deps: bump the notebook-stack group with 8 updates by dependabot[bot] · Pull Request #135 · OpenMS/pyopenms_viz

dependabot · 2026-01-13T12:56:55Z

Bumps the notebook-stack group with 8 updates:

Package	From	To
decorator	`5.1.1`	`5.2.1`
ipython	`8.31.0`	`8.38.0`
jupyter-client	`8.6.3`	`8.8.0`
nbclient	`0.10.2`	`0.10.4`
nbconvert	`7.16.5`	`7.16.6`
parso	`0.8.4`	`0.8.5`
platformdirs	`4.3.6`	`4.5.1`
prompt-toolkit	`3.0.48`	`3.0.52`

Updates decorator from 5.1.1 to 5.2.1

Changelog

Sourced from decorator's changelog.

5.2.1 (2025-02-24)

Shiv Krishna Jaiswal suggested how to manage che case of functions without name. Michał Górny contributed a fix for the generation of the source package.

5.2.0 (2025-02-22)

Changed the build procedure to use pyproject.toml and moved the tests outside of the generated wheel/tarball.

Added official support for Python 3.11, 3.12, 3.13 (thanks to Hugo van Kemenade).

Dropped official support for Python < 3.8: the module is expected to work on older Python versions, but I cannot test such versions on GitHub actions, so I cannot claim that it is officially supported.

Dafu Wu provided support for decorating partial functions, i.e. functions wrapped by functools.partial.

Commits

cdeab3c Managed functions without name
bbc430b Merge pull request #169 from mgorny/sdist
8c87cb2 Include tests and documentation in sdist
c996292 Merge pull request #166 from micheles/pyproject
24af8c8 Update Makefile [ci skip]
930ef0f Updated CHANGES.md
2e1d155 Moved tests outside of src
eac33cb Updated copyright
7849ea6 Replaced setup.py with pyproject
0a1832e Using asyncio.run
Additional commits viewable in compare view

Updates ipython from 8.31.0 to 8.38.0

Commits

f014fa1 release 8.38.0
07abfcf Make debugger work with Python 3.14 (#15085)
7f159ef Make debugger work with Python 3.14
fed55e3 back to dev
86a50d3 release 8.37.0
91ad381 Backport PR #14913 on branch 8.x (Update changelog for 8.37) (#14915)
d8c971e Backport PR #14913: Update changelog for 8.37
fcc41fa Backport PR #14910 on branch 8.x (Eliminate startup delay when slow-starting ...
576bc55 Backport PR #14910: Eliminate startup delay when slow-starting LLM completion...
21d9433 Backport PR #14898 on branch 8.x (Fix attribute completion for expressions wi...
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Updates jupyter-client from 8.6.3 to 8.8.0

Release notes

Sourced from jupyter-client's releases.

v8.8.0

8.8.0

(Full Changelog)

Enhancements made

Added kernel_protocol_version to kernelspec #1097 (@JohanMabille, @SylvainCorlay)

Faster message serialization #1064 (@fleming79, @Carreau, @henryiii, @krassowski, @minrk, @rgbkrk)

Path resolution by kernel manager and providers #1005 (@krassowski, @rgbkrk)

Maintenance and upkeep improvements

chore: update some parts of the pre-commit #1093 (@henryiii, @minrk, @rgbkrk)

Fix flaky client tests by waiting for first request's reply #1091 (@rgbkrk)

Re-enable qtconsole in downstream checks #1090 (@rgbkrk)

Fix channel cleanup by closing streams before stopping ioloop thread #1089 (@rgbkrk)

Fix downstream workflow #1087 (@rgbkrk)

Skip mypy on PyPy to avoid librt compilation issues #1086 (@rgbkrk)

Documentation improvements

Upgrade to version 5.5 #1096 (@JohanMabille, @SylvainCorlay)

Update messaging spec #1095 (@JohanMabille, @minrk, @rgbkrk)

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)

@Carreau (activity) | @ccordoba12 (activity) | @fleming79 (activity) | @henryiii (activity) | @JohanMabille (activity) | @krassowski (activity) | @minrk (activity) | @rgbkrk (activity) | @SylvainCorlay (activity)

v8.7.0

8.7.0

(Full Changelog)

Enhancements made

allow configuring client_class and client_factory #1081 (@rgbkrk)

Support date serialization in messages #1060 (@sebwills)

feat: added --missing flag to list and remove subcommands #1056 (@wpk-nist-gov)

Set protocol version to 5.4 #1054 (@JamesWrigley)

... (truncated)

Changelog

Sourced from jupyter-client's changelog.

