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Bump the uv group with 11 updates#66

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May 3, 2026
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Bump the uv group with 11 updates#66
d33bs merged 2 commits intomainfrom
dependabot/uv/uv-ef776e378d

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@dependabot dependabot Bot commented on behalf of github May 1, 2026

Bumps the uv group with 11 updates:

Package From To
bioio-ome-zarr 3.3.0 3.4.0
matplotlib 3.10.8 3.10.9
pyarrow 23.0.1 24.0.0
jax 0.9.2 0.10.0
pyvista 0.47.1 0.47.3
trame-vtk 2.11.6 2.11.8
trame-vuetify 3.2.1 3.2.2
vortex-data 0.67.0 0.69.0
poethepoet 0.42.1 0.45.0
pydata-sphinx-theme 0.16.1 0.17.1
jupyterlab 4.5.6 4.5.7

Updates bioio-ome-zarr from 3.3.0 to 3.4.0

Release notes

Sourced from bioio-ome-zarr's releases.

v3.4.0

What's Changed

Full Changelog: bioio-devs/bioio-ome-zarr@v3.3.0...v3.4.0

Commits
  • 3d1fd38 Merge pull request #139 from bioio-devs/feature/3d-viz-presets
  • 79e5b52 Merge branch 'main' into feature/3d-viz-presets
  • d0237ef Merge pull request #141 from bioio-devs/fix/pin-ome-zarr-models
  • f8262aa Pin pydantic<2.13 to fix CI failures
  • 965d73a Pin ome-zarr-models<1.6 to fix CI failures
  • d182214 remove unnecessary examples
  • 8d39591 Add downsample_z flag to get_default_config_for_viz for 3D viewer support
  • 9ca5713 Merge pull request #137 from bioio-devs/feature/share-ci
  • 44748c6 simplify params
  • 2a27e76 shared lint and test
  • Additional commits viewable in compare view

Updates matplotlib from 3.10.8 to 3.10.9

Release notes

Sourced from matplotlib's releases.

v3.10.9

This is a micro release of the v3.10.x series. Highlights of this release include:

  • Various minor bug and doc fixes
  • Security hardening validation of cyclers - Removing eval usage
  • Security hardening in Latex and PS calls - Removing shell escapes
Commits
  • dd8d78b REL: v3.10.9
  • 2fb1891 REL: Release prep v3.10.9
  • d0e923a Merge branch 'v3.10.8-doc' into v3.10.x
  • 1637932 Merge pull request #31558 from meeseeksmachine/auto-backport-of-pr-31556-on-v...
  • a83faac Backport PR #31556: FIX: Inverted PyErr_Occurred check in enum type caster (_...
  • a4f57ab Merge pull request #31545 from ksunden/backport-of-pr-31282-on-v3.10.x
  • 063288d Merge pull request #31544 from ksunden/backport-of-pr-31248-on-v3.10.x
  • b2ed196 Backport PR #31248: SEC: Remove eval() from validate_cycler
  • acc6024 Merge pull request #31282 from scottshambaugh/tex_no_shell
  • e3fb541 Merge pull request #31078 from meeseeksmachine/auto-backport-of-pr-31075-on-v...
  • Additional commits viewable in compare view

Updates pyarrow from 23.0.1 to 24.0.0

Release notes

Sourced from pyarrow's releases.

Apache Arrow 24.0.0

Release Notes URL: https://arrow.apache.org/release/24.0.0.html

Apache Arrow 24.0.0 RC0

Release Notes: Release Candidate: 24.0.0 RC0

Commits
  • 31b4b6c MINOR: [Release] Update versions for 24.0.0
  • 06dbc17 MINOR: [Release] Update .deb/.rpm changelogs for 24.0.0
  • a021d80 MINOR: [Release] Update CHANGELOG.md for 24.0.0
  • 2d6b12c GH-49716: [C++] FixedShapeTensorType::Deserialize should strictly validate se...
  • a74cb6a GH-49697: [C++][CI] Check IPC file body bounds are in sync with decoder outco...
  • 871a0c6 GH-49676: [Python][Packaging] Fix gRPC docker image layer being too big for h...
  • f9203b3 GH-49586: [C++][CI] StructToStructSubset test failure with libc++ 22.1.1 (#49...
  • fe298b4 GH-49628: [Python][Interchange protocol] Suppress warnings for pandas 4.0.0 a...
  • 1f94910 GH-49252: [GLib] Deprecate Feather features (#49673)
  • 5ba5c3c GH-49671: [CI][Docs] Don't run jobs for push by Dependabot (#49672)
  • Additional commits viewable in compare view

Updates jax from 0.9.2 to 0.10.0

Release notes

Sourced from jax's releases.

