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Bumps the package-updates group with 9 updates in the / directory:

Package From To
pydantic 2.13.3 2.13.4
zarr 3.1.6 3.2.1
numpy 2.4.4 2.4.5
coverage 7.13.5 7.14.0
ruff 0.15.12 0.15.13
mypy 1.20.2 2.1.0
types-pyyaml 6.0.12.20260408 6.0.12.20260518
types-shapely 2.1.0.20260408 2.1.0.20260518
zensical 0.0.37 0.0.42

Updates pydantic from 2.13.3 to 2.13.4

Release notes

Sourced from pydantic's releases.

v2.13.4 2026-05-06

v2.13.4 (2026-05-06)

What's Changed

Packaging

Fixes

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

Changelog

Sourced from pydantic's changelog.

v2.13.4 (2026-05-06)

GitHub release

What's Changed

Packaging

Fixes

Commits
  • cf67d4b Fix linting
  • f0d8a21 Prepare release v2.13.4
  • 5e3fe1d Check for pydantic tag pattern in CI
  • 7f9edcc Document tagging conventions
  • b46a0c9 Adapt pydantic-core linker flags on macOS
  • 50629c8 Update to PyPy 7.3.22
  • 8522ebb Preserve RootModel core metadata
  • a37f3af Adapt MISSING sentinel test to work with unreleased typing_extensions ver...
  • 909259a Remove Logfire example in documentation
  • 2c4174c Bump libc from 0.2.155 to 0.2.185
  • See full diff in compare view

Updates zarr from 3.1.6 to 3.2.1

Release notes

Sourced from zarr's releases.

v3.2.1

What's Changed

Full Changelog: zarr-developers/zarr-python@v3.2.0...v3.2.1

v3.2.0

What's Changed

... (truncated)

Changelog

Sourced from zarr's changelog.

3.2.1 (2026-05-05)

Bugfixes

  • Fixed a CastValue validation bug where the "can we use an out-of-range mode" check inspected the source dtype instead of the target dtype. This meant arrays with a float source dtype and an integer target dtype incorrectly raised a ValueError when configured with a wrap out-of-range mode. (#3938)
  • Fixed a bug where the codec pipeline evolved each codec against the original array spec instead of the spec produced by upstream array-to-array codecs. This caused failures whenever an upstream codec changed the dtype between codec boundaries — e.g. arrays using CastValue to convert a single-byte source dtype (int8) to a multi-byte target dtype (int16) raised a ValueError from BytesCodec about a missing endian configuration. (#3941)
  • Fixed breakage in existing fsspec-dependent workflows caused by associating the "memory" URL scheme with instances of ManagedMemoryStore instead of fsspec's memory-backed store. After this change, store URLs with a "memory" scheme are handled differently when fsspec is installed: with fsspec, a FsspecStore backed by a MemoryFileSystem is used. Without fsspec, a ManagedMemoryStore is used. (#3944)

3.2.0 (2026-04-30)

Features

  • Adds a new in-memory storage backend called ManagedMemoryStore. Instances of ManagedMemoryStore function similarly to MemoryStore, but instances of ManagedMemoryStore can be constructed from a URL like memory://store. (#3679)

  • Added array.read_missing_chunks configuration option. When set to False, reading missing chunks raises a ChunkNotFoundError instead of filling them with the array's fill value. (#3748)

  • Added Struct class (subclass of Structured) implementing the zarr-extensions struct dtype spec. Uses object-style field format and dict fill values. Legacy Structured remains available for backward compatibility. (#3781)

  • Add support for rectilinear (variable-sized) chunk grids. This feature is experimental and must be explicitly enabled via zarr.config.set({'array.rectilinear_chunks': True}).

    Rectilinear chunks can be used through:

    • Creating arrays: Pass nested sequences (e.g., [[10, 20, 30], [50, 50]]) to chunks in zarr.create_array, zarr.from_array, zarr.zeros, zarr.ones, zarr.full, zarr.open, and related functions, or to chunk_shape in zarr.create.
    • Opening existing arrays: Arrays stored with the rectilinear chunk grid are read transparently via zarr.open and zarr.open_array.
    • Rectilinear sharding: Shard boundaries can be rectilinear while inner chunks remain regular.

