deps(deps): bump the python-dependencies group with 23 updates by dependabot[bot] · Pull Request #734 · QuantClimate/GPJax

dependabot · 2026-07-27T08:48:32Z

Bumps the python-dependencies group with 23 updates:

Package	From	To
jax	`0.9.0`	`0.10.2`
optax	`0.2.6`	`0.2.8`
numpyro	`0.19.0`	`0.21.0`
jaxtyping	`0.3.6`	`0.3.11`
equinox	`0.13.5`	`0.13.8`
lineax	`0.1.0`	`0.1.1`
scipy	`1.17.0`	`1.17.1`
numpy	`2.4.1`	`2.4.6`
rich	`14.3.1`	`15.0.0`
mkdocs-material	`9.7.1`	`9.7.7`
mkdocs-jupyter	`0.25.1`	`0.26.3`
mkdocs-gen-files	`0.6.0`	`0.6.1`
mkdocs-literate-nav	`0.6.2`	`0.6.3`
matplotlib	`3.10.8`	`3.11.1`
ipython	`9.9.0`	`9.15.0`
ipykernel	`6.31.0`	`7.3.0`
blackjax	`1.3`	`1.6.2`
pymdown-extensions	`10.20.1`	`11.0.1`
nbconvert	`7.16.6`	`7.17.1`
scikit-learn	`1.8.0`	`1.9.0`
markdown-it-py	`4.0.0`	`4.2.0`
pygments	`2.19.2`	`2.20.0`
typing-extensions	`4.15.0`	`4.16.0`

Updates jax from 0.9.0 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.

JAX v0.10.1

New features

Added ResizeMethod.AREA to jax.image.resize, which matches TensorFlow's AREA resizing (#20098).

Added jax.scipy.linalg.hadamard for constructing Hadamard matrices (#10144).

Added jax.scipy.linalg.circulant for constructing circulant matrices (#10144).

Added jax.scipy.linalg.dft for constructing discrete Fourier transform matrices (#10144).

Added jax.scipy.linalg.leslie for constructing Leslie matrices (#10144).

Added jax.scipy.linalg.companion for constructing companion matrices from polynomial coefficients (#10144).

Added jax.scipy.linalg.fiedler for constructing symmetric Fiedler matrices (#10144).

Added jax.scipy.linalg.helmert for constructing Helmert matrices (#10144).

Moved RNG APIs from "implementations" to dtypes (#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 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 version of JAX, this will become an error, if you depend on using them as leaves, pass is_leaf to jax.tree.* methods.

... (truncated)

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
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Updates optax from 0.2.6 to 0.2.8

Release notes

Sourced from optax's releases.

Optax 0.2.8

What's Changed

Following the JAX 0.9.2 release, the jax_pmap_shmap_merge config flag was removed so that the jax.pmap implementation is always based on jax.jit and jax.shard_map, and opting into the old jax.pmap behavior is no longer an option. Optax had opted into the old behavior to give users time to migrate, and as of Optax 0.2.8 this is no longer supported. This changed shouldn't impact most users, but if you experience errors or performance regressions as a result of it, you can update your code following JAX's migration guide (or use JAX 0.9.2 or earlier and set jax.config.update("jax_pmap_shmap_merge", False)).

Explicitly specify the dtype of the gradient accumulator in the MultiStep transform. by @copybara-service[bot] in google-deepmind/optax#1605

feat: add preconditioning and coef presets to muon by @massena-t in google-deepmind/optax#1602

Backwards compatibility export for the newton schulz iterator by @copybara-service[bot] in google-deepmind/optax#1608

Remove TensorFlow dependency in Adversarial training example by @rajasekharporeddy in google-deepmind/optax#1609

Improve lookahead docstrings with example and usage notes by @rdyro in google-deepmind/optax#1619

Make sure inject_hyperparams uses the dtype inferred from parameters... by @copybara-service[bot] in google-deepmind/optax#1615

Memory-optimization for microbatching. by @copybara-service[bot] in google-deepmind/optax#1623

Remove TensorFlow dependency and migrate mlp_mnist to Flax NNX by @selamw1 in google-deepmind/optax#1536

Let inject use the highest dtype found in the params as the default dtype of params. by @copybara-service[bot] in google-deepmind/optax#1628

Support scheduling alpha for AdEMAmix by @copybara-service[bot] in google-deepmind/optax#1630

