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chore(deps): bump the python-dependencies group with 6 updates#4151
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Bumps the python-dependencies group with 6 updates:

Package From To
numpy 2.5.0 2.5.1
coverage 7.14.3 7.15.0
hypothesis 6.155.7 6.156.4
uv 0.11.26 0.11.28
markdown-exec[ansi] 1.12.1 1.12.3
mypy 2.1.0 2.2.0

Updates numpy from 2.5.0 to 2.5.1

Release notes

Sourced from numpy's releases.

v2.5.1 (July 4, 2026)

NumPy 2.5.1 Release Notes

The NumPy 2.5.1 is a patch release that fixes bugs discovered after the 2.5.0 release. The most noticeable is the fix is to the numpy datetime cython API which should allow downstream to support NumPy versions older than 2.5. Preparation for Python 3.15 continues along with typing improvements.

This release supports Python versions 3.12-3.14

Changes

  • The minimum supported GCC version has been updated from 9.3.0 to 10.3.0

    (gh-31843)

Contributors

A total of 10 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Adhyan Gupta +
  • Ankit Ahlawat
  • Charles Harris
  • Iason Krommydas
  • Joren Hammudoglu
  • Kumar Aditya
  • Nathan Goldbaum
  • Sebastian Berg
  • Ties Jan Hefting +
  • Vineet Kumar

Pull requests merged

A total of 20 pull requests were merged for this release.

  • #31707: MAINT: Prepare 2.5.x for further development
  • #31721: CI: fix new cython-lint errors (#31711)
  • #31723: MAINT: Update meson to match main
  • #31729: TST: use setup-sde instead of curl to get SDE binaries (#31727)
  • #31829: BUG: Relax finfo to be easier accessible for all user dtypes...
  • #31831: TYP: Fix flatiter.__next__ return type for object_ and...
  • #31832: BUG: avoid deadlocks using NpyString API (#31682)
  • #31833: BUG: fix out array leak in reduceat and accumulate when dtype...
  • #31835: BUG: fix numpy datetime cython APIs to be compatible with older...
  • #31836: TYP: Fix incorrect dtype inference of asarray([]) (#31732)
  • #31837: TYP: Fix np.ma.masked_array 2.5.0 regression
  • #31838: FIX: Refactor error handling in array_setstate to prevent typecode...
  • #31839: TST: xfail multithreaded BLAS test more generously
  • #31840: MAINT: Rename subroutine for crackfortran tests

... (truncated)

Commits
  • 5e1d03f Merge pull request #31863 from charris/prepare-2.5.1
  • ad0b66b REL: Prepare for the NumPy 2.5.1 release.
  • 9df8516 Merge pull request #31858 from charris/backport-31688
  • 4dee265 Merge pull request #31857 from charris/backport-31775
  • dc8d553 Merge pull request #31856 from charris/backport-31846
  • 67cb4a8 fix:Signed integer overflow in datetime.c (#31688)
  • baa2589 TST: Clean up imports, formatting, and assertions
  • 2fe5ba4 TEST: Refactor tests to use np.testing.assert_raises_regex per review
  • bb46581 MAINT: Remove deprecated Python recursion fix
  • 8f34214 MAINT: Move SeedSequence recursion guard to C-layer and add tests
  • Additional commits viewable in compare view

Updates coverage from 7.14.3 to 7.15.0

Release notes

Sourced from coverage's releases.

7.15.0

Version 7.15.0 — 2026-07-02

  • Since 7.14.0, reporting commands implicitly combine parallel data files. Now those commands have a new option --keep-combined to retain the data files after combining them instead of the default, which is to delete them. Finishes issue 2198.
  • Fix: the LCOV report would incorrectly count excluded functions as uncovered, as described in issue 2205. This is now fixed thanks to Martin Kuntz Jacobsen.
  • When running your program, coverage now correctly sets yourmodule.__spec__.loader as strongly recommended, avoiding the deprecation warning described in issue 2208. Thanks, A5rocks.
  • Fix: with Python 3.10, running with the -I (isolated mode) option didn’t correctly omit the current directory from the module search path, as described in issue 2103. That is now fixed thanks to Ilia Sorokin.

➡️  PyPI page: coverage 7.15.0. :arrow_right:  To install: python3 -m pip install coverage==7.15.0

Changelog

Sourced from coverage's changelog.

Version 7.15.0 — 2026-07-02

  • Since 7.14.0, reporting commands implicitly combine parallel data files. Now those commands have a new option --keep-combined to retain the data files after combining them instead of the default, which is to delete them. Finishes issue 2198_.

  • Fix: the LCOV report would incorrectly count excluded functions as uncovered, as described in issue 2205. This is now fixed thanks to Martin Kuntz Jacobsen <pull 2206_>.

