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Bump the python-requirements group in /envs with 18 updates #23

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Bumps the python-requirements group in /envs with 18 updates:

Package From To
simpleitk 2.5.0 2.5.2
coverage 7.8.2 7.10.7
jupyterlab 4.4.3 4.4.9
matplotlib 3.10.1 3.10.6
monai 1.4.0 1.5.1
pandas 2.2.3 2.3.3
plotly 6.1.2 6.3.1
pre-commit 4.2.0 4.3.0
pytest-cov 6.1.1 7.0.0
pytest-mock 3.14.1 3.15.1
pytest 8.3.5 8.4.2
rich 14.0.0 14.1.0
ruff 0.11.12 0.13.3
safetensors 0.5.3 0.6.2
scikit-learn 1.6.1 1.7.2
scipy 1.15.2 1.16.2
timm 1.0.15 1.0.20
wandb 0.19.11 0.22.1

Updates simpleitk from 2.5.0 to 2.5.2

Release notes

Sourced from simpleitk's releases.

Release v2.5.2

To upgrade to this Python binary package run: pip install --upgrade --pre simpleitk --find-links https://github.com/SimpleITK/SimpleITK/releases/tag/v2.5.2

What's Changed

Full Changelog: SimpleITK/SimpleITK@v2.5.0...v2.5.2

Commits
  • 2018b6b Update version to 2.5.2
  • f4f47df Merge pull request #2319 from blowekamp/release_ITK_5_4_4
  • 392ab24 Update ITK Superbuild version to 5.4.4
  • a4c5c44 Merge pull request #2306 from blowekamp/fix_docker_as
  • 756b401 Fix Docker FromAsCasing error for Doxygen
  • 2f12793 Merge pull request #2294 from blowekamp/image_series_reader_options
  • ad34fae Add ForceOrthogonalDirection and ReverseOrder options
  • See full diff in compare view

Updates coverage from 7.8.2 to 7.10.7

Changelog

Sourced from coverage's changelog.

Version 7.10.7 — 2025-09-21

  • Performance: with branch coverage in large files, generating HTML, JSON, or LCOV reports could take far too long due to some quadratic behavior when creating the function and class index pages. This is now fixed, closing issue 2048_. Thanks to Daniel Diniz for help diagnosing the problem.

  • Most warnings and a few errors now have links to a page in the docs explaining the specific message. Closes issue 1921_.

.. _issue 1921: nedbat/coveragepy#1921 .. _issue 2048: nedbat/coveragepy#2048

.. _changes_7-10-6:

Version 7.10.6 — 2025-08-29

  • Fix: source directories were not properly communicated to subprocesses that ran in different directories, as reported in issue 1499_. This is now fixed.

  • Performance: Alex Gaynor continues fine-tuning <pull 2038_>_ the speed of combination, especially with many contexts.

.. _issue 1499: nedbat/coveragepy#1499 .. _pull 2038: nedbat/coveragepy#2038

.. _changes_7-10-5:

Version 7.10.5 — 2025-08-23

  • Big speed improvements for coverage combine: it's now about twice as fast! Huge thanks to Alex Gaynor for pull requests 2032 <pull 2032_>, 2033 <pull 2033_>, and 2034 <pull 2034_>_.

.. _pull 2032: nedbat/coveragepy#2032 .. _pull 2033: nedbat/coveragepy#2033 .. _pull 2034: nedbat/coveragepy#2034

.. _changes_7-10-4:

Version 7.10.4 — 2025-08-16

... (truncated)

Commits
  • 92a2af5 docs: sample HTML for 7.10.7
  • 952afda docs: prep for 7.10.7
  • a301761 build: riscv64 wheels (#2055)
  • 5daff8d docs: now source is formatted with ruff
  • 04bbc3a docs: discuss cog in the contributing docs
  • c181b93 build: use cog --check-fail-msg to instruct devs
  • 33c4ba1 chore: make upgrade
  • 0744b73 chore: bump the action-dependencies group across 1 directory with 2 updates (...
  • 0d5a112 perf: bulk narrowing to avoid N**2. #2048
  • a868ed9 docs: mention Python Discord on the index page
  • Additional commits viewable in compare view

Updates jupyterlab from 4.4.3 to 4.4.9

Release notes

Sourced from jupyterlab's releases.

v4.4.9

4.4.9

(Full Changelog)

Bugs fixed

Contributors to this release

(GitHub contributors page for this release)

