Bump the python-packages group with 14 updates by dependabot[bot] · Pull Request #38 · WayScience/ome-arrow-benchmarks

dependabot · 2026-06-03T17:11:19Z

Bumps the python-packages group with 14 updates:

Package	From	To
duckdb	`1.4.4`	`1.5.3`
jupyterlab	`4.5.3`	`4.5.7`
jupytext	`1.19.1`	`1.19.3`
lancedb	`0.27.1`	`0.30.2`
matplotlib	`3.10.8`	`3.10.9`
numpy	`2.4.2`	`2.4.6`
ome-arrow	`0.0.5`	`0.0.9`
ome-zarr	`0.12.2`	`0.16.0`
pandas	`3.0.0`	`3.0.3`
poethepoet	`0.40.0`	`0.46.0`
pyarrow	`23.0.0`	`24.0.0`
tifffile	`2025.10.16`	`2026.3.3`
vortex-data	`0.58.0`	`0.73.0`
zarr	`3.1.5`	`3.1.6`

Updates duckdb from 1.4.4 to 1.5.3

Release notes

Sourced from duckdb's releases.

v1.5.3 Bugfix Release

See the DuckDB core release notes here: https://github.com/duckdb/duckdb/releases/tag/v1.5.3

What's Changed in DuckDB Python

Export all symbols by @evertlammerts in duckdb/duckdb-python#445

Fix concjunction OR by @evertlammerts in duckdb/duckdb-python#465

Use recursive mutex to deal with GIL <-> internal lock deadlocks by @evertlammerts in duckdb/duckdb-python#462

Allow self-joining of Polars lazyframes by @evertlammerts in duckdb/duckdb-python#466

Full Changelog: duckdb/duckdb-python@v1.5.2...v1.5.3

v1.5.2 Bugfix Release

See the DuckDB core release notes here: https://github.com/duckdb/duckdb/releases/tag/v1.5.2

What's Changed in duckdb-python

Type hints overhaul by @OutSquareCapital in duckdb/duckdb-python#352

Cache arrow schema for streaming types by @evertlammerts in duckdb/duckdb-python#423

Fix segfault on join with None by @evertlammerts in duckdb/duckdb-python#422

Fix stubs for path_or_buffer param by @evertlammerts in duckdb/duckdb-python#425

v1.5.1 Bugfix Release

DuckDB core v1.5.1 Changelog: duckdb/duckdb@v1.5.0...v1.5.1

What's Changed

Re-added basic support for the GEOMETRY type

DuckDB Python 1.5.0 "Variegata"

This is the 1.5.0 release of DuckDB's Python bindings. For a list of changes in DuckDB core, have a look at the DuckDB release notes and the blogpost.

Breaking Changes

Dropped Python 3.9 support. The minimum supported version is now Python 3.10.

Removed deprecated duckdb.typing and duckdb.functional modules. These were deprecated in 1.4.0. Use duckdb.sqltypes and duckdb.func instead.

Renamed column parameter to expression in relational API functions (e.g., min, max, sum, mean, etc.) to better reflect that these accept expressions, not just column names.

Deprecated fetch_arrow_table() and fetch_record_batch() on connections and relations. Use the new to_arrow_table() and to_arrow_reader() methods instead.

New Features

Polars LazyFrame projection and filter pushdown. DuckDB can now push down projections and filters when scanning Polars LazyFrames, including support for cast nodes and unstrict casts.

Polars Int128 / UInt128 support.

VARIANT type support — Python conversion, NumPy array wrapping, and type stubs.

TIME_NS type support — nanosecond-precision time values across Python, NumPy, and Spark type systems.

Profiling API — new get_profiling_info() and get_profiling_json() methods on connections, plus a refactored query_graph module with improved HTML visualization (dark mode, expandable phases, depth).

to_arrow_table() and to_arrow_reader() — new methods on connections and relations as the preferred Arrow export API.

Performance

__arrow_c_stream__ on relations — relations now export via the Arrow PyCapsule interface using PhysicalArrowCollector for zero-copy streaming.

Unified Arrow stream scanning via __arrow_c_stream__, with filter pushdown only when pyarrow is present.

