chore(deps): bump the python-dependencies group with 7 updates

[dependabot]

Bumps the python-dependencies group with 7 updates:

Package	From	To
numcodecs	0.16.5	0.17.0
fsspec	2026.7.0	2026.9.0
hypothesis	6.168.0	6.168.1
uv	0.12.15	0.12.18
botocore	1.43.0	1.43.101
s3fs	2026.7.0	2026.9.0
mkdocstrings-python	2.0.8	2.0.9

Updates numcodecs from 0.16.5 to 0.17.0

Release notes

Sourced from numcodecs's releases.

v0.17.0

What's Changed

• Don't report coverage on test directory by @​maxrjones in zarr-developers/numcodecs#803
• Bump ruff and update pre-commit legacy alias by @​DimitriPapadopoulos in zarr-developers/numcodecs#791
• update macos intel runner by @​ianhi in zarr-developers/numcodecs#819
• Exclude tests dir from code coverage by @​maxrjones in zarr-developers/numcodecs#823
• Suppress NumPy 2.4 VisibleDeprecationWarning for align=0 in test by @​maxrjones in zarr-developers/numcodecs#822
• Move tests out of installable distribution by @​maxrjones in zarr-developers/numcodecs#829
• Update README to markdown with working badges by @​maxrjones in zarr-developers/numcodecs#827
• Convert RST docs to markdown by @​maxrjones in zarr-developers/numcodecs#830
• Migrate build system from setuptools to meson-python by @​maxrjones in zarr-developers/numcodecs#826
• Drop Python 3.11 and NumPy <2.0 per SPEC-0 by @​maxrjones in zarr-developers/numcodecs#834
• Bump readthedocs build image by @​maxrjones in zarr-developers/numcodecs#833
• Fix typos by @​DimitriPapadopoulos in zarr-developers/numcodecs#832
• CI: Fix Meson mixup between Conda and system Python headers by @​DimitriPapadopoulos in zarr-developers/numcodecs#839
• zarr-python does not depend on crc32c anymore by @​DimitriPapadopoulos in zarr-developers/numcodecs#840
• chore: pin pytest and dedupe dependency groups by @​d-v-b in zarr-developers/numcodecs#844
• Skip test_pyzstd when pyzstd cannot be imported by @​d-v-b in zarr-developers/numcodecs#845
• update pcodec by @​mwlon in zarr-developers/numcodecs#817
• Add pytest-cov to dev dependency group by @​d-v-b in zarr-developers/numcodecs#846
• Bump GitHub actions by @​DimitriPapadopoulos in zarr-developers/numcodecs#838
• Add free-threaded CPython (3.14t) support by @​kumaraditya303 in zarr-developers/numcodecs#858
• CI: set an explicit python-version for test-crc32c and test-zarr by @​glaziermag in zarr-developers/numcodecs#856

New Contributors

• @​kumaraditya303 made their first contribution in zarr-developers/numcodecs#858
• @​glaziermag made their first contribution in zarr-developers/numcodecs#856

Full Changelog: zarr-developers/numcodecs@v0.16.5...v0.17.0

Changelog

Sourced from numcodecs's changelog.

0.17.0

Breaking changes

• The minimum supported Python version is now 3.12, and the minimum supported NumPy version is now 2.0, following SPEC-0. By {user}Max Jones <maxrjones>, {issue}834

• Tests are no longer installed as part of the numcodecs package. They have moved from numcodecs/tests/ to a top-level tests/ directory, so numcodecs.tests (including numcodecs.tests.common) can no longer be imported from an installed copy of numcodecs. Downstream packages that reused the test helpers should vendor the helpers they need. The tests and the fixture/ data are still shipped in the source distribution, so downstream packagers can continue to run the suite from an unpacked sdist. By {user}Max Jones <maxrjones>, {issue}829

• The DISABLE_NUMCODECS_CEXT environment variable is no longer supported, as a consequence of the migration to meson-python (see Maintenance below). By {user}Max Jones <maxrjones>, {issue}826

• The pcodec optional dependency now requires pcodec>=1,<2, up from pcodec>=0.3,<0.4. By {user}Martin Loncaric <mwlon>, {issue}817

• Two behavioral changes in numcodecs.blosc accompany the free-threading work (see Enhancements below): the undocumented numcodecs.blosc.get_mutex function is removed, replaced by a private threading.Lock that also guards set_nthreads, _init, _destroy and the global-context decompression path; and on platforms where multiprocessing.Lock() raises (no sem_open), Blosc's internal threads are now used from the main thread instead of always falling back to the single-threaded context functions. By {user}Kumar Aditya <kumaraditya303>, {issue}858

Deprecations

• PCodec(delta_spec="none") is deprecated in favor of PCodec(delta_spec="no_op") and now emits a DeprecationWarning. The "none" spelling still works and produces identical output, but it will be removed in a future version. By {user}Martin Loncaric <mwlon>, {issue}817

