Bump the python-packages group across 1 directory with 7 updates by dependabot[bot] · Pull Request #189 · cytomining/CytoDataFrame

dependabot · 2026-02-13T00:17:50Z

Bumps the python-packages group with 7 updates in the / directory:

Package	From	To
opencv-python	`4.13.0.90`	`4.13.0.92`
ome-arrow	`0.0.5`	`0.0.6`
pyvista	`0.46.5`	`0.47.0`
coverage	`7.13.2`	`7.13.4`
jupyterlab	`4.5.3`	`4.5.4`
jupyterlab-code-formatter	`3.0.2`	`3.0.3`
poethepoet	`0.40.0`	`0.41.0`

Updates opencv-python from 4.13.0.90 to 4.13.0.92

Release notes

Sourced from opencv-python's releases.

4.13.0.92

Follow up release for 4.13.0 with X server dependency fix. See #28438 for details.

Commits

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Updates ome-arrow from 0.0.5 to 0.0.6

Release notes

Sourced from ome-arrow's releases.

v0.0.6

Changes

Add pixel chunking to specification (@d33bs via #24)

Bump the uv group with 20 updates (@dependabot[bot] via #32)

Bump jupyterlab from 4.4.2 to 4.4.8 (@dependabot[bot] via #31)

Bump requests from 2.32.3 to 2.32.4 (@dependabot[bot] via #30)

Bump fonttools from 4.60.1 to 4.60.2 (@dependabot[bot] via #29)

Bump aiohttp from 3.13.2 to 3.13.3 (@dependabot[bot] via #27)

Bump protobuf from 5.29.5 to 6.33.5 (@dependabot[bot] via #26)

Bump urllib3 from 2.4.0 to 2.6.3 (@dependabot[bot] via #25)

Bump isort from 6.0.1 to 7.0.0 (@dependabot[bot] via #19)

Add image_type key to spec (@d33bs via #17)

Commits

8a6803e Add pixel chunking to specification (#24)
d30d507 Bump the uv group with 20 updates (#32)
03b2ce3 Bump jupyterlab from 4.4.2 to 4.4.8 (#31)
3043441 Bump requests from 2.32.3 to 2.32.4 (#30)
09f94c2 Bump fonttools from 4.60.1 to 4.60.2 (#29)
667b78f Bump aiohttp from 3.13.2 to 3.13.3 (#27)
c9cbfa5 Bump protobuf from 5.29.5 to 6.33.5 (#26)
816e432 Bump urllib3 from 2.4.0 to 2.6.3 (#25)
8fff9da Bump isort from 6.0.1 to 7.0.0 (#19)
e925345 Add image_type key to spec (#17)
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Updates pyvista from 0.46.5 to 0.47.0

Release notes

Sourced from pyvista's releases.

v0.47.0

What's Changed

Breaking Changes

Improve number_time_points property in EnsightReader by @riku-sakamoto in pyvista/pyvista#7804

Do not always get last image depth by @akaszynski in pyvista/pyvista#7953

Make CameraPosition.__repr__ explicit by @user27182 in pyvista/pyvista#7794

Use 2D labels by default with CubeAxesActor for VTK 9.6 by @user27182 in pyvista/pyvista#8248

New Features

Add Texture.color_mode and use 'direct' mode by default by @user27182 in pyvista/pyvista#7757

Add pass_point(cell)_ids to extract_points(cells) by @user27182 in pyvista/pyvista#7765

Add remove_existing_actor parameter to add_mesh by @tkoyama010 in pyvista/pyvista#7809

Add point keyword to Transform.compose by @user27182 in pyvista/pyvista#7869

Add optional downloads info to Report by @user27182 in pyvista/pyvista#7927

Add border_mode to resample filter by @user27182 in pyvista/pyvista#7964

Add bspline interpolator to resample filter by @user27182 in pyvista/pyvista#7965

Add command line interface with --version and report options by @user27182 in pyvista/pyvista#7463

Allow adding mesh to plotter from file by @user27182 in pyvista/pyvista#7976

Add plot command to pyvista CLI by @user27182 in pyvista/pyvista#7970

Use cyclopts as CLI library by @edabor in pyvista/pyvista#7991

Improve morphological filters for ImageData by @tkoyama010 in pyvista/pyvista#7833

Use binary filter dynamically with morphological operators by @user27182 in pyvista/pyvista#7996

Add convert CLI command for converting mesh file format by @user27182 in pyvista/pyvista#8005

Disallow no files for pyvista plot CLI by @edabor in pyvista/pyvista#8011

Add allow_new_attributes state manager class by @user27182 in pyvista/pyvista#7864