[JAX] Suppress type errors found by pytype after correcting definition of jax.typing.ArrayLike. by @copybara-service[bot] in google-deepmind/optax#1629

[JAX] Suppress type errors found by pytype after correcting definition of jax.typing.ArrayLike. by @copybara-service[bot] in google-deepmind/optax#1633

New Contributors

@massena-t made their first contribution in google-deepmind/optax#1602

@selamw1 made their first contribution in google-deepmind/optax#1536

Full Changelog: google-deepmind/optax@v0.2.7...v0.2.8

Optax 0.2.7

What's Changed

Update Optax version to 0.2.7.dev. by @copybara-service[bot] in google-deepmind/optax#1420

Fix doctest by @copybara-service[bot] in google-deepmind/optax#1424

Fix piecewise interpolate with 0 first split by @rdyro in google-deepmind/optax#1425

Expose weight decay as a schedule option in all alias optimizers. by @copybara-service[bot] in google-deepmind/optax#1427

Skip schedule free tests casting from complex to float. by @copybara-service[bot] in google-deepmind/optax#1428

Add monitor and measure_with_ema to Optax transformations. by @copybara-service[bot] in google-deepmind/optax#1430

Add consistent rms scaling for muon update by @shuningjin in google-deepmind/optax#1435

Add microbatch transformation to optax/experimental. by @copybara-service[bot] in google-deepmind/optax#1434

Add experimental aggregators in optax. by @copybara-service[bot] in google-deepmind/optax#1436

Add missing exports to optax/init.py. by @carlosgmartin in google-deepmind/optax#1433

Adding microbatch to the docs by @copybara-service[bot] in google-deepmind/optax#1443

Add a few sharding-related tests to optax. by @copybara-service[bot] in google-deepmind/optax#1450

Allow instantiating optimizers before jax has been initialized. by @copybara-service[bot] in google-deepmind/optax#1454

Adding gradient variance tracking. by @copybara-service[bot] in google-deepmind/optax#1451

Resolve remaining sharding test failures in optax. by @copybara-service[bot] in google-deepmind/optax#1457

Add optional "in_axes" and "argnames" kwargs to microbatch, which will allow for natural composition with jax.vmap. by @copybara-service[bot] in google-deepmind/optax#1442

Honor inject_hyperparams dtypes if passed as jax.Arrays. by @copybara-service[bot] in google-deepmind/optax#1460

Update reshape_batch_axis to include sharding information when in explicit sharding mode. by @copybara-service[bot] in google-deepmind/optax#1459

Fix typo in L-BFGS debug information section by @partev in google-deepmind/optax#1465

Deprecate second order utilities. by @copybara-service[bot] in google-deepmind/optax#1466

Deprecate optax.global_norm in favor of optax.tree.norm. by @carlosgmartin in google-deepmind/optax#1368

Add signum optimizer by @copybara-service[bot] in google-deepmind/optax#1463

Use internal warn_deprecated_function instead of the Chex version. by @copybara-service[bot] in google-deepmind/optax#1469

Define internal assert_trees_all_{close, equal} functions and use them in tests instead of the Chex versions. by @copybara-service[bot] in google-deepmind/optax#1481

Replace (non-test) Chex assertions, usually with ValueErrors. by @copybara-service[bot] in google-deepmind/optax#1483

Replace chex.Numeric with jax.typing.ArrayLike. Replace chex.Scalar with float/int as appropriate. by @copybara-service[bot] in google-deepmind/optax#1479

... (truncated)

Commits

107e9ad Release Optax version 0.2.8.
70df570 [JAX] Suppress type errors found by pytype after correcting definition of jax...
d015bc4 [JAX] Suppress type errors found by pytype after correcting definition of jax...
82601b4 Support scheduling alpha for AdEMAmix
a6ba37b Let inject use the highest dtype found in the params as the default dtype of ...
4a53ba3 Merge pull request #1536 from selamw1:mnl_nnx
b24c5fa Merge branch 'google-deepmind:main' into mnl_nnx
9ff5961 Memory-optimization for microbatching.
1e52e8c Make sure inject_hyperparams uses the dtype inferred from parameters...
a6c2942 Merge pull request #1619 from rdyro:lookahead-imprv
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Updates numpyro from 0.19.0 to 0.21.0

Release notes

Sourced from numpyro's releases.