Enhancements

• Add support for free-threaded CPython (3.14t). All Cython extensions are declared freethreading_compatible, so importing numcodecs no longer re-enables the GIL; free-threaded wheels are now built and 3.14t is part of the test matrix. Building from source now requires Cython 3.1 or newer. See Breaking changes above for the accompanying numcodecs.blosc changes. By {user}Kumar Aditya <kumaraditya303>, {issue}858

... (truncated)

Commits

• fcc79a1 docs: add release notes for 0.17.0 (#859)
• 9d93931 CI: set an explicit python-version for test-crc32c and test-zarr (#856)
• eff52c8 Add free-threaded CPython (3.14t) support (#858)
• 82c3635 Bump GitHub actions (#838)
• e813354 Add pytest-cov to dev dependency group (#846)
• f3d6187 update pcodec (#817)
• 53e5157 Skip test_pyzstd when pyzstd cannot be imported (#845)
• 99566f0 chore: pin pytest and dedupe dependency groups (#844)
• 2a0b67f zarr-python does not depend on crc32c anymore (#840)
• fa92ee7 CI: Fix Meson mixup between Conda and system Python headers (#839)
• Additional commits viewable in compare view

Updates fsspec from 2026.7.0 to 2026.9.0

Commits

• 0f76baa changelog (#2166)
• 695f831 Add age-based cleanup for simplecache (#2118)
• 42aa468 Mirror readinto from the pyarrow stream onto ArrowFile (#2111)
• 4a4e6ae Make the SFTP host key policy configurable (#2126)
• a0ce6db Normalize paths in AsyncFileSystemWrapper like the wrapped filesystem (#2159)
• c5fea6d Fix cat_ranges on whole-file caches after #2154 (#2163)
• 9efb18b Patch HAS_CPYTHON_API where _fast_slice reads it (#2164)
• 27bcd35 feat(AdaptiveReadaheadCache): introducing a new cache-type adaptive (#2093)
• a681aca Ignore a leading slash in TarFileSystem paths (#2148)
• 57c55f8 Make names relative in DirFileSystem.walk(detail=True) (#2160)
• Additional commits viewable in compare view

Updates hypothesis from 6.168.0 to 6.168.1

Commits

• 6cee8ce Bump hypothesis version to 6.168.1 and update changelog
• d97fdf3 Merge pull request #4879 from Liam-DeVoe/more-wheels
• 37da03c publish wheels for s390x and i686+musl
• See full diff in compare view

Updates uv from 0.12.15 to 0.12.18

Release notes

Sourced from uv's releases.

0.12.18

Release Notes

Released on 2026-09-22.

This release addresses GHSA-2cv4-cqwr-gwf7, which is a path traversal weakness during wheel installation on Windows. No other platforms are affected by this advisory.

Enhancements

• Add --output-format json to uv pip install and uv pip sync, including for --dry-run and --check (#21893)
• Add --check to uv pip install and uv pip sync to report planned changes without modifying the environment (#21844)
• Identify failures from get_requires_for_build_* hooks correctly in build errors (#21881)

Preview features

• Validate build requirements for uv build --no-build-isolation with --preview-features build-dependency-check; use --skip-dependency-check to opt out (#21880)

Performance

• Speed up uv_build editable wheel creation by omitting compression from temporary wheels (#21918)

Bug fixes

• Select package versions with wheels compatible with each Python resolution fork, correctly interpreting generic and stable-ABI wheel tags (#21835, #21836)
• Restore project, script, and lock files when uv add, uv remove, or uv version fails or is interrupted (#21860, #21856)
• Use configured dependency-metadata when checking whether installed requirements are satisfied (#21843)
• Reject archive entries that normalize to absolute Windows paths (#21923)
• Recognize distribution filenames and archive extensions when URL fragments contain ? (#21920)
• Generate correctly lowercased platform tags for BSD and Haiku releases (#21853)
• Avoid rebuilding a Windows relative path into an absolute form (#21923)

Install uv 0.12.18

Install prebuilt binaries via shell script

curl --proto '=https' --tlsv1.2 -LsSf https://releases.astral.sh/github/uv/releases/download/0.12.18/uv-installer.sh | sh

Install prebuilt binaries via powershell script

powershell -ExecutionPolicy Bypass -c "irm https://releases.astral.sh/github/uv/releases/download/0.12.18/uv-installer.ps1 | iex"

Download uv 0.12.18

File	Platform	Checksum
uv-aarch64-apple-darwin.tar.gz	Apple Silicon macOS	checksum

... (truncated)

Changelog

Sourced from uv's changelog.

0.12.18

Released on 2026-09-22.

This release addresses GHSA-2cv4-cqwr-gwf7, which is a path traversal weakness during wheel installation on Windows. No other platforms are affected by this advisory.