Add image concatenate filter by @user27182 in pyvista/pyvista#8013

Add connectivity region assignment mode by @edabor in pyvista/pyvista#8029

Add background_value keyword to concatenate filter by @user27182 in pyvista/pyvista#8031

Add Transform component properties by @user27182 in pyvista/pyvista#8051

Add multi-level option to Box by @user27182 in pyvista/pyvista#8068

Add png, jpg, tiff, nifti, bmp, pnm image writers by @user27182 in pyvista/pyvista#8084

Add writer classes by @user27182 in pyvista/pyvista#8094

Add DataObject.cast_to_multiblock by @user27182 in pyvista/pyvista#8106

Generalize dimensionality property for all datasets by @user27182 in pyvista/pyvista#8121

Add more arguments to spline by @tletut0ur in pyvista/pyvista#8072

Enable VtkErrorCatcher to catch VTK warnings by @user27182 in pyvista/pyvista#7863

Add warping spheres example and enable plotting PartitionedDataSet by @user27182 in pyvista/pyvista#8111

Allow using Plane with plane-based filters by @user27182 in pyvista/pyvista#8151

Add UnstructuredGrid.distinct_cell_types by @user27182 in pyvista/pyvista#8160

Enable setting dataset center by @user27182 in pyvista/pyvista#8174

Add length option to resize filter by @user27182 in pyvista/pyvista#8175

Add pv.to_trimesh and pv.from_trimesh functions by @user27182 in pyvista/pyvista#8176

Add select_interior_points filter to replace select_enclosed_points by @user27182 in pyvista/pyvista#8181

Support mesh validation for MultiBlock by @user27182 in pyvista/pyvista#8189

Add min/max cell dimensionality by @user27182 in pyvista/pyvista#8186

Add generic typing for mesh validation reports by @user27182 in pyvista/pyvista#8203

Add validate keyword to mesh constructors by @user27182 in pyvista/pyvista#8222

Add font_size, point_size, line_width and normals_scale keywords to plot_cell by @user27182 in pyvista/pyvista#8236

Generalize distinct_cell_types for all datasets by @user27182 in pyvista/pyvista#8224

... (truncated)

Commits

f6613b1 Merge branch 'main' into release/0.47
a738a6a Make upload step conditional on tag only (#8302)
96bed1e Avoid casting to ugrid for distinct cell types (#8298)
b41d5c2 bump to v0.47.0 (#8300)
259ebb3 revert all deprecation modifications
b77c749 fix theme testing
f4d2d4c allow setting axes box in themes
d05b37e skip gc check; remove unused image
27ba548 make error instead
eb7d55f remove add_axes(box=...) functionality and add_pick observer
Additional commits viewable in compare view

Updates coverage from 7.13.2 to 7.13.4

Changelog

Sourced from coverage's changelog.

Version 7.13.4 — 2026-02-09

Fix: the third-party code fix in 7.13.3 required examining the parent directories where coverage was run. In the unusual situation that one of the parent directories is unreadable, a PermissionError would occur, as described in issue 2129_. This is now fixed.

Fix: in test suites that change sys.path, coverage.py could fail with "RuntimeError: Set changed size during iteration" as described and fixed in pull 2130_. Thanks, Noah Fatsi.

We now publish ppc64le wheels, thanks to Pankhudi Jain <pull 2121_>_.

.. _pull 2121: coveragepy/coveragepy#2121 .. _issue 2129: coveragepy/coveragepy#2129 .. _pull 2130: coveragepy/coveragepy#2130

.. _changes_7-13-3:

Version 7.13.3 — 2026-02-03

Fix: in some situations, third-party code was measured when it shouldn't have been, slowing down test execution. This happened with layered virtual environments such as uv sometimes makes. The problem is fixed, closing issue 2082_. Now any directory on sys.path that is inside a virtualenv is considered third-party code.

.. _issue 2082: coveragepy/coveragepy#2082

.. _changes_7-13-2:

Commits

4f78d57 build: no need to publish status.json
f8616ff docs: sample HTML for 7.13.4
fcf8c68 docs: prep for 7.13.4
189ecfd docs: thanks Pankhudi Jain for ppc64le wheels #2121
58aade0 build: add support for ppc64le architecture (#2121)
8ea42c8 chore: bump actions/attest-build-provenance (#2131)
c09595f docs: Janine put a lot of effort into debugging issue #2128
8ee1760 docs: Greg wrote a great issue: #2129
76ba043 docs: thanks, Noah Fatsi
371fcc5 fix: set fixed paths_list in TreeMatcher init (#2130)
Additional commits viewable in compare view

Updates jupyterlab from 4.5.3 to 4.5.4

Release notes

Sourced from jupyterlab's releases.

v4.5.4

4.5.4

(Full Changelog)

Bugs fixed

Avoid using system clipboard in Notebook widget #18474 (@brichet)

