build(deps): bump the production group across 1 directory with 18 updates by dependabot[bot] · Pull Request #93 · emdgroup/matcha

dependabot · 2026-09-01T13:50:49Z

Bumps the production group with 17 updates in the / directory:

Package	From	To
numpy	`2.4.2`	`2.5.2`
pydantic	`2.12.5`	`2.13.5`
scikit-fingerprints	`1.18.0`	`2.1.0`
scikit-learn	`1.8.0`	`1.9.0`
scipy	`1.17.1`	`1.18.1`
umap-learn	`0.5.11`	`0.5.12`
mlflow-skinny	`3.10.0`	`3.15.2`
plotly	`6.5.2`	`7.0.0`
fastparquet	`2026.3.0`	`2026.5.0`
torch	`2.9.1`	`2.13.0`
torch-geometric	`2.7.0`	`2.8.0.post1`
optuna	`4.7.0`	`4.9.0`
optuna-integration	`4.7.0`	`4.9.0`
transformers	`4.57.6`	`5.16.1`
chemprop	`2.2.2`	`2.3.1`
myst-parser	`4.0.1`	`5.1.0`
sphinx-autoapi	`3.8.0`	`3.8.1`

Updates numpy from 2.4.2 to 2.5.2

Release notes

Sourced from numpy's releases.

v2.5.2 (Aug 9, 2026)

NumPy 2.5.2 Release Notes

The NumPy 2.5.2 is a patch release that fixes bugs discovered after the 2.5.1 release. The big news is that it includes wheels for the newly released Python 3.15.0rc1.

This release supports Python versions 3.12-3.15

C API changes

PyArray_StringDTypeObject is opaque under the abi3t stable ABI

The PyArray_StringDTypeObject was accidentally exposed in NumPy 2.5 when targeting the free-threading-compatible stable ABI (Py_TARGET_ABI3T). PyArray_StringDTypeObject is now an opaque struct: extensions compiled that way cannot access its fields, since the struct layout depends on the size of the object header. Any code that accessed PyArray_StringDTypeObject fields in an abi3t build would have crashed, so we are making this API change in a bugfix release.

The NpyString allocator API remains usable by passing the descriptor object pointer, e.g. NpyString_acquire_allocator((PyArray_StringDTypeObject *)descr).

(gh-31771)

Contributors

A total of 16 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

Abhijeetsingh Meena +

Charalampos Stratakis

Charles Harris

Chris Ninham +

David Woods

Geonho +

Gopu Yeshwanth Reddy +

Iason Krommydas

Ijtihed Kilani

Jelle Zijlstra +

Joren Hammudoglu

Kumar Aditya

Mike Boyle

Nathan Goldbaum

Raghuveer Devulapalli

Sebastian Berg

... (truncated)

Commits

48fecee REL: Prepare for the NumPy 2.5.2 release (#32226)
ecf599c Merge pull request #32221 from charris/backport-32151
3c7ac97 Merge pull request #32220 from charris/backport-32205
23b30f4 BUG: avoid segfaults when legacy copyswap slot is not defined (#32151)
4964ca8 TYP: isclose shape-typing fix for 2d array-likes (#32205)
c37ed94 MAINT: Skip limited_api tests on some platforms. (#32214)
5cfd73b Merge pull request #32206 from charris/update-cibuildwheel
d8262bc MAINT: Update cibuildwheel to v4.2.0
988d94d Merge pull request #32158 from charris/backport-32133
b2e4f97 BUG: avoid possible stack overflow in arraydescr_dealloc (#32133)
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Updates pydantic from 2.12.5 to 2.13.5

Release notes

Sourced from pydantic's releases.

v2.13.5 (2026-08-28)

What's Changed

Fixes

Allow reuse of validators when plugins are set by @Viicos in #13535

Fix missing GC traversal on some pydantic-core struct fields by @Viicos in #13624

Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer by @Viicos in #13629

Count validated model fields once in smart unions by @tamird in #13731

v2.13.4 2026-05-06

v2.13.4 (2026-05-06)

