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Update zarr requirement from <3.0.0a,>=2.12.0 to >=2.12.0,<4.0.0 in the pip-dependencies group #936

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Update zarr requirement from <3.0.0a,>=2.12.0 to >=2.12.0,<4.0.0 in the pip-dependencies group #936

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@dependabot dependabot bot commented on behalf of github Feb 1, 2025 •
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Updates the requirements on zarr to permit the latest version.
Updates zarr to 3.0.2

Release notes

Sourced from zarr's releases.

v3.0.2

What's Changed

New Contributors

Full Changelog: zarr-developers/zarr-python@v3.0.1...v3.0.2

Changelog

Sourced from zarr's changelog.

3.0.2 (2025-01-31)

Features


- Test ``getsize()`` and ``getsize_prefix()`` in ``StoreTests``. (:issue:`2693`)
- Test that a ``ValueError`` is raised for invalid byte range syntax in ``StoreTests``. (:issue:`2693`)
- Separate instantiating and opening a store in ``StoreTests``. (:issue:`2693`)
- Add a test for using Stores as a context managers in ``StoreTests``. (:issue:`2693`)
- Implemented ``LogingStore.open()``. (:issue:`2693`)
- ``LoggingStore`` is now a generic class. (:issue:`2693`)
- Change StoreTest's ``test_store_repr``, ``test_store_supports_writes``,
  ``test_store_supports_partial_writes``, and ``test_store_supports_listing``
  to to be implemented using ``@abstractmethod``, rather raising ``NotImplementedError``. (:issue:`2693`)
- Test the error raised for invalid buffer arguments in ``StoreTests``. (:issue:`2693`)
- Test that data can be written to a store that's not yet open using the store.set method in ``StoreTests``. (:issue:`2693`)
- Adds a new function ``init_array`` for initializing an array in storage, and refactors ``create_array``
  to use ``init_array``. ``create_array`` takes two new parameters: ``data``, an optional array-like object, and ``write_data``, a bool which defaults to ``True``.
  If ``data`` is given to ``create_array``, then the ``dtype`` and ``shape`` attributes of ``data`` are used to define the
  corresponding attributes of the resulting Zarr array. Additionally, if ``data`` given and ``write_data`` is ``True``,
  then the values in ``data`` will be written to the newly created array. (:issue:`2761`)

Bugfixes

  • Wrap sync fsspec filesystems with AsyncFileSystemWrapper. (:issue:2533)
  • Added backwards compatibility for Zarr format 2 structured arrays. (:issue:2681)
  • Update equality for LoggingStore and WrapperStore such that 'other' must also be a LoggingStore or WrapperStore respectively, rather than only checking the types of the stores they wrap. (:issue:2693)
  • Ensure that ZipStore is open before getting or setting any values. (:issue:2693)
  • Use stdout rather than stderr as the default stream for LoggingStore. (:issue:2693)
  • Match the errors raised by read only stores in StoreTests. (:issue:2693)
  • Fixed ZipStore to make sure the correct attributes are saved when instances are pickled. This fixes a previous bug that prevent using ZipStore with a ProcessPoolExecutor. (:issue:2762)
  • Updated the optional test dependencies to include botocore and fsspec. (:issue:2768)
  • Fixed the fsspec tests to skip if botocore is not installed. Previously they would have failed with an import error. (:issue:2768)
  • Optimize full chunk writes. (:issue:2782)

Improved Documentation


- Changed the machinery for creating changelog entries.
  Now individual entries should be added as files to the `changes` directory in the `zarr-python` repository, instead of directly to the changelog file. (:issue:`2736`)

Other



&lt;/tr&gt;&lt;/table&gt; 
</code></pre>
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>