Update CodeMirror versions, fixing a few selection issues #18466 (@krassowski)

Fix debugger variable panel to render value 0 properly #18464 (@itsmevichu)

Consider both the content type and pattern match in DocumentRegistry.getFileTypeForModel() #18409 (@krassowski)

false in saveAs to avoid fetching file body #18379 (@DeborahOlaboye)

Maintenance and upkeep improvements

Bump Lumino packages to the 2026.2.5 release, fixing iframe resizing #18440 (@jasongrout)

Documentation improvements

Clarify notebook and cell metadata API changes in JupyterLab 4 #18304 (@Krish-876)

Document a change in the Code Editor source updates via sharedModel in JupyterLab 4 #18260 (@Krish-876)

Fix Contents API fetch documentation of the content default #18383 (@ceasermikes002)

Add AI rules #18322 (@jtpio)

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)

@brichet (activity) | @ceasermikes002 (activity) | @DeborahOlaboye (activity) | @itsmevichu (activity) | @jasongrout (activity) | @jtpio (activity) | @krassowski (activity) | @Krish-876 (activity)

Commits

2ecc1ee [ci skip] Publish 4.5.4
19f81fc Backport PR #18474 on branch 4.5.x (Avoid using system clipboard in Notebook ...
b82e6d7 Backport PR #18466 on branch 4.5.x (Update CodeMirror versions, fixing a few ...
c70c36e Backport PR #18440 on branch 4.5.x (Bump Lumino packages to the 2026.2.5 rele...
23b9ff5 Backport PR #18464 on branch 4.5.x (Fix debugger variable panel to render val...
553d941 Backport PR #18409 on branch 4.5.x (Consider both the content type and patter...
d8acd39 Backport PR #18304 on branch 4.5.x (Clarify notebook and cell metadata API ch...
e021969 Backport PR #18260 on branch 4.5.x (Document a change in the Code Editor sour...
dc39ba5 Backport PR #18383 on branch 4.5.x (Fix Contents API fetch documentation of t...
fd57db9 Backport PR #18322: Add AI rules (#18395)
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Updates jupyterlab-code-formatter from 3.0.2 to 3.0.3

Release notes

Sourced from jupyterlab-code-formatter's releases.

v3.0.3

3.0.3

(Full Changelog)

Maintenance and upkeep improvements

Update snapshots bot checkout and permission check #373 (@martinRenou, @krassowski)

Other merged PRs

Drop NPM_TOKEN for trusted publishers setup #374 (@krassowski, @AA-Turner)

feat: improve isort configurability #370 (@lucas-bremond, @AA-Turner, @krassowski)

ruff format: don't pass -q #368 (@nelhage, @AA-Turner, @Hnasar, @krassowski)

Fix SyntaxWarning by using a raw string in the regex pattern #366 (@tsvikas, @krassowski, @shreve)

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)

@AA-Turner (activity) | @Hnasar (activity) | @krassowski (activity) | @lucas-bremond (activity) | @martinRenou (activity) | @nelhage (activity) | @shreve (activity) | @tsvikas (activity)

Changelog

Sourced from jupyterlab-code-formatter's changelog.

3.0.3

(Full Changelog)

Maintenance and upkeep improvements

Update snapshots bot checkout and permission check #373 (@martinRenou, @krassowski)

Other merged PRs

Drop NPM_TOKEN for trusted publishers setup #374 (@krassowski, @AA-Turner)

feat: improve isort configurability #370 (@lucas-bremond, @AA-Turner, @krassowski)

ruff format: don't pass -q #368 (@nelhage, @AA-Turner, @Hnasar, @krassowski)

Fix SyntaxWarning by using a raw string in the regex pattern #366 (@tsvikas, @krassowski, @shreve)

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)

@AA-Turner (activity) | @Hnasar (activity) | @krassowski (activity) | @lucas-bremond (activity) | @martinRenou (activity) | @nelhage (activity) | @shreve (activity) | @tsvikas (activity)

Commits

37119c1 Publish 3.0.3
2ba87d6 Drop NPM_TOKEN for trusted publishers setup (#374)
b15e1a8 feat: improve isort configurability (#370)
3f042ec ruff format: don't pass -q (#368)
fb54795 Update snapshots bot checkout and permission check (#373)
9d6e41e Fix SyntaxWarning by using a raw string in the regex pattern (#366)
See full diff in compare view

Updates poethepoet from 0.40.0 to 0.41.0

Release notes

Sourced from poethepoet's releases.

0.41.0

Enhancements

Full shell completions for global and task arguments in zsh and bash by @nat-n in nat-n/poethepoet#355

Full Changelog: nat-n/poethepoet@v0.40.0...v0.41.0

[!IMPORTANT] You must follow the instructions to (re)install the completion script for your preferred shell environment to benefit from the revamped tab completion covering task arguments.

