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deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 #1801

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merged 7 commits into from
May 6, 2024
Merged

deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 #1801

merged 7 commits into from
May 6, 2024

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jhamman
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@jhamman jhamman commented Apr 19, 2024 •
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This adds a simple deprecation warning to the following stores:

  • DBMStore
  • LMDBStore
  • SQLiteStore
  • MongoDBStore
  • RedisStore
  • ABSStore
  • NestedDirectoryStore (note: this was already just a special case of the Directory store for v2

closes #1756

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • GitHub Actions have all passed
  • Test coverage is 100% (Codecov passes)

@jhamman
deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, S…
b655d24 
…QLiteStore, MongoDBStore, RedisStore, and ABSStore
@jhamman jhamman requested a review from d-v-b April 19, 2024 03:55
jhamman
jhamman commented Apr 19, 2024
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zarr/_storage/store.py Outdated Show resolved Hide resolved
@jhamman jhamman added this to the 2.18.0 milestone Apr 19, 2024
@jhamman jhamman added the V3 Affects the v3 branch label Apr 19, 2024
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codecov bot commented Apr 22, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.98%. Comparing base (9d046ea) to head (f500c51).

Additional details and impacted files 
@@           Coverage Diff           @@
##             main    #1801   +/-   ##
=======================================
  Coverage   99.98%   99.98%           
=======================================
  Files          38       38           
  Lines       14659    14667    +8     
=======================================
+ Hits        14657    14665    +8     
  Misses          2        2
Files Coverage Δ
zarr/_storage/absstore.py 100.00% <100.00%> (ø)
zarr/_storage/store.py 100.00% <100.00%> (ø)
zarr/storage.py 100.00% <100.00%> (ø)

jhamman
jhamman commented Apr 24, 2024
View reviewed changes
zarr/storage.py
Comment on lines +1608 to +1612
.. deprecated:: 2.18.0
NestedDirectoryStore will be removed in Zarr-Python 3.0 where controlling
the chunk key encoding will be supported as part of the array metadata. See
`GH1274 <https://github.com/zarr-developers/zarr-python/issues/1274>`_
for more information.
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@jhamman jhamman Apr 24, 2024 •
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As far as I'm concerned, this is the only potentially controversial thing in this PR.

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The "Prefixed" Stores are a code smell since they define storage parameters in python-land only rather than in the zarr metadata. I support this change 👍

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jhamman commented May 1, 2024

@zarr-developers/python-core-devs - this is ready for a review. @d-v-b is out of town this week otherwise I'd be hounding him!

@jhamman jhamman merged commit 2f29144 into zarr-developers:main May 6, 2024
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@jhamman jhamman deleted the dep/stores branch May 6, 2024 22:33
@d-v-b d-v-b mentioned this pull request May 10, 2024
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@jeromekelleher jeromekelleher mentioned this pull request May 13, 2024
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jhamman added a commit that referenced this pull request Oct 11, 2024
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V3 main sync w/ merge (#2335)
ce5f53e 
* Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11 (#1586)

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.10...v1.8.11)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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* Bump conda-incubator/setup-miniconda from 2.3.0 to 3.0.1 (#1587)

Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2.3.0 to 3.0.1.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v2.3.0...v3.0.1)

---
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- dependency-name: conda-incubator/setup-miniconda
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  update-type: version-update:semver-major
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* * Cache result of FSStore._fsspec_installed (#1581)

Prevent runtime-overhead in doing this check multiple times

* Bump version of black in pre-commit (#1559)

* Use list comprehension where applicable (#1555)

Even if this is only a test, list comprehensions are faster than
repeatedly call append().

Also use tuple instead of list when possible.

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

* Bump numcodecs from 0.11.0 to 0.12.1 (#1580)

Bumps [numcodecs](https://github.com/zarr-developers/numcodecs) from 0.11.0 to 0.12.1.
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.11.0...v0.12.1)

---
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- dependency-name: numcodecs
  dependency-type: direct:development
  update-type: version-update:semver-minor
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* Use format specification mini-language to format string (#1558)

Co-authored-by: Joe Hamman <joe@earthmover.io>

* Single startswith() call instead of multiple ones (#1556)

It's faster and probably more readable.