8.8.0

(Full Changelog)

Enhancements made

Added kernel_protocol_version to kernelspec #1097 (@JohanMabille, @SylvainCorlay)

Faster message serialization #1064 (@fleming79, @Carreau, @henryiii, @krassowski, @minrk, @rgbkrk)

Path resolution by kernel manager and providers #1005 (@krassowski, @rgbkrk)

Maintenance and upkeep improvements

chore: update some parts of the pre-commit #1093 (@henryiii, @minrk, @rgbkrk)

Fix flaky client tests by waiting for first request's reply #1091 (@rgbkrk)

Re-enable qtconsole in downstream checks #1090 (@rgbkrk)

Fix channel cleanup by closing streams before stopping ioloop thread #1089 (@rgbkrk)

Fix downstream workflow #1087 (@rgbkrk)

Skip mypy on PyPy to avoid librt compilation issues #1086 (@rgbkrk)

Documentation improvements

Upgrade to version 5.5 #1096 (@JohanMabille, @SylvainCorlay)

Update messaging spec #1095 (@JohanMabille, @minrk, @rgbkrk)

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)

@Carreau (activity) | @ccordoba12 (activity) | @fleming79 (activity) | @henryiii (activity) | @JohanMabille (activity) | @krassowski (activity) | @minrk (activity) | @rgbkrk (activity) | @SylvainCorlay (activity)

8.7.0

(Full Changelog)

Enhancements made

allow configuring client_class and client_factory #1081 (@rgbkrk)

Support date serialization in messages #1060 (@sebwills)

feat: added --missing flag to list and remove subcommands #1056 (@wpk-nist-gov)

Set protocol version to 5.4 #1054 (@JamesWrigley)

Bugs fixed

don't include link-local addresses (169.254) in public_ips #1040 (@minrk)

jupyter-run: avoid traceback for NoSuchKernel #994 (@minrk)

... (truncated)

Commits

e27f54b Publish 8.8.0
523294f Upgrade to version 5.5 (#1096)
2820532 Added kernel_protocol_version to kernelspec (#1097)
7c3a325 Update messaging spec (#1095)
9589ed8 chore: update some parts of the pre-commit (#1093)
ee43cd3 Faster message serialization (#1064)
0bce36f Fix flaky client tests by waiting for first request's reply (#1091)
a53ade9 Path resolution by kernel manager and providers (#1005)
b32dcce Re-enable qtconsole in downstream checks (#1090)
cd14b0e Fix channel cleanup by closing streams before stopping ioloop thread (#1089)
Additional commits viewable in compare view

Updates nbclient from 0.10.2 to 0.10.4

Release notes

Sourced from nbclient's releases.

v0.10.4

0.10.4

(Full Changelog)

Merged PRs

Allow display_id to be None #338 (@davidbrochart, @YannickJadoul, @slayoo)

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)

@davidbrochart (activity) | @slayoo (activity) | @YannickJadoul (activity)

v0.10.3

0.10.3

(Full Changelog)

Merged PRs

Drop Python 3.9, test 3.14 and pypy-3.11 #337 (@davidbrochart)

correct execution count in test for ipython 9.8 and above #335 (@drorspei, @davidbrochart)

Update contribution with pytest instructions, remove tox. #331 (@dgrahn, @davidbrochart)

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)

@davidbrochart (activity) | @dgrahn (activity) | @drorspei (activity)

Changelog

Sourced from nbclient's changelog.

0.10.4

(Full Changelog)

Merged PRs

Allow display_id to be None #338 (@davidbrochart, @YannickJadoul, @slayoo)

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)

@davidbrochart (activity) | @slayoo (activity) | @YannickJadoul (activity)

0.10.3

(Full Changelog)

Merged PRs

Drop Python 3.9, test 3.14 and pypy-3.11 #337 (@davidbrochart)

correct execution count in test for ipython 9.8 and above #335 (@drorspei, @davidbrochart)

Update contribution with pytest instructions, remove tox. #331 (@dgrahn, @davidbrochart)

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)

@davidbrochart (activity) | @dgrahn (activity) | @drorspei (activity)

Commits

e500e95 Publish 0.10.4
af9b77a Allow display_id to be None (#338)
5a52a0a Publish 0.10.3
b42ad03 correct execution count in tests for ipython 9.8 and above (#335)
3352484 Drop Python 3.9, test 3.14 and pypy-3.11 (#337)
ec86eef Update contribution with hatch instructions, remove tox. (#331)
See full diff in compare view