0.21.0

What's Changed

Add pupport forward-mode differentiation with autoguide by @juanitorduz in pyro-ppl/numpyro#2163

Fix TraceEnum_ELBO ignoring is_auxiliary option by @juanitorduz in pyro-ppl/numpyro#2164

Fix: Tracer leaks during NUTS sampling on random_nnx_module when NNX module contains mutable state by @juanitorduz in pyro-ppl/numpyro#2162

FIX: Running MCMC within JIT causes tracer leaks by @juanitorduz in pyro-ppl/numpyro#2165

Example: Embarrassingly Parallel MCMC via Consensus Monte Carlo by @juanitorduz in pyro-ppl/numpyro#2167

Remove vectorize_particles from RenyiELBO docstring (Issue #2166) by @juanitorduz in pyro-ppl/numpyro#2168

fix repeated recompilation in no-progress-bar fori_collect path by @simeoncampos in pyro-ppl/numpyro#2171

Update GPJax notebook to simplified API by @thomaspinder in pyro-ppl/numpyro#2177

Effect handlers Tutorial by @juanitorduz in pyro-ppl/numpyro#2169

Generate outputs by @thomaspinder in pyro-ppl/numpyro#2179

improve type error message for 'fn' in sample function by @Qazalbash in pyro-ppl/numpyro#2175

Fix xla_pmap_p import for JAX versions that removed pmap by @saitcakmak in pyro-ppl/numpyro#2173

Change key type from prng_key to Array by @fehiepsi in pyro-ppl/numpyro#2178

feat(gh-2142): add VSBC diagnostic by @michaelellis003 in pyro-ppl/numpyro#2170

Allow zero rate for Poisson distribution. by @tillahoffmann in pyro-ppl/numpyro#2176

Bump to 0.21.0 by @fehiepsi in pyro-ppl/numpyro#2180

New Contributors

@simeoncampos made their first contribution in pyro-ppl/numpyro#2171

@saitcakmak made their first contribution in pyro-ppl/numpyro#2173

Full Changelog: pyro-ppl/numpyro@0.20.1...0.21.0

0.20.1

What's Changed

DOC: Minor wording changes to numpyro code comments by @star1327p in pyro-ppl/numpyro#2133

chore: files formatted with ruff-v0.15.0 by @Qazalbash in pyro-ppl/numpyro#2136

test: update test effected by the optax==0.2.7 release by @Qazalbash in pyro-ppl/numpyro#2137

test: adjust assertion for my_fn_calls based on optax version in test/test_optimizers.py by @Qazalbash in pyro-ppl/numpyro#2140

build: setup.py -> pyproject.toml by @Qazalbash in pyro-ppl/numpyro#2141

chore: replace legacy jax.random.PRNGKey with modern jax.random.key by @Qazalbash in pyro-ppl/numpyro#2134

Add PSIS k-hat diagnostic for variational inference by @michaelellis003 in pyro-ppl/numpyro#2139

doc: Fix a few typos in numpyro code comments by @star1327p in pyro-ppl/numpyro#2144

try fixing downloads datasets by @juanitorduz in pyro-ppl/numpyro#2151

chore: remove dm-haiku support from numpyro.contrib.module by @theorashid in pyro-ppl/numpyro#2150

Add GPJax notebook by @thomaspinder in pyro-ppl/numpyro#2149

GPJax Notebook is correctly display in docs by @juanitorduz in pyro-ppl/numpyro#2152

expose progress bar print rate option in MCMC by @mdmould in pyro-ppl/numpyro#2145

Always call jnp.finfo on array dtypes, not arrays themselves by @dylanhmorris in pyro-ppl/numpyro#2147

fix test because new jax 0.9.2 release by @juanitorduz in pyro-ppl/numpyro#2155

CI(gh-2126): transition to uv for dependency management and testing by @Qazalbash in pyro-ppl/numpyro#2129

fix test because new jax 0.9.2 release [v2] by @juanitorduz in pyro-ppl/numpyro#2156

Use PyThon 3.14 in the Test Suite (CI) by @juanitorduz in pyro-ppl/numpyro#2157

fix: remove frozen project build during doc generation by @Qazalbash in pyro-ppl/numpyro#2160

Bump NumPyro 0.20.1 by @juanitorduz in pyro-ppl/numpyro#2159

New Contributors

@michaelellis003 made their first contribution in pyro-ppl/numpyro#2139

... (truncated)