@​jupyterlab-probot | @​krassowski | @​martinRenou | @​meeseeksmachine

v4.4.8

4.4.8

(Full Changelog)

Bugs fixed

Maintenance and upkeep improvements

Documentation improvements

Contributors to this release

(GitHub contributors page for this release)

@​brichet | @​github-actions | @​HaudinFlorence | @​jtpio | @​jupyterlab-probot | @​krassowski | @​martinRenou | @​meeseeksmachine | @​Meriem-BenIsmail | @​williamstein

v4.4.7

4.4.7

... (truncated)

Commits

Updates matplotlib from 3.10.1 to 3.10.6

Release notes

Sourced from matplotlib's releases.

REL: v3.10.6

This is a bugfix release in the 3.10.x series.

Highlights from this release include:

- Fix regression of hi-dpi support for Qt
- Fix race condition in TexManager.make_dvi & make_png
- Various documentation and other bugfixes

REL: v3.10.5

This is the fourth bugfix release of the 3.10.x series.

Included in this release is distributed wheels for Python 3.14 (including freethreaded) and Windows ARM.

There are also several smaller bugfixes.

REL: v3.10.3

This is the third bugfix release of the 3.10.x series

Commits
  • 5cd38c3 REL: v3.10.6
  • b2358e7 Release prep v3.10.6
  • 2e04783 Merge branch 'v3.10.5-doc' into v3.10.x
  • d3365af Github stats v3.10.6
  • 81ed659 Merge pull request #30489 from meeseeksmachine/auto-backport-of-pr-30486-on-v...
  • 5351097 Merge pull request #30488 from meeseeksmachine/auto-backport-of-pr-30486-on-v...
  • 6b800b8 Merge pull request #30487 from meeseeksmachine/auto-backport-of-pr-30484-on-v...
  • 25a97fd Backport PR #30486: doc: Update warnings about python-build-standalone
  • 4b79495 Backport PR #30486: doc: Update warnings about python-build-standalone
  • a55b817 Backport PR #30484: FIX: be more cautious about checking widget size
  • Additional commits viewable in compare view

Updates monai from 1.4.0 to 1.5.1

Release notes

Sourced from monai's releases.

1.5.1

Added

  • PyTorch 2.7 and 2.8 support (#8429, #8530)
  • Create SECURITY.md (#8546)
  • Add kwargs in array and functional file (#8508)
  • Add .coderabbit.yaml File (#8513)
  • Add input validation to ImageStats class (#8501)
  • Add support for optional conditioning in PatchInferer, SliceInferer, and SlidingWindowInferer (#8400)
  • Add classifier free guidance unconditioned value (#8562)
  • Improved DiffusionModelEncoder to support output linear layers of different dimensions (#8578, #8580)

Fixed

  • Fix for insecure zip file extraction to address GHSA-x6ww-pf9m-m73m (#8568)
  • Fix for insecure use of torch.load and pickle to address GHSA-6vm5-6jv9-rjpj and GHSA-p8cm-mm2v-gwjm (#8566)
  • Torchvision fix for loading pretrained weights using current syntax (#8563)
  • Fix bug in MAISI vae (#8517)
  • Throw exception on invalid images in retinanet detector (#8515)
  • Fix: HistogramNormalized doc (#8543)
  • Fix build failure by pinning pyamg to versions below 5.3.0 (#8548)
  • Fix hardcoded input dim in DiffusionModelEncoder (#8514)
  • Fix for gdown downloading fails (#8576)

Changed

  • Update README badges to add research paper citations number (#8494)
  • CI: Add custom timeout to ci job in order to save resources (#8504)
  • Improve documentation on the datalist format (#8539)
  • Tests Cleanup and refactor (#8405, #8535)
  • Improve Orientation transform to use the "space" (LPS vs RAS) of a metatensor by default (#8473)
  • Updated supported version of Huggingface Transformers (#8574)

New Contributors

Full Changelog: Project-MONAI/MONAI@1.5.0...1.5.1

1.5.0

Added

  • Add platform-specific constraints to setup.cfg (#8260)
  • Add PythonicWorkflow (#8151)
  • Add SM architecture version check (#8199)
  • Add MedNext implementation (#8004)
  • Added a top button to CONSTRIBUTING.md (#8163)

... (truncated)

Changelog

Sourced from monai's changelog.