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>

* Bump pymongo from 4.5.0 to 4.6.1 (#1585)

Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.5.0 to 4.6.1.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.5.0...4.6.1)

---
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* Move codespell options around (#1196)

Starting with codespell 2.2.2, options can be specified in
`pyrpoject.toml` in addition to `setup.cfg`:
https://github.com/codespell-project/codespell#using-a-config-file

Specifying options in a config file instead of command line options in
`.pre-commit-config.yaml` ensures codespell uses the same options when
run as pre-commit hook or from the command line in the repository root
directory.

* Bump fsspec from 2023.10.0 to 2023.12.1 (#1600)

* Bump fsspec from 2023.10.0 to 2023.12.1

Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.10.0 to 2023.12.1.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.10.0...2023.12.1)

---
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- dependency-name: fsspec
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

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* Update s3fs as well

* Fix s3fs

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* Add type hints to zarr.create (#1536)

* Add type hints to zarr.create

* Use protocol for MetaArray

* Use protocol for Synchronizer

* Fix Path typing

* Add release note

* Fix dim separator typing

* Ignore ... in coverage reporting

* Fix chunk typing

---------

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* Remove unused mypy ignore comments (#1602)

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

* Bump actions/setup-python from 4.7.1 to 5.0.0 (#1605)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4.7.1 to 5.0.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4.7.1...v5.0.0)

---
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* Bump github/codeql-action from 2 to 3 (#1609)

Bumps [github/codeql-action](https://github.com/github/codeql-action) from 2 to 3.
- [Release notes](https://github.com/github/codeql-action/releases)
- [Changelog](https://github.com/github/codeql-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/github/codeql-action/compare/v2...v3)

---
updated-dependencies:
- dependency-name: github/codeql-action
  dependency-type: direct:production
  update-type: version-update:semver-major
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* chore: update pre-commit hooks (#1448)

* chore: update pre-commit hooks

updates:
- https://github.com/charliermarsh/ruff-pre-commit → https://github.com/astral-sh/ruff-pre-commit
- [github.com/astral-sh/ruff-pre-commit: v0.0.224 → v0.1.8](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.224...v0.1.8)
- [github.com/psf/black: 23.10.1 → 23.12.0](https://github.com/psf/black/compare/23.10.1...23.12.0)
- [github.com/codespell-project/codespell: v2.2.5 → v2.2.6](https://github.com/codespell-project/codespell/compare/v2.2.5...v2.2.6)
- [github.com/pre-commit/pre-commit-hooks: v4.4.0 → v4.5.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.4.0...v4.5.0)
- [github.com/pre-commit/mirrors-mypy: v1.3.0 → v1.7.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.3.0...v1.7.1)

* Attempt to fix ruff

* Use isinstance

---------

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* chore: update pre-commit hooks (#1618)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.8 → v0.1.9](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.8...v0.1.9)
- [github.com/psf/black: 23.12.0 → 23.12.1](https://github.com/psf/black/compare/23.12.0...23.12.1)
- [github.com/pre-commit/mirrors-mypy: v1.7.1 → v1.8.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.7.1...v1.8.0)

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* Bump fsspec from 2023.12.1 to 2023.12.2 (#1606)

* Bump fsspec from 2023.12.1 to 2023.12.2

Bumps [fsspec](https://github.com/fsspec/filesystem_spec) from 2023.12.1 to 2023.12.2.
- [Commits](https://github.com/fsspec/filesystem_spec/compare/2023.12.1...2023.12.2)

---
updated-dependencies:
- dependency-name: fsspec
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* Update requirements_dev_optional.txt

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* Bump pytest-doctestplus from 1.0.0 to 1.1.0 (#1619)

Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.0.0 to 1.1.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.0.0...v1.1.0)

---
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  dependency-type: direct:development
  update-type: version-update:semver-minor
...

