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@dependabot dependabot bot commented on behalf of github Apr 13, 2026

Updates the requirements on scyjava, pyimagej, jpype1, networkx, pymupdf, pyobjc-framework-cocoa, zarr, fsspec, pytest, sphinx, myst-nb and setuptools to permit the latest version.
Updates scyjava to 1.12.4

Commits
  • f05e305 Release version 1.12.4
  • 5000d73 Set jgo's lenient mode when resolving components
  • 4f1aa5b Fail fast with clear error for Java < 11
  • 50006f0 Bump to next development cycle
  • ada8393 Release version 1.12.3
  • 1f2a326 Fix string syntax
  • cf6df14 Update to jgo v2
  • 16fe82b Stop using jgo.jgo.maven_scijava_repository()
  • cc7e66d Make deprecation warnings visible during test runs
  • 55cb87e Bump to next development cycle
  • Additional commits viewable in compare view

Updates pyimagej to 1.8.0

Commits
  • 39d37fd Release version 1.8.0
  • e69d39d Make doctor checkup more comprehensive
  • dbe379e Update to jgo v2
  • 11f9669 Fix dependency version constraint whitespace
  • c0deae4 Update pyimagej.readthedocs.io -> py.imagej.net
  • f6a0757 Debug log each module/package opened and exported
  • bc8453a Simplify debug logging detection logic
  • 07dfe63 Use temp directory when converting labelings
  • 0788e10 Check if the JVM is running before checking version
  • 8c408a1 Actually fix the link
  • Additional commits viewable in compare view

Updates jpype1 to 1.7.0

Release notes

Sourced from jpype1's releases.

v1.7.0

  • 1.7.0 - 2026-04-04

    • Fixed compatibility with NumPy 2.3 breaking change where np.bool_ no longer inherits from Python bool. #1307

    • Migrated build system from legacy setup.py to cmake and scikit-build-core.

    • Added initial support and testing for Python 3.14. #1338

    • Updated pyproject.toml metadata for PEP 639 license compliance. #1337

    • Fixed a race condition in cross-module mutex initialization. #1333

    • Fixed PySlice_CheckFull for 32-bit architectures. #1336

    • Fixed unknown references in dbapi2 module. #1342

    • Fixed regression in relative classpath resolution and modernized org.jpype.jar discovery.

    • Optimized Azure CI pipelines with improved pip caching.

    • Added documentation for building tracing-instrumented extensions.

    • Added a support script to validate wheels.

    • Fixed compatibility with NumPy 2.3. #1320

    • Fixed a race condition upon JPype import on Windows. #1316

    • Made jedi support optional

Changelog

Sourced from jpype1's changelog.

Changelog

This changelog only contains changes from the first pypi release (0.5.4.3) onwards.

Latest Changes:

  • 1.7.1.dev0 - 2026-04-09

  • 1.7.0 - 2026-04-04

    • Fixed compatibility with NumPy 2.3 breaking change where np.bool_ no longer inherits from Python bool. #1307

    • Migrated build system from legacy setup.py to cmake and scikit-build-core.

    • Added initial support and testing for Python 3.14. #1338

    • Updated pyproject.toml metadata for PEP 639 license compliance. #1337

    • Fixed a race condition in cross-module mutex initialization. #1333

    • Fixed PySlice_CheckFull for 32-bit architectures. #1336

    • Fixed unknown references in dbapi2 module. #1342

    • Fixed regression in relative classpath resolution and modernized org.jpype.jar discovery.

    • Optimized Azure CI pipelines with improved pip caching.

    • Added documentation for building tracing-instrumented extensions.

    • Added a support script to validate wheels.

    • Fixed compatibility with NumPy 2.3. #1320

    • Fixed a race condition upon JPype import on Windows. #1316

    • Made jedi support optional

  • 1.6.0 - 2025-01-20

    • Java components have been converted to maven style module.

    • JArray is now registered as a Sequence.