[1.5.1] - 2025-09-22

What's Changed

Added

  • PyTorch 2.7 and 2.8 support (#8429, #8530)
  • Create SECURITY.md (#8546)
  • Add kwargs in array and functional file (#8508)
  • Add .coderabbit.yaml File (#8513)
  • Add input validation to ImageStats class (#8501)
  • Add support for optional conditioning in PatchInferer, SliceInferer, and SlidingWindowInferer (#8400)
  • Add classifier free guidance unconditioned value (#8562)
  • Improved DiffusionModelEncoder to support output linear layers of different dimensions (#8578, #8580)

Fixed

  • Fix for insecure zip file extraction to address GHSA-x6ww-pf9m-m73m (#8568)
  • Fix for insecure use of torch.load and pickle to address GHSA-6vm5-6jv9-rjpj and GHSA-p8cm-mm2v-gwjm (#8566)
  • Torchvision fix for loading pretrained weights using current syntax (#8563)
  • Fix bug in MAISI vae (#8517)
  • Throw exception on invalid images in retinanet detector (#8515)
  • Fix: HistogramNormalized doc (#8543)
  • Fix build failure by pinning pyamg to versions below 5.3.0 (#8548)
  • Fix hardcoded input dim in DiffusionModelEncoder (#8514)
  • Fix for gdown downloading fails (#8576)

Changed

  • Update README badges to add research paper citations number (#8494)
  • CI: Add custom timeout to ci job in order to save resources (#8504)
  • Improve documentation on the datalist format (#8539)
  • Tests Cleanup and refactor (#8405, #8535)
  • Improve Orientation transform to use the "space" (LPS vs RAS) of a metatensor by default (#8473)
  • Updated supported version of Huggingface Transformers (#8574)

[1.5.0] - 2025-06-13

What's Changed

Added

  • Add platform-specific constraints to setup.cfg (#8260)
  • Add PythonicWorkflow (#8151)
  • Add SM architecture version check (#8199)
  • Add MedNext implementation (#8004)
  • Added a top button to CONSTRIBUTING.md (#8163)
  • Adding CODEOWNERS (#8457)
  • Restormer Implementation (#8312)
  • Add rectified flow noise scheduler for accelerated diffusion model (#8374)
  • Add prediction type for rflow scheduler (#8386)
  • Add Average Precision to metrics (#8089)
  • Implementation of a Masked Autoencoder for representation learning (#8152)
  • Implement TorchIO transforms wrapper analogous to TorchVision transfo… (#7579)
  • 8328 nnunet bundle integration (#8329)
  • Adding Support Policy + Doc Updates (#8458)

... (truncated)

Commits

Updates pandas from 2.2.3 to 2.3.3

Release notes

Sourced from pandas's releases.

Pandas 2.3.3

We are pleased to announce the release of pandas 2.3.3. This release includes some improvements and fixes to the future string data type (preview feature for the upcoming pandas 3.0). We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.3.3 supports Python 3.9 and higher, and is the first release to support Python 3.14.

The release will be available on the conda-forge channel:

conda install pandas --channel conda-forge

Or via PyPI:

python3 -m pip install --upgrade pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Pandas 2.3.2

We are pleased to announce the release of pandas 2.3.2. This release includes some improvements and fixes to the future string data type (preview feature for the upcoming pandas 3.0). We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.3.2 supports Python 3.9 and higher.

The release will be available on the conda-forge channel:

conda install pandas --channel conda-forge

Or via PyPI:

python3 -m pip install --upgrade pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Pandas 2.3.1

We are pleased to announce the release of pandas 2.3.1. This release includes some improvements and fixes to the future string data type (preview feature for the upcoming pandas 3.0). We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.3.1 supports Python 3.9 and higher.

The release will be available on the conda-forge channel:

conda install pandas --channel conda-forge

Or via PyPI:

... (truncated)

Commits
  • 9c8bc3e RLS: 2.3.3
  • 6aa788a [backport 2.3.x] DOC: prepare 2.3.3 whatsnew notes for release (#62499) (#62508)
  • b64f0df [backport 2.3.x] BUG: avoid validation error for ufunc with string[python] ar...
  • 058eb2b [backport 2.3.x] BUG: String[pyarrow] comparison with mixed object (#62424) (...
  • 2ca088d [backport 2.3.x] DEPR: remove the Period resampling deprecation (#62480) (#62...
  • 92bf98f [backport 2.3.x] BUG: fix .str.isdigit to honor unicode superscript for older...
  • e57c7d6 Backport PR #62452 on branch 2.3.x (TST: Adjust tests for numexpr 2.13) (#62454)
  • e0fe9a0 Backport to 2.3.x: REGR: from_records not initializing subclasses properly (#...
  • 23a1085 BUG: improve future warning for boolean operations with missaligned indexes (...
  • 6113696 Backport PR #62396 on branch 2.3.x (PKG/DOC: indicate Python 3.14 support in ...
  • Additional commits viewable in compare view