Commits

e708f34 Bump to 0.21.0 (#2180)
984c743 Allow zero rate for Poisson distribution. (#2176)
df76b46 feat(gh-2142): add VSBC diagnostic (#2170)
cd7c515 Change key type from prng_key to Array (#2178)
18c2cc1 Fix xla_pmap_p import for JAX versions that removed pmap (#2173)
bf4e8ef improve type error message for 'fn' in sample function (#2175)
83de298 Generate outputs (#2179)
78c281c Effect handlers Tutorial (#2169)
c3ad496 Update GPJax notebook to simplified API (#2177)
e10f664 fix repeated recompilation in no-progress-bar fori_collect path (#2171)
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Updates jaxtyping from 0.3.6 to 0.3.11

Release notes

Sourced from jaxtyping's releases.

jaxtyping v0.3.11

Bugfix: the import hook now correctly handles the @no_type_check decorator. (Thanks @jeertmans! patrick-kidger/jaxtyping#393)

Full Changelog: patrick-kidger/jaxtyping@v0.3.10...v0.3.11

jaxtyping v0.3.10

Bugfixes

add u32[4] as a possible PRNGKeyArray type (Thanks @jondeaton! patrick-kidger/jaxtyping#388)

Make variadic objects (e.g. Float[Array, "..."]) survive cloudpickle round-trip. (Thanks @hmgaudecker! patrick-kidger/jaxtyping#391)

Infrastructure

Use dependency groups, uv, and local pre-commit hooks (patrick-kidger/jaxtyping#386)

Add pyrefly as a type checker in pre-commit and dev dependencies (Thanks @lolpack! patrick-kidger/jaxtyping#387)

New Contributors

@patrick-kidger-bot made their first contribution in patrick-kidger/jaxtyping#385

@lolpack made their first contribution in patrick-kidger/jaxtyping#387

@jondeaton made their first contribution in patrick-kidger/jaxtyping#388

@hmgaudecker made their first contribution in patrick-kidger/jaxtyping#391

Full Changelog: patrick-kidger/jaxtyping@v0.3.9...v0.3.10

jaxtyping v0.3.9

Bugfix: typechecking of pytrees of |-style unions, e.g. isinstance(..., PyTree[int | bool]), will no longer silently always pass. patrick-kidger/jaxtyping#381

Full Changelog: patrick-kidger/jaxtyping@v0.3.8...v0.3.9

jaxtyping v0.3.8

Another bugfix release for numpy.typing.ArrayLike on numpy 2.4.0, I think this time only needed Python 3.13+. #380

Full Changelog: patrick-kidger/jaxtyping@v0.3.7...v0.3.8

jaxtyping v0.3.7

Bugfix: SomeDtype[Union[numpy.typing.ArrayLike, ...], ...] will no longer crash in numpy 2.4.0. (#374)

Full Changelog: patrick-kidger/jaxtyping@v0.3.6...v0.3.7

Commits

f4083b2 v0.3.11
c80c7ad fix(lib): import_hook now correctly handles @no_type_check decorator
fca7077 Make _array_types sentinels survive cloudpickle round-trip.
a3e7bef add u32[4] as possible PRNGKeyArray type (#388)
1e79d13 Add pyrefly as a type checker in pre-commit and dev dependencies (#387)
1d54108 Use dependency groups, uv, and local pre-commit hooks (#386)
0609755 bump pymdown-extensions; pin pygments
f7e0088 0.3.9
aae2fa7 Fix typechecking of pytree of new-style union.
f6477d4 bump release pipeline to 3.12 to avoid jax weirdness on 3.11
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Updates equinox from 0.13.5 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.

Update awesome-list.md by @LambdaP in patrick-kidger/equinox#1225

Add return type to BoundMethod by @nstarman in patrick-kidger/equinox#1222

Added progress meters to equinox.internal (=not a public API) (Thanks @ASKabalan! patrick-kidger/equinox#1226)

New Contributors

@LambdaP made their first contribution in patrick-kidger/equinox#1225

@ASKabalan made their first contribution in patrick-kidger/equinox#1226

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

Equinox v0.13.7

Compatibility:

JAX v0.10.0 deprecated jax.core.find_top_trace; now using jax.extend.core.find_top_trace when available. (#1218)

JAX v0.10.0 removed jax.core.get_aval, jax.core.mapped_aval, jax.core.unmapped_aval; suppressed the resulting type errors. (#1218)

JAX v0.9.2 now compatible with equinox.internal.finalise_jaxpr. (Thanks @kasper0406! #1200)

