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chore(deps): bump the python group across 1 directory with 18 updates#3353
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@dependabot dependabot bot commented on behalf of github Mar 31, 2026

Updates the requirements on importlib-metadata, h5netcdf, rich, dask, tomlkit, responses, bayesian-optimization, gdstk, mypy, networkx, orbax-checkpoint, pydata-sphinx-theme, pygad, pytest-cov, rtree, ruff, sax and trame-vuetify to permit the latest version.
Updates importlib-metadata to 9.0.0

Changelog

Sourced from importlib-metadata's changelog.

v9.0.0

Deprecations and Removals

  • Added MetadataNotFound (subclass of FileNotFoundError) and updated Distribution.metadata/metadata() to raise it when the metadata files are missing instead of returning Nonepython/cpython#143387#532)

v8.9.0

Features

v8.8.0

Features

  • Removed Python 3.9 compatibility.

v8.7.1

Bugfixes

  • Fixed errors in FastPath under fork-multiprocessing. (#520)
  • Removed cruft from Python 3.8. (#524)

v8.7.0

Features

  • .metadata() (and Distribution.metadata) can now return None if the metadata directory exists but not metadata file is present. (#493)

Bugfixes

  • Raise consistent ValueError for invalid EntryPoint.value (#518)

... (truncated)

Commits

Updates h5netcdf from 1.0.2 to 1.8.1

Release notes

Sourced from h5netcdf's releases.

release 1.8.1

What's Changed

Full Changelog: h5netcdf/h5netcdf@v1.8.0...v1.8.1

release 1.8.0

What's Changed

Full Changelog: h5netcdf/h5netcdf@v1.7.3...v1.8.0

release 1.7.3

What's Changed

Full Changelog: h5netcdf/h5netcdf@v1.7.2...v1.7.3

release 1.7.2

What's Changed

Full Changelog: h5netcdf/h5netcdf@v1.7.1...v1.7.2

release 1.7.1

What's Changed

Full Changelog: h5netcdf/h5netcdf@v1.7.0...v1.7.1

release 1.7.0

What's Changed

... (truncated)

Changelog

Sourced from h5netcdf's changelog.

Change Log

Development Version (unreleased):

  • Fix CI issues with xarray nightly tests (add pytz dependency) and h5pyd tests (pin setuptools=81) (:issue:312, :pull:313) by Kai Mühlbauer <https://github.com/kmuehlbauer>_

Version 1.8.1 (January 23rd, 2026):

  • Add numpy to default dependencies, update install section to highlight backend installation, update error message on missing backend (:issue:310, :pull:311) by Kai Mühlbauer <https://github.com/kmuehlbauer>_

Version 1.8.0 (January 16st, 2026):

  • Fix ros3 test (:issue:295, :pull:296). By Ezequiel Cimadevilla Alvarez <https://github.com/zequihg50>_
  • Update pre-commit. By Kai Mühlbauer <https://github.com/kmuehlbauer>_
  • Fix h5py3 hdf5 1.10 CI run (:pull:303). By Kai Mühlbauer <https://github.com/kmuehlbauer>_
  • Support pyfive as an alternative backend ({pull}273). By Bryan Lawrence <https://github.com/bnlawrence>, David Hassell <https://github.com/davidhassell>, Valeriu Predoi <https://github.com/valeriupredoi>, Kai Mühlbauer <https://github.com/kmuehlbauer> and Stephan Hoyer <https://github.com/shoyer>_
  • Add support for filters() for Variables to match netCDF4 python API. By Mark Harfouche <https://github.com/hmaarrfk>_.