What's Changed

Packaging

Bump libc from 0.2.155 to 0.2.185 by @Viicos in #13109

Adapt pydantic-core linker flags on macOS by @washingtoneg and @Viicos in #13147

Fixes

Preserve RootModel core metadata by @Viicos in #13129

Full Changelog: pydantic/pydantic@v2.13.3...v2.13.4

v2.13.3 2026-04-20

v2.13.3 (2026-04-20)

What's Changed

Fixes

Handle AttributeError subclasses with from_attributes by @Viicos in #13096

Full Changelog: pydantic/pydantic@v2.13.2...v2.13.3

v2.13.2 2026-04-17

v2.13.2 (2026-04-17)

What's Changed

Fixes

Fix ValidationInfo.field_name missing with model_validate_json() by @Viicos in #13084

Full Changelog: pydantic/pydantic@v2.13.1...v2.13.2

v2.13.1 2026-04-15

... (truncated)

Changelog

Sourced from pydantic's changelog.

v2.13.5 (2026-08-28)

GitHub release

What's Changed

Fixes

Allow reuse of validators when plugins are set by @Viicos in #13535

Fix missing GC traversal on some pydantic-core struct fields by @Viicos in #13624

Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer by @Viicos in #13629

Count validated model fields once in smart unions by @tamird in #13731

v2.13.4 (2026-05-06)

GitHub release

What's Changed

Packaging

Bump libc from 0.2.155 to 0.2.185 by @Viicos in #13109

Adapt pydantic-core linker flags on macOS by @washingtoneg and @Viicos in #13147

Fixes

Preserve RootModel core metadata by @Viicos in #13129

v2.13.3 (2026-04-20)

GitHub release

What's Changed

Fixes

Handle AttributeError subclasses with from_attributes by @Viicos in #13096

v2.13.2 (2026-04-17)

GitHub release

What's Changed

Fixes

Fix ValidationInfo.field_name missing with model_validate_json() by @Viicos in #13084

v2.13.1 (2026-04-15)

... (truncated)

Commits

001dea0 Bump pypa/gh-action-pypi-publish action to v1.14.2
558379f Bump twine to v7.0.0
2cfd5d3 Do not check for docs build
a735bee Fix more Clippy lints
7eed4a1 Fix Clippy 0.1.95 warnings
b353bbb Prepare release v2.13.5
63d2ccc Count validated model fields once in smart unions
a53ec2e Speed up PyPy CI tests
d65e0f9 Workaround circular import error in Mypy
47a6dbf Fix missing GC traversal in pydantic-core for GeneralFieldsSerializer
Additional commits viewable in compare view

Updates scikit-fingerprints from 1.18.0 to 2.1.0

Release notes

Sourced from scikit-fingerprints's releases.

scikit-fingerprints 2.1.0

New features

Many new regression datasets: ExpansionRx - OpenADMET, ASAP Discovery - OpenADMET, Biogen ADME benchmark

Initial support for fingerprints based on pretrained neural networks. Currently, CLAMP has been implemented, with extensible interface.

Added MAGPIE fingerprint

Breaking changes

Butina split has been substantially rewritten, with prior implementation not necessarily reflecting the typical Butina clustering implementation. This will give different results on 2.1.0 compared to previous versions.

Removed deprecated functions, e.g. AUROC

Fixes, small modifications, internal changes

Better README

A bunch of new benchmarks

Faster CI

Faster datasets downloading

Faster LINGO fingerprint

Fixes to conformer handling in input/output

New Contributors

@rar-file made their first contribution in MLCIL/scikit-fingerprints#619

@rayair250-droid made their first contribution in MLCIL/scikit-fingerprints#626

Full Changelog: MLCIL/scikit-fingerprints@v2.0.0...v2.1.0

scikit-fingerprints 2.0.0

This is a major release to signify how scikit-fingerprints grew in scope and functionality since 1.0.0. It now covers not only molecular fingerprints, but also molecular filters, datasets, distances & similarities, applicability domain checkers, and much more. While this v2.0.0 does not bring significant breaking changes overall, it does change many smaller functionalities, in particular MAP4 fingerprint. Further, we want to underscore the wider scope of the library now, with many planned extensions down the line in 2.x versions.