Updates plotly from 6.1.2 to 6.3.1

Release notes

Sourced from plotly's releases.

v6.3.1

Updated

  • Update Plotly.js from version 3.1.0 to version 3.1.1. See the Plotly.js release notes for more information. [#5357]. Notable changes include:
    • Fix issue preventing Scattergl plots with text elements from rendering [plotly.js#7563]
  • Use native legends when converting from matplotlib [#5312], with thanks to @​robertoffmoura to the contribution!
  • Allow shared_yaxes to work with secondary axes [#5180], with thanks to @​gmjw for the contribution!

Fixed

  • Fix issue where width/height in plot layout were not respected during Kaleido image export [#5325]
  • Fix typo in default argument to _ternary_contour.py [#5315], with thanks to @​Lexachoc for the contribution!
  • Fix incorrect fig.show() behavior when ipython is installed [#5258]

Full Changelog: plotly/plotly.py@v6.3.0...v6.3.1

v6.3.0

Updated

  • Updated Plotly.js from version 3.0.1 to version 3.1.0. See the plotly.js release notes for more information. [#5318]

Added

  • Exposed plotly.io.get_chrome() as a function which can be called from within a Python script. [#5282]

Fixed

  • Resolved issue causing extraneous engine deprecation warnings [#5287], with thanks to @​jdbeel for the contribution!

v6.2.0

Added

  • Add SRI (Subresource Integrity) hash support for CDN script tags when using include_plotlyjs='cdn'. This enhances security by ensuring browser verification of CDN-served plotly.js files [#5165] (with thanks to @​ddworken)

Fixed

  • Allow setting Plotly.js path via pio.defaults [#5207]

Changed

  • Refactor validation code to reduce bundle size [#5214] (with thanks to @​bmaranville)
  • Add deprecation warnings when using Kaleido v0 or deprecated image export features [#5177]
Changelog

Sourced from plotly's changelog.

[6.3.1] - 2025-10-02

Updated

  • Update Plotly.js from version 3.1.0 to version 3.1.1. See the Plotly.js release notes for more information. [#5357]. Notable changes include:
    • Fix issue preventing Scattergl plots with text elements from rendering [plotly.js#7563]
  • Use native legends when converting from matplotlib [#5312], with thanks to @​robertoffmoura to the contribution!
  • Allow shared_yaxes to work with secondary axes [#5180], with thanks to @​gmjw for the contribution!

Fixed

  • Fix issue where width/height in plot layout were not respected during Kaleido image export [#5325]
  • Fix typo in default argument to _ternary_contour.py [#5315], with thanks to @​Lexachoc for the contribution!
  • Fix incorrect fig.show() behavior when ipython is installed [#5258]

[6.3.0] - 2025-08-12

Updated

  • Updated Plotly.js from version 3.0.1 to version 3.1.0. See the Plotly.js release notes for more information. [#5318]

Added

  • Exposed plotly.io.get_chrome() as a function which can be called from within a Python script. [#5282]

Fixed

  • Resolved issue causing extraneous engine deprecation warnings [#5287], with thanks to @​jdbeel for the contribution!

[6.2.0] - 2025-06-26

Added

  • Add SRI (Subresource Integrity) hash support for CDN script tags when using include_plotlyjs='cdn'. This enhances security by ensuring browser verification of CDN-served plotly.js files [#5165] (with thanks to @​ddworken)

Fixed

  • Allow setting Plotly.js path via pio.defaults [#5207]

