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deps(deps): bump the python-dependencies group with 7 updates - #820

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Bumps the python-dependencies group with 7 updates:

Package From To
ipykernel 7.3.0 7.4.0
jupytext 1.19.5 1.19.6
blackjax 1.6.2 1.7.1
xarray 2026.7.0 2026.9.0
ruff 0.16.9 0.16.10
pytest-beartype 0.2.0 0.3.0
hypothesis 6.168.2 6.168.4

Updates ipykernel from 7.3.0 to 7.4.0

Release notes

Sourced from ipykernel's releases.

v7.4.0

7.4.0

(Full Changelog)

New features added

Enhancements made

Bugs fixed

Maintenance and upkeep improvements

Contributors to this release

The following people contributed discussions, new ideas, code and documentation contributions, and review. See our definition of contributors.

(GitHub contributors page for this release)

@​BoykoNeov (activity) | @​Carreau (activity) | @​davidbrochart (activity) | @​glaziermag (activity) | @​Gravifer (activity) | @​ianthomas23 (activity) | @​jasongrout (activity) | @​JohanMabille (activity) | @​krassowski (activity) | @​kylebarron (activity) | @​minrk (activity) | @​NewUserHa (activity) | @​practicusai (activity) | @​sahvx655-wq (activity) | @​Scott5S (activity) | @​thomasjm (activity) | @​tovrstra (activity) | @​Yann-P (activity) | @​yves-surrel (activity) | @​ZupoLlask (activity)

Changelog

Sourced from ipykernel's changelog.

7.4.0

(Full Changelog)

New features added

Enhancements made

Bugs fixed

Maintenance and upkeep improvements

Contributors to this release

The following people contributed discussions, new ideas, code and documentation contributions, and review. See our definition of contributors.

(GitHub contributors page for this release)

@​BoykoNeov (activity) | @​Carreau (activity) | @​davidbrochart (activity) | @​glaziermag (activity) | @​Gravifer (activity) | @​ianthomas23 (activity) | @​jasongrout (activity) | @​JohanMabille (activity) | @​krassowski (activity) | @​kylebarron (activity) | @​minrk (activity) | @​NewUserHa (activity) | @​practicusai (activity) | @​sahvx655-wq (activity) | @​Scott5S (activity) | @​thomasjm (activity) | @​tovrstra (activity) | @​Yann-P (activity) | @​yves-surrel (activity) | @​ZupoLlask (activity)

Commits

Updates jupytext from 1.19.5 to 1.19.6

Release notes

Sourced from jupytext's releases.

Version 1.19.6

Security

  • The Quarto conversions now run in a private temporary directory, so that the output file that quarto convert names after its input can no longer be pre-created as a symlink by another user of the machine. Thanks to Naveed for the PR (#1615).
  • Paired paths from notebook formats metadata are now prevented from escaping the working tree, including when an absolute notebook path is used. Thanks to Naveed for addressing the issue (#1588).
  • The CLI now ignores trusted cell metadata when the notebook signature is invalid, so a trusted=true option in a paired text file cannot make untrusted notebook outputs trusted during --sync. Thanks to Naveed for the fix (#1617).
  • Custom cell_markers and endofcell values in the light format are now matched literally, preventing regular-expression injection, parsing errors, and excessive processing time on crafted notebooks. This also fixes writing OCaml notebooks with custom cell markers. Thanks to Naveed again for the PR (#1618).
  • We have merged Dependabot security updates for the JupyterLab extension and the documentation website (#1614, #1620, #1622, #1624, #1634, #1639, #1642, #1643, #1647, #1653, #1654).

Fixed

  • Menu entries such as "Rename Notebook…" name the file type again, instead of saying "default". Thanks to Michał Krassowski for this PR (#1632).
  • Mermaid %% comments inside a markdown cell are no longer mistaken for py:percent cell markers (#1533). Thanks to Sanjay Santhanam for his PR (#1609)
  • A whitespace-only final line in a percent-format cell is now preserved when reading and round-tripping the notebook (#1599). Thanks to lowbyteguy for the PR (#1610).
  • The JupyterLab extension's development install script now uses the correct jupyter-builder import (#1632). Thanks again to Michał Krassowski for this fix.
  • Fixed JupyterLab extension build issues related to Yarn package checksums. Thanks to Mahendra Paipuri for his contributions to #1614, #1620, and #1621.
  • Fixed pairing on Windows when a prefix root contains subdirectories, such as notebooks/tutorials///ipynb.

Changed

Added

  • We have added a development container that can be opened with VS Code’s Dev Containers extension (#1655).
  • Added support for the Jenner language. Thanks to Lawrence Sinclair for this contribution (#1493).
Changelog

Sourced from jupytext's changelog.