Arrow schema caching to avoid repeated lookups during scanning.

... (truncated)

Commits

811b135 DuckDB submodule pinned at v1.5.3
289bfbd Bump submodule
f87d6d9 Allow self-joining of Polars lazyframes (#466)
c88229d Allow self-joining of Polars lazyframes
559f6af Only disable unity builds for editable installs on OSX
97df049 fix .clangd
fd8889e Use recursive mutex to deal with GIL <-> internal lock deadlocks (#462)
7b77328 [duckdb-labs bot] Bump DuckDB submodule (#464)
9a86633 Fix concjunction OR (#465)
3d778de Fix concjunction OR
Additional commits viewable in compare view

Updates jupyterlab from 4.5.3 to 4.5.7

Release notes

Sourced from jupyterlab's releases.

v4.5.7

4.5.7

(Full Changelog)

Security patches

CVE-2026-42557 GHSA-mqcg-5x36-vfcg

CVE-2026-42266 GHSA-37w4-hwhx-4rc4

CVE-2026-40171 GHSA-rch3-82jr-f9w9

Bugs fixed

Video and Audio Content Providers: Fix JupyterLite support #18652 (@martinRenou)

Fix notebook hang when dropping cells #18808 (@MUFFANUJ)

Fix Contextual Help keyboard shortcut reliability and menu Help functionality #18747 (@itsmejay80)

Fix focusing input element when opening a dialog from Command Palette #18735 (@Carreau)

Fix native context menu blocked even when context menu is suppressed #18753 (@utsav-develops)

Fix flaky toolbar item placement in popup #18618 (@filipeoliveira05)

Update terminal default font family to honor macOS system-wide ui-monospace #18647 (@flaviomartins)

Maintenance and upkeep improvements

Fix linting issue #18819 (@krassowski)

Fix syntax for Python 3.9 on 4.5.x branch #18817 (@krassowski)

Remove unused CodeMirror v5 CSS rule #18785 (@Carreau)

Remove unused CSS rule forgotten after CodeMirror migration #18763 (@Carreau)

Remove unused progress bar CSS rule in execution indicator #18759 (@Carreau)

Remove dead .jp-VariableRenderer-TrustButton CSS rule #18762 (@Carreau)

Remove used .jp-Cell-Placeholder CSS rules #18761 (@Carreau)

Documentation improvements

Fix name of option for extension manager implementation in docs #18788 (@krassowski)

Remove 4.5.0 announcement from docs #18740 (@krassowski)

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) | @filipeoliveira05 (activity) | @flaviomartins (activity) | @itsmejay80 (activity) | @jtpio (activity) | @krassowski (activity) | @martinRenou (activity) | @MUFFANUJ (activity) | @utsav-develops (activity)

v4.5.6

4.5.6

... (truncated)

Commits

f514041 [ci skip] Publish 4.5.7
66fe9ad Backport PR #18652 on branch 4.5.x (Video and Audio Content Providers: Fix Ju...
f4455fa Fix syntax for Python 3.9 on 4.5.x branch (#18817)
d2322b5 Backport PR #18819 on branch 4.5.x (Fix linting issue) (#18820)
5d9cb8c Merge commit from fork
1de120b Merge commit from fork
6926100 Backport PR #18808 on branch 4.5.x (Fix notebook hang when dropping cells) (#...
67e6e88 Backport PR #18647 on branch 4.5.x (Update default font family to honor macOS...
bf21eb9 Backport PR #18747 on branch 4.5.x (Fix Contextual Help keyboard shortcut rel...
73cafa5 Backport PR #18788 on branch 4.5.x (Fix name of option for extension manager ...
Additional commits viewable in compare view

Updates jupytext from 1.19.1 to 1.19.3

Release notes

Sourced from jupytext's releases.

Version 1.19.3

Fixed

The Jupytext CLI issues a warning when a notebook is not trusted. Also, trust is preserved when empty outputs are added (follow-up on #1505)

Changed

The dependabot config has been updated to correctly bump extension packages, now allowing only production updates and ignoring dev dependencies (#1532). Thanks to Mahendra Paipuri for this PR!