    • Fixed conversion of float16 for subnormal numbers.

    • Fixed segmentation fault on null String.

    • Fixed bugs with java.util.List concat and repeat methods.

    • Enhancement to JProxy to handle wrapping an existing Python object with a Java

... (truncated)

Commits

Updates networkx to 3.2.1

Commits

Updates pymupdf to 1.26.5

Release notes

Sourced from pymupdf's releases.

PyMuPDF-1.26.5 released

Wheels for Windows, Linux and MacOS, and the sdist, are available on pypi.org and can be installed in the usual way, for example:

python -m pip install --upgrade pymupdf

[Linux-aarch64 wheels will be built and uploaded later.]

Changes in version 1.26.5

  • Use MuPDF-1.26.10.

  • Fixed issues:

  • Other:

    • Supported Python versions are now 3.9-3.14.
    • We now define all class methods explicitly instead of with dynamic assignment; this improves type hints.
    • Removed pymupdf.utils.Shape class, was duplicate of pymupdf.Shape.
    • Allow use of cibuildwheel to build and test on Pyodide.
    • Fixed various Pyodide bugs.
    • In documentation, added section about Linux wheels and glibc compatibility.
    • Improved documentation of pymupdf.open()'s arg.
    • Retrospectively mark 4544 <https://github.com/pymupdf/PyMuPDF/issues/4544>_ as fixed in 1.26.4.
Changelog

Sourced from pymupdf's changelog.

Change Log

**Changes in version **

  • Fixed issues:

  • Other:

    • Fixed incorrect generation of lineJoin j in PDF content, introduced in 1.27.2.2.

Changes in version 1.27.2.2 (2026-03-20)

  • Fixed issues:

    • Fixed 4902 <https://github.com/pymupdf/PyMuPDF/issues/4902>_: Incorrect linewidth in elements returned by Page.get_texttrace()
    • Fixed 4932 <https://github.com/pymupdf/PyMuPDF/issues/4932>_: "Page" has no attribute "find_tables" in PyMuPDF 1.27

  • Other:

    • Added Annot.__bool__().

Changes in version 1.27.2. (2026-03-10)

  • Use MuPDF-1.27.2.

  • Fixed issues:

    • Fixed 4903 <https://github.com/pymupdf/PyMuPDF/issues/4903>_: Typing broken because of *_forward_decl

  • Other:

    • Retrospectively marked #4907 as fixed in pymupdf-1.27.1.

    • Improved get_textpage_ocr().

      For partial OCR, all page areas outside legible text are now OCRed, not just those within images. This means that OCR will now also be performed for vector graphics, and for text containing illegible characters.

Changes in version 1.27.1 (2026-02-11)

  • Use MuPDF-1.27.1.

  • Fixed issues:

    • Fixed 4599 <https://github.com/pymupdf/PyMuPDF/issues/4599>_: page.cluster_drawings extract a lot of small clusters once upgraded to 1.26

... (truncated)

Commits
  • cc13f80 pipcl.py: Added asserts to avoid obscure build/runtime errors.
  • cd79b59 scripts/test.py: improved cibw command.
  • 97ed979 scripts/test.py: avoid test failures from cibw's recent default to include fr...
  • a707524 tests/test_release.py: avoid error from os.path.relpath() on windows.
  • aef5d64 scripts/test.py: fixed bug in manylinux cibuildwheel builds.
  • c4a83ea tests/: added test_4699() for upstream bug fixed with mupdf master.
  • 090e23e changes.txt: add date of most recent release 1.26.4.
  • 90e86e7 Add 3.14 to list of supported Python versions.
  • 13d89c0 src/init.py: fix call of pdf_is_ocg_hidden() with mupdf master.
  • d9d4ab8 changes.txt: updated to match all changes since 1.26.4 release.
  • Additional commits viewable in compare view

Updates pyobjc-framework-cocoa to 12.0

Release notes

Sourced from pyobjc-framework-cocoa's releases.

v12.0

  • Drop support for Python 3.9, which will go out of support before PyObjC 3.12 is released.