Updates nbconvert from 7.16.5 to 7.16.6

Release notes

Sourced from nbconvert's releases.

v7.16.6

7.16.6

(Full Changelog)

Bugs fixed

Prevent leading whitespace in markdown code blocks from being stripped #2203 (@peytondmurray)

Fix bullet list parsing in markdown #2177 (@douglas-raillard-arm)

Fix crash when running with optimization #2160 (@QuLogic)

Maintenance and upkeep improvements

remove any twitter mention #2206 (@Carreau)

Update base.tex.j2 for macro compatibility with newer versions of Pandoc #2196 (@PetalAdrift)

Contributors to this release

(GitHub contributors page for this release)

@Carreau | @douglas-raillard-arm | @gabemorris12 | @krassowski | @PetalAdrift | @peytondmurray | @QuLogic

Changelog

Sourced from nbconvert's changelog.

7.16.6

(Full Changelog)

Bugs fixed

Prevent leading whitespace in markdown code blocks from being stripped #2203 (@peytondmurray)

Fix bullet list parsing in markdown #2177 (@douglas-raillard-arm)

Fix crash when running with optimization #2160 (@QuLogic)

Maintenance and upkeep improvements

remove any twitter mention #2206 (@Carreau)

Update base.tex.j2 for macro compatibility with newer versions of Pandoc #2196 (@PetalAdrift)

Contributors to this release

(GitHub contributors page for this release)

@Carreau | @douglas-raillard-arm | @gabemorris12 | @krassowski | @PetalAdrift | @peytondmurray | @QuLogic

Commits

2ba5858 Publish 7.16.6
01c6ab2 Fix bullet list parsing in markdown (#2177)
0b36e8b Fix crash when running with optimization (#2160)
edd96d1 Update base.tex.j2 for macro compatibility with newer versions of Pandoc (#2196)
7ffb70a Prevent leading whitespace in markdown code blocks from being stripped (#2203)
9ffb94a remove any twitter mention (#2206)
See full diff in compare view

Updates parso from 0.8.4 to 0.8.5

Changelog

Sourced from parso's changelog.

0.8.5 (2025-08-23) ++++++++++++++++++

Add a fallback grammar for Python 3.14+

Commits

be9f5a4 Prepare release 0.8.5
7e4777b Merge pull request #234 from A5rocks/future-compatibility
e99dbdd Remove redundant warnings import
e22dc67 Avoid warning
baa3c90 Load newest grammar in face of a future grammar
23b1cdf Drop Python 3.7 in CI
a73af5c Fix pip install -e in docs
9328cff Update classifiers in setup.py (#230)
f670e6e ENH: add grammar file for py314 (#229)
338a576 Updated readme installation documentation, now we can copy it easier (#228)
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Updates platformdirs from 4.3.6 to 4.5.1

Release notes

Sourced from platformdirs's releases.

4.5.1

What's Changed

Fix no-ctypes fallback on windows by @youknowone in tox-dev/platformdirs#403

Full Changelog: tox-dev/platformdirs@4.5.0...4.5.1

4.5.0

What's Changed

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in tox-dev/platformdirs#376

Bump pypa/gh-action-pypi-publish from 1.12.4 to 1.13.0 in the all group by @dependabot[bot] in tox-dev/platformdirs#378

Bump pypa/gh-action-pypi-publish from 1.12.4 to 1.13.0 in /.github/workflows by @dependabot[bot] in tox-dev/platformdirs#379

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in tox-dev/platformdirs#381

Add support for Python 3.14 by @hugovk in tox-dev/platformdirs#382

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in tox-dev/platformdirs#383

Update Windows file paths in README by @ParadaCarleton in tox-dev/platformdirs#385

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in tox-dev/platformdirs#384

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in tox-dev/platformdirs#387

Bump astral-sh/setup-uv from 6 to 7 in the all group by @dependabot[bot] in tox-dev/platformdirs#388

Drop 3.9 support by @gaborbernat in tox-dev/platformdirs#389

New Contributors

@ParadaCarleton made their first contribution in tox-dev/platformdirs#385

Full Changelog: tox-dev/platformdirs@4.4.0...4.5.0

4.4.0

What's Changed

feat: improve homebrew path detection by @daeho-ro in tox-dev/platformdirs#370

New Contributors

@daeho-ro made their first contribution in tox-dev/platformdirs#370

Full Changelog: tox-dev/platformdirs@4.3.8...4.4.0

4.3.8

What's Changed

Add missing examples and fix order of examples in README by @gene1wood in tox-dev/platformdirs#355

