Bump the python-packages group with 10 updates by dependabot[bot] · Pull Request #60 · WayScience/ZedProfiler

dependabot · 2026-10-01T04:24:01Z

Bumps the python-packages group with 10 updates:

Package	From	To
bioio	`3.5.0`	`3.5.1`
bioio-tifffile	`1.3.0`	`1.3.1`
mahotas	`1.4.18`	`1.4.19`
matplotlib	`3.11.1`	`3.11.2`
pandas	`3.0.5`	`3.0.6`
pandera	`0.32.1`	`0.33.1`
ruff	`0.16.5`	`0.16.9`
plotly	`6.9.0`	`7.1.0`
isort	`8.0.1`	`9.0.1`
jupyterlab	`4.6.3`	`4.6.4`

Updates bioio from 3.5.0 to 3.5.1

Release notes

Sourced from bioio's releases.

v3.5.1

What's Changed

ci(dependabot): bump actions/setup-python from 6 to 7 by @dependabot[bot] in bioio-devs/bioio#214

docs: add community contributed plugins to registry by @BrianWhitneyAI in bioio-devs/bioio#219

Prefer reader fast paths for metadata and sub-region reads by @BrianWhitneyAI in bioio-devs/bioio#218

Add CITATION.cff and citation section to README by @BrianWhitneyAI in bioio-devs/bioio#215

Full Changelog: bioio-devs/bioio@v3.5.0...v3.5.1

Commits

a1bc21e Merge pull request #215 from bioio-devs/feature/doi-citation
02cfe0a Merge branch 'main' into feature/doi-citation
83adccd Merge pull request #218 from bioio-devs/feature/reader-fast-paths
ba48c9b update cit message
877cab6 update based on legal advice
6d97546 comment responses
c8273bc Merge branch 'main' into feature/doi-citation
8c27155 Merge branch 'main' into feature/reader-fast-paths
050e5e0 Merge pull request #219 from bioio-devs/docs/community-plugin-registry
8494939 docs: add community contributed plugins to registry
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Updates bioio-tifffile from 1.3.0 to 1.3.1

Commits

00b50f0 Merge pull request #55 from bioio-devs/bugfix/delayed-read-size-one-dims
fe8bdad Merge branch 'main' into bugfix/delayed-read-size-one-dims
b729c8b Build delayed read Zarr store from the series, not the file
75a7618 Merge pull request #53 from bioio-devs/dependabot/github_actions/actions/setu...
d726f22 ci(dependabot): bump actions/setup-python from 6 to 7
9b356fa Merge pull request #52 from bioio-devs/dependabot/github_actions/actions/chec...
3cad9d9 ci(dependabot): bump actions/checkout from 6 to 7
107ad72 Merge pull request #51 from bioio-devs/dependabot/github_actions/extractions/...
ad6e780 ci(dependabot): bump extractions/setup-just from 3 to 4
4c38d90 Merge pull request #49 from bioio-devs/feature/shared-ci-simplify
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Updates mahotas from 1.4.18 to 1.4.19

Release notes

Sourced from mahotas's releases.

Version 1.4.19

Bugfix release

Require Python 3.10+; support Python 3.14 and NumPy 2.x

Build with meson-python (setup.py removed)

Fix incorrect results in colour conversions (rgb2xyz, xyz2rgb, xyz2lab), gbernsen, dog, and find

Fix gaussian_filter1d ignoring out and failing with default axis=-1; fix gaussian_filter on some 3-D inputs

center_of_mass returns NaN for zero-sum labels

Allow spline order 0 in interpolate.zoom/interpolate.shift

Fix interpolate.shift/interpolate.zoom (order 0 or 1) and features.lbp on non-contiguous input (see #124)

Remove long-deprecated modules mahotas.lbp, mahotas.surf, mahotas.texture, mahotas.tas, mahotas.zernike, and mahotas.moments (use mahotas.features.*)

Changelog

Sourced from mahotas's changelog.

Version 1.4.19+

Fix hard crash (segfault/heap corruption) in several C++ extensions on platforms where char is unsigned by default (e.g., aarch64/ARM), which caused int8 arrays with negative values to be mishandled, including bypassing the safety check in features.haralick().

Documentation: document that from mahotas import * shadows the builtin open, the tested Python version range, the thresholding module layout (which functions return a threshold vs. an image), the bernsen/gbernsen gthresh default difference, the n argument of bwperim (including 3-D), and cdilate's semantics; document the I/O backends and fix the backend order and stale install instructions in the io error message; align the README and docs index feature lists.