  • When running your program, coverage now correctly sets yourmodule.__spec__.loader as strongly recommended <--loader--_>, avoiding the deprecation warning described in issue 2208. Thanks, A5rocks <pull 2209_>_.

  • Fix: with Python 3.10, running with the -I (isolated mode) option didn't correctly omit the current directory from the module search path, as described in issue 2103. That is now fixed thanks to Ilia Sorokin <pull 2211_>.

.. --loader--: https://docs.python.org/3/reference/datamodel.html#module.__loader_ .. _issue 2103: coveragepy/coveragepy#2103 .. _issue 2198: coveragepy/coveragepy#2198 .. _issue 2205: coveragepy/coveragepy#2205 .. _pull 2206: coveragepy/coveragepy#2206 .. _issue 2208: coveragepy/coveragepy#2208 .. _pull 2209: coveragepy/coveragepy#2209 .. _pull 2211: coveragepy/coveragepy#2211

.. _changes_7-14-3:

Commits
  • c8c8020 docs: sample HTML for 7.15.0
  • ae19db1 docs: prep for 7.15.0
  • 17b45a1 docs: --keep-combined in the man page
  • 6f9fa1e fix: preserve isolated sys.path on Python 3.10 (#2211)
  • 787af5f chore: bump actions/checkout in the action-dependencies group (#2210)
  • 1ed3998 fix: start attaching the loader on __spec__ #2208 (#2209)
  • 1ab1122 docs: remove stray comma
  • f24a91f feat: --keep-combined for reporting commands. #2198
  • 5e70751 test: canonicalize mock calls in test_cmdline to reduce diff noise
  • 65979cc fix: skip excluded functions in LCOV function totals (#2206)
  • Additional commits viewable in compare view

Updates hypothesis from 6.155.7 to 6.156.4

Commits
  • 8683661 Bump hypothesis version to 6.156.4 and update changelog
  • d55de5a Merge pull request #4793 from Liam-DeVoe/abi3-wheels
  • 81be9b1 Merge pull request #4792 from HypothesisWorks/fix-version-import
  • 503f86d ship abi3 wheels
  • 60c92c0 fix docs build in github release
  • a6ca790 Bump hypothesis version to 6.156.3 and update changelog
  • 3a49f9e Merge pull request #4786 from Liam-DeVoe/fix-release
  • 3ea2aef Bump hypothesis version to 6.156.2 and update changelog
  • 6bdf847 Merge pull request #4787 from dylan-bakr/patch-github-artifact-database-keyerror
  • 8edffba simplify comment
  • Additional commits viewable in compare view

Updates uv from 0.11.26 to 0.11.28

Release notes

Sourced from uv's releases.

0.11.28

Release Notes

Released on 2026-07-07.

Security

This release updates our ZIP library, astral-async-zip, to v0.0.20, which includes 15 changes that harden our ZIP handling against parser differentials. uv may reject ZIP archives with malformed or ambiguous content that were previously accepted.

See the upstream commits for a full list of changes.

Python

  • Upgrade GraalPy to 25.1.3 (#20069)

Enhancements

  • Improve trace logs for unexpected error chains (#20220)
  • Move lockfile update guidance to a hint (#20219)
  • Preserve indentation for multiline error causes (#20156)
  • Render user errors with their cause chains (#20217)
  • Route final command errors through the printer to respect -q and -qq (#20163)
  • Use standard rendering for uv build errors (#20159)
  • Use standard rendering for tool requirement errors (#20160)

Performance

  • Only compile bytecode for installed distributions in uv pip install (#19914)
  • Avoid allocating URL-safe Git revisions (#20194)
  • Avoid allocating canonical Python request strings (#20193)
  • Avoid allocating custom Astral mirror URLs (#20204)
  • Avoid allocating expanded compatibility tags (#20190)
  • Avoid allocating shell strings that need no escaping (#20196)
  • Avoid allocating static ABI descriptions (#20201)
  • Avoid allocating static Windows executable names (#20200)
  • Avoid allocating static dependency table names (#20199)
  • Avoid allocating static platform triple components (#20195)
  • Avoid allocating static resolver report labels (#20198)
  • Avoid allocating static unavailable-version messages (#20197)
  • Avoid allocating unchanged Python download architectures (#20202)
  • Avoid allocating unchanged paths during case normalization (#20203)
  • Avoid allocations when expanding group conflicts (#20211)
  • Avoid allocations when formatting requirements (#20206)
  • Avoid cloning credential lookup services (#20210)
  • Avoid cloning dry-run distributions (#20209)
  • Avoid cloning owned dependency metadata (#20212)
  • Avoid redundant direct URL clones (#20207)
  • Create metadata version errors lazily (#20205)
  • Optimize expanded tag compatibility checks (#20171)
  • Optimize parsing of single-digit three-part versions (#20118)

... (truncated)

Changelog

Sourced from uv's changelog.

