Bump the python-dependencies group across 1 directory with 4 updates

[dependabot]

Updates the requirements on cmocean, numpy, psutil and zarr to permit the latest version.
Updates cmocean to 4.0.3

Release notes

Sourced from cmocean's releases.

v4.0.3

Full Changelog: matplotlib/cmocean@v4.0.2...v4.0.3

Commits

• 59c3500 Update setup.py
• 48f4aa8 Update setup.py
• 3268ea7 Update setup.py
• edbb9c0 Update setup.py
• d98e5e6 Update setup.py
• 05a6a9f Merge pull request #106 from andrew-s28/inverted-cmaps
• 12cd24e Small fix to register inverted and reveresed cmaps properly
• 953b7da Adds access to inverted colormaps with _i appendix
• 64773a9 Merge pull request #103 from matplotlib/dependabot/github_actions/actions/set...
• f8e460e Merge pull request #104 from matplotlib/dependabot/github_actions/codecov/cod...
• Additional commits viewable in compare view

Updates numpy to 2.2.3

Release notes

Sourced from numpy's releases.

2.2.3 (Feb 13, 2025)

NumPy 2.2.3 Release Notes

NumPy 2.2.3 is a patch release that fixes bugs found after the 2.2.2 release. The majority of the changes are typing improvements and fixes for free threaded Python. Both of those areas are still under development, so if you discover new problems, please report them.

This release supports Python versions 3.10-3.13.

Contributors

A total of 9 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

• !amotzop
• Charles Harris
• Chris Sidebottom
• Joren Hammudoglu
• Matthew Brett
• Nathan Goldbaum
• Raghuveer Devulapalli
• Sebastian Berg
• Yakov Danishevsky +

Pull requests merged

A total of 21 pull requests were merged for this release.

• #28185: MAINT: Prepare 2.2.x for further development
• #28201: BUG: fix data race in a more minimal way on stable branch
• #28208: BUG: Fix from_float_positional errors for huge pads
• #28209: BUG: fix data race in np.repeat
• #28212: MAINT: Use VQSORT_COMPILER_COMPATIBLE to determine if we should...
• #28224: MAINT: update highway to latest
• #28236: BUG: Add cpp atomic support (#28234)
• #28237: BLD: Compile fix for clang-cl on WoA
• #28243: TYP: Avoid upcasting float64 in the set-ops
• #28249: BLD: better fix for clang / ARM compiles
• #28266: TYP: Fix timedelta64.__divmod__ and timedelta64.__mod__...
• #28274: TYP: Fixed missing typing information of set_printoptions
• #28278: BUG: backport resource cleanup bugfix from gh-28273
• #28282: BUG: fix incorrect bytes to stringdtype coercion
• #28283: TYP: Fix scalar constructors
• #28284: TYP: stub numpy.matlib
• #28285: TYP: stub the missing numpy.testing modules
• #28286: CI: Fix the github label for TYP: PR's and issues
• #28305: TYP: Backport typing updates from main
• #28321: BUG: fix race initializing legacy dtype casts
• #28324: CI: update test_moderately_small_alpha

... (truncated)

Changelog

Sourced from numpy's changelog.

This is a walkthrough of the NumPy 2.1.0 release on Linux, modified for building with GitHub Actions and cibuildwheels and uploading to the anaconda.org staging repository for NumPy <https://anaconda.org/multibuild-wheels-staging/numpy>_. The commands can be copied into the command line, but be sure to replace 2.1.0 by the correct version. This should be read together with the :ref:general release guide <prepare_release>.

Facility preparation

Before beginning to make a release, use the requirements/*_requirements.txt files to ensure that you have the needed software. Most software can be installed with pip, but some will require apt-get, dnf, or whatever your system uses for software. You will also need a GitHub personal access token (PAT) to push the documentation. There are a few ways to streamline things:

• Git can be set up to use a keyring to store your GitHub personal access token. Search online for the details.
• You can use the keyring app to store the PyPI password for twine. See the online twine documentation for details.

Prior to release

Add/drop Python versions

When adding or dropping Python versions, three files need to be edited:

• .github/workflows/wheels.yml # for github cibuildwheel
• tools/ci/cirrus_wheels.yml # for cibuildwheel aarch64/arm64 builds
• pyproject.toml # for classifier and minimum version check.

Make these changes in an ordinary PR against main and backport if necessary. Add [wheel build] at the end of the title line of the commit summary so that wheel builds will be run to test the changes. We currently release wheels for new Python versions after the first Python rc once manylinux and cibuildwheel support it. For Python 3.11 we were able to release within a week of the rc1 announcement.