Other:

Module.__new__ now returns Self rather than Module. (Thanks @RunnersNum40! #1207)

Switched to uv and dependency groups for development. (#1218)

New awesome-list entries:

Add Parax and ParamRF to awesome-list (Thanks @gvcallen! #1209)

add peex to awesome-list (Thanks @sammccallum! #1208)

Add GPJax to awesome-list (Thanks @thomaspinder! #1213)

Add chronos2 implementation to awesome-list (Thanks @theorashid! #1214)

New Contributors

@kasper0406 made their first contribution in patrick-kidger/equinox#1200

@patrick-kidger-bot made their first contribution in patrick-kidger/equinox#1205

@gvcallen made their first contribution in patrick-kidger/equinox#1209

@sammccallum made their first contribution in patrick-kidger/equinox#1208

@thomaspinder made their first contribution in patrick-kidger/equinox#1213

@theorashid made their first contribution in patrick-kidger/equinox#1214

Full Changelog: patrick-kidger/equinox@v0.13.6...v0.13.7

Equinox v0.13.6

Bug fix: overriding an AbstractClassVar with a concrete instance field will no longer cause a crash when attempting to instantiate the module. (#1198)

Full Changelog: patrick-kidger/equinox@v0.13.5...v0.13.6

Commits

dfadb04 0.13.8 release
d6ae901 Add progress meter to equinox
87f4072 Add return type to BoundMethod
53b3c75 Update awesome-list.md
5972a41 Bump version to 0.13.7
d77d057 Use dependency groups, uv, and local pre-commit hooks (#1218)
7f7b46c Update awesome-list.md
9e7cc3e Add GPJax to list (#1213)
e41cdac Change Module.__new__ return self type rather than Module (#1207)
940f903 add peex to awesome-list
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Updates lineax from 0.1.0 to 0.1.1

Release notes

Sourced from lineax's releases.

lineax v0.1.1

This is mostly a bug fix, documentation and under-the-hood performance improvement release with one new feature—the lx.invert transformation which produces an operator representing the inverse of a matrix. Use of coloring rules should make using implicit solvers in diffrax for tridiagonal Jacobian/FunctionLinearOperators at least an order of magnitude faster.

Breaking Changes

Extraction of diagonal/tridiagonals of now leverages the promise of a matrix being tagged as diagonal/tridiagonal more heavily. If you have previously used the tag for an operator that you just wanted lineax to TREAT as diagonal/tridiagonal you may now get incorrect results. In most cases the right fix probably be to first manually extract (tri)diagonal and construct the (Tri)DiagonalOperator explicitly, please raise an issue if you need any further assistance.

lineax.linear_solve now stop-gradient's automatically (#213), it is unlikely this will break any existing use-cases but may make manual stop-gradienting unecessary

Removed AuxLinearOperator (#203)

Features

Add invert helper function to wrap lineax.linear_solve in FunctionLinearOperator. Materialising an inverse is now as simple as lx.invert(op).as_matrix(). (#206)

Compatibility

lineax v0.1.1 now requires JAX >= 0.10.0 which provides a lowering to LAPACK/cuSolver's` ormqr for more efficient QR solve adopted in #219.

Bugfixes

Fix derived tag check rules for composite operators (e.g. Composed/Neg/Mul/AddLinearOperator) (#192)

Linearisation of functions custom_vjp's are now supported by lineax.linearize(JacobianLinearOperator(f, x, jac="bwd")) by using jax.linear_transpose under the hood. (#191)

Complex positive/negative semi-definite matrices no longer register as symmetric (#200)

lineax.LSMR no longer fails when initial residual is exactly zero. (HUGE thanks to @f0uriest for spotting this tricky and hard-to-spot bug #202)

Differentiating through linear_solve's no longer differentiates through solver.init this means using solver's with no or incorrect jvp rule is now possible (#212)

Performance

Coloring rules now used to massively speed up diagonal/tridiagonal extraction of tagged Jacobian/FunctionLinearOperators (#164, #165)

Normal and iterative solvers now apply lineax.linearise under the hood to avoid multiple sequential AD passes (#198)

Furthermore, lineax.Normal(lineax.Cholesky()) now materialises the inner operator before constructing the Gram matrix (#207)

ComposedLinearOperator.as_matrix no longer materialises each matrix first but instead batches mv of the first operator over the second matrix (#196)

JAX's ormqr now used for more efficient QR solves (#219)

Documentation

The lineax.LSMR iterative least square solver is now properly documented (#204) after @f0uriest's #202 bug-fixes make it more robust.