Changed

  • Refactor validation code to reduce bundle size [#5214] (with thanks to @​bmaranville)
  • Add deprecation warnings when using Kaleido v0 or deprecated image export features [#5177]
Commits
  • ecb00fe update uv lockfile
  • 4e96a43 version changes for v6.3.1
  • a0de8c9 Merge pull request #5361 from plotly/matplotlib-import-fix
  • 832b46c Merge branch 'main' into matplotlib-import-fix
  • b258862 Merge pull request #5180 from gmjw/secondary-y-shared
  • 2c5e2b6 fix matplotlib import
  • 610b7ee Merge branch 'main' into secondary-y-shared
  • fbbc9d6 Merge pull request #5322 from mgorny/plt-import
  • d2af541 Merge pull request #5258 from plotly/fix-default-renderer-when-ipython-installed
  • ead0c76 Merge branch 'main' into plt-import
  • Additional commits viewable in compare view

Updates pre-commit from 4.2.0 to 4.3.0

Release notes

Sourced from pre-commit's releases.

pre-commit v4.3.0

Features

Changelog

Sourced from pre-commit's changelog.

4.3.0 - 2025-08-09

Features

Commits
  • b74a22d v4.3.0
  • cc899de Merge pull request #3507 from bc-lee/dart-fix
  • 2a0bcea Downgrade Dart SDK version installed in the CI
  • f1cc7a4 Make Dart pre-commit hook compatible with the latest Dart SDKs
  • 72a3b71 Merge pull request #3504 from pre-commit/pre-commit-ci-update-config
  • c8925a4 [pre-commit.ci] pre-commit autoupdate
  • a5fe6c5 Merge pull request #3496 from ericphanson/eph/jl-startup
  • 6f1f433 Julia language: skip startup.jl file
  • c681721 Merge pull request #3499 from pre-commit/pre-commit-ci-update-config
  • 4fd4537 [pre-commit.ci] pre-commit autoupdate
  • Additional commits viewable in compare view

Updates pytest-cov from 6.1.1 to 7.0.0

Changelog

Sourced from pytest-cov's changelog.

7.0.0 (2025-09-09)

  • Dropped support for subprocesses measurement.

    It was a feature added long time ago when coverage lacked a nice way to measure subprocesses created in tests. It relied on a .pth file, there was no way to opt-out and it created bad interations with coverage's new patch system <https://coverage.readthedocs.io/en/latest/config.html#run-patch>_ added in 7.10 <https://coverage.readthedocs.io/en/7.10.6/changes.html#version-7-10-0-2025-07-24>_.

    To migrate to this release you might need to enable the suprocess patch, example for .coveragerc:

    .. code-block:: ini

    [run] patch = subprocess

    This release also requires at least coverage 7.10.6.

  • Switched packaging to have metadata completely in pyproject.toml and use hatchling <https://pypi.org/project/hatchling/>_ for building. Contributed by Ofek Lev in [#551](https://github.com/pytest-dev/pytest-cov/issues/551) <https://github.com/pytest-dev/pytest-cov/pull/551>_ with some extras in [#716](https://github.com/pytest-dev/pytest-cov/issues/716) <https://github.com/pytest-dev/pytest-cov/pull/716>_.

  • Removed some not really necessary testing deps like six.

6.3.0 (2025-09-06)

  • Added support for markdown reports. Contributed by Marcos Boger in [#712](https://github.com/pytest-dev/pytest-cov/issues/712) <https://github.com/pytest-dev/pytest-cov/pull/712>_ and [#714](https://github.com/pytest-dev/pytest-cov/issues/714) <https://github.com/pytest-dev/pytest-cov/pull/714>_.
  • Fixed some formatting issues in docs. Anonymous contribution in [#706](https://github.com/pytest-dev/pytest-cov/issues/706) <https://github.com/pytest-dev/pytest-cov/pull/706>_.

6.2.1 (2025-06-12)

  • Added a version requirement for pytest's pluggy dependency (1.2.0, released 2023-06-21) that has the required new-style hookwrapper API.

  • Removed deprecated license classifier (packaging).

  • Disabled coverage warnings in two more situations where they have no value:

    • "module-not-measured" in workers
    • "already-imported" in subprocesses

6.2.0 (2025-06-11)

  • The plugin now adds 3 rules in the filter warnings configuration to prevent common coverage warnings being raised as obscure errors::

    default:unclosed database in <sqlite3.Connection object at:ResourceWarning once::PytestCovWarning

... (truncated)