Version 1.4.19 2026-09-22 by luispedro

Require Python 3.10 or later; support Python 3.14 and NumPy 2.x (tested up to NumPy 2.5).

Build system: replace setup.py with meson-python (packaging metadata is now in pyproject.toml).

Import failures inside mahotas are now propagated instead of being replaced by a generic message.

Fix out handling in convolve1d() and gaussian_filter1d() on non-last axes, accept negative axes in convolve1d() (so gaussian_filter1d() with the default axis=-1 works), and fix gaussian_filter() failing on some 3-D inputs.

Fix interpolate.shift() and interpolate.zoom() with order 0 or 1 raising "input data has unexpected types" on non-C-contiguous input (e.g., slices or Fortran-ordered arrays). This also affected features.lbp() (issue #124).

Simplify mahotas.citation(): replace the Python-2-era sys.stdout.write workaround with print(text, end='').

Remove long-deprecated import shims mahotas.lbp, mahotas.surf, mahotas.texture, mahotas.tas, mahotas.zernike, and mahotas.moments. These had been emitting a DeprecationWarning at import for years; use the corresponding mahotas.features.* modules instead.

Documentation sweep: fix swapped docstrings of labeled_max and labeled_min, parameter-name mistakes in relabel/remove_regions, bad lbp_transform signature/description, "linear binary patterns" -> "local binary patterns" in lbp docstrings and CLI help, dog() and convolve1d signature lines, tophat_close self-See-Also, ambiguous Haralick output shape, freeimage.read shape ordering (height, width), zoom/shift mode list, spline_filter stray "axis." line, slic spacer typo, bbox/croptobbox n-D wording, stretch/stretch_rgb arg0/arg1 naming, _get_output description, several typos (empahsize, threashold, unecessary, Manhatan, Computers, mahotas.features.lb), and gbernsen gthresh "optional" mislabeling. No behavior changes.

Fix inverted np.choose in color conversions (rgb2xyz, xyz2rgb, xyz2lab): all three had the choice arrays swapped, producing incorrect values.

... (truncated)

Commits

d046201 RLS Version 1.4.19
61ae84f BUG Fix out handling in convolve1d/gaussian_filter1d on non-last axes
8bdfc85 DOC Update AGENTS.md with architecture and meson build notes
bd1eced BLD Add AGENTS.md
3deb2f3 BLD Fix wheel builds and update action pins
e6b36ab TST Add testing on Numpy 2.5
f698be5 BUG Fix shift/zoom (order 0/1) on non-contiguous input
7e50f33 MIN Use print() in citation() instead of sys.stdout.write
1d34e11 ENH Remove long-deprecated top-level import shims
0c68b1c RFCT Remove extraneous whitespace
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Updates matplotlib from 3.11.1 to 3.11.2

Release notes

Sourced from matplotlib's releases.

REL: v3.11.2

This is the second bugfix release of the 3.11.x series.

This release contains several bug-fixes and adjustments:

Speed up RGBA-stage image resampling

Fix hexbin clipping in PDF output

Fix \text with internal braces

Fix some crashes and make some checks more robust to unlikely cases

Fix frame skew when saving GIF animations with PillowWriter

Fix HiDPI handling in Qt toolbar and WebAgg embeddings

Fix ResizeEvent handling for TextBox

Fix bug with PGF hatch linewidth and color

Fix a bug with drawing an empty Collection

Fix incorrect glyphs in Cairo backends

Improve build system to prevent conflicts between wheels and system libraries

Commits

d3ca917 REL: v3.11.2
b76fea9 DOC: Set current version to 3.11.2
39c7f06 DOC: Prepare GitHub stats for 3.11.2
5dd13e3 Merge branch 'v3.11.1-doc' into release-3.11.2
aa484be Merge branch 'v3.11.0-doc' into v3.11.1-doc
0e10f83 Merge pull request #32330 from meeseeksmachine/auto-backport-of-pr-32324-on-v...
ebe947b Backport PR #32324: Don't force any diagnostics to be errors in bundled Harfbuzz
8f4b7c5 Merge pull request #32322 from meeseeksmachine/auto-backport-of-pr-32321-on-v...
93278ad Backport PR #32321: DOC: correct note about PyOS_InputHook
b0aee78 Merge pull request #32319 from meeseeksmachine/auto-backport-of-pr-32305-on-v...
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Updates pandas from 3.0.5 to 3.0.6

Release notes

Sourced from pandas's releases.

pandas 3.0.6

We are pleased to announce the release of pandas 3.0.6. This is a patch release in the 3.0.x series and includes some regression fixes and bug fixes. We recommend that all users of the 3.0.x series upgrade to this version. This is also the first release to support Python 3.15.