Removed deprecated stylelint packages (stylelint-config-prettier and stylelint-prettier) from the JupyterLab extension dependencies (#1530)

We have removed Python 3.9 testing from the CI (Python 3.9 reached EOL in October 2025)

Version 1.19.2

Fixed

Trusted notebooks remain trusted after jupytext --sync (#1505)

We have fixed the homepage link in package.json. Thanks to Michał Krassowski for making this PR (#1494)

Thanks to Brigitta Sipőcz for fixing a broken link in our CLI (#1428)

The --quiet flag now suppresses the creating missing directory warning when writing to a path that includes a prefix (#1533)

Changed

The CI workflow has been restructured to maximize parallelization. All test suites (pip, conda, UI) and the build step now run concurrently after pre-commit checks, instead of sequentially, reducing CI times (#1527)

We have skipped the tests that involve jupyterfs on Python 3.12+ as they started failing on the CI with no obvious way to fix them (#1509)

We have changed the configuration of Dependabot to get grouped dependency updates for our JupyterLab extension.

We have merged a series of Dependabot security updates: #1516, #1517, #1519, #1520, #1522, #1524

Changelog

Sourced from jupytext's changelog.

1.19.3 (2026-05-17)

Fixed

The Jupytext CLI issues a warning when a notebook is not trusted. Also, trust is preserved when empty outputs are added (follow-up on #1505)

Changed

The dependabot config has been updated to correctly bump extension packages, now allowing only production updates and ignoring dev dependencies (#1532). Thanks to Mahendra Paipuri for this PR!

Removed deprecated stylelint packages (stylelint-config-prettier and stylelint-prettier) from the JupyterLab extension dependencies (#1530)

We have removed Python 3.9 testing from the CI (Python 3.9 reached EOL in October 2025)

1.19.2 (2026-05-10)

Fixed

Trusted notebooks remain trusted after jupytext --sync (#1505)

We have fixed the homepage link in package.json. Thanks to Michał Krassowski for making this PR (#1494)

Thanks to Brigitta Sipőcz for fixing a broken link in our CLI (#1428)

The --quiet flag now suppresses the creating missing directory warning when writing to a path that includes a prefix (#1533)

Changed

The CI workflow has been restructured to maximize parallelization. All test suites (pip, conda, UI) and the build step now run concurrently after pre-commit checks, instead of sequentially, reducing CI times (#1527)

We have skipped the tests that involve jupyterfs on Python 3.12+ as they started failing on the CI with no obvious way to fix them (#1509)

We have changed the configuration of Dependabot to get grouped dependency updates for our JupyterLab extension.

We have merged a series of Dependabot security updates: #1516, #1517, #1519, #1520, #1522, #1524

Commits

48fdfd8 Fix: Adding cells with no outputs preserves trust status (#1531)
4706e65 chore: Update dependabot config (#1532)
2ec5404 build (deps): Remove deprecated stylelint packages (#1530)
309f97f Version 1.19.2 (#1529)
e4dded4 build(deps-dev): bump typescript from 5.9.3 to 6.0.3 in /jupyterlab/packages/...
2c262e5 Fix: --quiet also suppresses warning for directory creation (#1526)
0bfcec1 build(deps): bump fast-uri from 3.1.0 to 3.1.2 in /jupyterlab (#1524)
611e2c0 Explicitly close NotebookNotary signature store (#1528)
70b1f20 All tests run after coverage tests have passed (#1527)
399e934 Close SQLite database connections of Jupytext-created notaries
Additional commits viewable in compare view

Updates lancedb from 0.27.1 to 0.30.2

Release notes

Sourced from lancedb's releases.

