Changes

• #​12069: pluggy>=1.5.0 is now required.
• #​12167: cache <cache>{.interpreted-text role="ref"}: create supporting files (CACHEDIR.TAG, .gitignore, etc.) in a temporary directory to provide atomic semantics.

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

v0.23.2

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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):

• @​pitkajuh
• Jarrod Millman (@​jarrodmillman)
• Lars Grüter (@​lagru)
• Marianne Corvellec (@​mkcor)

4 reviewers added to this release (alphabetically):

• Egor Panfilov (@​soupault)
• Jarrod Millman (@​jarrodmillman)
• Lars Grüter (@​lagru)
• Marianne Corvellec (@​mkcor)

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

v0.23.1

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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):

• @​GParolini
• @​tokiAi
• Adrien Foucart (@​adfoucart)
• Anam Fatima (@​anamfatima1304)
• Ananya Srivastava (@​ana42742)
• Ben Harvie (@​benharvie)
• Christian Clauss (@​cclauss)
• Cris Luengo (@​crisluengo)
• Egor Panfilov (@​soupault)
• Grzegorz Bokota (@​Czaki)
• Jan Lebert (@​sitic)
• Jarrod Millman (@​jarrodmillman)
• Jeremy Farrell (@​farrjere)
• Juan Nunez-Iglesias (@​jni)
• Lars Grüter (@​lagru)
• Mao Nishino (@​mao1756)
• Marianne Corvellec (@​mkcor)
• Mark Harfouche (@​hmaarrfk)
• Matthew Feickert (@​matthewfeickert)
• Matthew Vine (@​MattTheCuber)
• Maxime Corbé (@​Maxime-corbe)
• Michał Górny (@​mgorny)
• Neil Shephard (@​ns-rse)
• Ole Streicher (@​olebole)
• Peter Suter (@​petsuter)
• Robert Haase (@​haesleinhuepf)
• Sean McKinney (@​jouyun)
• Stefan van der Walt (@​stefanv)
• vfdev (@​vfdev-5)

21 reviewers added to this release (alphabetically):

• @​GParolini
• Adrien Foucart (@​adfoucart)
• Anam Fatima (@​anamfatima1304)
• Ben Harvie (@​benharvie)
• Christian Clauss (@​cclauss)
• Cris Luengo (@​crisluengo)
• Egor Panfilov (@​soupault)
• Grzegorz Bokota (@​Czaki)
• Jarrod Millman (@​jarrodmillman)
• Jeremy Farrell (@​farrjere)
• Juan Nunez-Iglesias (@​jni)
• Lars Grüter (@​lagru)
• M Bussonnier (@​Carreau)
• Mao Nishino (@​mao1756)
• Marianne Corvellec (@​mkcor)
• Mark Harfouche (@​hmaarrfk)
• Maxime Corbé (@​Maxime-corbe)
• P. L. Lim (@​pllim)
• Peter Suter (@​petsuter)
• Sebastian Berg (@​seberg)
• Stefan van der Walt (@​stefanv)

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

v0.23.0

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[!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.

python/typing_extensions (typing_extensions)

v4.11.0

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This feature release provides improvements to various recently
added features, most importantly type parameter defaults (PEP 696).

There are no changes since 4.11.0rc1.

zopefoundation/zope.interface (zope.interface)

v6.3

Compare Source

================

• Add preliminary support for Python 3.13 as of 3.13a6.

---

Configuration

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👻 Immortal: This PR will be recreated if closed unmerged. Get config help if that's undesired.

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File name: poetry.lock

Updating dependencies
Resolving dependencies...

Creating virtualenv c2cwsgiutils-E2Cq1g0o-py3.12 in /home/ubuntu/.cache/pypoetry/virtualenvs

The current project's Python requirement (>=3.9,<4.0) is not compatible with some of the required packages Python requirement:
  - scikit-image requires Python >=3.10, so it will not be satisfied for Python >=3.9,<3.10

Because c2cwsgiutils depends on scikit-image (0.23.2) which requires Python >=3.10, version solving failed.

  • Check your dependencies Python requirement: The Python requirement can be specified via the `python` or `markers` properties
    
    For scikit-image, a possible solution would be to set the `python` property to ">=3.10,<4.0"

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    https://python-poetry.org/docs/dependency-specification/#using-environment-markers

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