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Updates the requirements on jax, equinox, trimesh, scipy, matplotlib, rich, typing-extensions, gdstk, mlx, tidy3d, h5py, pydantic, plotly, pyvista, trame, mcp, black, ipykernel, pre-commit, pymdown-extensions, pytest, pytest-cov, ruff, tox-uv, pydoclint, sphinx, sphinx-book-theme, nbsphinx, sphinx-autodoc-typehints and myst-nb to permit the latest version.
Updates jax to 0.10.2

Release notes

Sourced from jax's releases.

JAX v0.10.2

  • New features
    • Added jax.scipy.linalg.invhilbert for the closed-form inverse of the Hilbert matrix ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added jax.scipy.linalg.invpascal for the inverse of the Pascal matrix ([#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added jax.scipy.linalg.fiedler_companion for constructing the pentadiagonal Fiedler companion matrix of a polynomial ([#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added jax.ShapeDtypeStruct.like -- a shortcut for constructing a jax.ShapeDtypeStruct from an object with shape and dtype attributes.
  • We have made a number of improvements to JAX tracing performance.
Changelog

Sourced from jax's changelog.

JAX 0.10.2 (June 17, 2026)

  • New features
    • Added {func}jax.scipy.linalg.invhilbert for the closed-form inverse of the Hilbert matrix ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.invpascal for the inverse of the Pascal matrix ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.fiedler_companion for constructing the pentadiagonal Fiedler companion matrix of a polynomial ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.ShapeDtypeStruct.like -- a shortcut for constructing a {class}jax.ShapeDtypeStruct from an object with shape and dtype attributes.

JAX 0.10.1 (May 20, 2026)

  • New features

    • Added ResizeMethod.AREA to {func}jax.image.resize, which matches TensorFlow's AREA resizing ({jax-issue}[#20098](https://github.com/jax-ml/jax/issues/20098)).
    • Added {func}jax.scipy.linalg.hadamard for constructing Hadamard matrices ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.circulant for constructing circulant matrices ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.dft for constructing discrete Fourier transform matrices ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.leslie for constructing Leslie matrices ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.companion for constructing companion matrices from polynomial coefficients ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.fiedler for constructing symmetric Fiedler matrices ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.linalg.helmert for constructing Helmert matrices ({jax-issue}[#10144](https://github.com/jax-ml/jax/issues/10144)).
    • Added {func}jax.scipy.special.boxcox and {func}jax.scipy.special.boxcox1p for the Box-Cox power transformation.
    • Moved RNG APIs from "implementations" to dtypes ({jax-issue}[#27854](https://github.com/jax-ml/jax/issues/27854)):
      • Added jax.random.key_dtype to get the dtype corresponding to a PRNG implementation name.
      • jax.random.key and wrap_key_data now accept a dtype argument.

  • Breaking changes

    • with mesh: context manager has been deprecated. Please use with jax.set_mesh(mesh): instead.

  • Deprecations

    • Passing the copy, order, and ndmin arguments to {func}jax.numpy.array positionally is deprecated. Use keyword arguments instead. This matches the signature of numpy.array.
    • Python dict_values, generators, zip return type and iterators generally are deprecated by default when used as leaves in pytrees. In a future

... (truncated)

Commits
  • 990e6a0 Disable gpu_pallas_distributed_nvshmem_test_gpu which was failing at the
  • 4437b23 Synchronize PGLE profiler tests before stopping traces
  • 3815e4e Add a workaround for linux aarch64 python 3.14t pytest builds.
  • 272e378 Refactor Windows Docker GCE metadata access
  • 310278e Prepare for JAX release 0.10.2
  • 7db3a70 [Pallas:MGPU] Add support for batch dimensions to async_store_tmem.
  • 5597e90 [Mosaic:GPU] Disable set_xla_gpu_enable_allocator_spatial_partitioning for nv...
  • 728e4bf Add functionality to blanket disable the custom call safety checks in export.
  • 26113fa Merge pull request #38432 from vfdev-5:pallas-emit-pipeline-raises-error-empt...
  • c15bacc Pallas emit_pipeline raises ValueError on empty grid
  • Additional commits viewable in compare view

Updates equinox to 0.13.8

Release notes

Sourced from equinox's releases.

Equinox v0.13.8

This is a minor release, largely for internal maintenance purposes.

