Bump the python-packages group with 9 updates

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Bumps the python-packages group with 9 updates:

Package	From	To
numpy	2.5.2	2.5.3
torch	2.13.0+cu130	2.14.1+cu130
lxml	6.1.2	6.1.3
matplotlib	3.11.1	3.11.2
networkx	3.6.1	3.7
open3d	0.19.0	0.20.0
pandas	3.0.5	3.0.6
protobuf	7.36.0	7.36.2
scikit-learn	1.9.0	1.9.1

Updates numpy from 2.5.2 to 2.5.3

Release notes

Sourced from numpy's releases.

v2.5.3 (Sep 6, 2026)

NumPy 2.5.3 Release Notes

The NumPy 2.5.3 is a patch release that fixes bugs discovered after the 2.5.2 release. Apart from the usual bug and maintenance work, there are a number of StringDType related fixes for problems discovered during the ongoing string work in the main branch.

This release supports Python versions 3.12-3.15

Changes

• Casting a fixed-width byte string array (np.bytes_) to StringDType now raises TypeError when the bytes are not valid UTF-8. Previously the invalid bytes were stored as-is and later caused undefined behavior in string operations.

  (gh-32296)

• MaskedArray._fill_value would become stale when ufuncs that change dtype left the result holding a fill_value typed for the old dtype. The mismatch was silent until something later called _check_fill_value, such as .view(), and then a TypeError would be raised. Now, when the copied fill_value is no longer valid for the new dtype, fall back to the default fill_value for that dtype instead of propagating the stale value. This may raise a ComplexWarning if the fill_value is complex and the new dtype is real.

  (gh-32423)

Contributors

A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• Charles Harris
• Iason Krommydas
• James Davies +
• Joren Hammudoglu
• Maanas Arora
• Matti Picus
• Nathan Goldbaum
• Shikhar Goel +
• Yeonho Kim +

Pull requests merged

A total of 27 pull requests were merged for this release.

• #32235: MAINT: Prepare 2.5.x for further development

... (truncated)

Commits

• dd88c0c Merge pull request #32511 from charris/prepare-2.5.3
• edcac6a REL: Prepare for the NumPy 2.5.3 release
• fd4d908 Merge pull request #32509 from charris/backport-32496
• 65bb1da BUG: fix crash in ufunc.resolve_dtypes with a Python scalar type (#32496)
• 294956e Merge pull request #32506 from charris/backport-32503
• 26428d9 DOC: fix scipy docs links in intersphinx mapping (#32507)
• 5fab1cb DOC: use static scipy doc site for intershpinx (#32503)
• 7beed2f Merge pull request #32481 from ngoldbaum/stringdtype-backport
• 8972f70 Merge pull request #32478 from charris/backport-32466
• ab1b589 Merge pull request #32477 from charris/backport-32423
• Additional commits viewable in compare view

Updates torch from 2.13.0+cu130 to 2.14.1+cu130

Updates lxml from 6.1.2 to 6.1.3

Changelog

Sourced from lxml's changelog.

6.1.3 (2026-09-02)

Bugs fixed

• LP#2165901: External parameter entity parsing was allowed by default (with resolve_entities="internal"). Issue found by Tomer Fichman.

Commits

• 3c1a4c7 Prepare release of 6.1.3.
• c1191fc Update changelog.
• 03ec312 Disable parameter entity parsing when internal-only entity parsing is requested.
• 11d03e9 Build: Prevent duplicate Py3.8 wheel builds.
• 9efc586 Build: Exclude musllinux-ARM from Py3.8 wheel building to prevent slow emulat...
• 9716fb1 Build: Include older PyPy versions.
• 0f3327d Build: Exclude Win-Aarch64 from wheel build.
• 6967c96 Build: Make all built wheels downloadable even if they don't pass the release...
• 061218d Build: Exclude Py3.15 i686 wheels from validation (because they are intention...
• ce9fe0d Build: Fix Py3.8 windows build.
• See full diff in compare view

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...
• Additional commits viewable in compare view

Updates networkx from 3.6.1 to 3.7

Release notes

Sourced from networkx's releases.