See the full whatsnew for a list of all the changes.

Pandas 3.0 supports Python 3.11 and higher. The release can be installed from PyPI:
python -m pip install --upgrade pandas==3.0.*
Or from conda-forge
conda install -c conda-forge pandas=3.0
Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Commits

2905718 RLS: 3.0.6
3188ced [backport 3.0.x] BUG: read_csv(sep=None) raised TypeError instead of falling...
f097905 DOC: cleanup 3.0.6 whatsnew + mention Python 3.15 support (#68965) (#68969)
4f68223 [backport 3.0.x] BUG: fix setting with bool column mask into 1-column DataFra...
e3df0e8 [backport 3.0.x] BUG: full-slice setitem into a pyarrow-backed array shared m...
b7735f6 Backport PR #66117 on branch 3.0.x (BUG: interpolate leaving NAs unfilled for...
bca0b77 [backport 3.0.x] BUG: read_csv leaked the string-intern table when a column f...
bca1e5d [backport 3.0.x] BUG: prevent external mutation of RangeIndex._data (CoW) (#6...
c95b42c [3.0.x] CI: skip cython-lint on pre-commit.ci (#68910)
9cbd884 [backport 3.0.x] Backport of some already merged regression fixes (#68447)
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Updates pandera from 0.32.1 to 0.33.1

Release notes

Sourced from pandera's releases.

v0.33.1

What's Changed

docs: announce Pandera CLI and PyArrow support in banner by @cosmicBboy in unionai-oss/pandera#2456

fix: restore optional-column semantics for bare T | None annotations by @cosmicBboy in unionai-oss/pandera#2458

Warn when optional columns are missing via on_missing option by @ChrisJr404 in unionai-oss/pandera#2447

ci: add actionlint workflow and pre-commit hook by @chernojagne in unionai-oss/pandera#2436

New Contributors

@ChrisJr404 made their first contribution in unionai-oss/pandera#2447

@chernojagne made their first contribution in unionai-oss/pandera#2436

Full Changelog: unionai-oss/pandera@v0.33.0...v0.33.1

v0.33.0: Introducing pandera CLI, support pyarrow table

What's Changed

Report all missing required columns in lazy validation by @vineethsaivs in unionai-oss/pandera#2397

fix(pandas): report differing categories in dtype mismatch error by @sha-sta in unionai-oss/pandera#2391

fix(pandas-engine): treat an Enum annotation as a categorical dtype (#2052) by @cycsmail in unionai-oss/pandera#2399

fix(pandas): run column parsers before dataframe-level coercion by @sha-sta in unionai-oss/pandera#2400

fix(pandas): treat NA as coercible for masked nullable dtypes by @sha-sta in unionai-oss/pandera#2404

Fix parenthesized @dataframe_parser() decorator form by @vineethsaivs in unionai-oss/pandera#2408

fix(polars): avoid concat deprecation in lazy validation by @RedZapdos123 in unionai-oss/pandera#2411

fix: Repair coerce and parser options for xarray Datasets by @abaarsma in unionai-oss/pandera#2413

feat(narwhals): support the pandas schema API in the narwhals backend by @cosmicBboy in unionai-oss/pandera#2417

fix(io): deserialize parametrized Decimal dtypes from yaml/json by @cycsmail in unionai-oss/pandera#2434

fix(pandas): apply parsers to Index fields and schema components by @cycsmail in unionai-oss/pandera#2435

feat(pyarrow): add first-class pyarrow.Table schema validation by @sravankumarkunadi in unionai-oss/pandera#2427

Add a pandera CLI: validate, infer, and generate commands by @cosmicBboy in unionai-oss/pandera#2402

add backend info to the cli by @cosmicBboy in unionai-oss/pandera#2446

fix(pandas): respect Optional pydantic fields as nullable in PydanticModel columns (closes #2406) by @feiiiiii5 in unionai-oss/pandera#2429

doc: Fix "list" type annotation by @VeckoTheGecko in unionai-oss/pandera#2440

Support itemsize-parameterized numpy dtypes in the pandas engine by @mannemkarthik010 in unionai-oss/pandera#2437

fix: bind self correctly in check_input when an arg is passed by keyword by @Sanjays2402 in unionai-oss/pandera#2428

fix(polars): raise minimum polars version to 1.20.0 by @fhoehle in unionai-oss/pandera#2412

docs: fix duplicated "the" typos in Check and Hypothesis docstrings by @maupatel in unionai-oss/pandera#2445