  • Added AVFAudio as a separate toplevel package, instead of keeping it merged in into AVFoundation.

    The package is included in the pyobjc-framework-AVFoundation distribution.

  • Updated metadata for the macOS 26 SDK.

    As part of this introduce bindings for the following new framework bindings:

    • ARKit
    • CompositorServices
    • GameSave

    There are no bindings for the MetalPerformancePrimitives at this time, it is a low-level C++ library that would require a lot of work to create bindings.

  • In macOS 26 a number of type encodings for block arguments include a signature for the block interface. Update PyObjC runtime introspection to ignore that information.

  • Dropped old metadata scans. That is, all framework bindings are now created from the most recent macOS SDK headers with some manual additions and annotations.

    This change required adding manual entries for, in particular, constants that were renamed in by now old versions of macOS and have been removed from Apple's headers by now. These will be removed from PyObjC in a future update as well (but after a transition period where using them will raise a warning).

    This has the following user visible side effects (as far as they are visible, most of the the changes below affect versions of macOS that are long gone):

    • Accounts: The following constants are no longer available (on the old versions of macOS where these were available): ACFacebookAppVersionKey, ACFacebookPermissionGroupKey, ACFacebookPermissionGroupRead, ACFacebookPermissionGroupReadWrite, and ACFacebookPermissionGroupWrite.

    • AppKit: The NSFileWrapper class no longer supports with keyword arguments path, and serializedRepresentation, and the keyword set (URL, options, error).

    • AuthenticationServices: The classes ASAccountAuthenticationModificationReplacePasswordWithSignInWithAppleRequest and ASAccountAuthenticationModificationUpgradePasswordToStrongPasswordRequest no longer have a keyword argument set named (user, serviceIdentifier).

    • Automator: class AMBundleAction no longer accepts the keyword set (definition, fromArchive).

... (truncated)

Changelog

Sourced from pyobjc-framework-cocoa's changelog.

Version 12.0

  • Drop support for Python 3.9, which will go out of support before PyObjC 3.12 is released.

  • Added AVFAudio as a separate toplevel package, instead of keeping it merged in into AVFoundation.

    The package is included in the pyobjc-framework-AVFoundation distribution.

  • Updated metadata for the macOS 26 SDK.

    As part of this introduce bindings for the following new framework bindings:

    • ARKit
    • CompositorServices
    • GameSave

    There are no bindings for the MetalPerformancePrimitives at this time, it is a low-level C++ library that would require a lot of work to create bindings.

  • In macOS 26 a number of type encodings for block arguments include a signature for the block interface. Update PyObjC runtime introspection to ignore that information.

  • Dropped old metadata scans. That is, all framework bindings are now created from the most recent macOS SDK headers with some manual additions and annotations.

    This change required adding manual entries for, in particular, constants that were renamed in by now old versions of macOS and have been removed from Apple's headers by now. These will be removed from PyObjC in a future update as well (but after a transition period where using them will raise a warning).

    This has the following user visible side effects (as far as they are visible, most of the the changes below affect versions of macOS that are long gone):

    • Accounts: The following constants are no longer available (on the old versions of macOS where these were available): ACFacebookAppVersionKey, ACFacebookPermissionGroupKey, ACFacebookPermissionGroupRead, ACFacebookPermissionGroupReadWrite, and ACFacebookPermissionGroupWrite.

    • AppKit: The NSFileWrapper class no longer supports with keyword arguments path, and serializedRepresentation, and the keyword set (URL, options, error).

    • AuthenticationServices: The classes ASAccountAuthenticationModificationReplacePasswordWithSignInWithAppleRequest and ASAccountAuthenticationModificationUpgradePasswordToStrongPasswordRequest no longer have a keyword argument set named (user, serviceIdentifier).