NetworkX 3.7

networkx 3.7

We're happy to announce the release of networkx 3.7!

Highlights

• The isomorphism checking suite of tools has been upgraded. The VF2++ functions now provide subgraph isomorphism and subgraph monomorphism checking (#8506).
• Leiden based community detection algorithms are now supported via leiden_communities and leiden_partitions. This provides an alternative, often improved, community detection algorithm compared to the Louvain functions (#8509).
• The pygraphviz library is now provided via pip with wheels that include the GraphViz binaries. This should make the NetworkX interface to pygraphviz easier to use for graph layout and rendering (#8694).

API Changes

• Expire random lobster dep (#8499).
• API: Expire deprecations of could-be isomorphism aliases (#8498).
• Proposal to deprecate bfs_predecessors (#8494).
• Change maximal_independent_set to return set instead of list (#8564).
• Add centroid as alias to barycenter (#8622).
• API: Deprecate p2g module (#8855).

Enhancements

• Adding the Tree Optimization in Floyd Warshall (#8361).
• Kruskal MST early break for efficiency (#8296).
• create new generator that returns a random k-lift of a d-regular graph (#8045).
• Floyd Warshall: Adding support for weight parameter as a callable (#8386).
• [ENH] Flow algorithms: Add support for callable capacity parameter (#8406).
• fix: add suggestions from #8021 and #8029 to is_aperiodic (#8148).
• Improve chordal code readability by removing helper function (#8479).
• FEAT: Added basic random walk utilities #8378 (#8383).
• Implement Constant-Potts Model (for use with Leiden community detection) (#8507).
• The isomorphism checking suite of tools has been upgraded. The VF2++ functions now provide subgraph isomorphism and subgraph monomorphism checking (#8506).
• Adding optional sp arg to closeness_centrality (#8424).
• perf: replace built-in sum() with np.sum() in pagerank and katz (#8561).
• ENH: Add format parameter to adjacency_matrix (#8545).
• Proposal: Add density to nx.describe defaults (#8569).
• Add utility to extract faces from PlanarEmbedding (#8512).
• Improving views exceptions (#8588).
• Optimize _build_paths_from_predecessors stack logic for 30-40% speedup (#8460).
• EHN: Add nonedge argument to from_numpy_array and complete the roundtrip (#8552).
• State-of-the-art implementation of Tarjan's algorithm (#8615).
• Add description and keywords support to GEXF reader/writer (#8629).
• DOC: more barycenter and centroid equivalence (#8630).
• ENH: Add Barber's bipartite modularity quality function (#8618).
• Leiden based community detection algorithms are now supported via leiden_communities and leiden_partitions. This provides an alternative, often improved, community detection algorithm compared to the Louvain functions (#8509).
• ENH: Add Shen's overlapping modularity quality function (#8647).
• ENH: leiden test and doc_string improvements (#8656).
• Add butterflies() to bipartite cluster module (#8591).
• Avoid O(E) lookup in nx.display -issue8639 (#8663).
• Add HITS algorithm benchmark to benchmark suite (#8625).

... (truncated)

Commits

• 49ca229 Designate 3.7 release
• bd45cfe Update minimum dependencies (SPEC 0) (#8916)
• fee1ebc Bump release version
• 4106c33 Designate 3.7rc0 release
• 083e472 BUG: Hold the graph weakly in cached edge and degree views (#8892)
• 8977f1c Merge pull request #8896 from jarrodmillman/py3.15
• 2d91736 Remove failing tests
• 0d6ac7a make lint happy
• 9ca76bf move python_rc to py315 specific features
• ccf0995 Support for Py3.15
• Additional commits viewable in compare view

Updates open3d from 0.19.0 to 0.20.0

Release notes

Sourced from open3d's releases.

v0.20 release

Open3D v0.20 brings Gaussian Splatting to the Open3D renderer, makes Intel GPU workflows substantially more practical through expanded SYCL Tensor pipelines, and improves the developer experience with smaller installs, Python type checking, and new distribution options.