Add a backend-neutral FieldType[T] typing contract by @Dev-iL in unionai-oss/pandera#2448

fix: handle scalar groupby keys in _format_groupby_input by @feiiiiii5 in unionai-oss/pandera#2420

fix(decorators): support keyword-only / variadic functions in check_input by @feiiiiii5 in unionai-oss/pandera#2454

ci: only run unit tests for changed areas by @cosmicBboy in unionai-oss/pandera#2450

fix(docs): make intersphinx fetch resilient to transient failures by @cosmicBboy in unionai-oss/pandera#2452

fix(docs): scope pyspark JDK24 security-manager opt-in to JDK 24 only by @cosmicBboy in unionai-oss/pandera#2451

fix: respect pydantic serialization aliases by @mameikagou in unionai-oss/pandera#2449

New Contributors

@sha-sta made their first contribution in unionai-oss/pandera#2391

@abaarsma made their first contribution in unionai-oss/pandera#2413

@sravankumarkunadi made their first contribution in unionai-oss/pandera#2427

@feiiiiii5 made their first contribution in unionai-oss/pandera#2429

@VeckoTheGecko made their first contribution in unionai-oss/pandera#2440

@mannemkarthik010 made their first contribution in unionai-oss/pandera#2437

... (truncated)

Commits

62f55e2 ci: add actionlint workflow and pre-commit hook (#2436)
857a3b2 Warn when optional columns are missing via on_missing option (#2447)
2e307b7 fix: restore optional-column semantics for bare T | None annotations (#2458)
ccdabde docs: announce Pandera CLI and PyArrow support in banner (#2456)
c37a5b2 fix: respect pydantic serialization aliases (#2449)
b6ecd53 fix(docs): only apply pyspark JDK24 security-manager opt-in flag on JDK 24 (#...
384d48b fix(docs): make intersphinx fetch resilient to transient failures (#2452)
f1245c2 ci: only run unit tests for changed areas (#2450)
46b1495 fix(decorators): support keyword-only / variadic functions in check_input (#2...
9e268ac fix: handle scalar groupby keys in _format_groupby_input (#2420)
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Updates ruff from 0.16.5 to 0.16.9

Release notes

Sourced from ruff's releases.

0.16.9

Release Notes

Released on 2026-09-24.

Preview features

[ruff] Avoid false positives for overloaded division (RUF069) (#28309)

Bug fixes

[flake8-bugbear] Avoid false positives for calls with keyword arguments (B009, B010, B043) (#28776)

[flake8-tidy-imports] Allow lazy imports to be used in deferred annotations (TID255) (#28767)

Rule changes

Update LibCST-based fixes for Python 3.15 (#28616)

[flake8-pyi] Mention stubs in the diagnostic message (PYI002) (#28542)

Documentation

Fix horizontal overflow on the rules documentation page (#28699)

Update rules table with category information (#28651)

[flake8-annotations] Clarify that ANN401 checks return types in addition to arguments (#28334)

[flake8-bugbear] Document type-checker interaction (B010) (#28509)

[flake8-comprehensions] Document map/generator exception behavior (C417) (#27794)

[ruff] Mention related isort settings (RUF022) (#28719)

Contributors

@qinpei-dev

@sanjayrohith

@ntBre

@webdevsamran

@zaniebot

@ewdurbin

@MichaReiser

@spaceone

@IbrahimKhan12

@devtechedge

@GruffElixir

Install ruff 0.16.9

Install prebuilt binaries via shell script
curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/ruff/releases/download/0.16.9/ruff-installer.sh | sh

... (truncated)

Changelog

Sourced from ruff's changelog.

0.16.9

Released on 2026-09-24.