... (truncated)

Commits
  • 8e97298 Update release to to match reality
  • 8660317 Merge branch 'pyobjc-12' of github.com:ronaldoussoren/pyobjc into pyobjc-12
  • c442422 Fix test failure with python 3.15
  • 31efb5f Some pre-releaes updates
  • 6683d66 More test coverage updates
  • 03f9219 Test coverage improvements
  • b055e49 Improve test coverage
  • 1fe6997 Fix edge case in super-call.m
  • 350ad78 Fix tests on x86_64 and update shared files
  • 78d5c29 Fix some analyzer warnings
  • Additional commits viewable in compare view

Updates zarr to 2.18.2

Release notes

Sourced from zarr's releases.

v2.18.2

What's Changed

Full Changelog: zarr-developers/zarr-python@v2.18.1...v2.18.2

Changelog

Sourced from zarr's changelog.

Release notes

.. # Copy the warning statement under the latest release version # and unindent for pre-releases.

.. warning::
   Pre-release! Use :command:`pip install --pre zarr` to evaluate this release.

.. # Unindent the section between releases in order # to document your changes. On releases it will be # re-indented so that it does not show up in the notes.

.. note:: Zarr-Python 2.18.* is expected be the final release in the 2.* series. Work on Zarr-Python 3.0 is underway. See GH1777 <https://github.com/zarr-developers/zarr-python/issues/1777>_ for more details on the upcoming 3.0 release.

.. _release_2.18.2:

Enhancements


* Add Zstd codec to old V3 code path.
  By :user:`Ryan Abernathey <rabernat>` 

.. _release_2.18.1:


2.18.1


Maintenance


* Fix a regression when getting or setting a single value from arrays with size-1 chunks.
  By :user:`Deepak Cherian &lt;dcherian&gt;` :issue:`1874`

.. _release_2.18.0:


2.18.0


Enhancements

</code></pre>

<ul>

<li>Performance improvement for reading and writing chunks if any of the dimensions is size 1.

By :user:<code>Deepak Cherian &lt;dcherian&gt;</code> :issue:<code>1730</code>.</li>

</ul>

<p>Maintenance</p>

<pre><code>&lt;/tr&gt;&lt;/table&gt;

</code></pre>

</blockquote>

<p>... (truncated)</p>

</details>

<details>

<summary>Commits</summary>


<ul>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/0855bd6e99baef7bd99baaf1b6fdaefd4efd83a6&quot;&gt;&lt;code&gt;0855bd6&lt;/code&gt;&lt;/a> doc: update release notes for 2.18.2 (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1915&quot;&gt;#1915&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/3e98c3b1d6ed24b7b04fdbaa56ed2c42f5b1ef05&quot;&gt;&lt;code&gt;3e98c3b&lt;/code&gt;&lt;/a> Add zstd to old V3 supported codecs (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1914&quot;&gt;#1914&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/bf895332cdb8f028284f958c58cda773085d5e68&quot;&gt;&lt;code&gt;bf89533&lt;/code&gt;&lt;/a> reset release notes (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1886&quot;&gt;#1886&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/4bd9764c1857cb563d155ad797011dfd4a44616e&quot;&gt;&lt;code&gt;4bd9764&lt;/code&gt;&lt;/a> release notes for 2.18.1 (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1885&quot;&gt;#1885&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/908e920bfd52371a4148b19d305262a804bc0201&quot;&gt;&lt;code&gt;908e920&lt;/code&gt;&lt;/a> Fix a regression with scalar indexing due to <a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1800&quot;&gt;#1800&lt;/a> (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1875&quot;&gt;#1875&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/8264acebc5e1671c36bc434f14cac914f5a099e1&quot;&gt;&lt;code&gt;8264ace&lt;/code&gt;&lt;/a> chore: update pre-commit hooks (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1876&quot;&gt;#1876&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/8979205fbebd991974172ac23b436372911f4666&quot;&gt;&lt;code&gt;8979205&lt;/code&gt;&lt;/a> Group dependabot updates (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1854&quot;&gt;#1854&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/cb4230dd9a2a0c68b78384b24a2a5567df0b704a&quot;&gt;&lt;code&gt;cb4230d&lt;/code&gt;&lt;/a> Update release.rst (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1850&quot;&gt;#1850&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/056657ca5ed70aa3d77a9e2db42253fca39800b0&quot;&gt;&lt;code&gt;056657c&lt;/code&gt;&lt;/a> Release notes for 2.18.0 (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1843&quot;&gt;#1843&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/270aff18dc780a0a9e7409455277aae017190765&quot;&gt;&lt;code&gt;270aff1&lt;/code&gt;&lt;/a> Enable ruff/bugbear rules (B) and fix issues (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/1702&quot;&gt;#1702&lt;/a&gt;)&lt;/li>