Enhancements

• Add --output-format json to uv pip install and uv pip sync, including for --dry-run and --check (#21893)
• Add --check to uv pip install and uv pip sync to report planned changes without modifying the environment (#21844)
• Identify failures from get_requires_for_build_* hooks correctly in build errors (#21881)

Preview features

• Validate build requirements for uv build --no-build-isolation with --preview-features build-dependency-check; use --skip-dependency-check to opt out (#21880)

Performance

• Speed up uv_build editable wheel creation by omitting compression from temporary wheels (#21918)

Bug fixes

• Select package versions with wheels compatible with each Python resolution fork, correctly interpreting generic and stable-ABI wheel tags (#21835, #21836)
• Restore project, script, and lock files when uv add, uv remove, or uv version fails or is interrupted (#21860, #21856)
• Use configured dependency-metadata when checking whether installed requirements are satisfied (#21843)
• Reject archive entries that normalize to absolute Windows paths (#21923)
• Recognize distribution filenames and archive extensions when URL fragments contain ? (#21920)
• Generate correctly lowercased platform tags for BSD and Haiku releases (#21853)
• Avoid rebuilding a Windows relative path into an absolute form (#21923)

0.12.17

Released on 2026-09-18.

Enhancements

• Reject unsupported Git archive paths in lockfiles with a clear error instead of panicking during frozen exports (#21780)

Preview features

• Set minimum glibc and musl versions that universal resolutions must support with minimum-libc-version (#21651)
• Reject pylock.toml files whose wheel filenames do not match their declared package names or versions (#20746)
• Keep uv workspace metadata read-only unless --sync is provided (#21821)
• Apply uv check lock modes when retrieving workspace metadata (#21821)

Performance

• Speed up builds with many exclusion patterns by avoiding quadratic deduplication (#21650)
• Reduce resolver allocations when deduplicating package and distribution requests (#21810)

... (truncated)

Commits

• 01cb90c Hush some PEP 440 version warnings when dry-running Docker pushes (#21929)
• 9937fa2 Check remote wheel metadata prefetch ranges (#21919)
• 0f03963 Skip loading Python download metadata when listing installed interpreters (#2...
• 6d1b266 filter severity: labels in pr promotion automation (#21926)
• d269839 Bump version to 0.12.18 (#21924)
• 6716964 Avoid rebuilding a path into an absolute form (#21923)
• 4dd39e8 Use uncompressed editable wheels (#21918)
• 0c8da51 Add JSON output for uv pip install and uv pip sync (#21893)
• 0714322 Fix fragment boundaries in UrlString::base_str (#21920)
• 8460ef5 Share URL userinfo redaction (#21912)
• Additional commits viewable in compare view

Updates botocore from 1.43.0 to 1.43.101

Commits

• 93a35be Merge branch 'release-1.43.101'
• a9ac948 Bumping version to 1.43.101
• 42ec6e0 Update endpoints model
• a07e400 Update to latest models
• 3fe1b11 Track S3 region redirect feature id (#3804)
• 22c55b3 Merge branch 'release-1.43.100'
• b770c0d Merge branch 'release-1.43.100' into develop
• a5b65ca Bumping version to 1.43.100
• c150479 Update to latest models
• 85e265b Merge branch 'release-1.43.99'
• Additional commits viewable in compare view

Updates s3fs from 2026.7.0 to 2026.9.0

Commits

• 62f45e6 changelog (#1044)
• 85a6ec5 Retry transient errors on each listing page (#1042)
• 359cf57 Preserve coroutine errors without a response local (#1041)
• 6d5b34b version-guard and strict the big exclusive-write xfails, stale since moto 5.1...
• d3dd9b7 Fix requester pays propogation and bug with combining head_bucket and `req...
• See full diff in compare view

Updates mkdocstrings-python from 2.0.8 to 2.0.9

Release notes

Sourced from mkdocstrings-python's releases.

2.0.9

2.0.9 - 2026-09-22

Compare with 2.0.8

Bug Fixes

• Improve inventory object types (incorrectly called roles in mkdocstrings) (d754326 by Timothée Mazzucotelli). Issue-339, PR-340
• Expand relative cross-references against the object the docstring was written on (a9a4ca3 by Dev M). Issue-341, PR-342

Performance Improvements

• Small performance improvement when getting aliases and formatting/highlighting signatures (2263163 by Timothée Mazzucotelli).

Changelog

Sourced from mkdocstrings-python's changelog.

2.0.9 - 2026-09-22

Compare with 2.0.8

Bug Fixes

• Improve inventory object types (incorrectly called roles in mkdocstrings) (d754326 by Timothée Mazzucotelli). Issue-339, PR-340
• Expand relative cross-references against the object the docstring was written on (a9a4ca3 by Dev M). Issue-341, PR-342

Performance Improvements

• Small performance improvement when getting aliases and formatting/highlighting signatures (2263163 by Timothée Mazzucotelli).

Commits

• c888dc2 chore: Prepare release 2.0.9
• 2263163 perf: Small performance improvement when getting aliases and formatting/highl...
• d754326 fix: Improve inventory object types (incorrectly called roles in mkdocstrings)
• a9a4ca3 fix: Expand relative cross-references against the object the docstring was wr...
• See full diff in compare view

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.47%. Comparing base (d18fb50) to head (86839b7).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4461   +/-   ##
=======================================
  Coverage   94.47%   94.47%           
=======================================
  Files          93       93           
  Lines       13241    13241           
=======================================
  Hits        12510    12510           
  Misses        731      731           

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