1.19.6 (2026-10-04)

Security

  • The Quarto conversions now run in a private temporary directory, so that the output file that quarto convert names after its input can no longer be pre-created as a symlink by another user of the machine. Thanks to Naveed for the PR (#1615).
  • Paired paths from notebook formats metadata are now prevented from escaping the working tree, including when an absolute notebook path is used. Thanks to Naveed for addressing the issue (#1588).
  • The CLI now ignores trusted cell metadata when the notebook signature is invalid, so a trusted=true option in a paired text file cannot make untrusted notebook outputs trusted during --sync. Thanks to Naveed for the fix (#1617).
  • Custom cell_markers and endofcell values in the light format are now matched literally, preventing regular-expression injection, parsing errors, and excessive processing time on crafted notebooks. This also fixes writing OCaml notebooks with custom cell markers. Thanks to Naveed again for the PR (#1618).
  • We have merged Dependabot security updates for the JupyterLab extension and the documentation website (#1614, #1620, #1622, #1624, #1634, #1639, #1642, #1643, #1647, #1653, #1654).

Fixed

  • Menu entries such as "Rename Notebook…" name the file type again, instead of saying "default". Thanks to Michał Krassowski for this PR (#1632).
  • Mermaid %% comments inside a markdown cell are no longer mistaken for py:percent cell markers (#1533). Thanks to Sanjay Santhanam for his PR (#1609)
  • A whitespace-only final line in a percent-format cell is now preserved when reading and round-tripping the notebook (#1599). Thanks to lowbyteguy for the PR (#1610).
  • The JupyterLab extension's development install script now uses the correct jupyter-builder import (#1632). Thanks again to Michał Krassowski for this fix.
  • Fixed JupyterLab extension build issues related to Yarn package checksums. Thanks to Mahendra Paipuri for his contributions to #1614, #1620, and #1621.
  • Fixed pairing on Windows when a prefix root contains subdirectories, such as notebooks/tutorials///ipynb.

Changed

... (truncated)

Commits
  • 9fccc3d Version 1.19.6 (#1656)
  • 85c65a9 Add Jenner language support (#1493)
  • ca39ad2 Add development container (#1655)
  • 0176ff2 reject paired paths that escape the notebook directory tree (#1588)
  • 1eb4653 Ignore '%%' lines inside fenced blocks of py:percent markdown cells (#1609)
  • b1d7b65 build(deps): bump the jupytext-extension-security-updates group across 2 dire...
  • 85df69a build(deps): bump the actions-dependencies group with 3 updates (#1651)
  • c3bb81d run quarto convert in a private temp directory (#1615)
  • 9bbd990 build(deps): bump the jupytext-extension-security-updates group across 1 dire...
  • f96ae7d build(deps): bump the jupytext-extension-dependencies group across 2 director...
  • Additional commits viewable in compare view

Updates blackjax from 1.6.2 to 1.7.1

Release notes

Sourced from blackjax's releases.

1.7.1

Fix

  • MCLMC tuning: mclmc_find_L_and_step_size returned L = inf whenever a coordinate was degenerate (constant) over the stage-3 window. Since 1.7.0 (#1020) the effective sample size is 0 for such coordinates, and stage 3 divided by it. L is now averaged over the informative coordinates only, and stays unchanged if there are none (#1046).

What's Changed

Full Changelog: blackjax-devs/blackjax@1.7.0...1.7.1

1.7.0

Highlights

  • Faster sampling on jax ≥ 0.10.2: run_inference_algorithm, window/staged warmup and MCLMC tuning now jit-compile their loops. Eager lax.scan became 2–10× slower on CPU from jax 0.10.2 (jax-ml/jax#37465). On jax 0.11.2, NUTS/HMC benchmarks run ~1.3–1.4× faster than before (#1045).
  • New: coupled HMC (#1033); update_strategy exposed on the nested-sampling kernel (#1025); diagnostics-only divergence-concentration warning (#1016); GIST family packaged under blackjax/mcmc/composed/ (#1017); meta-adaptation moved into the adaptation/meta subpackage (#1001).
  • Fixes: nested-sampling birth contours after rejected MCMC updates (#1042); isokinetic kinetic increment (#1039); stepping-out under vmap (#1041); tied ranks in rank-normalized diagnostics (#1031); multi-chain metric='auto' crash on PyTree positions (#1013); GIST no-U-turn momentum pairing (#1012).
  • Dev lockfile: upgraded, including jax 0.11.2, numpy 2.5, pymc 6 and arviz 1.3 (#1043).

What's Changed

... (truncated)

Commits
  • cde2ab0 Guard MCLMC stage-3 L estimate against ess=0 degenerate dims (#1046)
  • 421add7 Upgrade uv.lock to latest compatible versions (#1043)
  • 0c69b5d Jit-compile the eagerly executed lax.scan loops (CPU slowdown on jax >= 0.10....
  • 351bb9a Document dense Pathfinder metric memory use (#1044)
  • e96cc19 Reset replacement birth contours after rejected MCMC updates (#1042)
  • 5b67f5a Evaluate the stepping-out test once per step under vmap (#1041)
  • fc7f331 Use two-sided nonnegative A in the isokinetic kinetic increment (#1039)
  • df074f9 Fix nightly + main CI: LAPS silent NaN death, and three float-boundary test d...
  • 74a2c1c Trim telemetry and coupled HMC prose and reuse test records (#1034)
  • 112dae7 Expose metric publication decisions without changing adaptation (#1032)
  • Additional commits viewable in compare view