<ul>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/cab29d21dd7ef88a2ccaab0749faa59db345c86e&quot;&gt;&lt;code&gt;cab29d2&lt;/code&gt;&lt;/a> prepare changelog for 3.0.2 release (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2783&quot;&gt;#2783&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/15d92601d23458bc0fc278c17a90e1e18de09e5a&quot;&gt;&lt;code&gt;15d9260&lt;/code&gt;&lt;/a> Optimize is_total_slice for chunksize == 1 (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2782&quot;&gt;#2782&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/fc08f31a0b4210c9d9b2071373c5ea7d55b66287&quot;&gt;&lt;code&gt;fc08f31&lt;/code&gt;&lt;/a> add init_array, and data kwarg for create_array (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2761&quot;&gt;#2761&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/e602aa1d19f26bb06669994231e524c55bcecbeb&quot;&gt;&lt;code&gt;e602aa1&lt;/code&gt;&lt;/a> Use ChunkKeyEncodingLike type alias (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2763&quot;&gt;#2763&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/0c895d18aa69b1d90866f2249e93986022ddc5e7&quot;&gt;&lt;code&gt;0c895d1&lt;/code&gt;&lt;/a> Some release note improvements (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2775&quot;&gt;#2775&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/b5016c020ad5e2691b025506e490ad3abb0fa7c5&quot;&gt;&lt;code&gt;b5016c0&lt;/code&gt;&lt;/a> Make botocore an optional test dependency (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2768&quot;&gt;#2768&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/fb37ff0942c7417a7767cc4d537de7173a9b3329&quot;&gt;&lt;code&gt;fb37ff0&lt;/code&gt;&lt;/a> Upload coverage after GPU tests (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2767&quot;&gt;#2767&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/458299857141a5470ba3956d8a1607f52ac33857&quot;&gt;&lt;code&gt;4582998&lt;/code&gt;&lt;/a> Bump pypa/gh-action-pypi-publish from 1.12.3 to 1.12.4 in the actions group (...</li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/80aea2ae5af416de15d1e4b95c50f214ee0151e4&quot;&gt;&lt;code&gt;80aea2a&lt;/code&gt;&lt;/a> Improve test coverage for storage classes (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2693&quot;&gt;#2693&lt;/a&gt;)&lt;/li>

<li><a href="https://github.com/zarr-developers/zarr-python/commit/9fd45451a9b4b0112b7dd9c180be5977d18570ac&quot;&gt;&lt;code&gt;9fd4545&lt;/code&gt;&lt;/a> Fix pickling of ZipStore (<a href="https://redirect.github.com/zarr-developers/zarr-python/issues/2762&quot;&gt;#2762&lt;/a&gt;)&lt;/li>

<li>Additional commits viewable in <a href="https://github.com/zarr-developers/zarr-python/compare/v2.12.0...v3.0.2&quot;&gt;compare view</a></li>

</ul>

</details>


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📚 Documentation preview 📚: https://earthaccess--936.org.readthedocs.build/en/936/

@dependabot dependabot bot added impact: dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Feb 1, 2025
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Binder 👈 Launch a binder notebook on this branch for commit 1736bb8

I will automatically update this comment whenever this PR is modified

Binder 👈 Launch a binder notebook on this branch for commit 1645206

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Why do we upper-bound Zarr? Is it recommended by the library?

@dependabot
Update zarr requirement in the pip-dependencies group
1645206 
Updates the requirements on [zarr](https://github.com/zarr-developers/zarr-python) to permit the latest version.

Updates `zarr` to 3.0.2
- [Release notes](https://github.com/zarr-developers/zarr-python/releases)
- [Changelog](https://github.com/zarr-developers/zarr-python/blob/main/docs/release-notes.rst)
- [Commits](zarr-developers/zarr-python@v2.12.0...v3.0.2)

---
updated-dependencies:
- dependency-name: zarr
  dependency-type: direct:production
  dependency-group: pip-dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot force-pushed the dependabot/pip/pip-dependencies-7b8f3a6ec2 branch from 1736bb8 to 1645206 Compare February 11, 2025 00:31
mfisher87
mfisher87 reviewed Feb 11, 2025
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I don't think we want the upper bound to be bumped? I didn't expect dependabot to do that.

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chuckwondo commented Feb 11, 2025 •
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Why do we upper-bound Zarr? Is it recommended by the library?

I suspect we use an upper bound because Zarr v3 is an extremely breaking difference from v2 (based on what little I know).

I don't think we want the upper bound to be bumped? I didn't expect dependabot to do that.

Yeah, that seems like odd behavior.

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I suspect we use an upper bound because Zarr v3 is an extremely breaking difference from v2 (based on what little I know).

Makes sense!

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Rejected because we do not want to update the upper bound of the zarr dependency. How can we tell dependabot "hands off"?

@mfisher87 mfisher87 closed this Feb 12, 2025
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dependabot bot commented on behalf of github Feb 12, 2025

This pull request was built based on a group rule. Closing it will not ignore any of these versions in future pull requests.

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@dependabot dependabot bot deleted the dependabot/pip/pip-dependencies-7b8f3a6ec2 branch February 12, 2025 16:29
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