    Breaking change: The validate method on BaseCodec and CodecPipeline now receives a ChunkGridMetadata instance instead of a ChunkGrid instance for the chunk_grid parameter. Third-party codecs that override validate and inspect the chunk grid will need to update their type annotations. No known downstream packages were using this parameter. (#3802)

  • Add cast_value and scale_offset codecs. (#3874)

Bugfixes

  • Fix SyncError raised when assigning a zarr.Array as the value in a __setitem__ call (e.g. dst[:] = src where src is a zarr array). The source array is now converted to a NumPy array before entering the async codec pipeline. (#3611)

... (truncated)

Commits
  • 85890b3 release : 3.2.1 release notes (#3942)
  • 37ae37b fix: defer to fsspec for memory url scheme (#3944)
  • 021662c fix: use contextual arrayspec when validating / evolving codecs (#3941)
  • ad374b5 cast_value data type validation was checking the source data type instead of ...
  • f8c0c5d feat:metadata package (#3919)
  • 3ede5e8 docs: build 3.2.0 release notes (#3932)
  • 870fabd chore/3.2.0 release notes (#3927)
  • ac667c1 chore: automate more of the release process (#3896)
  • 23e9635 feat: add cast_value and scale_offset codecs (#3874)
  • 279d400 fix(storage): preserve leading slashes in FsspecStore.path (#3926)
  • Additional commits viewable in compare view

Updates numpy from 2.4.4 to 2.4.5

Release notes

Sourced from numpy's releases.

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 +
  • Matti Picus
  • Nathan Goldbaum
  • Praneeth Kodumagulla +
  • Ralf Gommers
  • RoomWithOutRoof +
  • Sebastian Berg
  • Warren Weckesser
  • div +

Pull requests merged

A total of 28 pull requests were merged for this release.

  • #31093: MAINT: Prepare 2.4.x for further development
  • #31182: TYP: fix np.shape assignability issue for python lists (#31171)
  • #31197: ENH: Return rank 0 for empty matrices in matrix_rank (#30422)
  • #31198: CI/BUG: add native jobs for s390x, fix bug in pack_inner...
  • #31199: BUG: f2py map complex_long_double to NPY_CLONGDOUBLE
  • #31205: MAINT: f2py: Stop setting re._MAXCACHE to 50.
  • #31206: BUG: fix heap buffer overflow in timedelta to string casts
  • #31207: MAINT: Rename ppc64le and s390x workflow (#31121)
  • #31208: BUG: Fix matvec/vecmat in-place aliasing (out=input produces...
  • #31209: TYP: tile: accept numpy scalars and arrays as second argument...
  • #31211: DEP: Undo deprecation for np.dtype() signature used by old pickles...
  • #31212: REV: Manual revert of float16 svml use (#31178)
  • #31222: TYP: ix_ fix for boolean and non-1d input (#31218)
  • #31329: BUG: incorrect temp elision for new-style (NEP 43) user-defined...
  • #31330: TYP: fix sliding_window_view axis parameter typing

... (truncated)

Commits
  • 26e8185 Merge pull request #31441 from charris/prepare-2.4.5
  • 573110c REL: Prepare for the NumPy 2.4.5 release.
  • be6123a Merge pull request #31426 from jorenham/backport-31425
  • a286f52 TYP: Fix DTypeLike runtime type-checker support
  • f880727 Merge pull request #31404 from charris/backport-31399
  • 626d469 Merge pull request #31402 from charris/backport-31397
  • a42bd48 Merge pull request #31401 from charris/backport-31396
  • 207ad05 TYP: _NestedSequence type parameter default to work around a mypy issue (#3...
  • 309b637 BUG: exclude pycache directories from wheels (#31397)
  • 8ded93c BUG: Avoid UB in safe_[add,sub,mul] helpers (#31396)
  • Additional commits viewable in compare view

Updates coverage from 7.13.5 to 7.14.0

Changelog

Sourced from coverage's changelog.

Version 7.14.0 — 2026-05-10

  • Feature: now when running one of the reporting commands, if there are parallel data files that need combining, they will be implicitly combined before creating the report. There is no option to avoid the combination; let us know if you have a use case that requires it. Thanks, Tim Hatch <pull 2162_>. Closes issue 1781.

  • Fix: the output from combine was too verbose, listing each file considered. Now it shows a single line with the counts of files combined, files skipped, and files with errors. The -q flag suppresses this line. The old detailed lines are available with the new --debug=combine option.

  • Fix: running a Python file through a symlink now sets the sys.path correctly, matching regular Python behavior. Fixes issue 2157_.