New features

ensure_mols now supports InChI strings, which also means all fingerprints etc. safely take InChI input in addition to SMILES and Mol objects

TDC clearance_hepatocyte_az dataset removed due to low data quality

First clustering method: MaxMin clustering

Filtering only valid sequences in LRGB

Multithreading for MolFromSDFTransformer for new RDKit versions

Breaking changes

MAP4 fingerprint debugged, results will strongly differ from previous ones

random_state removed from classes that didn't use it

Fixes, small modifications, internal changes

A lot of small fixes, with code and docs style unification

Faster tests and CI

Many new benchmarks

New Contributors

@LiudengZhang made their first contribution in MLCIL/scikit-fingerprints#524

@florian-huber made their first contribution in MLCIL/scikit-fingerprints#528

@abbadonaz made their first contribution in MLCIL/scikit-fingerprints#512

@FloudMe77 made their first contribution in MLCIL/scikit-fingerprints#526

@deepakdamera made their first contribution in MLCIL/scikit-fingerprints#532

... (truncated)

Commits

c2cdfb6 Added BaseNeuralFingerprintTransformer base class (#683)
573a27d Various fixes (#664)
d69dcb5 Add MAGPIE fingerprint (#663)
fb89bac A few fixes (#662)
e49a9fa Add model caching (#654)
8589faf More robust conformer ID handling (#639)
350f2fe Remove uv audit (#643)
78111e8 Fix datasets tests (#636)
604694d Add Adam as maintainer
e504f0a Clarify contributing guidelines (#629)
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Updates scikit-learn from 1.8.0 to 1.9.0

Release notes

Sourced from scikit-learn's releases.

Scikit-learn 1.9.0

We're happy to announce the 1.9.0 release.

You can read the release highlights under https://scikit-learn.org/stable/auto_examples/release_highlights/plot_release_highlights_1_9_0.html and the long version of the change log under https://scikit-learn.org/stable/whats_new/v1.9.html

This release adds narwhals as a new dependency that will help to improve dataframe interoperability across the project.

This version supports Python versions 3.11 to 3.14.

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

Commits

77def0e trigger wheel builder [cd build]
ee7c0b0 generate changelog
3d7fb04 bump version
8954e7b DOC Release highlights for 1.9 (#34147)
73a3eab Fix: Array-API - avoid failing for numpy fit + predict with sparse or array-l...
8839aae DOC Thread-safety requirement for open_listener message consumer callback (#3...
4d2476a DOC Refactor array API docs page (#34054)
f9f812f 🔒 🤖 CI Update lock files for scipy-dev CI build(s) 🔒 🤖 ...
d779dc3 🔒 🤖 CI Update lock files for free-threaded CI build(s) 🔒 :rob...
6a03cf0 🔒 🤖 CI Update lock files for array-api CI build(s) 🔒 🤖 ...
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Updates scipy from 1.17.1 to 1.18.1

Release notes

Sourced from scipy's releases.

SciPy 1.18.1 Release Notes

SciPy 1.18.1 is a bug-fix release with no new features compared to 1.18.0. This release includes binaries on PyPI for Python 3.15, and the minimum required version of the GCC toolchain has been increased to 10.3.0.

Authors

Name (commits)

Wasim Akram (2) +

Jake Bowhay (1)

Michael Bratsch (1)

Dietrich Brunn (1)

Evgeni Burovski (1)

Aadya Chinubhai (1)

Lucas Colley (3)

Tekin Ertekin (1) +

Fuyugithub (2) +

Ralf Gommers (11)

Joren Hammudoglu (1)

Ijtihed Kilani (1) +

Andrew Nelson (2)

Ilhan Polat (1)

Tyler Reddy (39)

romao05 (1) +

Michael Simacek (1) +

Jacob Vanderplas (2)

A total of 18 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

Note that the source and binary assets associated with this release were published to PyPI using trusted publishing, and so the trusted assets and their hashes are made available more securely at https://pypi.org/project/scipy/1.18.1/ rather than providing them here in a less secure manner.