New Contributors

Full Changelog: patrick-kidger/equinox@v0.13.7...v0.13.8

Commits

Updates trimesh to 4.12.2

Release notes

Sourced from trimesh's releases.

Release 4.12.2

What's Changed

Full Changelog: mikedh/trimesh@4.12.1...4.12.2

Commits

Updates scipy to 1.17.1

Release notes

Sourced from scipy's releases.

SciPy 1.17.1 Release Notes

SciPy 1.17.1 is a bug-fix release with no new features compared to 1.17.0.

Authors

  • Name (commits)
  • Evgeni Burovski (5)
  • Lucas Colley (1)
  • Christoph Gohlke (1)
  • Ralf Gommers (6)
  • Matt Haberland (5)
  • Matthias Koeppe (1)
  • Nick ODell (1)
  • Ilhan Polat (10)
  • Tyler Reddy (44)
  • Martin Schuck (3)
  • Dan Schult (3)
  • stratakis (1) +
  • ਗਗਨਦੀਪ ਸਿੰਘ (Gagandeep Singh) (1)

A total of 13 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

Complete issue list, PR list, and release asset hashes are available in the associated README.txt.

Commits
  • 527eb7f REL: 1.17.1 release commit [wheel build]
  • f11663b Merge pull request #24584 from tylerjereddy/treddy_prep_1.17.1
  • 2c49e68 DOC: PR 24584 revisions
  • 400fa15 safely convert index dtypes to intc for csgraph and superLU
  • 8c70404 MAINT: PR 24584 revisions [wheel build]
  • 6dda8c1 BUG: PR 24584 revisions
  • 4a187e5 DOC: PR 24584 revisions
  • 463ee9f ENH: linalg/inv: re-enable overwrite_a for 2D inputs (#24442)
  • df746ee BUG: linalg: restore dtypes in inv, solve, det
  • 246bfee MAINT:optimize: Enable multi-phase init to DIRECT
  • Additional commits viewable in compare view

Updates matplotlib to 3.11.0

Release notes

Sourced from matplotlib's releases.

REL: v3.11.0

The largest change within this release is a complete overhaul of text and font processing. Through the use of libraqm, HarfBuzz, SheenBidi, and an updated release of FreeType, all text should now support modern font features, enabling full internationalization in all languages. Not all features of these libraries are supported yet, but we expect this work to enable further improvements in an easier manner.

Outside of text handling, there are several improvements to 3D Axes, performance, new accessible colour sequences, flexible figure management, and more. See the release notes for more information.

Commits
  • 69c7534 REL: v3.11.0
  • b7d912b DOC: Set 3.11 as preferred stable release
  • 7c3d502 Update Security Policy for 3.11
  • 964e73d DOC: Prepare GitHub stats for 3.11 final
  • bfa2633 Bump font manager version to final release
  • d0603b2 Merge pull request #31873 from meeseeksmachine/auto-backport-of-pr-31706-on-v...
  • edf5ebc Backport PR #31706: Fix clabel manual index
  • c0e80b7 Merge pull request #31872 from meeseeksmachine/auto-backport-of-pr-31868-on-v...
  • 2a14854 Backport PR #31868: DOC: Move errorbar examples to the statistics sections
  • ea43d96 Merge pull request #31871 from meeseeksmachine/auto-backport-of-pr-31870-on-v...
  • Additional commits viewable in compare view

Updates rich to 15.0.0

Release notes

Sourced from rich's releases.

The So Long 3.8 Release

A few fixes. The major version bump is to honor the passing of 3.8 support which reached its EOL in October 7, 2024

[15.0.0] - 2026-04-12

Changed

  • Breaking change: Dropped support for Python3.8

Fixed

Changelog

Sourced from rich's changelog.

[15.0.0] - 2026-04-12

Changed

  • Breaking change: Dropped support for Python3.8

Fixed

[14.3.4] - 2026-04-11

Changed

[14.3.3] - 2026-02-19

Fixed

[14.3.2] - 2026-02-01

Fixed

[14.3.1] - 2026-01-24

Fixed

[14.3.0] - 2026-01-24

Fixed

Added

... (truncated)

Commits

Updates typing-extensions to 4.16.0

Release notes

Sourced from typing-extensions's releases.