Note

• Now available.: open3d-cpu Python 3.11-3.14 wheels are not available in PyPI at the moment due to storage limits. We expect this to be resolved in a few days.
• Signed Windows and macOS viewers will be available shortly.

Highlights

Gaussian Splatting

GaussianSplatting.draw_from_csv.2026-04-28.at.2.56.52.PM.mp4

Gaussian splats and meshes in one Open3D scene.

python examples/python/visualization/draw_from_csv.py

Open3D can now render 3D Gaussian Splats in interactive and offscreen views, along with regular PBR meshes. Load tensor point clouds from Gaussian PLY, binary SPLAT, or compressed SPZ files, then compose them with triangle meshes using correct depth occlusion. This enables applications to combine radiance-field captures with conventional 3D assets in the same Open3D scene (PRs #7191, #7194, #7490, #7520, and #7525; contributed by @​lumurillo, @​billamiable, @​ssheorey, and @​jeevan6996).

The renderer supports anti-aliasing, depth output and offscreen rendering (see OffscreenRenderer). See the Gaussian Splatting tutorial, the mixed-scene Python example, and the C++ example.

Labeling geometry over a compressed SPZ Gaussian Splat.

Intel GPU Pipelines Through SYCL

rgbd_dense_slam_b580.mp4

Real time RGBD reconstruction with dense SLAM on an Intel B580 GPU

pip install open3d-xpu
cd examples/python/t_reconstruction_system
python dense_slam.py --device SYCL:0 --default_dataset lounge --path_npz lounge_sycl.npz

... (truncated)

Commits

• b6c5e19 Fix release packaging and CI uploads for v0.20 release (#7563)
• d32b4fc Version bump to v0.20 (#7561)
• 099051e Switch all rendering fully to Vulkan and update filament to latest. (#7550)
• 1a9eb99 Open3D agent skills + macOS jupyter extension + misc. CI fixes + update CUTLA...
• cf1516a Fix system zstd propagation to SPZ + misc. fixes for release assets (#7537)
• fb693b6 Reduce installed Open3D install size + many bug fixes (#7540)
• 22a6a30 Windows App (MSIX) and GPU selection for 3DGS on multi-GPU systems (#7534)
• 9bebbd8 Add Normal Distributions Transform (NDT) registration (#7517)
• cf67052 Fix Gaussian splat Vulkan render target setup (#7525)
• bdd1498 PyTorch XPU (SYCL): ML ops parity, shared SYCL runtime (#7529)
• Additional commits viewable in compare view

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)
• Additional commits viewable in compare view

Updates protobuf from 7.36.0 to 7.36.2

Updates scikit-learn from 1.9.0 to 1.9.1

Release notes

Sourced from scikit-learn's releases.

Scikit-learn 1.9.1

We're happy to announce the 1.9.1 release.

This release contains a few bug fixes and is the first version supporting Python 3.15.

You can see the changelog here: https://scikit-learn.org/stable/whats_new/v1.9.html#version-1-9-1

You can upgrade with pip as usual:

pip install -U scikit-learn

The conda-forge builds can be installed using:

conda install -c conda-forge scikit-learn

Thanks to everyone who contributed to this release !

Commits

• 866c0f5 generate changelog
• 12f135f update upper bounds
• 43ff2f2 bump version
• b851524 DOC Mark dev index as orphan (#34916)
• 01d56d4 DOC Fix wikipedia principal eigenvector example references (#34915)
• b86a1e2 🔒 🤖 CI Update lock files for array-api CI build(s) 🔒 🤖 ...
• d282698 🔒 🤖 CI Update lock files for main CI build(s) 🔒 🤖 (#34897)
• eb34279 🔒 🤖 CI Update lock files for free-threaded CI build(s) 🔒 :rob...
• 7581303 FIX: Fix QuantileTransformer(ignore_implicit_zeros=True) sub-sampling behav...
• ac47f4d FIX: avoid EfficiencyWarning in OPTICS with metric='precomputed' (#34692)
• Additional commits viewable in compare view

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