A complete list of issues and pull requests associated with this release is available in the associated README.txt.

SciPy 1.18.0 Release Notes

SciPy 1.18.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s).

... (truncated)

Commits

e4e854e REL: SciPy 1.18.1 rel commit
3c8e5f8 BLD, MAINT: pythran bounds for 1.18.1 (#25978)
54c0f95 BLD, MAINT: pythran bounds for 1.18.1
45a355d Merge pull request #25884 from tylerjereddy/treddy_backports_1.18.1
a717e28 DOC: PR 25884 revisions
bb489c0 DOC: PR 25884 revisions
09bca24 BLD: package: pin meson on win-64 to avoid clang-cl bug (#25913)
095fe56 DOC, BLD: PR 25884 revisions
e66ea64 DOC: update minimum GCC version in toolchain roadmap
c021653 TST: tolerance bumps and skips on 32-bit platforms
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Updates umap-learn from 0.5.11 to 0.5.12

Release notes

Sourced from umap-learn's releases.

release-0.5.12

What's Changed

Remove nomic atlas reference from plotting.rst by @cakiki in lmcinnes/umap#1238

[MINOR] Update README.rst by @cakiki in lmcinnes/umap#1241

Remove more atlas references / fix doc build warnings by @cakiki in lmcinnes/umap#1243

Fix for #1180 and #1200 - NaN loss on Parametric UMAP retraining. by @jacobgolding in lmcinnes/umap#1244

Edit distance fixes + fast short ascii method (Myers) by @jh83775 in lmcinnes/umap#1247

Fixing gradients in some metrics by @jh83775 in lmcinnes/umap#1248

Update parametric_umap.py by @M4rk0st0j in lmcinnes/umap#1249

Issue 1216 by @lmcinnes in lmcinnes/umap#1250

New Contributors

@M4rk0st0j made their first contribution in lmcinnes/umap#1249

Full Changelog: lmcinnes/umap@release-0.5.11...release-0.5.12

Commits

cdb0eeb Merge pull request #1250 from lmcinnes/issue_1216
f30d372 version bump
6927806 Just remove fastmath
7a7bc24 Merge pull request #1249 from M4rk0st0j/master
1642ec6 Merge pull request #1248 from jh83775/grad-fix
e45dc6d Update parametric_umap.py
dc05089 guard hellinger_grad against tiny negatives
afd16c8 formatting
31e484d add tests for softmax_hellinger
6d7be7d fix hellinger output type; add softmax_hellinger
Additional commits viewable in compare view

Updates mlflow-skinny from 3.10.0 to 3.15.2

Release notes

Sourced from mlflow-skinny's releases.

v3.15.2

MLflow 3.15.2 is a patch release that includes several major features and improvements.

Features:

[Evaluation] Support immutable evaluation dataset versions (#24845, @danielseong1)

[Evaluation] Add scorer_ensemble primitive for combining scorer results (#24749, @alkispoly-db)

Bug fixes:

[Evaluation] Preserve base judge invocation flow in MemAlign aligned judges (#24883, @veronicalyu320)

[Tracking] Pre-import databricks.sdk in Databricks to avoid telemetry deadlock (#24841, @aaronteo-db)

[Build / Tracking] Align runs.status constraint metadata (#24890, @joshuawong-db)

MLflow 3.15.1 is a patch release that includes bug fixes and documentation updates.

Bug fixes:

[Model Registry] Skip env_pack on ARM client images (#24762, @qyc)

[Scoring / Tracking] Harden version parsing against missing/non-PEP440 versions on Databricks Serverless (#24799, @PattaraS)

Documentation updates:

[Docs] Clarify scorer versioning documentation (#24769, @nihalmenon)

v3.15.0

MLflow 3.15.0 includes several major features and improvements

Major New Features

🧩 MCP Registry: A centralized catalog for registering, versioning, and sharing Model Context Protocol servers — with semantic-versioned configs, promotable aliases, tags, auto-discovered tools, and ready-made connection instructions for Claude Code and .mcp.json. Manage it from the UI, REST API, or Python!