<li>Additional commits viewable in <a href="https://github.com/zarr-developers/zarr-python/compare/v2.10.0...v2.18.2&quot;&gt;compare view</a></li>

</ul>

</details>


<br />


Updates fsspec to 2025.10.0



Commits

    

  • dcb167e changelog (#1941)
    • 

  • a6b9954 Support to ignore specific storage options when tokenizing (#1933)
    • 

  • 79dbdcd SFTPFile methods that override the AbstractFilesystem methods now strip proto...
    • 

  • 11eabae Add class attribute protocol to HTTPFileSystem (#1935)
    • 

  • 7690a43 Directly move Jupyter file (#1937)
    • 

  • be8c3c1 Fix Jupyter return error instead of raise (#1936)
    • 

  • 43e60fa Allow ls() on single file in arrowFS (#1931)
    • 

  • c23674c Add marker for chained filesystems for path passthrough (#1929)
    • 

  • e12aa75 Make WebHDFS ls() method compatible with superclass by supporting **kwargs (#...
    • 

  • 695f14e Fix lazy reference handling for .parquet/.parq files (#1923)
    • 

  • Additional commits viewable in compare view
    • 







Updates pytest to 8.4.2



Release notes

Sourced from pytest's releases.




8.4.2


pytest 8.4.2 (2025-09-03)


Bug fixes


    

  • 

    #13478: Fixed a crash when using console_output_style{.interpreted-text role="confval"} with times and a module is skipped.
    

    • 

  • 

    #13530: Fixed a crash when using pytest.approx{.interpreted-text role="func"} and decimal.Decimal{.interpreted-text role="class"} instances with the decimal.FloatOperation{.interpreted-text role="class"} trap set.
    

    • 

  • 

    #13549: No longer evaluate type annotations in Python 3.14 when inspecting function signatures.
    

    This prevents crashes during module collection when modules do not explicitly use from __future__ import annotations and import types for annotations within a if TYPE_CHECKING: block.
    

    • 

  • 

    #13559: Added missing [int]{.title-ref} and [float]{.title-ref} variants to the [Literal]{.title-ref} type annotation of the [type]{.title-ref} parameter in pytest.Parser.addini{.interpreted-text role="meth"}.
    

    • 

  • 

    #13563: pytest.approx{.interpreted-text role="func"} now only imports numpy if NumPy is already in sys.modules. This fixes unconditional import behavior introduced in [8.4.0]{.title-ref}.
    