Version 1.7.3 (October 21st, 2025):

  • Fix indexing with empty arrays and lists (:pull:297). By Kai Mühlbauer <https://github.com/kmuehlbauer>_

Version 1.7.2 (October 17th, 2025):

  • Fix regression where format was requested from group instance instead of root. Simplify logic to check and raise CompatibilityError. (:issue:293, :pull:294). By Kai Mühlbauer <https://github.com/kmuehlbauer>

Version 1.7.1 (October 16th, 2025):

  • Fix regression where attributes with list of strings were written with h5py low-level API instead of high-level API (:issue:291, :pull:292). By Kai Mühlbauer <https://github.com/kmuehlbauer>_

Version 1.7.0 (October 15th, 2025):

  • Fix unintentional changes in test suite (:pull:277). By Kai Mühlbauer <https://github.com/kmuehlbauer>_
  • Create ENUM with low level API to keep order-by-value, add h5dump based tests (:pull:285). By Kai Mühlbauer <https://github.com/kmuehlbauer>_ and David Huard <https://github.com/huard>_
  • Fix interoperability issues between netcdf4/h5netcdf, namely resizing variables using partial slices, creating string attributes with NULLTERM, proper attachment of _Netcdf4Coordinates and _Netcdf4Dimid as well as special string type fillvalues (:pull:286).

... (truncated)

Commits

Updates rich to 14.3.3

Release notes

Sourced from rich's releases.

The infinite Release

Fixed a infinite loop in split_graphemes

[14.3.3] - 2026-02-19

Fixed

Changelog

Sourced from rich's changelog.

[14.3.3] - 2026-02-19

Fixed

[14.3.2] - 2026-02-01

Fixed

[14.3.1] - 2026-01-24

Fixed

[14.3.0] - 2026-01-24

Fixed

Added

Changed

[14.2.0] - 2025-10-09

Changed

... (truncated)

Commits

Updates dask to 2026.3.0

Release notes

Sourced from dask's releases.

2026.3.0

Changes

See the Changelog for more information.

Commits
  • b1025f7 Version 2026.3.0
  • 0d40a60 Silence deprecations in global config if local config overrides them (#12315)
  • 30ea561 docs: document approximate algorithm and Dask-specific params in describe() (...
  • 8a9b92f docs: clarify coarsen reduction function contract (#12314)
  • 0993aa9 Fix misleading TypeError for scalar overflow in dask.array elemwise (#12301)
  • e0529bb Stricter warnings filter (#12274)
  • ac02b7d Clean up obsolete PANDAS_GE markers (#12279)
  • e4338c2 Bump actions/upload-artifact from 6 to 7 (#12311)
  • 714eaf4 fix: Added full_matrices parameter to dask.array.linalg.svd (#12292)
  • d115605 Remove mention of obsolete default value for 'boundary' parameter. (#12304)
  • Additional commits viewable in compare view

Updates tomlkit to 0.14.0

Release notes

Sourced from tomlkit's releases.

0.14.0

What's Changed

New Contributors

Full Changelog: python-poetry/tomlkit@0.13.3...0.14.0

Changelog

Sourced from tomlkit's changelog.

[0.14.0] - 2026-01-13

Changed

  • Drop support for Python older than 3.9. Remove 3.8 from the CI matrix.

Added

  • Custom encoders can now receive _parent and _sort_keys parameters to enable proper encoding of nested structures. (#429)
  • Add String.type property to get the string type. (#443)

Fixed

  • Fixed tomlkit.boolean() API to correctly handle boolean inputs. (#442)

[0.13.3] - 2025-06-05

Added

  • Add .item() method to array and tables to retrieve an item by key. (#390)

Fixed

  • Fix missing newline when parsing a separated array of tables without trailing new line. (#381)
  • Fix non-existing key error when deleting an item from an out-of-order table. (#383)
  • Ensure newline is added between the plain values and the first table. (#387)
  • Fix repeated whitespace when removing an array item. (#405)
  • Fix invalid serialization after removing array item if the comma is on its own line. (#408)
  • Fix serialization of a nested dotted key table. (#411)
  • Refine the error message when use non-string as single key. (#412)
  • Fix invalid serialization after overwriting a key of a out-of-order table. (#414)

[0.13.2] - 2024-08-14

Fixed

  • Fix deleting keys from an out-of-order table does not remove all table parts. (#379)

[0.13.1] - 2024-08-14

Fixed

  • Fix the Table.is_super_table() check for tables with dotted key as the only child. (#374)
  • Count table as a super table if it has children and all children are either tables or arrays of tables. (#377)

[0.13.0] - 2024-07-10

Changed

  • Expect a tomlkit-specific error instead of TypeError from a custom encoder. (#355)