🤖 MLflow Assistant enhancements: The in-app AI assistant now supports multiple LLM providers (Claude Code, Codex, and OpenAI-compatible/Gateway endpoints) chosen from a single settings page, displays live per-session token usage and estimated cost in the composer, and is easier to set up — mlflow agent setup can enable it in one prompt, with API keys stored securely in the Gateway's LLM Connections.

🗂️ Sharable table views: Save named views of the Runs table — capturing columns, order, widths, filters, and sort — and share them by URL.

⚡ Proxy-less artifact upload/download via presigned URLs: Large artifact transfers can now bypass the tracking server and talk directly to cloud storage (e.g. S3) through presigned URLs, cutting server load and timeouts on big files. We fall back to proxied transfer automatically for backward compatibility.

🖼️ Multi-modal attachments in LLM judges: {{ trace }} judges created with make_judge() can now see images captured in trace spans via a new get_span_image tool, which fetches attachments as base64 data URLs and passes them to multimodal models (Anthropic, Gemini, and OpenAI-compatible via litellm) — enabling evaluation of vision tasks, screenshots, and other visual content.

Other Assorted Features & Improvements:

[Tracing / Tracking] Add Pydantic AI 2.x autologging support (#24721, @B-Step62)

[Tracing / UI] [3/3] Add action recommendation for low-value issue detection result (#24580, @B-Step62)

[Gateway] Support per-endpoint budget policies in the AI Gateway (#24370, @joelrobin18)

[Evaluation / Gateway] Add sap-ai-core:/ provider for SAP AI Core Orchestration v2 with extra_headers support (#24356, @shivamxtech)

[Model Registry] [Model Registry] Migrate UC model artifact download to native temp-creds (#24576, @AknA13)

[Gateway / Tracing / UI] [2/3] Simplify issue detection start modal (#24579, @B-Step62)

[Tracing / UI] [1/3] Run issue detection in the background (#24578, @B-Step62)

[Tracing] [BUG] Fix otel parent context propagation (#24444, @iyashk)

[Model Registry] [Model Registry] Gate UC model-registry client on native /api/2.1 endpoints (#24517, @AknA13)

[Docs / Tracking] Enable artifacts-only mode with workspaces (#24452, @kramaranya)

[Tracing / UI] Stop eagerly prefetching full neighboring traces in tracing UI (#24411, @DaoDaoNoCode)

[Docs / Gateway] Authenticate OpenAI-protocol coding agents through the RBAC gateway (#24294, @joshuawong-db)

... (truncated)

Changelog

Sourced from mlflow-skinny's changelog.

3.15.2 (2026-08-25)

MLflow 3.15.2 is a patch release that includes several major features and improvements.

Features:

[Evaluation] Support immutable evaluation dataset versions (#24845, @danielseong1)

[Evaluation] Add scorer_ensemble primitive for combining scorer results (#24749, @alkispoly-db)

Bug fixes:

[Evaluation] Preserve base judge invocation flow in MemAlign aligned judges (#24883, @veronicalyu320)

[Tracking] Pre-import databricks.sdk in Databricks to avoid telemetry deadlock (#24841, @aaronteo-db)

[Build / Tracking] Align runs.status constraint metadata (#24890, @joshuawong-db)

3.15.1 (2026-08-03)

MLflow 3.15.1 is a patch release that includes bug fixes and documentation updates.

Bug fixes:

[Model Registry] Skip env_pack on ARM client images (#24762) (#24835, @qyc)

[Scoring / Tracking] Harden version parsing against missing/non-PEP440 versions on Databricks Serverless (+ lint rule) (#24799) (#24813, @PattaraS)

Documentation updates:

[Docs] Clarify scorer versioning documentation (#24769) (#24805, @nihalmenon)

3.15.0 (2026-07-31)

MLflow 3.15.0 includes several major features and improvements

Major New Features

🧩 MCP Registry: A centralized catalog for registering, versioning, and sharing Model Context Protocol servers — with semantic-versioned configs, promotable aliases, tags, auto-discovered tools, and ready-made connection instructions for Claude Code and .mcp.json. Manage it from the UI, REST API, or Python!