    • 



Improved documentation


    

  • #13577: Clarify that pytest_generate_tests is discovered in test modules/classes; other hooks must be in conftest.py or plugins.
    • 



Contributor-facing changes


    

  • #13480: Self-testing: fixed a few test failures when run with -Wdefault or a similar override.
    • 

  • #13547: Self-testing: corrected expected message for test_doctest_unexpected_exception in Python 3.14.
    • 

  • #13684: Make pytest's own testsuite insensitive to the presence of the CI environment variable -- by ogrisel{.interpreted-text role="user"}.
    • 








Commits

    

  • bfae422 Prepare release version 8.4.2
    • 

  • 8990538 Fix passenv CI in tox ini and make tests insensitive to the presence of the C...
    • 

  • ca676bf Merge pull request #13687 from pytest-dev/patchback/backports/8.4.x/e63f6e51c...
    • 

  • 975a60a Merge pull request #13686 from pytest-dev/patchback/backports/8.4.x/12bde8af6...
    • 

  • 7723ce8 Merge pull request #13683 from even-even/fix_Exeption_to_Exception_in_errorMe...
    • 

  • b7f0568 Merge pull request #13685 from CoretexShadow/fix/docs-pytest-generate-tests
    • 

  • 2c94c4a add missing colon (#13640) (#13641)
    • 

  • c3d7684 Merge pull request #13606 from pytest-dev/patchback/backports/8.4.x/5f9938563...
    • 

  • dc6e3be Merge pull request #13605 from The-Compiler/training-update-2025-07
    • 

  • f87289c Fix crash with times output style and skipped module (#13573) (#13579)
    • 

  • Additional commits viewable in compare view
    • 







Updates sphinx to 7.4.7



Release notes

Sourced from sphinx's releases.




Sphinx 7.4.7


Changelog: https://www.sphinx-doc.org/en/master/changes.html







Changelog

Sourced from sphinx's changelog.




Release 7.4.7 (released Jul 20, 2024)


Bugs fixed


    

  • #12096: Warn when files are overwritten in the build directory.
Patch by Adam Turner and Bénédikt Tran.
    • 

  • #12620: Ensure that old-style object description options are respected.
Patch by Adam Turner.
    • 

  • #12601, #12625: Support callable objects in :py:class:~typing.Annotated type
metadata in the Python domain.
Patch by Adam Turner.
    • 

  • #12601, #12622: Resolve :py:class:~typing.Annotated warnings with
sphinx.ext.autodoc,
especially when using :mod:dataclasses as type metadata.
Patch by Adam Turner.
    • 

  • #12589, #12626: autosummary: Fix warnings with :rst:role:!autolink.
Patch by Adam Turner.
    • 



Release 7.4.6 (released Jul 18, 2024)


Bugs fixed


    

  • #12589, #9743, #12609: autosummary: Do not add the package prefix when
generating autosummary directives for modules within a package.
Patch by Adam Turner.
    • 

  • #12613: Reduce log severity for ambiguity detection during inventory loading.
Patch by James Addison.
    • 



Release 7.4.5 (released Jul 16, 2024)


Bugs fixed


    

  • #12593, #12600: Revert coercing the type of selected :confval:html_sidebars
values to a list.
Log an error message when string values are detected.
Patch by Adam Turner.
    • 

  • #12594: LaTeX: since 7.4.0, :rst:dir:seealso and other "light" admonitions
now break PDF builds if they contain a :dudir:figure directive; and also
if they are contained in a table cell (rendered by tabulary).
Patch by Jean-François B.
    • 



Release 7.4.4 (released Jul 15, 2024)





... (truncated)





Commits

    

  • 0d912c8 Bump to 7.4.7 final
    • 

  • bbc97e0 autosummary: Filter invalid import prefixes in autolink (#12626)
    • 

  • 6c486a5 Fix detecting file changes for the overwritten file warning (#12627)
    • 

  • 2bd973e autodoc: Fix warnings with dataclasses in Annotated metadata (#12622)
    • 

  • dd77f85 Support callables in Annotated types (#12625)
    • 

  • 1ed4ca7 Mark test_build_manpage as XFAIL following changes in Docutils master
    • 

  • cd8ce07 Update message catalogues following reverted commits
    • 

  • c6cd25f Partially revert "Update message catalogues (#11626)"
    • 

  • fa2ba7d Partially Revert "[bot]: Update message catalogues (#12563)"
    • 

  • e439c6f Ensure that old-style object description options are respected (#12620)
    • 