JAX v0.10.0

  • New features:

    • Added ResizeMethod.CUBIC_PYTORCH to jax.image.resize to match PyTorch's bicubic resize (#15768).
    • We now support differentiation of jax.lax.linalg.qr for wide matrices and when full_matrices is True.
    • LAPACK operations are now parallelized along the batch dimension on CPU.
    • Added perturb_singular argument to jax.lax.linalg.tridiagonal_solve to handle singular matrices by perturbing near-zero pivots in the LU decomposition. This is useful for solving numerically singular systems when computing eigenvectors by inverse iteration.
    • jax.scipy.linalg.eigh_tridiagonal now supports computing eigenvectors on CPU and GPU.
    • Added the jax.numpy.ndarray.byteswap method.

  • Breaking changes:

    • PartitionSpec objects no longer report themselves to be equal to tuples. Convert tuples to PartitionSpec objects before testing equality.
    • The .vma property has been removed from jax.core.ShapedArray. Use .manual_axis_type.varying instead.
    • JAX CPU devices now report their names as cpu:0, cpu:1, etc. instead of TFRT_CPU_0, TFRT_CPU_1.
    • The config state jax_pmap_shmap_merge has been removed. jax.pmap will now always use the new implementation that wraps jax.jit(jax.shard_map). Please see https://docs.jax.dev/en/latest/migrate_pmap.html for more information.
    • jax.device_put_sharded and jax.device_put_replicated have been removed from the public API and now raise an AttributeError when accessed. Please see https://docs.jax.dev/en/latest/migrate_pmap.html#drop-in-replacements for drop-in replacements.
    • The C++ pmap infrastructure has been removed. The following public APIs are no longer available:
      • jax.sharding.PmapSharding
      • From jaxlib.xla_extension: PmapFunction, pmap, NoSharding, Chunked, Unstacked, ShardedAxis, Replicated, ShardingSpec.
      • From jax.interpreters.pxla: MapTracer, PmapExecutable, parallel_callable, shard_args, xla_pmap_p, Chunked, NoSharding, Replicated, ShardedAxis, ShardingSpec, Unstacked, spec_to_indices.
    • The deprecated keyword arguments a, a_min, and a_max to jax.numpy.clip have been removed.
    • Functions jax.numpy.hstack, jax.numpy.vstack, jax.numpy.dstack, jax.numpy.column_stack, jax.numpy.atleast_1d, jax.numpy.atleast_2d, and jax.numpy.atleast_3d no longer accept non-ArrayLike inputs. Doing so previously issued a DeprecationWarning.
    • jax.scipy.stats.rankdata now returns floating point values in all cases, following a similar change in the SciPy 1.18 release.

... (truncated)

Changelog

Sourced from jax's changelog.

JAX 0.10.0 (April 16, 2026)

  • New features:

    • Added ResizeMethod.CUBIC_PYTORCH to {func}jax.image.resize to match PyTorch's bicubic resize ({jax-issue}[#15768](https://github.com/jax-ml/jax/issues/15768)).
    • We now support differentiation of {func}jax.lax.linalg.qr for wide matrices and when full_matrices is True.
    • LAPACK operations are now parallelized along the batch dimension on CPU.
    • Added perturb_singular argument to {func}jax.lax.linalg.tridiagonal_solve to handle singular matrices by perturbing near-zero pivots in the LU decomposition. This is useful for solving numerically singular systems when computing eigenvectors by inverse iteration.
    • {func}jax.scipy.linalg.eigh_tridiagonal now supports computing eigenvectors on CPU and GPU.
    • Added the {meth}jax.numpy.ndarray.byteswap method.

  • Breaking changes:

    • PartitionSpec objects no longer report themselves to be equal to tuples. Convert tuples to PartitionSpec objects before testing equality.
    • The .vma property has been removed from jax.core.ShapedArray. Use .manual_axis_type.varying instead.
    • JAX CPU devices now report their names as cpu:0, cpu:1, etc. instead of TFRT_CPU_0, TFRT_CPU_1.
    • The config state jax_pmap_shmap_merge has been removed. jax.pmap will now always use the new implementation that wraps jax.jit(jax.shard_map). Please see https://docs.jax.dev/en/latest/migrate_pmap.html for more information.
    • jax.device_put_sharded and jax.device_put_replicated have been removed from the public API and now raise an AttributeError when accessed. Please see https://docs.jax.dev/en/latest/migrate_pmap.html#drop-in-replacements for drop-in replacements.
    • The C++ pmap infrastructure has been removed. The following public APIs are no longer available:
      • jax.sharding.PmapSharding
      • From jaxlib.xla_extension: PmapFunction, pmap, NoSharding, Chunked, Unstacked, ShardedAxis, Replicated, ShardingSpec.
      • From jax.interpreters.pxla: MapTracer, PmapExecutable, parallel_callable, shard_args, xla_pmap_p, Chunked, NoSharding, Replicated, ShardedAxis, ShardingSpec, Unstacked, spec_to_indices.
    • The deprecated keyword arguments a, a_min, and a_max to jax.numpy.clip have been removed.
    • Functions jax.numpy.hstack, jax.numpy.vstack, jax.numpy.dstack, jax.numpy.column_stack, jax.numpy.atleast_1d, jax.numpy.atleast_2d, and jax.numpy.atleast_3d no longer accept non-ArrayLike inputs. Doing so previously issued a DeprecationWarning.
    • {func}jax.scipy.stats.rankdata now returns floating point values in

... (truncated)

Commits
  • a33ed61 Add a libtpu version guard in test_dce_sink_prevents_xla_dce
  • 79e8ef9 Remove unused EXTRA_INDEX environment variable
  • 83e0ac5 Allow shell globbing for libtpu wheel path in pytest_tpu.yml
  • 08a228a Prepare for JAX release 0.10.0
  • 2362cc7 Fix a bug in WeakValueInterner.
  • c12e417 Addressed an old pytype TODO
  • 1d0523d Skip a test in OSS that relies on stdout
  • 01c0f46 [Pallas] Make VMEM explicit on pallas_call TPU kernel inputs during tracing.
  • ad793d6 Use @​immutable for ShapeDtypeStruct and object.setattr in the constructor.
  • 40e7c70 Disable the eigh tests under asan.
  • Additional commits viewable in compare view

Updates pyvista from 0.47.1 to 0.47.3

Release notes

Sourced from pyvista's releases.

v0.47.2

What's Changed

Bug fixes or behavior changes

Full Changelog: pyvista/pyvista@v0.47.1...v0.47.2

Commits

Updates trame-vtk from 2.11.6 to 2.11.8

Release notes

Sourced from trame-vtk's releases.

v2.11.8 (2026-04-24)

Bug Fixes

  • vtk9.7: Replace GetSize() call by GetNumberOfValues() (eed8a5a)

fix #111

Detailed Changes: v2.11.7...v2.11.8

v2.11.7 (2026-04-13)

Bug Fixes

  • static_viewer: Include in repo to skip auto fetch on vtk.js (9302c6b)

Detailed Changes: v2.11.6...v2.11.7

Changelog

Sourced from trame-vtk's changelog.

v2.11.8 (2026-04-24)

Bug Fixes

  • vtk9.7: Replace GetSize() call by GetNumberOfValues() (eed8a5a)

fix #111

v2.11.7 (2026-04-13)

Bug Fixes

  • static_viewer: Include in repo to skip auto fetch on vtk.js (9302c6b)
Commits
  • 466ba94 2.11.8
  • eed8a5a fix(vtk9.7): replace GetSize() call by GetNumberOfValues()
  • ce0e2ed 2.11.7
  • 9302c6b fix(static_viewer): Include in repo to skip auto fetch on vtk.js
  • See full diff in compare view

Updates trame-vuetify from 3.2.1 to 3.2.2

Release notes

Sourced from trame-vuetify's releases.

v3.2.2 (2026-04-28)

Bug Fixes

  • vuetify2: Add version in URL for vue2 (62d3de6)

Detailed Changes: v3.2.1...v3.2.2

Changelog

Sourced from trame-vuetify's changelog.

v3.2.2 (2026-04-28)

Bug Fixes

  • vuetify2: Add version in URL for vue2 (62d3de6)
Commits

Updates vortex-data from 0.67.0 to 0.69.0

Release notes

Sourced from vortex-data's releases.

0.69.0

What's Changed

... (truncated)

Commits

Updates poethepoet from 0.42.1 to 0.45.0

Release notes

Sourced from poethepoet's releases.

0.45.0

Enhancements

Fixes

New Contributors

Full Changelog: nat-n/poethepoet@v0.44.0...v0.45.0

0.44.0

Enhancements

Breaking changes**

  • Transitive includes are now loaded by default. Previously, if an included config file contained its own include entries, those second-order includes were silently ignored. They are now followed recursively using depth-first loading. This may cause previously ignored config files to be loaded, potentially introducing new tasks or environment variables. To preserve the old behavior for a specific include, set recursive = false on that include entry. See the include guide for details.