🤖 MLflow Assistant enhancements: The in-app AI assistant now supports multiple LLM providers (Claude Code, Codex, and OpenAI-compatible/Gateway endpoints) chosen from a single settings page, displays live per-session token usage and estimated cost in the composer, and is easier to set up — mlflow agent setup can enable it in one prompt, with API keys stored securely in the Gateway's LLM Connections.

🗂️ Sharable table views: Save named views of the Runs table — capturing columns, order, widths, filters, and sort — and share them by URL.

⚡ Proxy-less artifact upload/download via presigned URLs: Large artifact transfers can now bypass the tracking server and talk directly to cloud storage (e.g. S3) through presigned URLs, cutting server load and timeouts on big files. We fall back to proxied transfer automatically for backward compatibility.

🖼️ Multi-modal attachments in LLM judges: {{ trace }} judges created with make_judge() can now see images captured in trace spans via a new get_span_image tool, which fetches attachments as base64 data URLs and passes them to multimodal models (Anthropic, Gemini, and OpenAI-compatible via litellm) — enabling evaluation of vision tasks, screenshots, and other visual content.

Other Assorted Features & Improvements:

[Tracing / Tracking] Add Pydantic AI 2.x autologging support (#24721, @B-Step62)

[Tracing / UI] [3/3] Add action recommendation for low-value issue detection result (#24580, @B-Step62)

[Gateway] Support per-endpoint budget policies in the AI Gateway (#24370, @joelrobin18)

[Evaluation / Gateway] Add sap-ai-core:/ provider for SAP AI Core Orchestration v2 with extra_headers support (#24356, @shivamxtech)

[Model Registry] [Model Registry] Migrate UC model artifact download to native temp-creds (#24576, @AknA13)

[Gateway / Tracing / UI] [2/3] Simplify issue detection start modal (#24579, @B-Step62)

[Tracing / UI] [1/3] Run issue detection in the background (#24578, @B-Step62)

[Tracing] [BUG] Fix otel parent context propagation (#24444, @iyashk)

... (truncated)

Commits

ca15da9 Add build-docs workflow for publishing release docs (#24857) (#25331)
b2af107 Bump version to 3.15.2 (#25327)
e3efd50 Backport runs.status constraint metadata alignment (#24890)
878e786 Backport MLFLOW_TRACE_ARCHIVAL_CONFIG delenv in workspace store tests
c2e8848 Pin litellm<1.97 in test-requirements for genai job
dd646e3 Backport httpx2 lock assertion for unpinned openai
dde2279 Pin ag2<1 and litellm<1.97 to fix branch-3.15 CI
d5198d7 Preserve base judge invocation flow in MemAlign aligned judges (#24883)
fb67e7d [GenAI] Support immutable evaluation dataset versions (#24845)
0b363e6 Pre-import databricks.sdk in Databricks to avoid telemetry deadlock (#24841)
Additional commits viewable in compare view

Updates plotly from 6.5.2 to 7.0.0

Release notes

Sourced from plotly's releases.

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.

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 [#7884, #7913]

Fix GeoJSON bounding-box computation for choropleth and scattergeo traces whose geometry crosses the antimeridian [#7891]

v7.0.0rc0

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]

Fixed

Raise a clear ValueError when an unsupported marginal plot type is passed to Plotly Express, instead of failing later with a cryptic 'NoneType' object has no attribute 'constructor' message [#5625], with thanks to @eugen-goebel for the contribution!

Updated

Update plotly.js from version 3.6.0 to version 4.0.0-rc.0 [#5673]. This is a major-version release candidate 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], with thanks to @degzhaus for the contribution!

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 color [#7536]. There are some changes to supported color string formats as a result:

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

... (truncated)

Changelog

Sourced from plotly's changelog.