Other repo infra PR's not affecting Python package include #214, #216 and #218.

New Contributors

@patrick-kidger-bot 🤖 made their first contribution in patrick-kidger/lineax#216

Full Changelog: patrick-kidger/lineax@v0.1.0...v0.1.1

Commits

2bf9824 0.1.1 release (#220)
53edb88 Use ormqr for more efficient QR solve (#219)
07b477b added LSMR to docs (#204)
0cb6090 Add invert helper function to wrap linear_solve in FunctionLinearOperator (#206)
164a74f Streamline tridiagonalisation of JacobianLinearOperator/FunctionLinearOperato...
886ea57 Efficient diagonal extraction when operator is promised to be diagonal
eb8cb0d Use dependency groups, uv, and local pre-commit hooks
83cf26f bump pymdown-extensions; pin pygments
b6f3087 prevent linear_solve calling jvp of solver.init
5e00f8c Fix construct_singular_matrix not respecting tags
Additional commits viewable in compare view

Updates scipy from 1.17.0 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
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Updates numpy from 2.4.1 to 2.4.6

Release notes

Sourced from numpy's releases.

v2.4.6 (May 18, 2026)

NumPy 2.4.6 Release Notes

NumPy 2.4.6 is a quick release that fixes a regression discovered in the 2.4.5 release.

This release supports Python versions 3.11-3.14

Contributors

A total of 4 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

!EarlMilktea

Charles Harris

Sebastian Berg

Warren Weckesser

Pull requests merged

A total of 4 pull requests were merged for this release.

#31444: MAINT: Prepare 2.4.x for further development

#31453: BUG: Fix regression in arr.conj()

#31459: BUG: np.linalg.svd(..., hermitian=True) returns non-unitary...

#31460: BUG: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator...

v2.4.5 (May 15, 2026)

NumPy 2.4.5 Release Notes

NumPy 2.4.5 is a patch release that fixes bugs discover...
Description has been truncated