... (truncated)

Commits
  • 090a28e chore(deps-dev): bump setuptools from 70.0.0 to 78.1.1 (#453)
  • 9bccd76 chore: bump version to 0.14.0 in pyproject.toml and init.py
  • e457892 chore(deps-dev): bump urllib3 from 2.2.2 to 2.6.3 (#452)
  • 82970a1 chore: update pre-commit hooks and refactor imports for consistency
  • edba395 chore: update Python version and GitHub Actions to use latest versions (#451)
  • 5495784 feat: add String.type property to retrieve the string type
  • a61a4d5 [pre-commit.ci] pre-commit autoupdate (#444)
  • 87ace5e [pre-commit.ci] pre-commit autoupdate (#438)
  • 3687d0d fix: update boolean function to handle both string and boolean inputs correctly
  • 6042e0c feat: enhance custom encoders to accept _parent and _sort_keys parameters (#436)
  • Additional commits viewable in compare view

Updates responses to 0.26.0

Release notes

Sourced from responses's releases.

0.26.0

  • When using assert_all_requests_are_fired=True, assertions about unfired requests are now raised even when an exception occurs in the context manager or decorated function. Previously, these assertions were suppressed when exceptions occurred. This new behavior provides valuable debugging context about which mocked requests were or weren't called.
  • Consider the Retry-After header when handling retries
Changelog

Sourced from responses's changelog.

0.26.0

  • When using assert_all_requests_are_fired=True, assertions about unfired requests are now raised even when an exception occurs in the context manager or decorated function. Previously, these assertions were suppressed when exceptions occurred. This new behavior provides valuable debugging context about which mocked requests were or weren't called.
  • Consider the Retry-After header when handling retries

0.25.8

  • Fix bug where the content type is always recorded as either text/plain or application/json. See #770
  • Allow asserts on add_callback() matches. See #727

0.25.7

  • Added support for python 3.13

0.25.6

  • Added py.typed to package_data

0.25.5

  • Fix readme issue that prevented 0.25.4 from being published to pypi.

0.25.4

  • Responses can now match requests that use data with file-like objects. Files will be read as bytes and stored in the request mock. See #736
  • RequestsMock.matchers was added. This property is an alias to responses.matchers. See #739
  • Removed tests from packaged wheels. See #746
  • Improved recorder API to ease use in REPL environments. See #745

0.25.3

  • Fixed recorder not saving and loading response headers with yaml files. See #715

0.25.2

  • Mulligan on 0.25.1 to run release pipeline correctly.

... (truncated)

Commits
  • 94913d0 release: 0.26.0
  • 051b79e Make assert_all_requests_are_fired always assert on exception (#782)
  • 0905cb8 Fix query_param_matcher not matching empty query parameter values (#787)
  • e0c6faa ci(release): Switch from action-prepare-release to Craft (#785)
  • 1be3a73 fix: Consider the Retry-After header when handling retries (#784)
  • c6730fb Merge branch 'release/0.25.8'
  • See full diff in compare view

Updates bayesian-optimization to 3.2.1

Release notes

Sourced from bayesian-optimization's releases.

v3.2.1

What's Changed

New Contributors

Full Changelog: bayesian-optimization/BayesianOptimization@v3.2.0...v3.2.1

Commits

Updates gdstk to 1.0.0

Changelog

Sourced from gdstk's changelog.

1.0.0 - 2026-02-21

Added

  • Support for layer names from/to OASIS files (#322, thanks nmz787-intel for the contribution).

Fixed

  • Missing docs for gds_timestamp.

0.9.62 - 2026-01-03

Added

  • Support for exporting empty flexpaths to GDSII/OASIS.

Fixed

  • Bug in point-in-polygon checks.
  • Array printing.

0.9.61 - 2025-08-28

Added

  • Support for non-standard repetition vectors in GDSII (#293, #299, thanks svollenweider, WesYu).

Fixed

  • Bug in OASIS output when using explicit repetitions (#307, thanks RedFalsh).
  • Time stamp format in GDSII (#308, thanks albachten).