4.16.0

No changes since 4.16.0rc2.

Changes since 4.15.0:

  • Make typing_extensions.TypeAliasType's __module__ attribute writable. Backport of CPython PR #149172.
  • Fix setting of __required_keys__ and __optional_keys__ when inheriting keys with the same name.
  • Add support for AsyncIterator, io.Reader, io.Writer and os.PathLike protocols as bases for other protocols.
  • Fix incorrect behaviour on Python 3.9 and Python 3.10 that meant that calling isinstance with typing_extensions.Concatenate[...] or typing_extensions.Unpack[...] as the first argument could have a different result in some situations depending on whether or not a profiling function had been set using sys.setprofile. This affected both CPython and PyPy implementations. Patch by Brian Schubert.
  • Fix __init_subclass__() behavior in the presence of multiple inheritance involving an @deprecated-decorated base class. Backport of CPython PR #138210 by Brian Schubert.
  • Raise TypeError when attempting to subclass typing_extensions.ParamSpec on Python 3.9. The typing implementation has always raised an error, and the typing_extensions implementation has raised an error on Python 3.10+ since typing_extensions v4.6.0. Patch by Brian Schubert.
  • Add the bound, covariant, contravariant, and infer_variance parameters to TypeVarTuple.
  • Officially support the bound, covariant, contravariant and infer_variance parameters to ParamSpec. Improve the validation of these parameters at runtime.
  • Rename typing_extensions.Sentinel to typing_extensions.sentinel, following the name that has been adopted for builtins.sentinel on Python 3.15. typing_extensions.Sentinel is retained as a soft-deprecated alias for backwards compatibility.
  • Add support for pickling sentinels.
  • Sentinels now preserve their identity when copied or deep-copied.
  • Deprecate passing name as a keyword argument or repr as a positional argument to the sentinel constructor.
  • The default repr of a sentinel X = sentinel("X") is now X rather than <X>.
  • Deprecate arbitrary attribute assignments to sentinels.
  • Deprecate subclassing sentinels.
  • Add support for Python 3.15.
  • Avoid a DeprecationWarning when deprecated is applied to a coroutine function on Python 3.14.0.
Changelog

Sourced from typing-extensions's changelog.

Release 4.16.0 (July 2, 2025)

No user-facing changes since 4.16.0rc2.

Release 4.16.0rc2 (June 25, 2026)

  • Avoid a DeprecationWarning when deprecated is applied to a coroutine function on Python 3.14.0.

Release 4.16.0rc1 (June 24, 2026)

  • Make typing_extensions.TypeAliasType's __module__ attribute writable. Backport of CPython PR #149172.
  • Fix setting of __required_keys__ and __optional_keys__ when inheriting keys with the same name.
  • Add support for AsyncIterator, io.Reader, io.Writer and os.PathLike protocols as bases for other protocols.
  • Fix incorrect behaviour on Python 3.9 and Python 3.10 that meant that calling isinstance with typing_extensions.Concatenate[...] or typing_extensions.Unpack[...] as the first argument could have a different result in some situations depending on whether or not a profiling function had been set using sys.setprofile. This affected both CPython and PyPy implementations. Patch by Brian Schubert.
  • Fix __init_subclass__() behavior in the presence of multiple inheritance involving an @deprecated-decorated base class. Backport of CPython PR #138210 by Brian Schubert.
  • Raise TypeError when attempting to subclass typing_extensions.ParamSpec on Python 3.9. The typing implementation has always raised an error, and the typing_extensions implementation has raised an error on Python 3.10+ since typing_extensions v4.6.0. Patch by Brian Schubert.
  • Add the bound, covariant, contravariant, and infer_variance parameters to TypeVarTuple.
  • Officially support the bound, covariant, contravariant and infer_variance parameters to ParamSpec. Improve the validation of these parameters at runtime.
  • Rename typing_extensions.Sentinel to typing_extensions.sentinel, following the name that has been adopted for builtins.sentinel on Python 3.15. typing_extensions.Sentinel is retained as a soft-deprecated alias for backwards compatibility.
  • Add support for pickling sentinels.
  • Sentinels now preserve their identity when copied or deep-copied.
  • Deprecate passing name as a keyword argument or repr as a positional argument to the sentinel constructor.
  • The default repr of a sentinel X = sentinel("X") is now X rather than <X>.
  • Deprecate arbitrary attribute assignments to sentinels.
  • Deprecate subclassing sentinels.
  • Add support for Python 3.15.