Commits

b15e96e feat: Full shell completions for global and task argument in zsh and bash (#355)
58aaa8b docs: correct invalid docs for uv executor options
6b7691f docs: fix typos (#350)
6a59da1 docs: Fix links in docs (#341)
9898f95 docs: Fix documented option types (#342)
See full diff in compare view

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d33bs · 2026-02-13T00:25:00Z

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Bumps the python-packages group with 7 updates in the / directory: | Package | From | To | | --- | --- | --- | | [opencv-python](https://github.com/opencv/opencv-python) | `4.13.0.90` | `4.13.0.92` | | [ome-arrow](https://github.com/wayscience/ome-arrow) | `0.0.5` | `0.0.6` | | [pyvista](https://github.com/pyvista/pyvista) | `0.46.5` | `0.47.0` | | [coverage](https://github.com/coveragepy/coveragepy) | `7.13.2` | `7.13.4` | | [jupyterlab](https://github.com/jupyterlab/jupyterlab) | `4.5.3` | `4.5.4` | | [jupyterlab-code-formatter](https://github.com/jupyterlab-contrib/jupyterlab_code_formatter) | `3.0.2` | `3.0.3` | | [poethepoet](https://github.com/nat-n/poethepoet) | `0.40.0` | `0.41.0` | Updates `opencv-python` from 4.13.0.90 to 4.13.0.92 - [Release notes](https://github.com/opencv/opencv-python/releases) - [Commits](https://github.com/opencv/opencv-python/commits) Updates `ome-arrow` from 0.0.5 to 0.0.6 - [Release notes](https://github.com/wayscience/ome-arrow/releases) - [Commits](WayScience/ome-arrow@v0.0.5...v0.0.6) Updates `pyvista` from 0.46.5 to 0.47.0 - [Release notes](https://github.com/pyvista/pyvista/releases) - [Commits](pyvista/pyvista@v0.46.5...v0.47.0) Updates `coverage` from 7.13.2 to 7.13.4 - [Release notes](https://github.com/coveragepy/coveragepy/releases) - [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst) - [Commits](coveragepy/coveragepy@7.13.2...7.13.4) Updates `jupyterlab` from 4.5.3 to 4.5.4 - [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@4.5.3...@jupyterlab/lsp@4.5.4) Updates `jupyterlab-code-formatter` from 3.0.2 to 3.0.3 - [Release notes](https://github.com/jupyterlab-contrib/jupyterlab_code_formatter/releases) - [Changelog](https://github.com/jupyterlab-contrib/jupyterlab_code_formatter/blob/master/CHANGELOG.md) - [Commits](jupyterlab-contrib/jupyterlab_code_formatter@v3.0.2...v3.0.3) Updates `poethepoet` from 0.40.0 to 0.41.0 - [Release notes](https://github.com/nat-n/poethepoet/releases) - [Commits](nat-n/poethepoet@v0.40.0...v0.41.0) --- updated-dependencies: - dependency-name: opencv-python dependency-version: 4.13.0.92 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: ome-arrow dependency-version: 0.0.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: pyvista dependency-version: 0.47.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: coverage dependency-version: 7.13.4 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: jupyterlab dependency-version: 4.5.4 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: jupyterlab-code-formatter dependency-version: 3.0.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: poethepoet dependency-version: 0.41.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com>

dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Feb 13, 2026

dependabot bot requested review from d33bs and jenna-tomkinson as code owners February 13, 2026 00:17

dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Feb 13, 2026

dependabot bot force-pushed the dependabot/pip/python-packages-3c7f571925 branch from 42ed516 to 536ea5d Compare February 13, 2026 00:34

chore: auto-apply pre-commit fixes

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d33bs merged commit 87f3b88 into main Feb 13, 2026
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d33bs deleted the dependabot/pip/python-packages-3c7f571925 branch February 13, 2026 01:09

d33bs mentioned this pull request Feb 13, 2026

Fix dependency update and test issues #190

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Bump the python-packages group across 1 directory with 7 updates#189

Bump the python-packages group across 1 directory with 7 updates#189
d33bs merged 2 commits intomainfrom
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4.13.0.92

v0.0.6

Changes

v0.47.0

What's Changed

Breaking Changes

New Features

Version 7.13.4 — 2026-02-09

Version 7.13.3 — 2026-02-03

v4.5.4

4.5.4

Bugs fixed

Maintenance and upkeep improvements

Documentation improvements

Contributors to this release

v3.0.3

3.0.3

Maintenance and upkeep improvements

Other merged PRs

Contributors to this release

3.0.3

Maintenance and upkeep improvements

Other merged PRs

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0.41.0

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