Commits
  • 224d896 Bump version: 6.3.0 → 7.0.0
  • 73424e3 Cleanup the docs a bit.
  • 36f1cc2 Bump pins in template.
  • f299c59 Bump the github-actions group with 2 updates
  • 25f0b2e Update docs/config.rst
  • bb23eac Improve configuration docs
  • a19531e Switch from build/pre-commit to uv/prek - this should make this faster.
  • 82f9993 Update changelog.
  • 211b5cd Fix links.
  • 97aadd7 Update some ci config, reformat and apply some lint fixes.
  • Additional commits viewable in compare view

Updates pytest-mock from 3.14.1 to 3.15.1

Release notes

Sourced from pytest-mock's releases.

v3.15.1

2025-09-16

  • #529: Fixed itertools._tee object has no attribute error -- now duplicate_iterators=True must be passed to mocker.spy to duplicate iterators.

v3.15.0

2025-09-04

  • Python 3.8 (EOL) is no longer supported.
  • #524: Added spy_return_iter to mocker.spy, which contains a duplicate of the return value of the spied method if it is an Iterator.
Changelog

Sourced from pytest-mock's changelog.

3.15.1

2025-09-16

  • [#529](https://github.com/pytest-dev/pytest-mock/issues/529) <https://github.com/pytest-dev/pytest-mock/issues/529>_: Fixed itertools._tee object has no attribute error -- now duplicate_iterators=True must be passed to mocker.spy to duplicate iterators.

3.15.0

2025-09-04

  • Python 3.8 (EOL) is no longer supported.
  • [#524](https://github.com/pytest-dev/pytest-mock/issues/524) <https://github.com/pytest-dev/pytest-mock/pull/524>_: Added spy_return_iter to mocker.spy, which contains a duplicate of the return value of the spied method if it is an Iterator.
Commits
  • e1b5c62 Release 3.15.1
  • 184eb19 Set spy_return_iter only when explicitly requested (#537)
  • 4fa0088 [pre-commit.ci] pre-commit autoupdate (#536)
  • f5aff33 Fix test failure with pytest 8+ and verbose mode (#535)
  • adc4187 Bump actions/setup-python from 5 to 6 in the github-actions group (#533)
  • 95ad570 [pre-commit.ci] pre-commit autoupdat...

    Description has been truncated

@dependabot
Bump the python-requirements group in /envs with 18 updates
25afda5 
Bumps the python-requirements group in /envs with 18 updates:

| Package | From | To |
| --- | --- | --- |
| [simpleitk](https://github.com/SimpleITK/SimpleITK) | `2.5.0` | `2.5.2` |
| [coverage](https://github.com/nedbat/coveragepy) | `7.8.2` | `7.10.7` |
| [jupyterlab](https://github.com/jupyterlab/jupyterlab) | `4.4.3` | `4.4.9` |
| [matplotlib](https://github.com/matplotlib/matplotlib) | `3.10.1` | `3.10.6` |
| [monai](https://github.com/Project-MONAI/MONAI) | `1.4.0` | `1.5.1` |
| [pandas](https://github.com/pandas-dev/pandas) | `2.2.3` | `2.3.3` |
| [plotly](https://github.com/plotly/plotly.py) | `6.1.2` | `6.3.1` |
| [pre-commit](https://github.com/pre-commit/pre-commit) | `4.2.0` | `4.3.0` |
| [pytest-cov](https://github.com/pytest-dev/pytest-cov) | `6.1.1` | `7.0.0` |
| [pytest-mock](https://github.com/pytest-dev/pytest-mock) | `3.14.1` | `3.15.1` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.3.5` | `8.4.2` |
| [rich](https://github.com/Textualize/rich) | `14.0.0` | `14.1.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.11.12` | `0.13.3` |
| [safetensors](https://github.com/huggingface/safetensors) | `0.5.3` | `0.6.2` |
| [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.6.1` | `1.7.2` |
| [scipy](https://github.com/scipy/scipy) | `1.15.2` | `1.16.2` |
| [timm](https://github.com/huggingface/pytorch-image-models) | `1.0.15` | `1.0.20` |
| [wandb](https://github.com/wandb/wandb) | `0.19.11` | `0.22.1` |


Updates `simpleitk` from 2.5.0 to 2.5.2
- [Release notes](https://github.com/SimpleITK/SimpleITK/releases)
- [Commits](SimpleITK/SimpleITK@v2.5.0...v2.5.2)

Updates `coverage` from 7.8.2 to 7.10.7
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.8.2...7.10.7)