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* Bump pytest from 7.4.3 to 7.4.4 (#1622)

* chore: update pre-commit hooks (#1626)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.9 → v0.1.11](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.9...v0.1.11)

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* Create TEAM.md (#1628)

* Drop python 3.8 and numpy 1.20 (#1557)

* Drop 3.8 and add 3.12

* Try removing line_profiler

* Also bump the minimal numpy to 1.21

* Drop 3.12 again

* Revert "Try removing line_profiler"

This reverts commit 837854bec99a9d25aece2ead9666f01690d228cc.

* Update release.rst

---------

Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: jakirkham <jakirkham@gmail.com>

* Add Norman Rzepka to core-dev team (#1630)

* chore: update pre-commit hooks (#1633)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.11 → v0.1.13](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.11...v0.1.13)

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* Bump actions/download-artifact from 3 to 4 (#1611)

* Bump actions/download-artifact from 3 to 4

Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](https://github.com/actions/download-artifact/compare/v3...v4)

---
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- dependency-name: actions/download-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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* Also bump upload-artifact

see https://github.com/actions/download-artifact?tab=readme-ov-file#breaking-changes

> Downloading artifacts that were created from action/upload-artifact@v3 and below are not supported.

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* Update tutorial.rst to include section about accessing Zip Files on S3 (#1615)

* Update tutorial.rst to include section about accessing Zip Files on S3

Per discussion here, add information about about accessing zip files on s3:
https://github.com/zarr-developers/zarr-python/discussions/1613

* Update release.rst

* Implement d-v-b's suggestions

---------

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Co-authored-by: Josh Moore <josh@openmicroscopy.org>

* doc(v3): add v3 roadmap and design document (#1583)

* doc(v3): add v3 roadmap and design document

* Update v3-roadmap-and-design.md

* updates after latest round of reviews

* Update v3-roadmap-and-design.md

Co-authored-by: Norman Rzepka <code@normanrz.com>

* Update v3-roadmap-and-design.md

Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>

---------

Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>

* chore: update pre-commit hooks (#1636)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.13 → v0.1.14](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.13...v0.1.14)

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* Fix zarr sync (#1663)

This patch removes fasteners and disables zarr.sync which uses process and thread

Co-authored-by: Wei Ouyang <oeway007@gmail.com>

* Update release.rst (#1621)

* Update release.rst

* Update release.rst

* Change 2.16.2 → 2.17.0

* Update moto for test_s3

* Skip bsddb3 tests to prevent warning failure

* Fix more user warning tests

* Fix even more user warning tests

* Skip coverage for importorskips

* Move to have_X skip method for deps

* Update release.rst (PR#1663)

* Fix test_core.py 'compile' issues

* Add black formatting

* Drop Windows/3.9 build due to unrelated failures

* fix typo

---------

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>

* Bump numpy from 1.24.3 to 1.26.1 (#1543)

Bumps [numpy](https://github.com/numpy/numpy) from 1.24.3 to 1.26.1.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.24.3...v1.26.1)

---
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* chore: update pre-commit hooks (#1642)

* chore: update pre-commit hooks

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.1.14...v0.2.1)
- [github.com/psf/black: 23.12.1 → 24.2.0](https://github.com/psf/black/compare/23.12.1...24.2.0)

* run black incl. comments for '...'

---------

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* Bump ipywidgets from 8.1.0 to 8.1.1 (#1538)

Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.0 to 8.1.1.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.0...8.1.1)

---
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  update-type: version-update:semver-patch
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* Proper argument for numpy.reshape (#1425)

`numpy.reshape` not only accepts a tuple of ints, but also a simple int.

Besides `(10)` is not a tuple and is identical to `10`, unlike `(10,)`.

* Bump ipywidgets from 8.1.1 to 8.1.2 (#1666)

Bumps [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) from 8.1.1 to 8.1.2.
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.1...8.1.2)

---
updated-dependencies:
- dependency-name: ipywidgets
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* docs: ZIP-related tweaks (#1641)

* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style

* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes

* docs: use 'ZIP archive' instead of 'zip file'; clarify utility of caching in s3 + ZIP example; style

* docs: update release notes, correct spelling of greg lee's name in past release notes, and fix markup in past release notes

* Bump numpy from 1.26.1 to 1.26.4 (#1669)