Release 4.15.0 (August 25, 2025)

... (truncated)

Commits

Updates gdstk to 1.0.0

Changelog

Sourced from gdstk's changelog.

1.0.0 - 2026-02-21

Added

  • Support for layer names from/to OASIS files (#322, thanks nmz787-intel for the contribution).

Fixed

  • Missing docs for gds_timestamp.

0.9.62 - 2026-01-03

Added

  • Support for exporting empty flexpaths to GDSII/OASIS.

Fixed

  • Bug in point-in-polygon checks.
  • Array printing.

0.9.61 - 2025-08-28

Added

  • Support for non-standard repetition vectors in GDSII (#293, #299, thanks svollenweider, WesYu).

Fixed

  • Bug in OASIS output when using explicit repetitions (#307, thanks RedFalsh).
  • Time stamp format in GDSII (#308, thanks albachten).

0.9.60 - 2025-04-15

Fixed

  • Added support to 32-bit layers and datatypes.

0.9.59 - 2025-02-11

Fixed

  • Treat string properties as binary byte arrays in OASIS.

0.9.58 - 2024-11-25

Changed

  • Empty paths now give a warning when being converted to polygons or stored in GDSII/OASIS.

Fixed

  • Missing paths when vertices were separated exactly by the tolerance (#277)

0.9.57 - 2024-11-07

Fixed

  • Bug when removing GDSII properties (#276, thanks jatoben).

0.9.56 - 2024-10-28

Added

  • Support for Python 3.13.

Fixed

  • Copy Raith data in Cell::get_flexpaths.

0.9.55 - 2024-08-31

Fixed

  • Memory bug fix for Raith data

0.9.54 - 2024-08-31

Changed

... (truncated)

Commits
  • 9575737 Release v1.0.0
  • 9315981 Add OASIS layername feature: array-based implementation and serialization
  • 25a7c51 Update _gdstk.pyi to include gds_timestamp
  • 13dffc4 Add gds_timestamp to docs
  • 525494b Release v0.9.62
  • 5b12244 Bug fixes for point in polygon checks and array printing
  • 5e871f6 Add support for exporting empty flexpaths to gds/oas
  • 9ceec43 Enable python 3.14 builds
  • 5f5def6 Release 0.9.61
  • 26857c7 Fix for #304: explicit repetition in OASIS
  • Additional commits viewable in compare view

Updates mlx to 0.31.2

Release notes

Sourced from mlx's releases.

v0.31.2

Highlights

What's Changed

... (truncated)

Commits
  • 68cf2fd Fix mx.prod vjp for complex types (#3433)
  • c594e6e Fix use after move in Compiled primitive (#3427)
  • 7d40a4f Throw meaningful error when Metal device is not found (#3428)
  • 5f519ef Fix bytes_per_key truncation in random kernels (Metal + CUDA) (#3432)
  • 705c828 Fix synchronize for ThreadLocalStream (#3429)
  • b4ddf9b Fix flaky TestVmap.test_vmap_masked_scatter (#3421)
  • 1f5a413 Make Scheduler::enqueue thread safe (#3423)
  • a6222f5 Speed up NAX split-K by better tuning and routing and fix NAX addmm (#3422)
  • fa4320d [CUDA] Handle residue k in qmm_naive (#3379)
  • 859f22f [CUDA] GatherQMM matrix-matrix sm80/naive path (#3417)
  • Additional commits viewable in compare view

Updates tidy3d to 2.11.2

Release notes

Sourced from tidy3d's releases.

v2.11.2

What's Changed

Added

  • Added documentation page explaining the three S-parameter definitions (pseudo, power, symmetric_pseudo) in TerminalComponentModeler, including mathematical derivations, symmetry properties, and power calculations.
  • TerminalComponentModeler now warns when its freqs exceeds the soft limit used by frequency-domain monitors.
  • Added local EME support for expressing a propagated S-matrix in user-supplied port modes.

Changed

  • Added Result.real_cost to the design plugin so pre/post runs can report billed FlexCredit usage after execution.
  • Increased the maximum number of EME cells from 100 to 500.