  • Fix: Collector.flush_data could fail with "RuntimeError: Set changed size during iteration" when a tracer in another thread added a line to the per-file set that add_lines (or add_arcs) was iterating. The values passed to CoverageData are now snapshotted via dict.copy() and set.copy(), which are atomic under the GIL. Thanks, Alex Vandiver <pull 2165_>_.

  • Fix: the soft keyword lazy is now bolded in HTML reports.

  • We are no longer testing eventlet support. Eventlet started issuing stern deprecation warnings that break our tests. Our support code is still there.

.. _issue 1781: coveragepy/coveragepy#1781 .. _issue 2157: coveragepy/coveragepy#2157 .. _pull 2162: coveragepy/coveragepy#2162 .. _pull 2165: coveragepy/coveragepy#2165

.. _changes_7-13-5:

Commits
  • 646351b docs: sample HTML for 7.14.0
  • 39cd015 docs: prep for 7.14.0
  • 649e8aa docs: thanks Alex Vandiver for #2165
  • 8cd392e fix: snapshot data in Collector.flush_data to avoid threading race (#2165)
  • c48e0ed fix: less output for combining
  • c2a3a28 docs: explain the change from #2162
  • 1cd47aa fix: implicit combine-during-report now removes the combined data files
  • 2d99fd7 feat: automatically combine coverage in report, thanks Tim Hatch (#2162)
  • 9fbdcdf fix: lazy soft keywords are bolded
  • 5de7d02 build: oops, misplaced quote
  • Additional commits viewable in compare view

Updates ruff from 0.15.12 to 0.15.13

Release notes

Sourced from ruff's releases.

0.15.13

Release Notes

Released on 2026-05-14.

Preview features

  • Add a rule to flag lazy imports that are eagerly evaluated (#25016)
  • [pylint] Standardize diagnostic message (PLR0914, PLR0917) (#24996)

Bug fixes

  • Fix F811 false positive for class methods (#24933)
  • Fix setting selection for multi-folder workspace (#24819)
  • [eradicate] Fix false positive for lines with leading whitespace (ERA001) (#25122)
  • [flake8-pyi] Fix false positive for f-string debug specifier (PYI016) (#24098)

Rule changes

  • Always include panic payload in panic diagnostic message (#24873)
  • Restrict PYI034 for in-place operations to enclosing class (#24511)
  • Improve error message for parameters that are declared global (#24902)
  • Update known stdlib (#25103)

Performance

  • [isort] Avoid constructing glob::Patterns for literal known modules (#25123)

CLI

  • Add TOML examples to --config help text (#25013)
  • Colorize ruff check 'All checks passed' (#25085)

Configuration

  • Increase max allowed value of line-length setting (#24962)

Documentation

  • Add D203 to rules that conflict with the formatter (#25044)
  • Clarify COM819 and formatter interaction (#25045)
  • Clarify that NotImplemented is a value, not an exception (F901) (#25054)
  • Update number of lint rules supported (#24942)

Other changes

  • Simplify the playground's markdown template (#24924)

Contributors

... (truncated)

Changelog

Sourced from ruff's changelog.

0.15.13

Released on 2026-05-14.

Preview features

  • Add a rule to flag lazy imports that are eagerly evaluated (#25016)
  • [pylint] Standardize diagnostic message (PLR0914, PLR0917) (#24996)

Bug fixes

  • Fix F811 false positive for class methods (#24933)
  • Fix setting selection for multi-folder workspace (#24819)
  • [eradicate] Fix false positive for lines with leading whitespace (ERA001) (#25122)
  • [flake8-pyi] Fix false positive for f-string debug specifier (PYI016) (#24098)

Rule changes

  • Always include panic payload in panic diagnostic message (#24873)
  • Restrict PYI034 for in-place operations to enclosing class (#24511)
  • Improve error message for parameters that are declared global (#24902)
  • Update known stdlib (#25103)

Performance

  • [isort] Avoid constructing glob::Patterns for literal known modules (#25123)

CLI

  • Add TOML examples to --config help text (#25013)
  • Colorize ruff check 'All checks passed' (#25085)

Configuration

  • Increase max allowed value of line-length setting (#24962)

Documentation

  • Add D203 to rules that conflict with the formatter (#25044)
  • Clarify COM819 and formatter interaction (#25045)
  • Clarify that NotImplemented is a value, not an exception (F901) (#25054)
  • Update number of lint rules supported (#24942)

Other changes

  • Simplify the playground's markdown template (#24924)

Contributors

... (truncated)