0.9.60 - 2025-04-15

Fixed

  • Added support to 32-bit layers and datatypes.

0.9.59 - 2025-02-11

Fixed

  • Treat string properties as binary byte arrays in OASIS.

0.9.58 - 2024-11-25

Changed

  • Empty paths now give a warning when being converted to polygons or stored in GDSII/OASIS.

Fixed

  • Missing paths when vertices were separated exactly by the tolerance (#277)

0.9.57 - 2024-11-07

Fixed

  • Bug when removing GDSII properties (#276, thanks jatoben).

0.9.56 - 2024-10-28

Added

  • Support for Python 3.13.

Fixed

  • Copy Raith data in Cell::get_flexpaths.

0.9.55 - 2024-08-31

Fixed

  • Memory bug fix for Raith data

0.9.54 - 2024-08-31

Changed

... (truncated)

Commits
  • 9575737 Release v1.0.0
  • 9315981 Add OASIS layername feature: array-based implementation and serialization
  • 25a7c51 Update _gdstk.pyi to include gds_timestamp
  • 13dffc4 Add gds_timestamp to docs
  • 525494b Release v0.9.62
  • 5b12244 Bug fixes for point in polygon checks and array printing
  • 5e871f6 Add support for exporting empty flexpaths to gds/oas
  • 9ceec43 Enable python 3.14 builds
  • 5f5def6 Release 0.9.61
  • 26857c7 Fix for #304: explicit repetition in OASIS
  • Additional commits viewable in compare view

Updates mypy from 1.13.0 to 1.19.1

Changelog

Sourced from mypy's changelog.

Mypy 1.19.1

  • Fix noncommutative joins with bounded TypeVars (Shantanu, PR 20345)
  • Respect output format for cached runs by serializing raw errors in cache metas (Ivan Levkivskyi, PR 20372)
  • Allow types.NoneType in match cases (A5rocks, PR 20383)
  • Fix mypyc generator regression with empty tuple (BobTheBuidler, PR 20371)
  • Fix crash involving Unpack-ed TypeVarTuple (Shantanu, PR 20323)
  • Fix crash on star import of redefinition (Ivan Levkivskyi, PR 20333)
  • Fix crash on typevar with forward ref used in other module (Ivan Levkivskyi, PR 20334)
  • Fail with an explicit error on PyPy (Ivan Levkivskyi, PR 20389)

Acknowledgements

Thanks to all mypy contributors who contributed to this release:

  • A5rocks
  • BobTheBuidler
  • bzoracler
  • Chainfire
  • Christoph Tyralla
  • David Foster
  • Frank Dana
  • Guo Ci
  • iap
  • Ivan Levkivskyi
  • James Hilton-Balfe
  • jhance
  • Joren Hammudoglu
  • Jukka Lehtosalo
  • KarelKenens
  • Kevin Kannammalil
  • Marc Mueller
  • Michael Carlstrom
  • Michael J. Sullivan
  • Piotr Sawicki
  • Randolf Scholz
  • Shantanu
  • Sigve Sebastian Farstad
  • sobolevn
  • Stanislav Terliakov
  • Stephen Morton
  • Theodore Ando
  • Thiago J. Barbalho
  • wyattscarpenter

I’d also like to thank my employer, Dropbox, for supporting mypy development.

Mypy 1.18

We’ve just uploaded mypy 1.18.1 to the Python Package Index (PyPI). Mypy is a static type checker for Python. This release includes new features, performance

... (truncated)

Commits

Updates networkx to 3.4.2

Release notes

Sourced from networkx's releases.

NetworkX 3.4.2

We're happy to announce the release of networkx 3.4.2!

Bug Fixes

  • Fix docstrings of dispatchable functions (#7679).
  • Fix draw_networkx_nodes return type (#7685).

Documentation

  • Add disclaimer about LLM driven PRs (#7683).

Maintenance

  • Fix doc warnings from recently added docs (#7682).

Contributors

6 authors added to this release (alphabetically):

4 reviewers added to this release (alphabetically):

These lists are automatically generated, and may not be complete or may contain duplicates.