Fixed

  • Fixed mode solver to place PEC boundaries at the closest grid boundary outside the monitor plane, matching user expectations when using the plane bounds as PEC locations (common in RF workflows). Added solver_field_bounds to ensure accurate field interpolation near the hard boundary.
  • Fixed eps_model() across Tidy3D media classes to consistently accept scalar, list, and NumPy array frequency inputs, including custom and anisotropic media.
  • Fixed ModeSimulation.from_mode_solver() to infer a wavelength from the mode-solver-associated simulation source when converting simulations that use auto grid without an explicit grid_spec.wavelength.
  • Fixed TFSF source validation to reject setups whose in-domain region collapses to zero extent along both tangential directions, such as 1D simulations.
  • Fixed CustomPoleResidue adjoint postprocessing to preserve the frequency axis for zero-gradient multi-frequency chunks.
  • Stabilized Tidy3D model JSON float formatting across supported pydantic-core versions.
  • Fixed EME S-matrix basis conversion for EMEModeSweep results that request different numbers of modes at different sweep points.
  • Fixed TerminalComponentModeler to snap WavePort internal absorbers and mode sources to the updated simulation grid (which includes the wavelength override and mesh overrides) rather than the original user-provided grid, preventing absorbers from landing off-grid in the final simulation.
  • Fixed inline PyVista plots in Jupyter on Python 3.13+ so they render interactively instead of failing or falling back to a static image.

Full Changelog: flexcompute/tidy3d@v2.11.1...v2.11.2

Changelog

Sourced from tidy3d's changelog.

[2.11.2] - 2026-05-03

Added

  • Added documentation page explaining the three S-parameter definitions (pseudo, power, symmetric_pseudo) in TerminalComponentModeler, including mathematical derivations, symmetry properties, and power calculations.
  • TerminalComponentModeler now warns when its freqs exceeds the soft limit used by frequency-domain monitors.
  • Added local EME support for expressing a propagated S-matrix in user-supplied port modes.

Changed

  • Added Result.real_cost to the design plugin so pre/post runs can report billed FlexCredit usage after execution.
  • Increased the maximum number of EME cells from 100 to 500.

Fixed

  • Fixed mode solver to place PEC boundaries at the closest grid boundary outside the monitor plane, matching user expectations when using the plane bounds as PEC locations (common in RF workflows). Added solver_field_bounds to ensure accurate field interpolation near the hard boundary.
  • Fixed eps_model() across Tidy3D media classes to consistently accept scalar, list, and NumPy array frequency inputs, including custom and anisotropic media.
  • Fixed ModeSimulation.from_mode_solver() to infer a wavelength from the mode-solver-associated simulation source when converting simulations that use auto grid without an explicit grid_spec.wavelength.
  • Fixed TFSF source validation to reject setups whose in-domain region collapses to zero extent along both tangential directions, such as 1D simulations.
  • Fixed CustomPoleResidue adjoint postprocessing to preserve the frequency axis for zero-gradient multi-frequency chunks.
  • Stabilized Tidy3D model JSON float formatting across supported pydantic-core versions.
  • Fixed EME S-matrix basis conversion for EMEModeSweep results that request different numbers of modes at different sweep points.
  • Fixed TerminalComponentModeler to snap WavePort internal absorbers and mode sources to the updated simulation grid (which includes the wavelength override and mesh overrides) rather than the original user-provided grid, preventing absorbers from landing off-grid in the final simulation.
  • Fixed inline PyVista plots in Jupyter on Python 3.13+ so they render interactively instead of failing or falling back to a static image.

[2.11.1] - 2026-04-21

Added

  • Added local EME propagation via EMESimulation.propagate(mode_data) and a per-element staged pipeline (mode_simulations, stage_cell_modes, compute_cell_overlap, compute_interface_overlap, compute_cell_smatrix, compute_interface_smatrix, compute_smatrix). For iterative design with many sweeps on the same modal basis, compute_overlaps(mode_data) + propagate_from_overlaps(cell_overlaps, interface_overlaps) amortizes the overlap stage. Intermediate results (EMEStageCellOverlap, EMEStageInterfaceSMatrix, etc.) are serializable and reusable across parameter sweeps. EMEFreqSweep is not supported; use EMESimulation.freqs directly. The local path does not support anisotropic media in bent cells with bend_medium_frame="global"; use bend_medium_frame="co_rotating" or the remote backend in that case.
  • Added filter_func support to MethodGrid and MethodMonteCarlo in the design plugin so invalid parameter combinations can now be skipped during parameter sweeps.
  • Added plot_field_components() to ModeSimulationData and ModeSolver for plotting multiple mode field components in one call.
  • Added FieldProjector.from_near_field_data() for projecting directly from custom or modified FieldData.