Updates `jupyterlab` from 4.4.3 to 4.4.9
- [Release notes](https://github.com/jupyterlab/jupyterlab/releases)
- [Changelog](https://github.com/jupyterlab/jupyterlab/blob/main/RELEASE.md)
- [Commits](https://github.com/jupyterlab/jupyterlab/compare/@jupyterlab/lsp@4.4.3...@jupyterlab/lsp@4.4.9)

Updates `matplotlib` from 3.10.1 to 3.10.6
- [Release notes](https://github.com/matplotlib/matplotlib/releases)
- [Commits](matplotlib/matplotlib@v3.10.1...v3.10.6)

Updates `monai` from 1.4.0 to 1.5.1
- [Release notes](https://github.com/Project-MONAI/MONAI/releases)
- [Changelog](https://github.com/Project-MONAI/MONAI/blob/dev/CHANGELOG.md)
- [Commits](Project-MONAI/MONAI@1.4.0...1.5.1)

Updates `pandas` from 2.2.3 to 2.3.3
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.2.3...v2.3.3)

Updates `plotly` from 6.1.2 to 6.3.1
- [Release notes](https://github.com/plotly/plotly.py/releases)
- [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md)
- [Commits](plotly/plotly.py@v6.1.2...v6.3.1)

Updates `pre-commit` from 4.2.0 to 4.3.0
- [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@v4.2.0...v4.3.0)

Updates `pytest-cov` from 6.1.1 to 7.0.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.1.1...v7.0.0)

Updates `pytest-mock` from 3.14.1 to 3.15.1
- [Release notes](https://github.com/pytest-dev/pytest-mock/releases)
- [Changelog](https://github.com/pytest-dev/pytest-mock/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-mock@v3.14.1...v3.15.1)

Updates `pytest` from 8.3.5 to 8.4.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](pytest-dev/pytest@8.3.5...8.4.2)

Updates `rich` from 14.0.0 to 14.1.0
- [Release notes](https://github.com/Textualize/rich/releases)
- [Changelog](https://github.com/Textualize/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v14.0.0...v14.1.0)

Updates `ruff` from 0.11.12 to 0.13.3
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.11.12...0.13.3)

Updates `safetensors` from 0.5.3 to 0.6.2
- [Release notes](https://github.com/huggingface/safetensors/releases)
- [Changelog](https://github.com/huggingface/safetensors/blob/main/RELEASE.md)
- [Commits](huggingface/safetensors@v0.5.3...v0.6.2)

Updates `scikit-learn` from 1.6.1 to 1.7.2
- [Release notes](https://github.com/scikit-learn/scikit-learn/releases)
- [Commits](scikit-learn/scikit-learn@1.6.1...1.7.2)

Updates `scipy` from 1.15.2 to 1.16.2
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.15.2...v1.16.2)

Updates `timm` from 1.0.15 to 1.0.20
- [Release notes](https://github.com/huggingface/pytorch-image-models/releases)
- [Commits](huggingface/pytorch-image-models@v1.0.15...v1.0.20)

Updates `wandb` from 0.19.11 to 0.22.1
- [Release notes](https://github.com/wandb/wandb/releases)
- [Changelog](https://github.com/wandb/wandb/blob/main/CHANGELOG.md)
- [Commits](wandb/wandb@v0.19.11...v0.22.1)

---
updated-dependencies:
- dependency-name: simpleitk
  dependency-version: 2.5.2
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-requirements
- dependency-name: coverage
  dependency-version: 7.10.7
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: jupyterlab
  dependency-version: 4.4.9
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-requirements
- dependency-name: matplotlib
  dependency-version: 3.10.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-requirements
- dependency-name: monai
  dependency-version: 1.5.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: pandas
  dependency-version: 2.3.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: plotly
  dependency-version: 6.3.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: pre-commit
  dependency-version: 4.3.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: pytest-cov
  dependency-version: 7.0.0
  dependency-type: direct:production
  update-type: version-update:semver-major
  dependency-group: python-requirements
- dependency-name: pytest-mock
  dependency-version: 3.15.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: pytest
  dependency-version: 8.4.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: rich
  dependency-version: 14.1.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: ruff
  dependency-version: 0.13.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: safetensors
  dependency-version: 0.6.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: scikit-learn
  dependency-version: 1.7.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: scipy
  dependency-version: 1.16.2
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
- dependency-name: timm
  dependency-version: 1.0.20
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-requirements
- dependency-name: wandb
  dependency-version: 0.22.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: python-requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update python code labels Oct 6, 2025
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