Commits

Updates orbax-checkpoint to 0.11.33

Commits
  • 6a36d40 Increment Orbax version.
  • 0becf51 Update pytest command to use an ignore list from a YAML file.
  • 4cf67f6 Allow restore+broadcast logic to not require a single-replica sharding parame...
  • daec61e Normalize device kind strings when looking up HBM memory.
  • 46eea87 #v1 In-line CompositeHandler logic into Orbax Layouts
  • 53b2890 #v1 Strip down composite handler class and refactor functionality.
  • c339d50 Internal Change
  • cbdd63f #v1 Fork handler resolution functionality from composite_handler into resolut...
  • cf5a1ce Fix Pytree Metadata resolution and refactor V0 Layout logic
  • 2520b09 #p2p Support CPU memory ops in multislice functions
  • ...

    Description has been truncated


    [!NOTE]
    Medium Risk
    Dependency constraints are widened and several versions are bumped (including some major-version allowances), which may introduce upstream behavior changes or resolver conflicts despite no code changes.

    Overview
    Updates pyproject.toml dependency constraints to allow newer releases across runtime and dev/test/doc extras.

    Notable bumps include h5netcdf to 1.8.1, widening upper bounds for importlib-metadata, rich, dask, tomlkit, and responses, plus dev tooling/library updates such as mypy, networkx, pytest-cov, ruff, rtree, gdstk, sax, trame-vuetify, and pygad.

    Written by Cursor Bugbot for commit 02b53f6. This will update automatically on new commits. Configure here.

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Cursor Bugbot has reviewed your changes and found 1 potential issue.

Fix All in Cursor

Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.

[project.optional-dependencies]
dev = [
"bayesian-optimization<2",
"bayesian-optimization<4",
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Version bump allows incompatible bayesian-optimization API versions

High Severity

The bayesian-optimization constraint changed from <2 to <4, but the codebase uses UtilityFunction (removed in v2.0.0) and the old suggest(utility) API pattern. In tidy3d/plugins/design/method.py, from bayes_opt import BayesianOptimization, UtilityFunction will raise ImportError with v2.0+, caught misleadingly as "module not found." The entire Bayesian optimization design plugin becomes non-functional when v2.x or v3.x is resolved.

Additional Locations (1)
Fix in Cursor Fix in Web

Updates the requirements on [importlib-metadata](https://github.com/python/importlib_metadata), [h5netcdf](https://github.com/h5netcdf/h5netcdf), [rich](https://github.com/Textualize/rich), [dask](https://github.com/dask/dask), [tomlkit](https://github.com/sdispater/tomlkit), [responses](https://github.com/getsentry/responses), [bayesian-optimization](https://github.com/bayesian-optimization/BayesianOptimization), [gdstk](https://github.com/heitzmann/gdstk), [mypy](https://github.com/python/mypy), [networkx](https://github.com/networkx/networkx), [orbax-checkpoint](https://github.com/google/orbax), [pydata-sphinx-theme](https://github.com/pydata/pydata-sphinx-theme), [pygad](https://github.com/ahmedfgad/GeneticAlgorithmPython), [pytest-cov](https://github.com/pytest-dev/pytest-cov), [rtree](https://github.com/Toblerity/rtree), [ruff](https://github.com/astral-sh/ruff), [sax](https://github.com/flaport/sax) and [trame-vuetify](https://github.com/Kitware/trame-vuetify) to permit the latest version.

Updates `importlib-metadata` to 9.0.0
- [Release notes](https://github.com/python/importlib_metadata/releases)
- [Changelog](https://github.com/python/importlib_metadata/blob/main/NEWS.rst)
- [Commits](python/importlib_metadata@v6.0.0...v9.0.0)

Updates `h5netcdf` from 1.0.2 to 1.8.1
- [Release notes](https://github.com/h5netcdf/h5netcdf/releases)
- [Changelog](https://github.com/h5netcdf/h5netcdf/blob/main/CHANGELOG.rst)
- [Commits](h5netcdf/h5netcdf@v1.0.2...v1.8.1)