Preview features

[ruff] Avoid false positives for overloaded division (RUF069) (#28309)

Bug fixes

[flake8-bugbear] Avoid false positives for calls with keyword arguments (B009, B010, B043) (#28776)

[flake8-tidy-imports] Allow lazy imports to be used in deferred annotations (TID255) (#28767)

Rule changes

Update LibCST-based fixes for Python 3.15 (#28616)

[flake8-pyi] Mention stubs in the diagnostic message (PYI002) (#28542)

Documentation

Fix horizontal overflow on the rules documentation page (#28699)

Update rules table with category information (#28651)

[flake8-annotations] Clarify that ANN401 checks return types in addition to arguments (#28334)

[flake8-bugbear] Document type-checker interaction (B010) (#28509)

[flake8-comprehensions] Document map/generator exception behavior (C417) (#27794)

[ruff] Mention related isort settings (RUF022) (#28719)

Contributors

@qinpei-dev

@sanjayrohith

@ntBre

@webdevsamran

@zaniebot

@ewdurbin

@MichaReiser

@spaceone

@IbrahimKhan12

@devtechedge

@GruffElixir

0.16.8

Released on 2026-09-16.

Bug fixes

Visit functional TypedDict keyword arguments correctly (#28584)

[flake8-simplify] Detect nested async with under sync parent (SIM117) (#27821)

[flake8-simplify] Preserve operand order in SIM109 fix (#27824)

... (truncated)

Commits

0be08a2 Bump version to 0.16.9 (#28882)
b4920b7 Rename ruff_cli to ruff_command_line (#28881)
47c751b Update dependency astral-sh/uv to v0.12.18 (#28880)
8c244e5 [flake8-comprehensions] Document map/generator exception behavior (C417...
5edf5a1 Use target form in rooster.version_files (#28876)
915bb2b [ty] Prefer existing @ paths over response files in Ruff and ty (#28877)
4710e1a ci(github): update version number in placeholder of issue template (#28871)
eedfc62 [ty] Propagate outer type context through cast calls (#28855)
ceaa6a0 [ty] Contain rendered code within Markdown fences (#28869)
dba0f30 authorize ruff-pre-commit dispatch via OIDC (#28867)
Additional commits viewable in compare view

Updates plotly from 6.9.0 to 7.1.0

Release notes

Sourced from plotly's releases.

v7.1.0

Added

Support marginal_x/marginal_y="heatmap" in density_heatmap, drawing a single-row/column heatmap strip in the margin colored by the same z/histfunc aggregate as the main plot and sharing its color scale [#5706], with thanks to @lucasjamar for the contribution!

Add support for custom tick values in mpl_to_plotly when the matplotlib tick positions don't follow an arithmetic progression, including custom tick labels and tick values on date axes [#5262], with thanks to @robertoffmoura for the contribution!

Fixed

Fix Plotly Express treating unsigned integer columns (uint8, uint16, uint32, uint64) in pandas DataFrames as categorical, which caused px.bar and other functions to pick the wrong orientation and render unexpected plots [#4291, #4344], with thanks to @Belagum for the contribution!

Fix mpl_to_plotly not setting paper_bgcolor and plot_bgcolor from the matplotlib figure and axes backgrounds, so converted figures match the source figure's background colors [#5285], with thanks to @robertoffmoura for the contribution!

Fix rendering issue causing a too-large div when calling Figure.show() in Google Colab [#5718]

Fix the sphinx-gallery scraper so that it generates thumbnails for figures shown with fig.show() or displayed as the last expression of a code block [#5701], with thanks to @larsoner for the contribution!

The scaper now warns once (instead of failing the build) when static image export is unavailable

The sphinx-gallery scraper no longer scrapes files belonging to other examples during parallel builds [#5701], with thanks to @larsoner for the contribution!

Updated

Update plotly.js from version 4.0.0 to version 4.1.1 [#5722, #5730]. See the plotly.js release notes for v4.1.0 and v4.1.1 for details. Notable changes include:

Add an opt-in modebar button for downloading Plotly figures as JSON [#7990, #8022]

Add legend.groupdoubleclick to set the group behavior for a legend double-click [#7997]

Increase default double-click delay threshold to 500ms (from 300) [#8014]

Fix issue with per-point marker color for hover labels in scattergl, quiver traces [#8027]

Update maplibre-gl to v6 to address CVE-2026-85061 [#8035]

Note: Safari 15, Chrome 56, Firefox 51 and later are now required for map traces

Update hex_to_rgb function to raise error for invalid-length hex codes, and emit warning for hex codes containing alpha [#5729], with thanks to @dylanpulver for the contribution!

v7.0.0

Fixed

Fix hex_to_rgb parsing of 3-digit shorthand hexadecimal colors such as #FFF [#5662], with thanks to @genrichez for the contribution!

Improve px.*_map() auto-fitting behavior when zoom and center are not specified [#5686]

Add <!doctype html> to the to_html() template to comply with modern web standards [#5693], with thanks to @mishrakushal for the contribution!