Changed

  • Improved near-field projection performance.
  • Strip autograd tracers from DataArray plotting functions before plotting.
  • Keep original simulation data from being zeroed out during the adjoint pipeline.
  • Updated adjoint shape integration to sample interface permittivity directly from anisotropic simulation permittivity data.

Fixed

  • Fixed ValueError shape mismatch in Simulation.epsilon() when a CustomMedium uses ScalarFieldDataArray with a frequency dimension, by squeezing the leftover f dimension after spatial interpolation in eps_diagonal_on_grid.
  • Fixed wrapped angle_theta handling for glancing-incidence checks so values like -pi/2 and 5*pi/2 are validated consistently in ModeSpec and angled field sources.
  • Added frontend validation for TCAD refinement regions and lines so unsupported degenerate shapes are rejected before submission.
  • Fixed plot function override for tidy3d data arrays.

[2.11.0] - 2026-04-06

... (truncated)

Commits
  • b03bb7c docs: update latest submodules
  • 262ab6c chore(tidy3d-client): restore github release workflow (FXC-7289) (#3366)
  • 7bcbcdc chore(changelog): 🤖 build release notes for 2.11.2 (#4976)
  • bd01173 hotfix(tidy3d-client): pre-launch trame Jupyter server to bypass nest_asyncio...
  • d1a8aa7 chore(tidy3d-client): move self-hosted docs source to compute (#4942)
  • 81df8fd docs(tidy3d-client): document CustomDoping charge docs (FXC-6418) (#4951)
  • 809916e hotfix(tidy3d-client, tidy3d-solver): refine semiconductor-conductor distance...
  • 3608a7d hotfix(tidy3d-client): snap absorber and source to updated grid in TerminalCo...
  • b54507c docs(tidy3d-client): add S-parameter definitions documentation page (FX...

    Description has been truncated

@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Jun 27, 2026
@dependabot dependabot Bot changed the title build(deps): bump the pip-dependencies group with 30 updates build(deps): bump the pip-dependencies group across 1 directory with 30 updates Jul 4, 2026
@dependabot
dependabot Bot force-pushed the dependabot/pip/pip-dependencies-e0658a4a71 branch from 465a8ed to 800f6a5 Compare July 4, 2026 11:06
@dependabot
build(deps): bump the pip-dependencies group across 1 directory with …
980b7a4 
…30 updates

Updates the requirements on [jax](https://github.com/jax-ml/jax), [equinox](https://github.com/patrick-kidger/equinox), [trimesh](https://github.com/mikedh/trimesh), [scipy](https://github.com/scipy/scipy), [matplotlib](https://github.com/matplotlib/matplotlib), [rich](https://github.com/Textualize/rich), [typing-extensions](https://github.com/python/typing_extensions), [gdstk](https://github.com/heitzmann/gdstk), [mlx](https://github.com/ml-explore/mlx), [tidy3d](https://github.com/flexcompute/tidy3d), [h5py](https://github.com/h5py/h5py), [pydantic](https://github.com/pydantic/pydantic), [plotly](https://github.com/plotly/plotly.py), [pyvista](https://github.com/pyvista/pyvista), [trame](https://github.com/Kitware/trame), [mcp](https://github.com/modelcontextprotocol/python-sdk), [black](https://github.com/psf/black), [ipykernel](https://github.com/ipython/ipykernel), [pre-commit](https://github.com/pre-commit/pre-commit), [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions), [pytest](https://github.com/pytest-dev/pytest), [pytest-cov](https://github.com/pytest-dev/pytest-cov), [ruff](https://github.com/astral-sh/ruff), [tox-uv](https://github.com/tox-dev/tox-uv), [pydoclint](https://github.com/jsh9/pydoclint), [sphinx](https://github.com/sphinx-doc/sphinx), [sphinx-book-theme](https://github.com/executablebooks/sphinx-book-theme), [nbsphinx](https://github.com/spatialaudio/nbsphinx), [sphinx-autodoc-typehints](https://github.com/tox-dev/sphinx-autodoc-typehints) and [myst-nb](https://github.com/executablebooks/myst-nb) to permit the latest version.