Python LanceDB v0.30.2

🎉 New Features

feat: update lance dependency to v3.0.1 by @lancedb-robot in lancedb/lancedb#3168

feat(rust): parallel inserts for remote tables via multipart write by @wjones127 in lancedb/lancedb#3071

feat: progress bar for add() by @wjones127 in lancedb/lancedb#3067

feat: update lance dependency to v4.0.0-rc.3 by @westonpace in lancedb/lancedb#3187

feat(node): support Float16, Float64, and Uint8 vector queries by @VedantMadane in lancedb/lancedb#3193

feat(python): add type-safe expression builder API by @pratik0316 in lancedb/lancedb#3150

🐛 Bug Fixes

fix(ci): bump AWS SDK MSRV pins to March 2025 release by @esteban in lancedb/lancedb#3179

fix: raise instead of return ValueError by @dantasse in lancedb/lancedb#3189

fix(rust): handle Mutex lock poisoning gracefully across codebase by @lennylxx in lancedb/lancedb#3196

ci: mitigate template injection attack in build_linux_wheel by @aikido-autofix[bot] in lancedb/lancedb#3195

fix(python): don't assign dict.update() return value in _sanitize_data by @lennylxx in lancedb/lancedb#3198

fix: table.add(mode='overwrite') infers vector column types by @majiayu000 in lancedb/lancedb#3184

fix(embeddings): add missing urllib.request import in url_retrieve by @lennylxx in lancedb/lancedb#3190

fix(python): use correct exception types in namespace tests by @wjones127 in lancedb/lancedb#3206

fix(python): skip test_url_retrieve_downloads_image when PIL not installed by @wjones127 in lancedb/lancedb#3208

fix: respect max_batch_length for Rust vector and hybrid queries by @myandpr in lancedb/lancedb#3172

fix: change _client reference to _conn by @dantasse in lancedb/lancedb#3188

📚 Documentation

docs: fix rendering issues with missing index types in API docs by @prrao87 in lancedb/lancedb#3143

Other Changes

Revert "feat: allow passing azure client/tenant ID through remote SDK" by @wkalt in lancedb/lancedb#3185

🔧 Build and CI

ci: fix unused PreprocessingOutput by @esteban in lancedb/lancedb#3180

ci: mitigate template injection attack in build_linux_wheel by @aikido-autofix[bot] in lancedb/lancedb#3195

Python LanceDB v0.30.2-beta.1

🎉 New Features

feat: update lance dependency to v4.0.0-rc.3 by @westonpace in lancedb/lancedb#3187

Python LanceDB v0.30.2-beta.0

🎉 New Features

feat: update lance dependency to v3.0.1 by @lancedb-robot in lancedb/lancedb#3168

feat(rust): parallel inserts for remote tables via multipart write by @wjones127 in lancedb/lancedb#3071

feat: progress bar for add() by @wjones127 in lancedb/lancedb#3067

🐛 Bug Fixes

... (truncated)

Commits

5d55012 Bump version: 0.30.2-beta.2 → 0.30.2
c57cb31 Bump version: 0.30.2-beta.1 → 0.30.2-beta.2
97754f5 fix: change _client reference to _conn (#3188)
7b1c063 feat(python): add type-safe expression builder API (#3150)
c7f189f chore: upgrade lance to stable 4.0.0 (#3207)
a0a2942 fix: respect max_batch_length for Rust vector and hybrid queries (#3172)
e3d53dd fix(python): skip test_url_retrieve_downloads_image when PIL not installed (#...
66804e9 fix(python): use correct exception types in namespace tests (#3206)
9f85d4c fix(embeddings): add missing urllib.request import in url_retrieve (#3190)
1ba19d7 feat(node): support Float16, Float64, and Uint8 vector queries (#3193)
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Updates matplotlib from 3.10.8 to 3.10.9

Release notes

Sourced from matplotlib's releases.

v3.10.9

This is a micro release of the v3.10.x series. Highlights of this release include:

Various minor bug and doc fixes

Security hardening validation of cyclers - Removing eval usage

Security hardening in Latex and PS calls - Removing shell escapes

Commits

dd8d78b REL: v3.10.9
2fb1891 REL: Release prep v3.10.9
d0e923a Merge branch 'v3.10.8-doc' into v3.10.x
1637932 Merge pull request #31558 from meeseeksmachine/auto-backport-of-pr-31556-on-v...
a83faac Backport PR #31556: FIX: Inverted PyErr_Occurred check in enum type caster (_...
a4f57ab Merge pull request #31545 from ksunden/backport-of-pr-31282-on-v3.10.x
063288d Merge pull request #31544 from ksunden/backport-of-pr-31248-on-v3.10.x
b2ed196 Backport PR #31248: SEC: Remove eval() from validate_cycler
acc6024 Merge pull request #31282 from scottshambaugh/tex_no_shell
e3fb541 Merge pull request #31078 from meeseeksmachine/auto-backport-of-pr-31075-on-v...
Additional commits viewable in compare view