Full Changelog: nat-n/poethepoet@v0.43.0...v0.44.0

0.43.0

Enhancements

Breaking changes

This release includes a refactor of how task variables are managed, improving boolean arg semantics and introducing private variables. These changes may affect a small number of existing configurations:

  • Boolean args now produce unset env vars when false. Previously false mapped to the string "False"; now the env var is removed entirely. This gives consistent falsy behavior across shells and parameter expansion operators (:-, :+). Tasks checking for the literal string "False" or using os.environ["flag"] will need updating.

  • Private env vars are filtered from subprocesses. Variables starting with _ and containing no uppercase characters (e.g. _secret) are now treated as private — available for config-time interpolation but excluded from the task subprocess environment. This is unlikely to affect existing configurations, but any task that relies on a subprocess reading a _lowercase env var will need to rename it.

  • Private arg option names strip leading underscores. An arg named _flag with no explicit options now generates --flag instead of --_flag. A new validation rejects duplicate CLI options across args.

See the migration guide for details and recommended fixes.

New Contributors

Full Changelog: nat-n/poethepoet@v0.42.1...v0.43.0

Commits
  • 244cf0b Bump version to 0.45.0
  • 3a6c09a feat: support forwarding free arguments via $POE_EXTRA_ARGS (#380)
  • a1edcda fix: preserve quotes in :+/:- operator arguments (#333) (#377)
  • 3e60a85 fix: handle cancelled asyncio tasks correctly (#378)
  • bbdd435 fix: handle ctrl+c attempt on windows if running bat/cmd scripts (#382)
  • 67a623d Bump version to 0.44.0
  • 472f390 feat!: support recursive includes #317 (#372)
  • 3168956 chore: optimize tests to run 17pc faster (#371)
  • 6a25fba chore: bump version to 0.43.0
  • 83091a5 feat!: treat false boolean args as unset env vars and add private vars (#359)
  • Additional commits viewable in compare view

Updates pydata-sphinx-theme from 0.16.1 to 0.17.1

Release notes

Sourced from pydata-sphinx-theme's releases.

v0.17.1

What's Changed

Fixes

Improvements

Dependencies

New Contributors

Full Changelog: pydata/pydata-sphinx-theme@v0.17.0...v0.17.1

v0.17.0

What's Changed

... (truncated)

Commits
  • a4986fa bump: 0.17.0 → 0.17.1 (#2355)
  • ff8be64 Fix default behavior when shorten_urls is unset (#2351)
  • 0867759 Replace broken Unsplash image URLs with Picsum in light-dark guide (#2341)
  • 56157e9 Bump octokit/request-action from 2.4.0 to 3.0.0 (#2346)
  • 8cce21d Bump pydata/pydata-sphinx-theme/.github/workflows/CI.yml from e8db643b990df73...
  • 30b4830 Bump pydata/pydata-sphinx-theme/.github/workflows/docs.yml from 43f9003549c49...
  • 6673b56 Fix docs build with sphinx 'extensions' config key (#2352)
  • ebc3f17 Fix search input receiving keystrokes after escape dismiss in Safari (#2338)
  • 8e67694 feat: add disable_search theme option (#2315)
  • cd00a86 bump: 0.16.2.dev0 -> 0.17.0
  • Additional commits viewable in compare view

Updates jupyterlab from 4.5.6 to 4.5.7

Release notes

Sourced from jupyterlab's releases.

v4.5.7

4.5.7

(Full Changelog)

Security patches

Bugs fixed

Maintenance and upkeep improvements

Documentation improvements

Contributors to this release

The following people contributed discussions, new ideas, code and documentation contributions, and review. See

@dependabot
Bump the uv group with 11 updates
4220c96 
Bumps the uv group with 11 updates:

| Package | From | To |
| --- | --- | --- |
| [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | `3.3.0` | `3.4.0` |
| [matplotlib](https://github.com/matplotlib/matplotlib) | `3.10.8` | `3.10.9` |
| [pyarrow](https://github.com/apache/arrow) | `23.0.1` | `24.0.0` |
| [jax](https://github.com/jax-ml/jax) | `0.9.2` | `0.10.0` |
| [pyvista](https://github.com/pyvista/pyvista) | `0.47.1` | `0.47.3` |
| [trame-vtk](https://github.com/Kitware/trame-vtk) | `2.11.6` | `2.11.8` |
| [trame-vuetify](https://github.com/Kitware/trame-vuetify) | `3.2.1` | `3.2.2` |
| [vortex-data](https://github.com/spiraldb/vortex) | `0.67.0` | `0.69.0` |
| [poethepoet](https://github.com/nat-n/poethepoet) | `0.42.1` | `0.45.0` |
| [pydata-sphinx-theme](https://github.com/pydata/pydata-sphinx-theme) | `0.16.1` | `0.17.1` |
| [jupyterlab](https://github.com/jupyterlab/jupyterlab) | `4.5.6` | `4.5.7` |