Updates `rich` to 14.3.3
- [Release notes](https://github.com/Textualize/rich/releases)
- [Changelog](https://github.com/Textualize/rich/blob/master/CHANGELOG.md)
- [Commits](Textualize/rich@v13.0.0...v14.3.3)

Updates `dask` to 2026.3.0
- [Release notes](https://github.com/dask/dask/releases)
- [Changelog](https://github.com/dask/dask/blob/main/docs/release-procedure.md)
- [Commits](dask/dask@2025.12.0...2026.3.0)

Updates `tomlkit` to 0.14.0
- [Release notes](https://github.com/sdispater/tomlkit/releases)
- [Changelog](https://github.com/python-poetry/tomlkit/blob/master/CHANGELOG.md)
- [Commits](python-poetry/tomlkit@0.13.2...0.14.0)

Updates `responses` to 0.26.0
- [Release notes](https://github.com/getsentry/responses/releases)
- [Changelog](https://github.com/getsentry/responses/blob/master/CHANGES)
- [Commits](getsentry/responses@0.25.8...0.26.0)

Updates `bayesian-optimization` to 3.2.1
- [Release notes](https://github.com/bayesian-optimization/BayesianOptimization/releases)
- [Commits](bayesian-optimization/BayesianOptimization@0.4...v3.2.1)

Updates `gdstk` to 1.0.0
- [Release notes](https://github.com/heitzmann/gdstk/releases)
- [Changelog](https://github.com/heitzmann/gdstk/blob/main/CHANGELOG.md)
- [Commits](heitzmann/gdstk@v0.9.49...v1.0.0)

Updates `mypy` from 1.13.0 to 1.19.1
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.13.0...v1.19.1)

Updates `networkx` to 3.4.2
- [Release notes](https://github.com/networkx/networkx/releases)
- [Commits](networkx/networkx@networkx-2.6.3...networkx-3.4.2)

Updates `orbax-checkpoint` to 0.11.33
- [Release notes](https://github.com/google/orbax/releases)
- [Changelog](https://github.com/google/orbax/blob/main/CHANGELOG.md)
- [Commits](google/orbax@v0.0.0...v0.11.33)

Updates `pydata-sphinx-theme` to 0.16.1
- [Release notes](https://github.com/pydata/pydata-sphinx-theme/releases)
- [Changelog](https://github.com/pydata/pydata-sphinx-theme/blob/main/RELEASE.md)
- [Commits](pydata/pydata-sphinx-theme@v0.13.3...v0.16.1)

Updates `pygad` from 3.3.1 to 3.5.0
- [Release notes](https://github.com/ahmedfgad/GeneticAlgorithmPython/releases)
- [Commits](ahmedfgad/GeneticAlgorithmPython@3.3.1...3.5.0)

Updates `pytest-cov` to 7.1.0
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](pytest-dev/pytest-cov@v6.0.0...v7.1.0)

Updates `rtree` from 1.2.0 to 1.4.1
- [Release notes](https://github.com/Toblerity/rtree/releases)
- [Changelog](https://github.com/Toblerity/rtree/blob/main/CHANGES.rst)
- [Commits](Toblerity/rtree@1.2.0...1.4.1)

Updates `ruff` from 0.11.11 to 0.15.7
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.11.11...0.15.7)

Updates `sax` to 0.14.2
- [Release notes](https://github.com/flaport/sax/releases)
- [Changelog](https://github.com/flaport/sax/blob/main/CHANGELOG.md)
- [Commits](flaport/sax@0.11.0...0.14.2)

Updates `trame-vuetify` to 3.2.1
- [Release notes](https://github.com/Kitware/trame-vuetify/releases)
- [Changelog](https://github.com/Kitware/trame-vuetify/blob/master/CHANGELOG.md)
- [Commits](Kitware/trame-vuetify@v2.0.1...v3.2.1)

---
updated-dependencies:
- dependency-name: importlib-metadata
  dependency-version: 9.0.0
  dependency-type: direct:production
  dependency-group: python
- dependency-name: h5netcdf
  dependency-version: 1.8.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
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...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot force-pushed the dependabot/pip/python-2c427f93bf branch from 56d2d8f to 02b53f6 Compare April 3, 2026 11:08
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