[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 ...
Description has been truncated

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…ates Bumps the production group with 17 updates in the / directory: | Package | From | To | | --- | --- | --- | | [numpy](https://github.com/numpy/numpy) | `2.4.2` | `2.5.2` | | [pydantic](https://github.com/pydantic/pydantic) | `2.12.5` | `2.13.5` | | [scikit-fingerprints](https://github.com/scikit-fingerprints/scikit-fingerprints) | `1.18.0` | `2.1.0` | | [scikit-learn](https://github.com/scikit-learn/scikit-learn) | `1.8.0` | `1.9.0` | | [scipy](https://github.com/scipy/scipy) | `1.17.1` | `1.18.1` | | [umap-learn](https://github.com/lmcinnes/umap) | `0.5.11` | `0.5.12` | | [mlflow-skinny](https://github.com/mlflow/mlflow) | `3.10.0` | `3.15.2` | | [plotly](https://github.com/plotly/plotly.py) | `6.5.2` | `7.0.0` | | [fastparquet](https://github.com/dask/fastparquet) | `2026.3.0` | `2026.5.0` | | [torch](https://github.com/pytorch/pytorch) | `2.9.1` | `2.13.0` | | [torch-geometric](https://github.com/pyg-team/pytorch_geometric) | `2.7.0` | `2.8.0.post1` | | [optuna](https://github.com/optuna/optuna) | `4.7.0` | `4.9.0` | | [optuna-integration](https://github.com/optuna/optuna-integration) | `4.7.0` | `4.9.0` | | [transformers](https://github.com/huggingface/transformers) | `4.57.6` | `5.16.1` | | [chemprop](https://github.com/chemprop/chemprop) | `2.2.2` | `2.3.1` | | [myst-parser](https://github.com/executablebooks/MyST-Parser) | `4.0.1` | `5.1.0` | | [sphinx-autoapi](https://github.com/readthedocs/sphinx-autoapi) | `3.8.0` | `3.8.1` | Updates `numpy` from 2.4.2 to 2.5.2 - [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...v2.5.2) Updates `pydantic` from 2.12.5 to 2.13.5 - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/v2.13.5/HISTORY.md) - [Commits](pydantic/pydantic@v2.12.5...v2.13.5) Updates `scikit-fingerprints` from 1.18.0 to 2.1.0 - [Release notes](https://github.com/scikit-fingerprints/scikit-fingerprints/releases) - [Commits](MLCIL/scikit-fingerprints@v1.18.0...v2.1.0) Updates `scikit-learn` from 1.8.0 to 1.9.0 - [Release notes](https://github.com/scikit-learn/scikit-learn/releases) - [Commits](scikit-learn/scikit-learn@1.8.0...1.9.0) Updates `scipy` from 1.17.1 to 1.18.1 - [Release notes](https://github.com/scipy/scipy/releases) - [Commits](scipy/scipy@v1.17.1...v1.18.1) Updates `umap-learn` from 0.5.11 to 0.5.12 - [Release notes](https://github.com/lmcinnes/umap/releases) - [Changelog](https://github.com/lmcinnes/umap/blob/master/doc/release_notes.rst) - [Commits](lmcinnes/umap@release-0.5.11...release-0.5.12) Updates `mlflow-skinny` from 3.10.0 to 3.15.2 - [Release notes](https://github.com/mlflow/mlflow/releases) - [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md) - [Commits](mlflow/mlflow@v3.10.0...v3.15.2) Updates `plotly` from 6.5.2 to 7.0.0 - [Release notes](https://github.com/plotly/plotly.py/releases) - [Changelog](https://github.com/plotly/plotly.py/blob/main/CHANGELOG.md) - [Commits](plotly/plotly.py@v6.5.2...v7.0.0) Updates `mlflow` from 3.10.0 to 3.15.2 - [Release notes](https://github.com/mlflow/mlflow/releases) - [Changelog](https://github.com/mlflow/mlflow/blob/master/CHANGELOG.md) - [Commits](mlflow/mlflow@v3.10.0...v3.15.2) Updates `fastparquet` from 2026.3.0 to 2026.5.0 - [Commits](dask/fastparquet@2026.3.0...2026.5.0) Updates `torch` from 2.9.1 to 2.13.0 - [Release notes](https://github.com/pytorch/pytorch/releases) - [Changelog](https://github.com/pytorch/pytorch/blob/main/RELEASE.md) - [Commits](pytorch/pytorch@v2.9.1...v2.13.0) Updates `torch-geometric` from 2.7.0 to 2.8.0.post1 - [Release notes](https://github.com/pyg-team/pytorch_geometric/releases) - [Changelog](https://github.com/pyg-team/pytorch_geometric/blob/2.8.0.post1/CHANGELOG.md) - [Commits](pyg-team/pytorch_geometric@2.7.0...2.8.0.post1) Updates `optuna` from 4.7.0 to 4.9.0 - [Release notes](https://github.com/optuna/optuna/releases) - [Commits](optuna/optuna@v4.7.0...v4.9.0) Updates `optuna-integration` from 4.7.0 to 4.9.0 - [Release notes](https://github.com/optuna/optuna-integration/releases) - [Commits](optuna/optuna-integration@v4.7.0...v4.9.0) Updates `transformers` from 4.57.6 to 5.16.1 - [Release notes](https://github.com/huggingface/transformers/releases) - [Commits](huggingface/transformers@v4.57.6...v5.16.1) Updates `chemprop` from 2.2.2 to 2.3.1 - [Release notes](https://github.com/chemprop/chemprop/releases) - [Commits](chemprop/chemprop@v2.2.2...v2.3.1) Updates `myst-parser` from 4.0.1 to 5.1.0 - [Release notes](https://github.com/executablebooks/MyST-Parser/releases) - [Changelog](https://github.com/executablebooks/MyST-Parser/blob/master/CHANGELOG.md) - [Commits](executablebooks/MyST-Parser@v4.0.1...v5.1.0) Updates `sphinx-autoapi` from 3.8.0 to 3.8.1 - [Release notes](https://github.com/readthedocs/sphinx-autoapi/releases) - [Changelog](https://github.com/readthedocs/sphinx-autoapi/blob/main/CHANGELOG.rst) - [Commits](readthedocs/sphinx-autoapi@v3.8.0...v3.8.1) --- updated-dependencies: - dependency-name: chemprop dependency-version: 2.3.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: fastparquet dependency-version: 2026.5.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: mlflow dependency-version: 3.15.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: mlflow-skinny dependency-version: 3.15.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: myst-parser dependency-version: 5.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: numpy dependency-version: 2.5.2 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: optuna dependency-version: 4.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: optuna-integration dependency-version: 4.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: plotly dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: pydantic dependency-version: 2.13.5 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: scikit-fingerprints dependency-version: 2.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: scikit-learn dependency-version: 1.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: scipy dependency-version: 1.18.1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: sphinx-autoapi dependency-version: 3.8.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: production - dependency-name: torch dependency-version: 2.13.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: torch-geometric dependency-version: 2.8.0.post1 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: production - dependency-name: transformers dependency-version: 5.16.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: production - dependency-name: umap-learn dependency-version: 0.5.12 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: production ... 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dependabot Bot requested a review from dahvida as a code owner September 1, 2026 13:50

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v2.5.2 (Aug 9, 2026)

NumPy 2.5.2 Release Notes

C API changes

PyArray_StringDTypeObject is opaque under the abi3t stable ABI

Contributors

v2.13.5 (2026-08-28)

What's Changed

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v2.13.4 2026-05-06

v2.13.4 (2026-05-06)

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v2.13.3 2026-04-20

v2.13.3 (2026-04-20)

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v2.13.2 2026-04-17

v2.13.2 (2026-04-17)

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v2.13.1 2026-04-15

v2.13.5 (2026-08-28)

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v2.13.4 (2026-05-06)

What's Changed

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v2.13.3 (2026-04-20)

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v2.13.2 (2026-04-17)

What's Changed

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v2.13.1 (2026-04-15)

scikit-fingerprints 2.1.0

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Fixes, small modifications, internal changes

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scikit-fingerprints 2.0.0

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Scikit-learn 1.9.0

SciPy 1.18.1 Release Notes

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SciPy 1.18.0 Release Notes

release-0.5.12

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v3.15.2

Bug fixes:

Documentation updates:

v3.15.0

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3.15.2 (2026-08-25)

3.15.1 (2026-08-03)

3.15.0 (2026-07-31)

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v7.0.0

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