Apply histfunc/z aggregation to marginal_x/marginal_y="histogram" subplots in density_heatmap/density_contour, instead of always showing raw bin counts [#3521], with thanks to @lucasjamar for the contribution!

Fix mpl_to_plotly silently dropping matplotlib path collections in data coordinates (such as violin plots, pcolor, event plots, stack plots, fill_between, and stem plots) by rendering them as filled polygons or lines [#5702], with thanks to @robertoffmoura for the contribution!

Removed

Remove the deprecated Figure Factory functions create_2d_density, create_annotated_heatmap, create_bullet, create_candlestick, create_choropleth, create_distplot, create_facet_grid, create_gantt, create_hexbin_mapbox, create_ohlc, create_scatterplotmatrix, and create_violin [#5627]

Remove support for Kaleido versions less than v1.0.0 for static image generation [#5677]

Remove support for Orca for static image generation [#5677]

Remove engine argument from functions fig.write_image(),fig.to_image(), pio.write_image(), pio.write_images(), pio.to_image(), pio.full_figure_for_development(), and from renderer constructors [#5677]

Updated

Update plotly.js from version 3.6.0 to version 4.0.0 [#5673]. This is a major-version release with many changes. See the plotly.js release notes for the full list. The most significant changes include:

Add quiver trace type to visualize vector fields using arrows [#7710, #7945]

Add "Share Chart" modebar button for generating a chart-sharing link via Plotly Cloud [#7909]

Remove scattermapbox, choroplethmapbox, densitymapbox trace types, the mapbox subplot, and the mapboxAccessToken config option [#7860]. Use the equivalent *map traces instead.

The corresponding graph_objects and Plotly Express functions have also been removed in plotly.py; use the map versions instead

Drop support for MathJax v2, and add support for v4 [#7898]. MathJax is the JavaScript library used for rendering mathematical equations in plotly charts.

Switch color processing library from TinyColor to culori [#7536, #7962]. There are some changes to supported color string formats as a result:

rgb()/rgba() strings with decimal 0–1 fractions are no longer supported

hsv() color strings are no longer supported

Strings with invalid syntax such as hsl(120, 50% 50%) are no longer supported

New supported formats: '#ff0000aa', '#f00a', 'rgb(255 0 0)', 'rgba(255 0 0 / 0.5)', 'hsl(0 100% 50% / 0.5)', 'hsla(0, 100%, 50%, 0.5)', 'hwb(0, 0%, 0%)', lab(), lch(), oklab(), oklch(), color(), hsl(0.5turn 60% 40%), hsl(none 60% 40%)

Replace country-regex with country-iso-search to search for country names in choropleth, scattergeo traces [#7856]. Most country names are handled exactly the same; a small number of legacy entries have been removed.

... (truncated)

Changelog

Sourced from plotly's changelog.

[7.1.0] - 2026-09-15

Added

Support marginal_x/marginal_y="heatmap" in density_heatmap, drawing a single-row/column heatmap strip in the margin colored by the same z/histfunc aggregate as the main plot and sharing its color scale [#5706], with thanks to @lucasjamar for the contribution!

Add support for custom tick values in mpl_to_plotly when the matplotlib tick positions don't follow an arithmetic progression, including custom tick labels and tick values on date axes [#5262], with thanks to @robertoffmoura for the contribution!

Fixed

Fix Plotly Express treating unsigned integer columns (uint8, uint16, uint32, uint64) in pandas DataFrames as categorical, which caused px.bar and other functions to pick the wrong orientation and render unexpected plots [#4291, #4344], with thanks to @Belagum for the contribution!

Fix mpl_to_plotly not setting paper_bgcolor and plot_bgcolor from the matplotlib figure and axes backgrounds, so converted figures match the source figure's background colors [#5285], with thanks to @robertoffmoura for the contribution!

Fix rendering issue causing a too-large div when calling Figure.show() in Google Colab [#5718]

Fix the sphinx-gallery scraper so that it generates thumbnails for figures shown with fig.show() or displayed as the last expression of a code block [#5701], with thanks to @larsoner for the contribution!

The scaper now warns once (instead of failing the build) when static image export is unavailable

The sphinx-gallery scraper no longer scrapes files belonging to other examples during parallel builds [#5701], with thanks to @larsoner for the contribution!