Updates `jax` to 0.10.2
- [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-v0.4.36...jax-v0.10.2)

Updates `equinox` to 0.13.8
- [Release notes](https://github.com/patrick-kidger/equinox/releases)
- [Commits](patrick-kidger/equinox@v0.11.10...v0.13.8)

Updates `trimesh` to 4.12.2
- [Release notes](https://github.com/mikedh/trimesh/releases)
- [Commits](mikedh/trimesh@4.5.3...4.12.2)

Updates `scipy` to 1.17.1
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.11.0...v1.17.1)

Updates `matplotlib` to 3.11.0
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.9.4...v3.11.0)

Updates `rich` to 15.0.0
- [Release notes](https://github.com/Textualize/rich/releases)
- [Changelog](https://github.com/Textualize/rich/blob/main/CHANGELOG.md)
- [Commits](Textualize/rich@v13.9.4...v15.0.0)

Updates `typing-extensions` to 4.16.0
- [Release notes](https://github.com/python/typing_extensions/releases)
- [Changelog](https://github.com/python/typing_extensions/blob/main/CHANGELOG.md)
- [Commits](python/typing_extensions@4.14.1...4.16.0)

Updates `gdstk` to 1.0.0
- [Release notes](https://github.com/heitzmann/gdstk/releases)
- [Changelog](https://github.com/heitzmann/gdstk/blob/main/CHANGELOG.md)
- [Commits](heitzmann/gdstk@v0.9.0...v1.0.0)

Updates `mlx` to 0.31.2
- [Release notes](https://github.com/ml-explore/mlx/releases)
- [Commits](ml-explore/mlx@v0.18.0...v0.31.2)

Updates `tidy3d` to 2.11.2
- [Release notes](https://github.com/flexcompute/tidy3d/releases)
- [Changelog](https://github.com/flexcompute/tidy3d/blob/develop/CHANGELOG.md)
- [Commits](flexcompute/tidy3d@v2.8.0...v2.11.2)

Updates `h5py` to 3.16.0
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](h5py/h5py@3.10.0...3.16.0)

Updates `pydantic` to 2.13.4
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v2.6.0...v2.13.4)

Updates `plotly` to 6.8.0
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md)
- [Commits](plotly/plotly.py@v5.22.0...v6.8.0)

Updates `pyvista` to 0.48.4
- [Release notes](https://github.com/pyvista/pyvista/releases)
- [Commits](pyvista/pyvista@v0.44.0...v0.48.4)

Updates `trame` to 3.13.2
- [Release notes](https://github.com/Kitware/trame/releases)
- [Changelog](https://github.com/Kitware/trame/blob/master/CHANGELOG.md)
- [Commits](Kitware/trame@v3.6.0...v3.13.2)

Updates `mcp` to 1.28.1
- [Release notes](https://github.com/modelcontextprotocol/python-sdk/releases)
- [Changelog](https://github.com/modelcontextprotocol/python-sdk/blob/main/RELEASE.md)
- [Commits](modelcontextprotocol/python-sdk@v1.0.0...v1.28.1)

Updates `black` to 26.5.1
- [Release notes](https://github.com/psf/black/releases)
- [Changelog](https://github.com/psf/black/blob/main/CHANGES.md)
- [Commits](psf/black@24.10.0...26.5.1)

Updates `ipykernel` to 7.3.0
- [Release notes](https://github.com/ipython/ipykernel/releases)
- [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md)
- [Commits](ipython/ipykernel@v6.29.5...v7.3.0)

Updates `pre-commit` to 4.6.0
- [Release notes](https://github.com/pre-commit/pre-commit/releases)
- [Changelog](https://github.com/pre-commit/pre-commit/blob/main/CHANGELOG.md)
- [Commits](pre-commit/pre-commit@v4.0.1...v4.6.0)

Updates `pymdown-extensions` to 11.0.1
- [Release notes](https://github.com/facelessuser/pymdown-extensions/releases)
- [Commits](facelessuser/pymdown-extensions@10.12...11.0.1)