Updates xarray from 2026.7.0 to 2026.9.0

Release notes

Sourced from xarray's releases.

v2026.09.0

This release adds read support for Zarr V3 rectilinear (variable-sized) chunks, Arrow PyCapsule export for :py:class:DataArray, a new :py:meth:DataArray.plot.lines plotting method, :py:class:DataTree support in :py:func:apply_ufunc, and flox-accelerated groupby medians. Bottleneck is now disabled by default, the remaining zarr-python 2 compatibility code has been removed, and the minimum h5netcdf version is now 1.8. It also includes many bug fixes.

This is the last xarray release that will support Python 3.11. Future releases will require Python 3.12 or later.

Thanks to the 45 contributors to this release: ANIRUDDHA ADAK, Ahmet Kamer Çivi, Albert Yau, Andrew Scherer, Anirban Mandal, Aryan Singh K., Asish Kumar, Chandan P, Charles Turner, Deepak Cherian, Devraj Pal, Dipak Chaudhari, Eltsefon Mark, Evan Lyall, Illviljan, Joe Hamman, Johnson K C, Jules Chéron, Justus Magin, Kropiunig, Marcus Campbell, Mark Harfouche, Matt Van Horn, Matthew Rocklin, Matthias Schabel, Michael Niklas, Nick Hodgskin, Patrick N. Raanes, Peter Hron, Puneet Dixit, QinXi, Samuel Le Meur-Diebolt, Spencer Clark, Stanley C, Stephan Hoyer, Thomas Kluyver, Tom Nicholas, dsk0425-sketch, genrichez, hushen, imam, omsatpute61-afk, stepit, whn and ✨Sarah Z✨

What's Changed

Bumps the python-dependencies group with 7 updates:

| Package | From | To |
| --- | --- | --- |
| [ipykernel](https://github.com/ipython/ipykernel) | `7.3.0` | `7.4.0` |
| [jupytext](https://github.com/jupytext/jupytext) | `1.19.5` | `1.19.6` |
| [blackjax](https://github.com/blackjax-devs/blackjax) | `1.6.2` | `1.7.1` |
| [xarray](https://github.com/pydata/xarray) | `2026.7.0` | `2026.9.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.16.9` | `0.16.10` |
| [pytest-beartype](https://github.com/beartype/pytest-beartype) | `0.2.0` | `0.3.0` |
| [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.168.2` | `6.168.4` |


Updates `ipykernel` from 7.3.0 to 7.4.0
- [Release notes](https://github.com/ipython/ipykernel/releases)
- [Changelog](https://github.com/ipython/ipykernel/blob/main/CHANGELOG.md)
- [Commits](ipython/ipykernel@v7.3.0...v7.4.0)

Updates `jupytext` from 1.19.5 to 1.19.6
- [Release notes](https://github.com/jupytext/jupytext/releases)
- [Changelog](https://github.com/jupytext/jupytext/blob/main/CHANGELOG.md)
- [Commits](jupytext/jupytext@v1.19.5...v1.19.6)

Updates `blackjax` from 1.6.2 to 1.7.1
- [Release notes](https://github.com/blackjax-devs/blackjax/releases)
- [Commits](blackjax-devs/blackjax@1.6.2...1.7.1)

Updates `xarray` from 2026.7.0 to 2026.9.0
- [Release notes](https://github.com/pydata/xarray/releases)
- [Commits](pydata/xarray@v2026.07.0...v2026.09.0)

Updates `ruff` from 0.16.9 to 0.16.10
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/0.16.10/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.16.9...0.16.10)

Updates `pytest-beartype` from 0.2.0 to 0.3.0
- [Release notes](https://github.com/beartype/pytest-beartype/releases)
- [Changelog](https://github.com/beartype/pytest-beartype/blob/main/doc/RELEASE.rst)
- [Commits](beartype/pytest-beartype@v0.2.0...v0.3.0)

Updates `hypothesis` from 6.168.2 to 6.168.4
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](HypothesisWorks/hypothesis@v6.168.2...v6.168.4)

---
updated-dependencies:
- dependency-name: ipykernel
  dependency-version: 7.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: jupytext
  dependency-version: 1.19.6
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: blackjax
  dependency-version: 1.7.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: xarray
  dependency-version: 2026.9.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: ruff
  dependency-version: 0.16.10
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: pytest-beartype
  dependency-version: 0.3.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: hypothesis
  dependency-version: 6.168.4
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added the dependencies Pull requests that update a dependency file label Oct 12, 2026
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@github-actions github-actions Bot added size/m ci Continuous Integration documentation Improvements or additions to documentation performance Performance security tests labels Oct 12, 2026
@thomaspinder
thomaspinder merged commit 0ebf115 into main Oct 14, 2026
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dependabot Bot deleted the dependabot/uv/python-dependencies-ffda494721 branch October 14, 2026 03:05
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