Updated

Update plotly.js from version 4.0.0 to version 4.1.1 [#5722, #5730]. See the plotly.js release notes for v4.1.0 and v4.1.1 for details. Notable changes include:

Add an opt-in modebar button for downloading Plotly figures as JSON [#7990, #8022]

Add legend.groupdoubleclick to set the group behavior for a legend double-click [#7997]

Increase default double-click delay threshold to 500ms (from 300) [#8014]

Fix issue with per-point marker color for hover labels in scattergl, quiver traces [#8027]

Update maplibre-gl to v6 to address CVE-2026-85061 [#8035]

Note: Safari 15, Chrome 56, Firefox 51 and later are now required for map traces

Update hex_to_rgb function to raise error for invalid-length hex codes, and emit warning for hex codes containing alpha [#5729], with thanks to @dylanpulver for the contribution!

[7.0.0] - 2026-08-25

Fixed

Fix hex_to_rgb parsing of 3-digit shorthand hexadecimal colors such as #FFF [#5662], with thanks to @genrichez for the contribution!

Improve px.*_map() auto-fitting behavior when zoom and center are not specified [#5686]

Add <!doctype html> to the to_html() template to comply with modern web standards [#5693], with thanks to @mishrakushal for the contribution!

Apply histfunc/z aggregation to marginal_x/marginal_y="histogram" subplots in density_heatmap/density_contour, instead of always showing raw bin counts [#3521], with thanks to @lucasjamar for the contribution!

Fix mpl_to_plotly silently dropping matplotlib path collections in data coordinates (such as violin plots, pcolor, event plots, stack plots, fill_between, and stem plots) by rendering them as filled polygons or lines [#5702], with thanks to @robertoffmoura for the contribution!

Updated

Update plotly.js from version 3.6.0 to version 4.0.0 [#5673]. This is a major-version release with many changes. See the plotly.js release notes for the full list. The most significant changes include:

Add quiver trace type to visualize vector fields using arrows [#7710, #7945]

Add "Share Chart" modebar button for generating a chart-sharing link via Plotly Cloud [#7909]

Remove scattermapbox, choroplethmapbox, densitymapbox trace types, the mapbox subplot, and the mapboxAccessToken config option [#7860]. Use the equivalent *map traces instead.

The corresponding graph_objects and Plotly Express functions have also been removed in plotly.py; use the map versions instead

Drop support for MathJax v2, and add support for v4 [#7898]. MathJax is the JavaScript library used for rendering mathematical equations in plotly charts.

Switch color processing library from TinyColor to culori [#7536, #7962]. There are some changes to supported color string formats as a result:

rgb()/rgba() strings with decimal 0–1 fractions are no longer supported

hsv() color strings are no longer supported

Strings with invalid syntax such as hsl(120, 50% 50%) are no longer supported

New supported formats: '#ff0000aa', '#f00a', 'rgb(255 0 0)', 'rgba(255 0 0 / 0.5)', 'hsl(0 100% 50% / 0.5)', 'hsla(0, 100%, 50%, 0.5)', 'hwb(0 0% 0%)', lab(), lch(), oklab(), oklch(), color(), hsl(0.5turn 60% 40%), hsl(none 60% 40%)

Replace country-regex with country-iso-search to search for country names in choropleth, scattergeo traces [#7856]. Most country names are handled exactly the same; a small number of legacy entries have been removed.

Change layout.geo.fitbounds default from false to 'locations' [#7895]. geo subplots will now auto-fit the initial view to the trace data by default.

Dynamically compute center and zoom values for scattermap and densitymap traces. The initial map view will now auto-fit to the trace data by default. Add layout.map.fitbounds attribute (default 'locations') to enable or disable auto-fitting behavior [https://zedprofiler--60.org.readthedocs.build/en/60/