  • Additional commits viewable in compare view
    • 







Updates myst-nb to 1.3.0



Release notes

Sourced from myst-nb's releases.




v1.3.0



What's Changed



New Contributors



Full Changelog: https://github.com/executablebooks/MyST-NB/compare/v1.2.0...v1.3.0







Changelog

Sourced from myst-nb's changelog.




v1.3.0 - 2025-07-13


(full changelog)


What's Changed


Enhancements made



Maintenance and upkeep improvements



New Contributors



v1.2.0 - 2025-02-07


(full changelog)


Enhancements made



Bugs Fixed



Maintenance and upkeep improvements






... (truncated)





Commits

    

  • 6bb973c Preparing for release v1.3
    • 

  • 23b2d62 And one more bot to ignore
    • 

  • ff699ca Adding more bots to ignore
    • 

  • 1e2d1a4 docs: nicer types in docs (#688)
    • 

  • 4020e26 MAINT: limit ipython in tox job, too (#687)
    • 

  • b7387d5 ENH: Add handling of image based PendingGlueReference in `generate_any_node...
    • 

  • 29d6e15 [pre-commit.ci] pre-commit autoupdate (#685)
    • 

  • 1ddc3a5 Add scroll_outputs configuration (#683)
    • 

  • 9fe8848 build(deps): bump codecov/codecov-action in the actions group (#676)
    • 

  • fc73430 Improve output cells in dark mode (#679)
    • 

  • Additional commits viewable in compare view
    • 







Updates setuptools to 82.0.1



Changelog

Sourced from setuptools's changelog.




v82.0.1


Bugfixes


    

  • Fix the loading of launcher manifest.xml file. (#5047)
    • 

  • Replaced deprecated json.__version__ with fixture in tests. (#5186)
    • 



Improved Documentation


    

  • Add advice about how to improve predictability when installing sdists. (#5168)
    • 



Misc



v82.0.0


Deprecations and Removals


    

  • pkg_resources has been removed from Setuptools. Most common uses of pkg_resources have been superseded by the importlib.resources <https://docs.python.org/3/library/importlib.resources.html>_ and importlib.metadata <https://docs.python.org/3/library/importlib.metadata.html>_ projects. Projects and environments relying on pkg_resources for namespace packages or other behavior should depend on older versions of setuptools. (#3085)
    • 



v81.0.0


Deprecations and Removals


    

  • Removed support for the --dry-run parameter to setup.py. This one feature by its nature threads through lots of core and ancillary functionality, adding complexity and friction. Removal of this parameter will help decouple the compiler functionality from distutils and thus the eventual full integration of distutils. These changes do affect some class and function signatures, so any derivative functionality may require some compatibility shims to support their expected interface. Please report any issues to the Setuptools project for investigation. (#4872)
    • 



v80.10.2


Bugfixes


    

  • Update vendored dependencies. (#5159)
    • 



Misc





... (truncated)





Commits

    

  • 5a13876 Bump version: 82.0.0 → 82.0.1
    • 

  • 51ab8f1 Avoid using (deprecated) 'json.version' in tests (#5194)
    • 

  • f9c37b2 Docs/CI: Fix intersphinx references (#5195)
    • 

  • 8173db2 Docs: Fix intersphinx references
    • 

  • 09bafbc Fix past tense on newsfragment
    • 

  • 461ea56 Add news fragment
    • 

  • c4ffe53 Avoid using (deprecated) 'json.version' in tests
    •

@dependabot
Build(deps): Bump the python-packages group with 12 updates
c1f27f0 
Updates the requirements on [scyjava](https://github.com/scijava/scyjava), [pyimagej](https://github.com/imagej/pyimagej), [jpype1](https://github.com/jpype-project/jpype), [networkx](https://github.com/networkx/networkx), [pymupdf](https://github.com/pymupdf/pymupdf), [pyobjc-framework-cocoa](https://github.com/ronaldoussoren/pyobjc), [zarr](https://github.com/zarr-developers/zarr-python), [fsspec](https://github.com/fsspec/filesystem_spec), [pytest](https://github.com/pytest-dev/pytest), [sphinx](https://github.com/sphinx-doc/sphinx), [myst-nb](https://github.com/executablebooks/myst-nb) and [setuptools](https://github.com/pypa/setuptools) to permit the latest version.