New Contributors

@gene1wood made their first contribution in tox-dev/platformdirs#355

Full Changelog: tox-dev/platformdirs@4.3.7...4.3.8

... (truncated)

Commits

e4dbdb8 Fix no-ctypes fallback on windows (#403)
4cc78aa [pre-commit.ci] pre-commit autoupdate (#401)
b624d78 [pre-commit.ci] pre-commit autoupdate (#400)
eb06e7e Bump actions/checkout from 5 to 6 in the all group (#399)
85efbe9 [pre-commit.ci] pre-commit autoupdate (#397)
704c603 [pre-commit.ci] pre-commit autoupdate (#394)
a018178 [pre-commit.ci] pre-commit autoupdate (#393)
9920b9b Bump the all group with 2 updates (#392)
c804724 [pre-commit.ci] pre-commit autoupdate (#391)
a6a2489 [pre-commit.ci] pre-commit autoupdate (#390)
Additional commits viewable in compare view

Updates prompt-toolkit from 3.0.48 to 3.0.52

Release notes

Sourced from prompt-toolkit's releases.

3.0.52

New features:

Add choice() shortcut for selecting an option amongst a list of choices (see documentation for examples).

Add support for ANSI dim text formatting.

Add frame=... option for prompt() and choice() shortcuts to allow for displaying a frame around the input prompt.

Fixes:

Fix button width when non English characters are displayed.

Implement flushing in Windows VT100 input.

Fix signal handling for GraalPy.

Fix handling of zero sized dimensions.

3.0.51

New features:

Use pyproject.toml instead of setup.py.

Fixes:

Fix edge case in formatted_text.split_lines when the input starts with a line ending.

3.0.50

Fixes:

Fixes non user impacting regression on the output rendering. Don't render cursor hide/show ANSI escape codes if not needed.

3.0.49

New features:

On Windows, use virtual terminal input when available.

Support for multiline suggestions.

Fixes:

Handle InvalidStateError during termination when using run_in_terminal/patch_stdout. This can happen in some cases during cancellation, probably when using anyio.

Fix cursor that remains in hidden state when the application exits. This can happen when the application doesn't show the cursor and erase_when_done is being used.

Breaking changes:

Drop support for Python 3.7

Changelog

Sourced from prompt-toolkit's changelog.

3.0.52: 2025-08-27

New features:

Add choice() shortcut for selecting an option amongst a list of choices (see documentation for examples).

Add support for ANSI dim text formatting.

Add frame=... option for prompt() and choice() shortcuts to allow for displaying a frame around the input prompt.

Fixes:

Fix button width when non English characters are displayed.

Implement flushing in Windows VT100 input.

Fix signal handling for GraalPy.

Fix handling of zero sized dimensions.

3.0.51: 2025-04-15

New features:

Use pyproject.toml instead of setup.py.

Fixes:

Fix edge case in formatted_text.split_lines when the input starts with a line ending.

3.0.50: 2025-01-20

Fixes:

Fixes non user impacting regression on the output rendering. Don't render cursor hide/show ANSI escape codes if not needed.

3.0.49: 2025-01-20

New features:

On Windows, use virtual terminal input when available.

Support for multiline suggestions.

Fixes:

Handle InvalidStateError during termination when using run_in_terminal/patch_stdout. This can happen in some cases during cancellation, probably when using anyio.

Fix cursor that remains in hidden state when the application exits. This can happen when the application doesn't show the cursor and erase_when_done is being used.

Breaking changes:

... (truncated)

Commits

d8adbe9 Release 3.0.52
5fde041 Follow-up: accept 'show_frame' in 'prompt_async()' and accept extra key bindi...
2b9cd93 Add choice shortcut for selecting an option amongst a list of choices. (#2005)
a446019 Re-add project URLs after migration to pyproject.toml (#1986)
5c852f8 Fix images in README.rst (#1987)
bfec07f Fix signal handling in _restore_sigint_from_ctypes for GraalPy (#2000)
af26eec Implement flushing in Windows VT100 input (#2001)
c435303 Fix button width when non English characters are displayed
3374ae9 Update docs theme to Nefertiti 0.8.6 (#2002)
54c5c85 Stop using @abstractproperty which is deprecated. (#2004)
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github-actions · 2026-01-17T16:33:04Z

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