Commits
  • 2afb467 Bump 0.15.13 (#25157)
  • 3008796 [ty] classify TypeVar semantic tokens as type parameters (#24891)
  • 79470e3 [isort] Avoid constructing glob::Patterns for literal known modules (#25123)
  • 2522549 Remove shellcheck from prek (#25154)
  • 7db7170 [ty] Support TypedDict key completions in incomplete, anonymous contexts (#25...
  • bb3dd53 [ty] Run full iteration analysis on narrowed typevars (#25143)
  • 828cdb7 [ty] Isolate file-watching test environment (#25151)
  • 89e1d86 [ty] Preserve TypedDict keys through dict unpacking (#24523)
  • 86f3064 [ty] Avoid accessing args[0] for static_assert (#25149)
  • ed819f9 [ty] Treat custom enum __new__ values as dynamic (#25136)
  • Additional commits viewable in compare view

Updates mypy from 1.20.2 to 2.1.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Mypy 2.1

We’ve just uploaded mypy 2.1.0 to the Python Package Index (PyPI). Mypy is a static type checker for Python. This release includes new features, performance improvements and bug fixes. You can install it as follows:

python3 -m pip install -U mypy

You can read the full documentation for this release on Read the Docs.

librt.vecs: Fast Growable Array Type for Mypyc

The new librt.vecs module provides an efficient growable array type vec that is optimized for mypyc use. It provides fast, packed arrays with integer and floating point value types, which can be several times faster than list, and tens of times faster than array.array in code compiled using mypyc. It also supports nested vec objects and non-value-type items, such as vec[vec[str]].

Refer to the documentation for the details.

Contributed by Jukka Lehtosalo.

librt.random: Fast Pseudo-Random Number Generation

The new librt.random module provides fast pseudo-random number generation that is optimized for code compiled using mypyc. It can be 3x to 10x faster than the stdlib random module in compiled code.

Refer to the documentation for the details.

Contributed by Jukka Lehtosalo (PR 21433).

Mypyc Improvements

  • Make compilation order with multiple files consistent (Piotr Sawicki, PR 21419)
  • Fix crash on accessing StopAsyncIteration (Piotr Sawicki, PR 21406)
  • Fix incremental compilation with separate flag (Vaggelis Danias, PR 21299)

Fixes to Crashes

  • Fix crash on partial type with --allow-redefinition and global declaration (Jukka Lehtosalo, PR 21428)
  • Fix broken awaitable generator patching (Ivan Levkivskyi, PR 21435)

Changes to Messages

... (truncated)

Commits

Updates types-pyyaml from 6.0.12.20260408 to 6.0.12.20260518

Commits

Updates types-shapely from 2.1.0.20260408 to 2.1.0.20260518

Commits

Updates zensical from 0.0.37 to 0.0.42

Release notes

Sourced from zensical's releases.

0.0.42

Summary

This version includes a number of bug fixes and refactorings to improve the stability and accuracy of link validation, and fixes a reload loop when the custom_dir, which is auto-watched, is explicitly added to watch. Moreover, GLightbox is now only downloaded when needed, which fixes an issue when using Zensical in air-gapped environments.

Changelog

Bug fixes

  • 6b54e14 ui – update ui to v0.0.18
  • cdee1e8 zensical – disabling link validation doesn't disable link and reference collection (#659)
  • 4355dad compat – harden link validation for files with CRLF line endings
  • a418c6b compat – link validation doesn't ignore fenced code blocks when \r is present
  • b31dd14 compat – $ at end of line breaks link validation (#659)
  • 17c67a2 compat – remove abbreviations from table of contents (#669)
  • 6eb2f4d compat – reserve theme name zensical
  • a5a8641 zensical – only wait for config update after a first successful build (#670)
  • 8207554 compat – don't consider [] and [][] link references (#663)
  • c338b27 compat – two backticks with no closing run trip up link parser (#663, #665)
  • d707aa9 compat – prevent reload loop by de-duplicating watched theme files (#655)

Refactorings

  • 53f593f compat – avoid mutating configurations list
  • a77087a compat – reorganize config module

0.0.41

Summary

This version adds support for integrating tabular data as Markdown tables, covering the functionality of the mkdocs-table-reader-plugin, as well as the watch option to automatically rebuild on changes in unmonitored files. Table reading is implemented as part of macros, which we shipped in 0.0.40. You can now embed CSV and other file formats with:

{{ read_csv("data/team.csv") }}

Additionally, the stability of link validation has been drastically improved, reducing the rate of false positives. We're working on support for validating links using autorefs, which we'll provide in one of the next versions.