Bumps [numpy](https://github.com/numpy/numpy) from 1.26.1 to 1.26.4.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.1...v1.26.4)

---
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  dependency-type: direct:development
  update-type: version-update:semver-patch
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* Change occurrences of % and format() to f-strings (#1423)

Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>

* chore: update pre-commit hooks (#1672)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.1...v0.2.2)

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* Bump pymongo from 4.6.1 to 4.6.2 (#1674)

Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.6.1 to 4.6.2.
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/4.6.2/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.1...4.6.2)

---
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  dependency-type: direct:development
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* Bump conda-incubator/setup-miniconda from 3.0.1 to 3.0.2 (#1677)

Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.1 to 3.0.2.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.1...v3.0.2)

---
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- dependency-name: conda-incubator/setup-miniconda
  dependency-type: direct:production
  update-type: version-update:semver-patch
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* Update config.yml with Zulip

* Type dimension separator (#1620)

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

* Replace Gitter with new Zulip Chat link (#1685)

* Replace Gitter with Zulip

* Replace Gitter with Zulip in remaining places

* Bump redis from 5.0.1 to 5.0.2 (#1688)

Bumps [redis](https://github.com/redis/redis-py) from 5.0.1 to 5.0.2.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.1...v5.0.2)

---
updated-dependencies:
- dependency-name: redis
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.12 (#1691)

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.12.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.11...v1.8.12)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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* Bump pytest-doctestplus from 1.1.0 to 1.2.0 (#1693)

Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.1.0 to 1.2.0.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.1.0...v1.2.0)

---
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- dependency-name: pytest-doctestplus
  dependency-type: direct:development
  update-type: version-update:semver-minor
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* Fix RTD build (#1694)

* Update release.rst for v2.17.1 (#1673)

* Update release.rst for v2.17.1

* Change the copyright year from 2023 → 2024.

* Update release.rst for v2.17.1

* Bump pytest-timeout from 2.2.0 to 2.3.1 (#1697)

Bumps [pytest-timeout](https://github.com/pytest-dev/pytest-timeout) from 2.2.0 to 2.3.1.
- [Commits](https://github.com/pytest-dev/pytest-timeout/compare/2.2.0...2.3.1)

---
updated-dependencies:
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  update-type: version-update:semver-minor
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* Bump conda-incubator/setup-miniconda from 3.0.2 to 3.0.3 (#1690)

Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.2 to 3.0.3.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.2...v3.0.3)

---
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- dependency-name: conda-incubator/setup-miniconda
  dependency-type: direct:production
  update-type: version-update:semver-patch
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* docs(tutorial.rst): fix link to GCSMap (#1689)

* Update installation.rst stating version support policy (#1665)

* Update installation.rst stating version support policy

* Update docs/installation.rst

Co-authored-by: Joe Hamman <jhamman1@gmail.com>

* Update docs/installation.rst

---------

Co-authored-by: Joe Hamman <jhamman1@gmail.com>

* Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.8.14 (#1700)

Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.12 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.12...v1.8.14)

---
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- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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* Bump pytest-doctestplus from 1.2.0 to 1.2.1 (#1699)

Bumps [pytest-doctestplus](https://github.com/scientific-python/pytest-doctestplus) from 1.2.0 to 1.2.1.
- [Release notes](https://github.com/scientific-python/pytest-doctestplus/releases)
- [Changelog](https://github.com/scientific-python/pytest-doctestplus/blob/main/CHANGES.rst)
- [Commits](https://github.com/scientific-python/pytest-doctestplus/compare/v1.2.0...v1.2.1)

---
updated-dependencies:
- dependency-name: pytest-doctestplus
  dependency-type: direct:development
  update-type: version-update:semver-patch
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* Bump redis from 5.0.2 to 5.0.3 (#1698)

Bumps [redis](https://github.com/redis/redis-py) from 5.0.2 to 5.0.3.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.2...v5.0.3)

---
updated-dependencies:
- dependency-name: redis
  dependency-type: direct:development
  update-type: version-update:semver-patch
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* Add Python 3.12 to CI (#1719)

* Update python-package.yml

* bump numpy versions

* bump min python version

* Update release.rst

* Bump pytest-cov from 4.1.0 to 5.0.0 (#1722)

Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 4.1.0 to 5.0.0.
- [Changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-cov/compare/v4.1.0...v5.0.0)

---
updated-dependencies:
- dependency-name: pytest-cov
  dependency-type: direct:development
  update-type: version-update:semver-major
...