0.11.28

Released on 2026-07-07.

Security

This release updates our ZIP library, astral-async-zip, to v0.0.20, which includes 15 changes that harden our ZIP handling against parser differentials. uv may reject ZIP archives with malformed or ambiguous content that were previously accepted.

See the upstream commits for a full list of changes.

Python

  • Upgrade GraalPy to 25.1.3 (#20069)

Enhancements

  • Improve trace logs for unexpected error chains (#20220)
  • Move lockfile update guidance to a hint (#20219)
  • Preserve indentation for multiline error causes (#20156)
  • Render user errors with their cause chains (#20217)
  • Route final command errors through the printer to respect -q and -qq (#20163)
  • Use standard rendering for uv build errors (#20159)
  • Use standard rendering for tool requirement errors (#20160)

Performance

  • Only compile bytecode for installed distributions in uv pip install (#19914)
  • Avoid allocating URL-safe Git revisions (#20194)
  • Avoid allocating canonical Python request strings (#20193)
  • Avoid allocating custom Astral mirror URLs (#20204)
  • Avoid allocating expanded compatibility tags (#20190)
  • Avoid allocating shell strings that need no escaping (#20196)
  • Avoid allocating static ABI descriptions (#20201)
  • Avoid allocating static Windows executable names (#20200)
  • Avoid allocating static dependency table names (#20199)
  • Avoid allocating static platform triple components (#20195)
  • Avoid allocating static resolver report labels (#20198)
  • Avoid allocating static unavailable-version messages (#20197)
  • Avoid allocating unchanged Python download architectures (#20202)
  • Avoid allocating unchanged paths during case normalization (#20203)
  • Avoid allocations when expanding group conflicts (#20211)
  • Avoid allocations when formatting requirements (#20206)
  • Avoid cloning credential lookup services (#20210)
  • Avoid cloning dry-run distributions (#20209)
  • Avoid cloning owned dependency metadata (#20212)
  • Avoid redundant direct URL clones (#20207)
  • Create metadata version errors lazily (#20205)
  • Optimize expanded tag compatibility checks (#20171)
  • Optimize parsing of single-digit three-part versions (#20118)

... (truncated)

Commits

Updates markdown-exec[ansi] from 1.12.1 to 1.12.3

Release notes

Sourced from markdown-exec[ansi]'s releases.

1.12.3

1.12.3 - 2026-07-07

Compare with 1.12.2

Bug Fixes

  • Provide Pyodide options to Zensical (abcb044 by Timothée Mazzucotelli). Issue-100

Code Refactoring

  • Rename material-block source display option to block (2cefa97 by Timothée Mazzucotelli).
  • Update Pyodide hardcoded version to 314.0.2 (eef2661 by Timothée Mazzucotelli).

1.12.2

1.12.2 - 2026-07-05

Compare with 1.12.1

Code Refactoring

  • Better integrate with Zensical (e4f60c1 by Timothée Mazzucotelli). PR-99
Changelog

Sourced from markdown-exec[ansi]'s changelog.

1.12.3 - 2026-07-07

Compare with 1.12.2

Bug Fixes

  • Provide Pyodide options to Zensical (abcb044 by Timothée Mazzucotelli). Issue-100

Code Refactoring

  • Rename material-block source display option to block (2cefa97 by Timothée Mazzucotelli).
  • Update Pyodide hardcoded version to 314.0.2 (eef2661 by Timothée Mazzucotelli).

1.12.2 - 2026-07-05

Compare with 1.12.1

Code Refactoring

  • Better integrate with Zensical (e4f60c1 by Timothée Mazzucotelli). PR-99
Commits
  • c14e4db chore: Prepare release 1.12.3
  • 8cf25c4 docs: Add more mentions of Zensical, fix Mermaid, minor improvements
  • abcb044 fix: Provide Pyodide options to Zensical
  • 258ffb7 ci: Fix setup-uv version
  • 93ffa0d ci: Only download objects.inv on Python 3.12 / Ubuntu, upgrade actions versions
  • a74d0ad ci: Fix lint warning about missing stacklevel
  • 77147e2 docs: Update README to mention Zensical
  • c2f5a1e docs: Update Pyodide docs for Zensical
  • 2cefa97 refactor: Rename material-block source display option to block
  • 37b5696 docs: Fix output of the pydeps example (remove links in SVG)
  • Additional commits viewable in compare view

Updates mypy from 2.1.0 to 2.2.0

Changelog

Sourced from mypy's changelog.

Mypy Release Notes

Next Release

Packaging changes

Mypy 2.3

We've just uploaded mypy 2.3.0 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.