Backport pull requests

Changes that have been marked for this release must be backported to the maintenance/2.1.x branch.

Update 2.1.0 milestones

... (truncated)

Commits

• a274561 Merge pull request #28322 from charris/prepare-2.2.3
• 5ab0f71 REL: Prepare for the NumPy 2.2.3 release [wheel build]
• 010ad9b Merge pull request #28324 from charris/update-test_dirichlet_moderately_small...
• 6338746 CI: update test_moderately_small_alpha [wheel build]
• 56f8d5b Merge pull request #28321 from charris/backport-28290
• 48515a3 MAINT: Update some testing files from main
• 96ca7e3 MAINT: respond to code review
• c20ac88 MAINT: use a try/finally to make the deadlock protection more robust
• d494647 MAINT: fix indentation and clarify comment
• 3f8fbd6 MAINT: go back to try/except
• Additional commits viewable in compare view

Updates psutil to 7.0.0

Changelog

Sourced from psutil's changelog.

7.0.0

2025-02-13

Enhancements

• 669_, [Windows]: net_if_addrs()_ also returns the broadcast address instead of None.
• 2480_: Python 2.7 is no longer supported. Latest version supporting Python 2.7 is psutil 6.1.X. Install it with: pip2 install psutil==6.1.*.
• 2490_: removed long deprecated Process.memory_info_ex() method. It was deprecated in psutil 4.0.0, released 8 years ago. Substitute is Process.memory_full_info().

Bug fixes

• 2496_, [Linux]: Avoid segfault (a cPython bug) on Process.memory_maps() for processes that use hundreds of GBs of memory.
• 2502_, [macOS]: virtual_memory()_ now relies on host_statistics64 instead of host_statistics. This is the same approach used by vm_stat CLI tool, and should grant more accurate results.

Compatibility notes

• 2480_: Python 2.7 is no longer supported.
• 2490_: removed long deprecated Process.memory_info_ex() method.

6.1.1

2024-12-19

Enhancements

• 2471_: use Vulture CLI tool to detect dead code.

Bug fixes

• 2418_, [Linux]: fix race condition in case /proc/PID/stat does not exist, but /proc/PID does, resulting in FileNotFoundError.
• 2470_, [Linux]: users()_ may return "localhost" instead of the actual IP address of the user logged in.

6.1.0

2024-10-17

Enhancements

... (truncated)

Commits

• ea5b556 pre-release
• d6e28b7 try to fix tests
• 104bb32 test cpu_times() for process children
• 16c091b test cpu_times() for process children
• eee09da [OSX] proc.c: Fix goo.gl link in comment for source reference (#2505)
• 17e2780 ci: build aarch64 wheel on GHA aarch64 runner (#2503)
• 1ba8667 pin black version to 24.X, because new 25.X breaks style
• 9c114a5 [OSX] use host_statistics64 to get memory metrics (#2502)
• 08d7d43 pin black version to 24.X, because new 25.X breaks style
• a509e5a 669 windows broadcast addr (#2501)
• Additional commits viewable in compare view

Updates zarr to 3.0.4

Release notes

Sourced from zarr's releases.

v3.0.4

What's Changed

• Unnecessary lambda expression by @​DimitriPapadopoulos in zarr-developers/zarr-python#2828
• don't serialize empty tuples for v2 filters, and warn when reading such metadata by @​d-v-b in zarr-developers/zarr-python#2847
• Fix a bug when setting complete chunks by @​dcherian in zarr-developers/zarr-python#2851
• feat/batch creation by @​d-v-b in zarr-developers/zarr-python#2665

Full Changelog: zarr-developers/zarr-python@v3.0.3...v3.0.4

Changelog

Sourced from zarr's changelog.