Updates numpy from 2.4.2 to 2.4.6

Release notes

Sourced from numpy's releases.

v2.4.6 (May 18, 2026)

NumPy 2.4.6 Release Notes

NumPy 2.4.6 is a quick release that fixes a regression discovered in the 2.4.5 release.

This release supports Python versions 3.11-3.14

Contributors

A total of 4 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

!EarlMilktea

Charles Harris

Sebastian Berg

Warren Weckesser

Pull requests merged

A total of 4 pull requests were merged for this release.

#31444: MAINT: Prepare 2.4.x for further development

#31453: BUG: Fix regression in arr.conj()

#31459: BUG: np.linalg.svd(..., hermitian=True) returns non-unitary...

#31460: BUG: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator...

v2.4.5 (May 15, 2026)

NumPy 2.4.5 Release Notes

NumPy 2.4.5 is a patch release that fixes bugs discovered after the 2.4.4 release, has some typing improvements, and maintains infrastructure.

This release supports Python versions 3.11-3.14

Contributors

A total of 17 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

Aleksei Nikiforov

Anarion Zuo +

Ankit Ahlawat

Breno Favaretto +

Charles Harris

Igor Krivenko +

Ijtihed Kilani +

Joren Hammudoglu

Maarten Baert +

... (truncated)

Commits

b832a09 Merge pull request #31462 from charris/prepare-2.4.6
57cc147 REL: Prepare for the NumPy 2.4.6 release
0c72b0b Merge pull request #31459 from charris/backport-31347
9778d26 BUG: core: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator. (#...
e0e3876 BUG: core: Don't call INCREF/DECREF on descr in NpyStringAcquireAllocator. (#...
d1bffeb BUG: np.linalg.svd(..., hermitian=True) returns non-unitary vh (#31347)
8d8d7e5 Merge pull request #31453 from seberg/issue-31452
bddaab7 BUG: Fix regression in arr.conj()
37a1ecc Merge pull request #31444 from charris/begin-2.4.6
3c0e043 MAINT: Prepare 2.4.x for further development
Additional commits viewable in compare view

Updates ome-arrow from 0.0.5 to 0.0.9

Release notes

Sourced from ome-arrow's releases.

v0.0.9

Changes

Add torch/jax array ingest support to OMEArrow (@d33bs via #56)

Bump aiohttp from 3.13.3 to 3.13.4 (@dependabot[bot] via #55)

Bump the uv group with 10 updates (@dependabot[bot] via #54)

Bump release-drafter/release-drafter from 6 to 7 in the github-actions group (@dependabot[bot] via #53)

Bump pygments from 2.19.1 to 2.20.0 (@dependabot[bot] via #52)

Bump requests from 2.32.4 to 2.33.0 (@dependabot[bot] via #51)

Bump ujson from 5.11.0 to 5.12.0 (@dependabot[bot] via #50)

Bump black from 26.1.0 to 26.3.1 (@dependabot[bot] via #48)

Bump tornado from 6.5.1 to 6.5.5 (@dependabot[bot] via #47)

Bump actions/upload-artifact from 4 to 7 in the github-actions group (@dependabot[bot] via #44)

Bump the uv group with 7 updates (@dependabot[bot] via #45)

v0.0.8

Changes

Add lazy read capabilities (@d33bs via #43)

v0.0.7

Changes

Provide tensor-friendly methods for torch and jax through OMEArrow.to_dlpack (@d33bs via #34)

Bump the uv group across 1 directory with 3 updates (@dependabot[bot] via #39)

Bump pillow from 12.1.0 to 12.1.1 (@dependabot[bot] via #37)

Bump nbconvert from 7.16.6 to 7.17.0 (@dependabot[bot] via #36)

Bump the uv group with 4 updates (@dependabot[bot] via #35)