The Upcoming Switch to the New Native Parser

We are planning to enable the new native parser (--native-parser) by default soon. We recommend that you test the native parser in your projects and report any issues in the mypy issue tracker.

Mypyc Free-threading Memory Safety

Free-threaded Python builds that don't have the GIL require additional synchronization primitives or lock-free algorithms to ensure memory safety when there are race conditions (for example, when a thread reads a list item while another thread writes the same list item concurrently). This release greatly improves memory safety of free threading.

List operations are now memory-safe on free threaded Python builds, even in the presence of race conditions. This has some performance cost. For list-heavy workloads, using librt.vecs.vec instead of list is often significantly faster, but note that vec is not (and likely won't be) fully memory safe, and the user is expected to avoid race conditions. The newly introduced librt.threading.Lock helps with this. Using variable-length tuples can also be more efficient than lists, since tuples are immutable and don't require expensive synchronization to ensure memory safety.

Instance attribute access is also (mostly) memory safe now on free-threaded builds in the presence of race conditions. We are planning to fix the remaining unsafe cases in a future release.

Full list of changes:

  • Make attribute access memory safe on free-threaded builds (Jukka Lehtosalo, PR 21705)
  • Fix unsafe borrowing of instance attributes with free-threading (Jukka Lehtosalo, PR 21688)
  • Make list get/set item more memory safe on free-threaded builds (Jukka Lehtosalo, PR 21683)
  • Don't borrow list items on free-threaded builds (Jukka Lehtosalo, PR 21679)
  • Make multiple assignment from list memory-safe on free-threaded builds (Jukka Lehtosalo, PR 21684)

... (truncated)

Commits

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@dependabot
chore(deps): bump the python-dependencies group with 6 updates
f9b63c5 
Bumps the python-dependencies group with 6 updates:

| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `2.5.0` | `2.5.1` |
| [coverage](https://github.com/coveragepy/coveragepy) | `7.14.3` | `7.15.0` |
| [hypothesis](https://github.com/HypothesisWorks/hypothesis) | `6.155.7` | `6.156.4` |
| [uv](https://github.com/astral-sh/uv) | `0.11.26` | `0.11.28` |
| [markdown-exec[ansi]](https://github.com/pawamoy/markdown-exec) | `1.12.1` | `1.12.3` |
| [mypy](https://github.com/python/mypy) | `2.1.0` | `2.2.0` |


Updates `numpy` from 2.5.0 to 2.5.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.5.0...v2.5.1)

Updates `coverage` from 7.14.3 to 7.15.0
- [Release notes](https://github.com/coveragepy/coveragepy/releases)
- [Changelog](https://github.com/coveragepy/coveragepy/blob/main/CHANGES.rst)
- [Commits](coveragepy/coveragepy@7.14.3...7.15.0)

Updates `hypothesis` from 6.155.7 to 6.156.4
- [Release notes](https://github.com/HypothesisWorks/hypothesis/releases)
- [Commits](HypothesisWorks/hypothesis@v6.155.7...v6.156.4)

Updates `uv` from 0.11.26 to 0.11.28
- [Release notes](https://github.com/astral-sh/uv/releases)
- [Changelog](https://github.com/astral-sh/uv/blob/main/CHANGELOG.md)
- [Commits](astral-sh/uv@0.11.26...0.11.28)

Updates `markdown-exec[ansi]` from 1.12.1 to 1.12.3
- [Release notes](https://github.com/pawamoy/markdown-exec/releases)
- [Changelog](https://github.com/pawamoy/markdown-exec/blob/main/CHANGELOG.md)
- [Commits](pawamoy/markdown-exec@1.12.1...1.12.3)

Updates `mypy` from 2.1.0 to 2.2.0
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v2.1.0...v2.2.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-version: 2.5.1
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: coverage
  dependency-version: 7.15.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: hypothesis
  dependency-version: 6.156.4
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
- dependency-name: uv
  dependency-version: 0.11.28
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: markdown-exec[ansi]
  dependency-version: 1.12.3
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: python-dependencies
- dependency-name: mypy
  dependency-version: 2.2.0
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: python-dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file python:uv Pull requests that update python:uv code labels Jul 16, 2026
@codecov

codecov Bot commented Jul 17, 2026 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.84%. Comparing base (3265452) to head (ef2475a).

Additional details and impacted files 
@@           Coverage Diff           @@
##             main    #4151   +/-   ##
=======================================
  Coverage   93.84%   93.84%           
=======================================
  Files          91       91           
  Lines       12570    12570           
=======================================
  Hits        11796    11796           
  Misses        774      774
🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@d-v-b

d-v-b commented Jul 17, 2026 •
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I investigated locally, mypy fails on the newer version of numpy because type annotations changed in the numpy type stubs. Fixing it requires changing some type annotations (at least) in our indexing code

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