Release notes

.. towncrier release notes start

3.0.3 (2025-02-14)

Features

- Improves performance of FsspecStore.delete_dir for remote filesystems supporting concurrent/batched deletes, e.g., s3fs. (:issue:`2661`)
- Added :meth:`zarr.config.enable_gpu` to update Zarr's configuration to use GPUs. (:issue:`2751`)
- Avoid reading chunks during writes where possible. :issue:`757` (:issue:`2784`)
- :py:class:`LocalStore` learned to ``delete_dir``. This makes array and group deletes more efficient. (:issue:`2804`)
- Add `zarr.testing.strategies.array_metadata` to generate ArrayV2Metadata and ArrayV3Metadata instances. (:issue:`2813`)
- Add arbitrary `shards` to Hypothesis strategy for generating arrays. (:issue:`2822`)
Bugfixes

• Fixed bug with Zarr using device memory, instead of host memory, for storing metadata when using GPUs. (:issue:2751)
• The array returned by zarr.empty and an empty zarr.core.buffer.cpu.NDBuffer will now be filled with the specified fill value, or with zeros if no fill value is provided. This fixes a bug where Zarr format 2 data with no fill value was written with un-predictable chunk sizes. (:issue:2755)
• Fix zip-store path checking for stores with directories listed as files. (:issue:2758)
• Use removeprefix rather than replace when removing filename prefixes in FsspecStore.list (:issue:2778)
• Enable automatic removal of needs release notes with labeler action (:issue:2781)
• Use the proper label config (:issue:2785)
• Alters the behavior of create_array to ensure that any groups implied by the array's name are created if they do not already exist. Also simplifies the type signature for any function that takes an ArrayConfig-like object. (:issue:2795)
• Enitialise empty chunks to the default fill value during writing and add default fill values for datetime, timedelta, structured, and other (void* fixed size) data types (:issue:2799)
• Ensure utf8 compliant strings are used to construct numpy arrays in property-based tests (:issue:2801)
• Fix pickling for ZipStore (:issue:2807)
• Update numcodecs to not overwrite codec configuration ever. Closes :issue:2800. (:issue:2811)
• Fix fancy indexing (e.g. arr[5, [0, 1]]) with the sharding codec (:issue:2817)

Improved Documentation

- Added new user guide on :ref:`user-guide-gpu`. (:issue:`2751`)
3.0.2 (2025-01-31)
Features

</tr></table> 
</code></pre>
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/8d2fb47252a7ed5eb163ccfb0401e4e0486f72f6&quot;&gt;&lt;code&gt;8d2fb47&lt;/code&gt;&lt;/a> feat/batch creation (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2665&quot;&gt;#2665&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/8b59a38463dca7b3c908aa3db7d5321a80a3c285&quot;&gt;&lt;code&gt;8b59a38&lt;/code&gt;&lt;/a> Fix a bug when setting complete chunks (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2851&quot;&gt;#2851&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/96c967786c42e235f4d07dfcdd2a3a72bcd508e1&quot;&gt;&lt;code&gt;96c9677&lt;/code&gt;&lt;/a> don't serialize empty tuples for v2 filters, and warn when reading such metad...</li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/e8bfb6484aeb543c21b9b0f6de2e0f0a034fc5d7&quot;&gt;&lt;code&gt;e8bfb64&lt;/code&gt;&lt;/a> Unnecessary lambda expression (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2828&quot;&gt;#2828&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/5a36e175325c1f6e55b0638009b8aa7e5ab89a05&quot;&gt;&lt;code&gt;5a36e17&lt;/code&gt;&lt;/a> Changelog for v3.0.3 (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2836&quot;&gt;#2836&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/8ad4cd69335a32d85b0b1c380572596b1e9f26b7&quot;&gt;&lt;code&gt;8ad4cd6&lt;/code&gt;&lt;/a> Run fsspec tests in min_deps env (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2835&quot;&gt;#2835&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/48f7c9af3b49e3221c65c3447e869437c0fb7575&quot;&gt;&lt;code&gt;48f7c9a&lt;/code&gt;&lt;/a> Feat: improves delete_dir for s3fs-backed FsspecStore (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2661&quot;&gt;#2661&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/23abb5b0cfb8b9565985e7e682a498405d630b34&quot;&gt;&lt;code&gt;23abb5b&lt;/code&gt;&lt;/a> Add more setitem property tests (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2825&quot;&gt;#2825&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/f8bc3153162e85ad41f62cdb6c693239868b85c6&quot;&gt;&lt;code&gt;f8bc315&lt;/code&gt;&lt;/a> create_array creates explicit groups (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2795&quot;&gt;#2795&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/3c25dacdd41e9a67f32c2cfac364292bb34d9370&quot;&gt;&lt;code&gt;3c25dac&lt;/code&gt;&lt;/a> Add shards to array strategy (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2822&quot;&gt;#2822&lt;/a&gt;)&lt;/li>

<li>Additional commits viewable in <a href="https://github.com/zarr-developers/zarr-python/compare/v2.13.0...v3.0.4&quot;&gt;compare view</a></li>

</ul>

</details>
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