Updates `scyjava` to 1.12.4
- [Commits](scijava/scyjava@1.12.1...1.12.4)

Updates `pyimagej` to 1.8.0
- [Commits](imagej/pyimagej@1.7.0...1.8.0)

Updates `jpype1` to 1.7.0
- [Release notes](https://github.com/jpype-project/jpype/releases)
- [Changelog](https://github.com/jpype-project/jpype/blob/master/doc/CHANGELOG.rst)
- [Commits](jpype-project/jpype@v1.5.0...v1.7.0)

Updates `networkx` to 3.2.1
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-3.0...networkx-3.2.1)

Updates `pymupdf` to 1.26.5
- [Release notes](https://github.com/pymupdf/pymupdf/releases)
- [Changelog](https://github.com/pymupdf/PyMuPDF/blob/main/changes.txt)
- [Commits](pymupdf/PyMuPDF@1.26.3...1.26.5)

Updates `pyobjc-framework-cocoa` to 12.0
- [Release notes](https://github.com/ronaldoussoren/pyobjc/releases)
- [Changelog](https://github.com/ronaldoussoren/pyobjc/blob/main/docs/changelog.rst)
- [Commits](ronaldoussoren/pyobjc@v11.1...v12.0)

Updates `zarr` to 2.18.2
- [Release notes](https://github.com/zarr-developers/zarr-python/releases)
- [Changelog](https://github.com/zarr-developers/zarr-python/blob/v2.18.2/docs/release.rst)
- [Commits](zarr-developers/zarr-python@v2.10.0...v2.18.2)

Updates `fsspec` to 2025.10.0
- [Commits](fsspec/filesystem_spec@2023.1.0...2025.10.0)

Updates `pytest` to 8.4.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@6.0.0...8.4.2)

Updates `sphinx` to 7.4.7
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/v7.4.7/CHANGES.rst)
- [Commits](sphinx-doc/sphinx@v5.0.0...v7.4.7)

Updates `myst-nb` to 1.3.0
- [Release notes](https://github.com/executablebooks/myst-nb/releases)
- [Changelog](https://github.com/executablebooks/MyST-NB/blob/main/CHANGELOG.md)
- [Commits](executablebooks/MyST-NB@v0.15.0...v1.3.0)

Updates `setuptools` to 82.0.1
- [Release notes](https://github.com/pypa/setuptools/releases)
- [Changelog](https://github.com/pypa/setuptools/blob/main/NEWS.rst)
- [Commits](pypa/setuptools@v61.0.0...v82.0.1)

---
updated-dependencies:
- dependency-name: scyjava
  dependency-version: 1.12.4
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: pyimagej
  dependency-version: 1.8.0
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: jpype1
  dependency-version: 1.7.0
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: networkx
  dependency-version: 3.2.1
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: pymupdf
  dependency-version: 1.26.5
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: pyobjc-framework-cocoa
  dependency-version: '12.0'
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: zarr
  dependency-version: 2.18.2
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: fsspec
  dependency-version: 2025.10.0
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: pytest
  dependency-version: 8.4.2
  dependency-type: direct:development
  dependency-group: python-packages
- dependency-name: sphinx
  dependency-version: 7.4.7
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: myst-nb
  dependency-version: 1.3.0
  dependency-type: direct:production
  dependency-group: python-packages
- dependency-name: setuptools
  dependency-version: 82.0.1
  dependency-type: direct:production
  dependency-group: python-packages
...

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@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Apr 13, 2026
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