Bumps the python-dependencies group with 23 updates: | Package | From | To | | --- | --- | --- | | [jax](https://github.com/jax-ml/jax) | `0.9.0` | `0.10.2` | | [optax](https://github.com/google-deepmind/optax) | `0.2.6` | `0.2.8` | | [numpyro](https://github.com/pyro-ppl/numpyro) | `0.19.0` | `0.21.0` | | [jaxtyping](https://github.com/patrick-kidger/jaxtyping) | `0.3.6` | `0.3.11` | | [equinox](https://github.com/patrick-kidger/equinox) | `0.13.5` | `0.13.8` | | [lineax](https://github.com/google/lineax) | `0.1.0` | `0.1.1` | | [scipy](https://github.com/scipy/scipy) | `1.17.0` | `1.17.1` | | [numpy](https://github.com/numpy/numpy) | `2.4.1` | `2.4.6` | | [rich](https://github.com/Textualize/rich) | `14.3.1` | `15.0.0` | | [mkdocs-material](https://github.com/squidfunk/mkdocs-material) | `9.7.1` | `9.7.7` | | [mkdocs-jupyter](https://github.com/danielfrg/mkdocs-jupyter) | `0.25.1` | `0.26.3` | | [mkdocs-gen-files](https://github.com/oprypin/mkdocs-gen-files) | `0.6.0` | `0.6.1` | | [mkdocs-literate-nav](https://github.com/oprypin/mkdocs-literate-nav) | `0.6.2` | `0.6.3` | | [matplotlib](https://github.com/matplotlib/matplotlib) | `3.10.8` | `3.11.1` | | [ipython](https://github.com/ipython/ipython) | `9.9.0` | `9.15.0` | | [ipykernel](https://github.com/ipython/ipykernel) | `6.31.0` | `7.3.0` | | [blackjax](https://github.com/blackjax-devs/blackjax) | `1.3` | `1.6.2` | | [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions) | `10.20.1` | `11.0.1` | | [nbconvert](https://github.com/jupyter/nbconvert) | `7.16.6` | `7.17.1` | | [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.8.0` | `1.9.0` | | [markdown-it-py](https://github.com/executablebooks/markdown-it-py) | `4.0.0` | `4.2.0` | | [pygments](https://github.com/pygments/pygments) | `2.19.2` | `2.20.0` | | [typing-extensions](https://github.com/python/typing_extensions) | `4.15.0` | `4.16.0` | Updates `jax` from 0.9.0 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-v0.9.0...jax-v0.10.2) Updates `optax` from 0.2.6 to 0.2.8 - [Release notes](https://github.com/google-deepmind/optax/releases) - [Commits](google-deepmind/optax@v0.2.6...v0.2.8) Updates `numpyro` from 0.19.0 to 0.21.0 - [Release notes](https://github.com/pyro-ppl/numpyro/releases) - [Commits](pyro-ppl/numpyro@0.19.0...0.21.0) Updates `jaxtyping` from 0.3.6 to 0.3.11 - [Release notes](https://github.com/patrick-kidger/jaxtyping/releases) - [Commits](patrick-kidger/jaxtyping@v0.3.6...v0.3.11) Updates `equinox` from 0.13.5 to 0.13.8 - [Release notes](https://github.com/patrick-kidger/equinox/releases) - [Commits](patrick-kidger/equinox@v0.13.5...v0.13.8) Updates `lineax` from 0.1.0 to 0.1.1 - [Release notes](https://github.com/google/lineax/releases) - [Commits](patrick-kidger/lineax@v0.1.0...v0.1.1) Updates `scipy` from 1.17.0 to 1.17.1 - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.17.0...v1.17.1) Updates `numpy` from 2.4.1 to 2.4.6 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v2.4.1...v2.4.6) Updates `rich` from 14.3.1 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@v14.3.1...v15.0.0) Updates `mkdocs-material` from 9.7.1 to 9.7.7 - [Release notes](https://github.com/squidfunk/mkdocs-material/releases) - [Changelog](https://github.com/squidfunk/mkdocs-material/blob/master/CHANGELOG) - [Commits](squidfunk/mkdocs-material@9.7.1...9.7.7) Updates `mkdocs-jupyter` from 0.25.1 to 0.26.3 - [Changelog](https://github.com/danielfrg/mkdocs-jupyter/blob/main/CHANGELOG.md) - [Commits](https://github.com/danielfrg/mkdocs-jupyter/commits) Updates `mkdocs-gen-files` from 0.6.0 to 0.6.1 - [Release notes](https://github.com/oprypin/mkdocs-gen-files/releases) - [Commits](oprypin/mkdocs-gen-files@v0.6.0...v0.6.1) Updates `mkdocs-literate-nav` from 0.6.2 to 0.6.3 - [Release notes](https://github.com/oprypin/mkdocs-literate-nav/releases) - [Commits](oprypin/mkdocs-literate-nav@v0.6.2...v0.6.3) Updates `matplotlib` from 3.10.8 to 3.11.1 - [Release notes](https://github.com/matplotlib/matplotlib/releases) - [Commits](matplotlib/matplotlib@v3.10.8...v3.11.1) Updates `ipython` from 9.9.0 to 9.15.0 - [Release notes](https://github.com/ipython/ipython/releases) - [Commits](ipython/ipython@9.9.0...9.15.0) Updates `ipykernel` from 6.31.0 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@v6.31.0...v7.3.0) Updates `blackjax` from 1.3 to 1.6.2 - [Release notes](https://github.com/blackjax-devs/blackjax/releases) - [Commits](blackjax-devs/blackjax@1.3...1.6.2) Updates `pymdown-extensions` from 10.20.1 to 11.0.1 - [Release notes](https://github.com/facelessuser/pymdown-extensions/releases) - [Commits](https://github.com/facelessuser/pymdown-extensions/commits/11.0.1) Updates `nbconvert` from 7.16.6 to 7.17.1 - [Release notes](https://github.com/jupyter/nbconvert/releases) - [Changelog](https://github.com/jupyter/nbconvert/blob/main/CHANGELOG.md) - [Commits](jupyter/nbconvert@v7.16.6...v7.17.1) Updates `scikit-learn` from 1.8.0 to 1.9.0 - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@1.8.0...1.9.0) Updates `markdown-it-py` from 4.0.0 to 4.2.0 - [Release notes](https://github.com/executablebooks/markdown-it-py/releases) - [Changelog](https://github.com/executablebooks/markdown-it-py/blob/master/CHANGELOG.md) - [Commits](executablebooks/markdown-it-py@v4.0.0...v4.2.0) Updates `pygments` from 2.19.2 to 2.20.0 - [Release notes](https://github.com/pygments/pygments/releases) - [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES) - [Commits](pygments/pygments@2.19.2...2.20.0) Updates `typing-extensions` from 4.15.0 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@4.15.0...4.16.0) --- updated-dependencies: - dependency-name: jax dependency-version: 0.10.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: optax dependency-version: 0.2.8 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: numpyro dependency-version: 0.21.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: jaxtyping dependency-version: 0.3.11 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: equinox dependency-version: 0.13.8 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: lineax dependency-version: 0.1.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: scipy dependency-version: 1.17.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: numpy dependency-version: 2.4.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: rich dependency-version: 15.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: python-dependencies - dependency-name: mkdocs-material dependency-version: 9.7.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: mkdocs-jupyter dependency-version: 0.26.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: mkdocs-gen-files dependency-version: 0.6.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: mkdocs-literate-nav dependency-version: 0.6.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-dependencies - dependency-name: matplotlib dependency-version: 3.11.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: ipython dependency-version: 9.15.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: ipykernel dependency-version: 7.3.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: python-dependencies - dependency-name: blackjax dependency-version: 1.6.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: pymdown-extensions dependency-version: 11.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: python-dependencies - dependency-name: nbconvert dependency-version: 7.17.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: scikit-learn dependency-version: 1.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: markdown-it-py dependency-version: 4.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: pygments dependency-version: 2.20.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies - dependency-name: typing-extensions dependency-version: 4.16.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-dependencies ... Signed-off-by: dependabot[bot] <support@github.com>