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

c33e70e Add torch/jax array ingest support to OMEArrow (#56)
d0c1ce0 Bump aiohttp from 3.13.3 to 3.13.4 (#55)
c241b8e Bump the uv group with 10 updates (#54)
16601e2 Bump release-drafter/release-drafter from 6 to 7 in the github-actions group ...
58757f7 Bump pygments from 2.19.1 to 2.20.0 (#52)
a12fc7a Bump requests from 2.32.4 to 2.33.0 (#51)
30ef9df Bump ujson from 5.11.0 to 5.12.0 (#50)
5205c90 Bump black from 26.1.0 to 26.3.1 (#48)
9d8c8ab Bump tornado from 6.5.1 to 6.5.5 (#47)
8403fdf Bump actions/upload-artifact from 4 to 7 in the github-actions group (#44)
Additional commits viewable in compare view

Updates ome-zarr from 0.12.2 to 0.16.0

Release notes

Sourced from ome-zarr's releases.

v0.16.0

What's Changed

Support sharding by @melonora in ome/ome-zarr-py#534

Document sharding by @jo-mueller in ome/ome-zarr-py#569

feat: do not delay writing metadata by @jo-mueller in ome/ome-zarr-py#568

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in ome/ome-zarr-py#558

chore: fix defaults for scale factors by @jo-mueller in ome/ome-zarr-py#567

Full Changelog: ome/ome-zarr-py@v0.15.0...v0.16.0

v0.15.0

What's Changed

More Pythons tested by @jo-mueller in ome/ome-zarr-py#551

Use markdown and Jupyter notebooks in doc pages by @jo-mueller in ome/ome-zarr-py#548

Fix downloading ome-zarr 0.5 by @psobolewskiPhD in ome/ome-zarr-py#562

BREAKING CHANGE: Deprecate writing v01, v02 and v03 by @jo-mueller in ome/ome-zarr-py#557

update codespell github action by @melonora in ome/ome-zarr-py#565

Full Changelog: ome/ome-zarr-py@v0.14.0...v0.15.0

v0.14.0

What's Changed

Fix documentation grammar, typos, and formatting by @DimitriPapadopoulos in ome/ome-zarr-py#528

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in ome/ome-zarr-py#533

deprecate scaler class by @jo-mueller in ome/ome-zarr-py#516

Streamline writing by @jo-mueller in ome/ome-zarr-py#531

Fix Test pre-releases by @pwalczysko in ome/ome-zarr-py#543

refactor: write scales to zarr group s by @jo-mueller in ome/ome-zarr-py#544

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in ome/ome-zarr-py#539

PEP 735 compliance: dependency groups by @DimitriPapadopoulos in ome/ome-zarr-py#537

fix: use newer skimage kwargs by @jo-mueller in ome/ome-zarr-py#541

New Contributors

@pwalczysko made their first contribution in ome/ome-zarr-py#543

Full Changelog: ome/ome-zarr-py@v0.13.0...v0.14.0

v0.13.0

What's Changed

Fix zarr.group() to zarr.open_group() in test_read_v05 by @will-moore in ome/ome-zarr-py#488

Use consistent version string for zarr lower bound by @jdblischak in ome/ome-zarr-py#487

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in ome/ome-zarr-py#483

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in ome/ome-zarr-py#490

Tests ome zarr models py by @will-moore in ome/ome-zarr-py#461

Default write_labels() uses nearest_neighbour to scale by @will-moore in ome/ome-zarr-py#489

[pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in ome/ome-zarr-py#493

ome_zarr view doesn't try to check for images by @will-moore in ome/ome-zarr-py#499

Handle Range headers in http server by @will-moore in ome/ome-zarr-py#500

... (truncated)

Commits

2f92fce Merge pull request #567 from jo-mueller/default-scaler-none
3e6c8a2 Merge pull request #558 from ome/pre-commit-ci-update-config
2a8ebc7 [pre-commit.ci] pre-commit autoupdate
c542100 Merge pull request #568 from jo-mueller/no-delay-metadata-write
e803618 Merge pull request #569 from jo-mueller/document-sharding
4ab3bbb docs: add note on file number limit
673c05e docs: document resolution-level-specific shard sizes
5692c6e docs: document sharding
3f3da46 Merge pull request #534 from melonora/support_sharding
566fb3d fix: account for chunks being None
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Updates pandas from 3.0.0 to 3.0.3

Release notes

Sourced from pandas's releases.

pandas 3.0.3

We are pleased to announce the release of pandas 3.0.3. 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.