Updates `bioio-ome-zarr` from 3.3.0 to 3.4.0
- [Release notes](https://github.com/bioio-devs/bioio-ome-zarr/releases)
- [Commits](bioio-devs/bioio-ome-zarr@v3.3.0...v3.4.0)

Updates `matplotlib` from 3.10.8 to 3.10.9
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.10.8...v3.10.9)

Updates `pyarrow` from 23.0.1 to 24.0.0
- [Release notes](https://github.com/apache/arrow/releases)
- [Commits](apache/arrow@apache-arrow-23.0.1...apache-arrow-24.0.0)

Updates `jax` from 0.9.2 to 0.10.0
- [Release notes](https://github.com/jax-ml/jax/releases)
- [Changelog](https://github.com/jax-ml/jax/blob/main/CHANGELOG.md)
- [Commits](jax-ml/jax@jax-v0.9.2...jax-v0.10.0)

Updates `pyvista` from 0.47.1 to 0.47.3
- [Release notes](https://github.com/pyvista/pyvista/releases)
- [Commits](pyvista/pyvista@v0.47.1...v0.47.3)

Updates `trame-vtk` from 2.11.6 to 2.11.8
- [Release notes](https://github.com/Kitware/trame-vtk/releases)
- [Changelog](https://github.com/Kitware/trame-vtk/blob/master/CHANGELOG.md)
- [Commits](Kitware/trame-vtk@v2.11.6...v2.11.8)

Updates `trame-vuetify` from 3.2.1 to 3.2.2
- [Release notes](https://github.com/Kitware/trame-vuetify/releases)
- [Changelog](https://github.com/Kitware/trame-vuetify/blob/master/CHANGELOG.md)
- [Commits](Kitware/trame-vuetify@v3.2.1...v3.2.2)

Updates `vortex-data` from 0.67.0 to 0.69.0
- [Release notes](https://github.com/spiraldb/vortex/releases)
- [Commits](vortex-data/vortex@0.67.0...0.69.0)

Updates `poethepoet` from 0.42.1 to 0.45.0
- [Release notes](https://github.com/nat-n/poethepoet/releases)
- [Commits](nat-n/poethepoet@v0.42.1...v0.45.0)

Updates `pydata-sphinx-theme` from 0.16.1 to 0.17.1
- [Release notes](https://github.com/pydata/pydata-sphinx-theme/releases)
- [Changelog](https://github.com/pydata/pydata-sphinx-theme/blob/main/RELEASE.md)
- [Commits](pydata/pydata-sphinx-theme@v0.16.1...v0.17.1)

Updates `jupyterlab` from 4.5.6 to 4.5.7
- [Release notes](https://github.com/jupyterlab/jupyterlab/releases)
- [Changelog](https://github.com/jupyterlab/jupyterlab/blob/main/RELEASE.md)
- [Commits](https://github.com/jupyterlab/jupyterlab/compare/@jupyterlab/lsp@4.5.6...@jupyterlab/lsp@4.5.7)

---
updated-dependencies:
- dependency-name: bioio-ome-zarr
  dependency-version: 3.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv
- dependency-name: matplotlib
  dependency-version: 3.10.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv
- dependency-name: pyarrow
  dependency-version: 24.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: uv
- dependency-name: jax
  dependency-version: 0.10.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: uv
- dependency-name: pyvista
  dependency-version: 0.47.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv
- dependency-name: trame-vtk
  dependency-version: 2.11.8
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv
- dependency-name: trame-vuetify
  dependency-version: 3.2.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: uv
- dependency-name: vortex-data
  dependency-version: 0.69.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: uv
- dependency-name: poethepoet
  dependency-version: 0.45.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: uv
- dependency-name: pydata-sphinx-theme
  dependency-version: 0.17.1
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: uv
- dependency-name: jupyterlab
  dependency-version: 4.5.7
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: uv
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels May 1, 2026
@d33bs d33bs merged commit 3871d42 into main May 3, 2026
12 checks passed
@d33bs d33bs deleted the dependabot/uv/uv-ef776e378d branch May 3, 2026 18:47
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