dependabot · 2026-07-27T08:48:33Z

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The following labels could not be found: automated. Please create it before Dependabot can add it to a pull request.

Please fix the above issues or remove invalid values from dependabot.yml.

Dependabot never updated the dev tooling. Its uv parser only reads `build-system.requires`, `project.dependencies`, `project.optional-dependencies`, `tool.poetry` and `dependency-groups`; `tool.uv` is consulted solely for `sources`. So the legacy `[tool.uv].dev-dependencies` block was invisible to it, and #734 bumped 23 packages without touching ruff, pytest, asv, hypothesis or poethepoet, all of which are several releases behind. Move the 19 entries verbatim to `[dependency-groups].dev`. uv already warns that `tool.uv.dev-dependencies` is deprecated in favour of `dependency-groups.dev`, and installs the `dev` group by default, so `uv sync --frozen` in CI is unaffected. `uv lock` reproduces uv.lock byte for byte. Also fix the documented install command. `uv sync --extra dev` appears in five files but no `dev` extra has ever existed -- only `docs` -- so the command fails today. With the dev group installed by default the correct form is plain `uv sync`.

dependabot Bot assigned thomaspinder Jul 27, 2026

dependabot Bot added the dependencies Pull requests that update a dependency file label Jul 27, 2026

dependabot Bot temporarily deployed to docs-preview July 27, 2026 09:11 Inactive

thomaspinder merged commit f9b7b8b into main Jul 27, 2026
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dependabot Bot deleted the dependabot/uv/python-dependencies-4ca496eb65 branch July 27, 2026 09:31

thomaspinder mentioned this pull request Jul 27, 2026

build(deps): migrate dev dependencies to PEP 735 dependency-groups #735

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deps(deps): bump the python-dependencies group with 23 updates - #734

deps(deps): bump the python-dependencies group with 23 updates#734
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dependabot Bot commented on behalf of github Jul 27, 2026

JAX v0.10.2

JAX v0.10.1

JAX 0.10.2 (June 17, 2026)

JAX 0.10.1 (May 20, 2026)

Optax 0.2.8

What's Changed

New Contributors

Optax 0.2.7

What's Changed

0.21.0

What's Changed

New Contributors

0.20.1

What's Changed

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jaxtyping v0.3.11

jaxtyping v0.3.10

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jaxtyping v0.3.9

jaxtyping v0.3.8

jaxtyping v0.3.7

Equinox v0.13.8

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Equinox v0.13.7

New Contributors

Equinox v0.13.6

lineax v0.1.1

Breaking Changes

Features

Compatibility

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Performance

Documentation

New Contributors

SciPy 1.17.1 Release Notes

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v2.4.6 (May 18, 2026)

NumPy 2.4.6 Release Notes

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Pull requests merged

v2.4.5 (May 15, 2026)

NumPy 2.4.5 Release Notes

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