Bumps the python-packages group with 10 updates: | Package | From | To | | --- | --- | --- | | [bioio](https://github.com/bioio-devs/bioio) | `3.5.0` | `3.5.1` | | [bioio-tifffile](https://github.com/bioio-devs/bioio-tifffile) | `1.3.0` | `1.3.1` | | [mahotas](https://github.com/luispedro/mahotas) | `1.4.18` | `1.4.19` | | [matplotlib](https://github.com/matplotlib/matplotlib) | `3.11.1` | `3.11.2` | | [pandas](https://github.com/pandas-dev/pandas) | `3.0.5` | `3.0.6` | | [pandera](https://github.com/pandera-dev/pandera) | `0.32.1` | `0.33.1` | | [ruff](https://github.com/astral-sh/ruff) | `0.16.5` | `0.16.9` | | [plotly](https://github.com/plotly/plotly.py) | `6.9.0` | `7.1.0` | | [isort](https://github.com/PyCQA/isort) | `8.0.1` | `9.0.1` | | [jupyterlab](https://github.com/jupyterlab/jupyterlab) | `4.6.3` | `4.6.4` | Updates `bioio` from 3.5.0 to 3.5.1 - [Release notes](https://github.com/bioio-devs/bioio/releases) - [Commits](bioio-devs/bioio@v3.5.0...v3.5.1) Updates `bioio-tifffile` from 1.3.0 to 1.3.1 - [Release notes](https://github.com/bioio-devs/bioio-tifffile/releases) - [Commits](bioio-devs/bioio-tifffile@v1.3.0...v1.3.1) Updates `mahotas` from 1.4.18 to 1.4.19 - [Release notes](https://github.com/luispedro/mahotas/releases) - [Changelog](https://github.com/luispedro/mahotas/blob/main/ChangeLog) - [Commits](luispedro/mahotas@v1.4.18...v1.4.19) Updates `matplotlib` from 3.11.1 to 3.11.2 - [Release notes](https://github.com/matplotlib/matplotlib/releases) - [Commits](matplotlib/matplotlib@v3.11.1...v3.11.2) Updates `pandas` from 3.0.5 to 3.0.6 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](pandas-dev/pandas@v3.0.5...v3.0.6) Updates `pandera` from 0.32.1 to 0.33.1 - [Release notes](https://github.com/pandera-dev/pandera/releases) - [Commits](unionai-oss/pandera@v0.32.1...v0.33.1) Updates `ruff` from 0.16.5 to 0.16.9 - [Release notes](https://github.com/astral-sh/ruff/releases) - [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md) - [Commits](astral-sh/ruff@0.16.5...0.16.9) Updates `plotly` from 6.9.0 to 7.1.0 - [Release notes](https://github.com/plotly/plotly.py/releases) - [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md) - [Commits](plotly/plotly.py@v6.9.0...v7.1.0) Updates `isort` from 8.0.1 to 9.0.1 - [Release notes](https://github.com/PyCQA/isort/releases) - [Changelog](https://github.com/PyCQA/isort/blob/main/CHANGELOG.md) - [Commits](PyCQA/isort@8.0.1...9.0.1) Updates `jupyterlab` from 4.6.3 to 4.6.4 - [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@4.6.3...@jupyterlab/lsp@4.6.4) --- updated-dependencies: - dependency-name: bioio dependency-version: 3.5.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: bioio-tifffile dependency-version: 1.3.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: mahotas dependency-version: 1.4.19 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: matplotlib dependency-version: 3.11.2 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: pandas dependency-version: 3.0.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: pandera dependency-version: 0.33.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: ruff dependency-version: 0.16.9 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: plotly dependency-version: 7.1.0 dependency-type: direct:development update-type: version-update:semver-major dependency-group: python-packages - dependency-name: isort dependency-version: 9.0.1 dependency-type: direct:development update-type: version-update:semver-major dependency-group: python-packages - dependency-name: jupyterlab dependency-version: 4.6.4 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com>

coderabbitai · 2026-10-01T04:24:32Z

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CI checks pass; reviewed dependency changes.

dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Oct 1, 2026

dependabot Bot requested review from MikeLippincott, d33bs and gwaybio as code owners October 1, 2026 04:24

dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Oct 1, 2026

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d33bs merged commit 99c6b3c into main Oct 1, 2026
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dependabot Bot deleted the dependabot/uv/python-packages-0eed80a6f0 branch October 1, 2026 16:22

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Bump the python-packages group with 10 updates - #60

Bump the python-packages group with 10 updates#60
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v3.5.1

What's Changed

Version 1.4.19

REL: v3.11.2

pandas 3.0.6

v0.33.1

What's Changed

New Contributors

v0.33.0: Introducing pandera CLI, support pyarrow table

What's Changed

New Contributors

0.16.9

Release Notes

Preview features

Bug fixes

Rule changes

Documentation

Contributors

Install ruff 0.16.9

Install prebuilt binaries via shell script

0.16.9

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Documentation

Contributors

0.16.8

Bug fixes

v7.1.0

Added

Fixed

Updated

v7.0.0

Fixed

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Updated

[7.1.0] - 2026-09-15

Added

Fixed

Updated

[7.0.0] - 2026-08-25

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v0.33.0: Introducing `pandera` CLI, support pyarrow table