Updates `pytest` to 9.1.1
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.4...9.1.1)

Updates `pytest-cov` to 7.1.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.0.0...v7.1.0)

Updates `ruff` to 0.15.20
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.8.2...0.15.20)

Updates `tox-uv` to 1.35.2
- [Release notes](https://github.com/tox-dev/tox-uv/releases)
- [Commits](tox-dev/tox-uv@1.16.1...1.35.2)

Updates `pydoclint` to 0.9.1
- [Release notes](https://github.com/jsh9/pydoclint/releases)
- [Changelog](https://github.com/jsh9/pydoclint/blob/main/CHANGELOG.md)
- [Commits](jsh9/pydoclint@0.6.6...0.9.1)

Updates `sphinx` to 9.0.4
- [Release notes](https://github.com/sphinx-doc/sphinx/releases)
- [Changelog](https://github.com/sphinx-doc/sphinx/blob/v9.0.4/CHANGES.rst)
- [Commits](sphinx-doc/sphinx@v0.1.61611...v9.0.4)

Updates `sphinx-book-theme` to 1.2.0
- [Release notes](https://github.com/executablebooks/sphinx-book-theme/releases)
- [Changelog](https://github.com/executablebooks/sphinx-book-theme/blob/main/CHANGELOG.md)
- [Commits](executablebooks/sphinx-book-theme@v1.1.4...v1.2.0)

Updates `nbsphinx` to 0.9.8
- [Release notes](https://github.com/spatialaudio/nbsphinx/releases)
- [Changelog](https://github.com/spatialaudio/nbsphinx/blob/master/NEWS.rst)
- [Commits](spatialaudio/nbsphinx@0.9.0...0.9.8)

Updates `sphinx-autodoc-typehints` to 3.6.1
- [Release notes](https://github.com/tox-dev/sphinx-autodoc-typehints/releases)
- [Commits](tox-dev/sphinx-autodoc-typehints@3.2.0...3.6.1)

Updates `myst-nb` to 1.4.0
- [Release notes](https://github.com/executablebooks/myst-nb/releases)
- [Changelog](https://github.com/executablebooks/MyST-NB/blob/main/CHANGELOG.md)
- [Commits](executablebooks/MyST-NB@v1.3.0...v1.4.0)

---
updated-dependencies:
- dependency-name: black
  dependency-version: 26.5.1
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: equinox
  dependency-version: 0.13.8
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: gdstk
  dependency-version: 1.0.0
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: h5py
  dependency-version: 3.16.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: ipykernel
  dependency-version: 7.3.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: jax
  dependency-version: 0.10.2
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: matplotlib
  dependency-version: 3.11.0
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: mcp
  dependency-version: 1.28.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: mlx
  dependency-version: 0.31.2
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: myst-nb
  dependency-version: 1.4.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: nbsphinx
  dependency-version: 0.9.8
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: plotly
  dependency-version: 6.8.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: pre-commit
  dependency-version: 4.6.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: pydantic
  dependency-version: 2.13.4
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: pydoclint
  dependency-version: 0.8.6
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: pymdown-extensions
  dependency-version: 10.21.3
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: pytest
  dependency-version: 9.1.1
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: pytest-cov
  dependency-version: 7.1.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: pyvista
  dependency-version: 0.48.4
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: rich
  dependency-version: 15.0.0
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: ruff
  dependency-version: 0.15.18
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: scipy
  dependency-version: 1.17.1
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: sphinx
  dependency-version: 9.0.4
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: sphinx-autodoc-typehints
  dependency-version: 3.6.1
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: sphinx-book-theme
  dependency-version: 1.2.0
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: tidy3d
  dependency-version: 2.11.2
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: tox-uv
  dependency-version: 1.35.2
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: trame
  dependency-version: 3.13.2
  dependency-type: direct:development
  dependency-group: pip-dependencies
- dependency-name: trimesh
  dependency-version: 4.12.2
  dependency-type: direct:production
  dependency-group: pip-dependencies
- dependency-name: typing-extensions
  dependency-version: 4.15.0
  dependency-type: direct:production
  dependency-group: pip-dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot
dependabot Bot force-pushed the dependabot/pip/pip-dependencies-e0658a4a71 branch from 800f6a5 to 980b7a4 Compare July 11, 2026 11:06
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