Changelog

Features

  • d24ea24 compat – support table reader functionality

... (truncated)

Commits
  • 7a141c5 chore: release v0.0.42
  • 6b54e14 fix: update ui to v0.0.18
  • cdee1e8 fix: disabling link validation doesn't disable link and reference collection ...
  • 7a5d97a Merge pull request #680 from zensical/fix/validation-edge-cases
  • 4355dad fix: harden link validation for files with CRLF line endings
  • a418c6b fix: link validation doesn't ignore fenced code blocks when \r is present
  • b31dd14 fix: $ at end of line breaks link validation (#659)
  • 17c67a2 fix: remove abbreviations from table of contents (#669)
  • 6eb2f4d fix: reserve theme name zensical
  • a5a8641 fix: only wait for config update after a first successful build (#670)
  • Additional commits viewable in compare view

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@dependabot
Bump the package-updates group across 1 directory with 9 updates
0c33914 
Bumps the package-updates group with 9 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [pydantic](https://github.com/pydantic/pydantic) | `2.13.3` | `2.13.4` |
| [zarr](https://github.com/zarr-developers/zarr-python) | `3.1.6` | `3.2.1` |
| [numpy](https://github.com/numpy/numpy) | `2.4.4` | `2.4.5` |
| [coverage](https://github.com/coveragepy/coveragepy) | `7.13.5` | `7.14.0` |
| [ruff](https://github.com/astral-sh/ruff) | `0.15.12` | `0.15.13` |
| [mypy](https://github.com/python/mypy) | `1.20.2` | `2.1.0` |
| [types-pyyaml](https://github.com/python/typeshed) | `6.0.12.20260408` | `6.0.12.20260518` |
| [types-shapely](https://github.com/python/typeshed) | `2.1.0.20260408` | `2.1.0.20260518` |
| [zensical](https://github.com/zensical/zensical) | `0.0.37` | `0.0.42` |



Updates `pydantic` from 2.13.3 to 2.13.4
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/v2.13.4/HISTORY.md)
- [Commits](pydantic/pydantic@v2.13.3...v2.13.4)

Updates `zarr` from 3.1.6 to 3.2.1
- [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@v3.1.6...v3.2.1)

Updates `numpy` from 2.4.4 to 2.4.5
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.4.4...v2.4.5)

Updates `coverage` from 7.13.5 to 7.14.0
- [Release notes](https://github.com/coveragepy/coveragepy/releases)
- [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.13.5...7.14.0)

Updates `ruff` from 0.15.12 to 0.15.13
- [Release notes](https://github.com/astral-sh/ruff/releases)
- [Changelog](https://github.com/astral-sh/ruff/blob/main/CHANGELOG.md)
- [Commits](astral-sh/ruff@0.15.12...0.15.13)

Updates `mypy` from 1.20.2 to 2.1.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.20.2...v2.1.0)

Updates `types-pyyaml` from 6.0.12.20260408 to 6.0.12.20260518
- [Commits](https://github.com/python/typeshed/commits)

Updates `types-shapely` from 2.1.0.20260408 to 2.1.0.20260518
- [Commits](https://github.com/python/typeshed/commits)

Updates `zensical` from 0.0.37 to 0.0.42
- [Release notes](https://github.com/zensical/zensical/releases)
- [Commits](zensical/zensical@v0.0.37...v0.0.42)

---
updated-dependencies:
- dependency-name: pydantic
  dependency-version: 2.13.4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: package-updates
- dependency-name: zarr
  dependency-version: 3.2.1
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: package-updates
- dependency-name: numpy
  dependency-version: 2.4.5
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: package-updates
- dependency-name: coverage
  dependency-version: 7.14.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: package-updates
- dependency-name: ruff
  dependency-version: 0.15.13
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: package-updates
- dependency-name: mypy
  dependency-version: 2.1.0
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: package-updates
- dependency-name: types-pyyaml
  dependency-version: 6.0.12.20260518
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: package-updates
- dependency-name: types-shapely
  dependency-version: 2.1.0.20260518
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: package-updates
- dependency-name: zensical
  dependency-version: 0.0.42
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: package-updates
...

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@dependabot dependabot Bot added dependencies Pull requests that update a dependency major Concerns a bug with major severity python Pull requests that update python code labels May 18, 2026
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dependencies Pull requests that update a dependency major Concerns a bug with major severity python Pull requests that update python code

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