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.

pandas 3.0.2

We are pleased to announce the release of pandas 3.0.2. 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.

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.

pandas 3.0.1

We are pleased to announce the release of pandas 3.0.1. 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.

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

Pandas 3.0.0 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

... (truncated)

Commits

72f2fea RLS: 3.0.3 (

Bumps the python-packages group with 14 updates: | Package | From | To | | --- | --- | --- | | [duckdb](https://github.com/duckdb/duckdb-python) | `1.4.4` | `1.5.3` | | [jupyterlab](https://github.com/jupyterlab/jupyterlab) | `4.5.3` | `4.5.7` | | [jupytext](https://github.com/mwouts/jupytext) | `1.19.1` | `1.19.3` | | [lancedb](https://github.com/lancedb/lancedb) | `0.27.1` | `0.30.2` | | [matplotlib](https://github.com/matplotlib/matplotlib) | `3.10.8` | `3.10.9` | | [numpy](https://github.com/numpy/numpy) | `2.4.2` | `2.4.6` | | [ome-arrow](https://github.com/wayscience/ome-arrow) | `0.0.5` | `0.0.9` | | [ome-zarr](https://github.com/ome/ome-zarr-py) | `0.12.2` | `0.16.0` | | [pandas](https://github.com/pandas-dev/pandas) | `3.0.0` | `3.0.3` | | [poethepoet](https://github.com/nat-n/poethepoet) | `0.40.0` | `0.46.0` | | [pyarrow](https://github.com/apache/arrow) | `23.0.0` | `24.0.0` | | [tifffile](https://github.com/cgohlke/tifffile) | `2025.10.16` | `2026.3.3` | | [vortex-data](https://github.com/spiraldb/vortex) | `0.58.0` | `0.73.0` | | [zarr](https://github.com/zarr-developers/zarr-python) | `3.1.5` | `3.1.6` | Updates `duckdb` from 1.4.4 to 1.5.3 - [Release notes](https://github.com/duckdb/duckdb-python/releases) - [Commits](duckdb/duckdb-python@v1.4.4...v1.5.3) Updates `jupyterlab` from 4.5.3 to 4.5.7 - [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@4.5.7) Updates `jupytext` from 1.19.1 to 1.19.3 - [Release notes](https://github.com/mwouts/jupytext/releases) - [Changelog](https://github.com/mwouts/jupytext/blob/main/CHANGELOG.md) - [Commits](jupytext/jupytext@v1.19.1...v1.19.3) Updates `lancedb` from 0.27.1 to 0.30.2 - [Release notes](https://github.com/lancedb/lancedb/releases) - [Changelog](https://github.com/lancedb/lancedb/blob/main/release_process.md) - [Commits](lancedb/lancedb@v0.27.1...python-v0.30.2) Updates `matplotlib` from 3.10.8 to 3.10.9 - [Release notes](https://github.com/matplotlib/matplotlib/releases) - [Commits](matplotlib/matplotlib@v3.10.8...v3.10.9) Updates `numpy` from 2.4.2 to 2.4.6 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v2.4.2...v2.4.6) Updates `ome-arrow` from 0.0.5 to 0.0.9 - [Release notes](https://github.com/wayscience/ome-arrow/releases) - [Commits](WayScience/ome-arrow@v0.0.5...v0.0.9) Updates `ome-zarr` from 0.12.2 to 0.16.0 - [Release notes](https://github.com/ome/ome-zarr-py/releases) - [Changelog](https://github.com/ome/ome-zarr-py/blob/master/CHANGELOG.md) - [Commits](ome/ome-zarr-py@v0.12.2...v0.16.0) Updates `pandas` from 3.0.0 to 3.0.3 - [Release notes](https://github.com/pandas-dev/pandas/releases) - [Commits](pandas-dev/pandas@v3.0.0...v3.0.3) Updates `poethepoet` from 0.40.0 to 0.46.0 - [Release notes](https://github.com/nat-n/poethepoet/releases) - [Commits](nat-n/poethepoet@v0.40.0...v0.46.0) Updates `pyarrow` from 23.0.0 to 24.0.0 - [Release notes](https://github.com/apache/arrow/releases) - [Commits](apache/arrow@apache-arrow-23.0.0...apache-arrow-24.0.0) Updates `tifffile` from 2025.10.16 to 2026.3.3 - [Release notes](https://github.com/cgohlke/tifffile/releases) - [Changelog](https://github.com/cgohlke/tifffile/blob/master/CHANGES.rst) - [Commits](cgohlke/tifffile@v2025.10.16...v2026.3.3) Updates `vortex-data` from 0.58.0 to 0.73.0 - [Release notes](https://github.com/spiraldb/vortex/releases) - [Commits](vortex-data/vortex@0.58.0...0.73.0) Updates `zarr` from 3.1.5 to 3.1.6 - [Release notes](https://github.com/zarr-developers/zarr-python/releases) - [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/docs/release-notes.md) - [Commits](zarr-developers/zarr-python@v3.1.5...v3.1.6) --- updated-dependencies: - dependency-name: duckdb dependency-version: 1.5.3 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: jupyterlab dependency-version: 4.5.7 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: jupytext dependency-version: 1.19.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: lancedb dependency-version: 0.30.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: matplotlib dependency-version: 3.10.9 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: numpy dependency-version: 2.4.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: ome-arrow dependency-version: 0.0.9 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: ome-zarr dependency-version: 0.16.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: pandas dependency-version: 3.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages - dependency-name: poethepoet dependency-version: 0.46.0 dependency-type: direct:development update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: pyarrow dependency-version: 24.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: python-packages - dependency-name: tifffile dependency-version: 2026.3.3 dependency-type: direct:production update-type: version-update:semver-major dependency-group: python-packages - dependency-name: vortex-data dependency-version: 0.73.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: python-packages - dependency-name: zarr dependency-version: 3.1.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: python-packages ... Signed-off-by: dependabot[bot] <support@github.com>

dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Jun 3, 2026

Update pyproject.toml

695bde0

d33bs approved these changes Jun 3, 2026

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d33bs merged commit c11b3c3 into main Jun 3, 2026
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d33bs deleted the dependabot/uv/python-packages-80a1c9bdec branch June 3, 2026 17:20

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Bump the python-packages group with 14 updates#38

Bump the python-packages group with 14 updates#38
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dependabot Bot commented on behalf of github Jun 3, 2026

v1.5.3 Bugfix Release

What's Changed in DuckDB Python

v1.5.2 Bugfix Release

What's Changed in duckdb-python

v1.5.1 Bugfix Release

What's Changed

DuckDB Python 1.5.0 "Variegata"

Breaking Changes

New Features

Performance

v4.5.7

4.5.7

Security patches

Bugs fixed

Maintenance and upkeep improvements

Documentation improvements

Contributors to this release

v4.5.6

4.5.6

Version 1.19.3

Version 1.19.2

1.19.3 (2026-05-17)

1.19.2 (2026-05-10)

Python LanceDB v0.30.2

🎉 New Features

🐛 Bug Fixes

📚 Documentation

Other Changes

🔧 Build and CI

Python LanceDB v0.30.2-beta.1

🎉 New Features

Python LanceDB v0.30.2-beta.0

🎉 New Features

🐛 Bug Fixes

v3.10.9

v2.4.6 (May 18, 2026)

NumPy 2.4.6 Release Notes

Contributors

Pull requests merged

v2.4.5 (May 15, 2026)

NumPy 2.4.5 Release Notes

Contributors

v0.0.9

Changes

v0.0.8

Changes

v0.0.7

Changes

v0.0.6

Changes

v0.16.0

What's Changed

v0.15.0

What's Changed

v0.14.0

What's Changed

New Contributors

v0.13.0

What's Changed

pandas 3.0.3

pandas 3.0.2

pandas 3.0.1

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