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* chore: update pre-commit hooks (#1708)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.2.2...v0.3.3)
- [github.com/psf/black: 24.2.0 → 24.3.0](https://github.com/psf/black/compare/24.2.0...24.3.0)
- [github.com/pre-commit/mirrors-mypy: v1.8.0 → v1.9.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.8.0...v1.9.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>

* chore: update pre-commit hooks (#1723)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.3 → v0.3.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.3...v0.3.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Fix release notes (following #1719) (#1725)

* Override ipython repr methods. (#1724)

Closes #1716

This avoids expensive lookups against object stores.

* Bump pymongo from 4.6.2 to 4.6.3 (#1729)

* Remove v1 and v2 specification (#1582)

* Remove v1 and v2 specification

* fix warning

---------

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

* chore: update pre-commit hooks (#1738)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Optimize Array.info and Group.info (#1733)

* Optimize Array.info.

Avoid repeated computes of the same value (getsize)

* Don't have InfoReporter query items twice.

Apparently IPython will run both __repr__ and _repr_html_
so we were calling `getsize` twice.

* Group too

* Apply suggestions from code review

Co-authored-by: Joe Hamman <jhamman1@gmail.com>

---------

Co-authored-by: Joe Hamman <jhamman1@gmail.com>

* Bump actions/setup-python from 5.0.0 to 5.1.0 (#1736)

Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.0.0 to 5.1.0.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.0.0...v5.1.0)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

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* Couple fixes (#1737)

* Use `is` when comparing `type` of two objects

* Unnecessary `None` provided as default

* Fix tests with Pytest 8 (#1714)

* Bump pytest version

* Use editable install when testing

---------

Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>

* Avoid redundant __contains__ (#1739)

Let's try grabbing the array.json and group.json files,
and check for `*NotFoundError`, instead of using contains first.

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

* Array & Group: Use already loaded attributes to populate cache. (#1734)

* Array: Use already loaded attributes to populate cache.

* Group: Use already loaded attributes to populate cache.

* Fix

* Add release note

* Optimize attribute setting (#1741)

* Optimize attribute setting

* Add release note

---------

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

* Make sure fs exceptions are raised if not MissingFs exceptions (clone) (#1604)

* Make sure fs exceptions are raised if not Missing

* lint

* add missing argument in tests, lint

* clear memory filesystem during test

* improve commenting

* add memory_store fixture, getitems performance

* Update release.rst

* improve FSStore.test_exception coverage

---------

Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Joe Hamman <joe@earthmover.io>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>

* chore(release): update changelog for 2.17.2 (#1775)

* chore(docs): reset release notes as unreleased (#1776)

* Bump codecov/codecov-action from 3 to 4 (#1647)

* Bump codecov/codecov-action from 3 to 4

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)

---
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- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

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* Set codecov env

---------

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Co-authored-by: Josh Moore <josh@openmicroscopy.org>

* Update release.rst for v2.17.2 (#1778)

* Update release.rst for v2.17.2

* Minor edits

---------

Co-authored-by: Joe Hamman <joe@earthmover.io>

* Deprecate the experimental v3 implementation (#1802)

* deprecate(exp-v3): Add a future warning about the pending removal of the experimental v3 implementation

* ignore warning

* add test

* chore: update pre-commit hooks (#1779)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
- [github.com/psf/black: 24.3.0 → 24.4.0](https://github.com/psf/black/compare/24.3.0...24.4.0)
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Fix `is_total_slice` for size-1 dimensions (#1800)

Closes #1730

Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Joe Hamman <joe@earthmover.io>

* add note to the top of the release page noting the plan for 2.18.* and 3.0 (#1816)

* Bump conda-incubator/setup-miniconda from 3.0.3 to 3.0.4 (#1824)

Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 3.0.3 to 3.0.4.
- [Release notes](https://github.com/conda-incubator/setup-miniconda/releases)
- [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md)
- [Commits](https://github.com/conda-incubator/setup-miniconda/compare/v3.0.3...v3.0.4)

---
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- dependency-name: conda-incubator/setup-miniconda
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

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* dep(docs): deprecate experimental v3 support in docs (#1807)

* dep(docs): deprecate experimental v3 support in docs

* Apply suggestions from code review

Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>

---------

Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>

* Bump h5py from 3.10.0 to 3.11.0 (#1786)

Bumps [h5py](https://github.com/h5py/h5py) from 3.10.0 to 3.11.0.
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.10.0...3.11.0)

---
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- dependency-name: h5py
  dependency-type: direct:development
  update-type: version-update:semver-minor
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* Bump redis from 5.0.3 to 5.0.4 (#1810)

Bumps [redis](https://github.com/redis/redis-py) from 5.0.3 to 5.0.4.
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.3...v5.0.4)

---
updated-dependencies:
- dependency-name: redis
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

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* deprecate(stores): add deprecation warnings to stores that we plan to remove in v3 (#1801)

* deprecate(stores): add deprecation warnings to DBMStore, LMDBStore, SQLiteStore, MongoDBStore, RedisStore, and ABSStore

* filter warnings in pytest config

* more deprecation warnings in docstrings

* add release note

* use np.inf instead of PINF/NINF (#1842)

* use np.inf instead of PINF/NINF

* update release notes

* chore: update pre-commit hooks (#1825)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.1...v0.4.3)
- [github.com/psf/black: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Enable ruff/bugbear rules (B) and fix issues (#1702)

* Enable ruff/bugbear rules (B)

As suggested by Repo-Review.

* Fix ruff/bugbear issue (B007)

B007 Loop control variable `key` not used within loop body

https://docs.astral.sh/ruff/rules/unused-loop-control-variable/

* Fix ruff/bugbear issue (B015)

B015 Pointless comparison. Did you mean to assign a value?
     Otherwise, prepend `assert` or remove it.

https://docs.astral.sh/ruff/rules/useless-comparison/

* Fix ruff/bugbear issues (B028)

B028 No explicit `stacklevel` keyword argument found

https://docs.astral.sh/ruff/rules/no-explicit-stacklevel/

* Fix ruff/bugbear issues (B904)

B904 Within an `except` clause, raise exceptions with `raise ... from err` or
     `raise ... from None` to distinguish them from errors in exception handling

https://docs.astral.sh/ruff/rules/raise-without-from-inside-except/

* Document changes in docs/release.rst

* Disable ruff/bugbear rule (B017)

B017 `pytest.raises(Exception)` should be considered evil

https://docs.astral.sh/ruff/rules/assert-raises-exception/

---------

Co-authored-by: Joe Hamman <joe@earthmover.io>

* Release notes for 2.18.0 (#1843)

* doc: cleanup release notes for 2.18.0

* Update release.rst (#1850)

* Group dependabot updates (#1854)

* chore: update pre-commit hooks (#1876)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.4.3 → v0.4.4](https://github.com/astral-sh/ruff-pre-commit/compare/v0.4.3...v0.4.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Fix a regression with scalar indexing due to #1800 (#1875)

* release notes for 2.18.1 (#1885)

* reset release notes (#1886)

* Add zstd to old V3 supported codecs (#1914)

* add zstd to old V3 supported codecs

* get to full test coverage and add release note

* fix pre-commit

* doc: update release notes for 2.18.2 (#1915)

* Drop support for Python 3.9

* Revert "Drop support for Python 3.9"

This reverts commit a054afbbdaf7c8560d0ce5df77af969bc863e335.

* Update TEAM.md (#2071)

* [v2] Fix doctests with numpy 2.0 (#2073)

* Fix version number in built docs (#2044)

* Fix orthogonal indexing with scalar. (#1947)

Co-authored-by: David Stansby <dstansby@gmail.com>

* Bump the requirements group across 1 directory with 7 updates (#2092)

Bumps the requirements group with 7 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [numpy](https://github.com/numpy/numpy) | `1.26.4` | `2.0.1` |
| [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) | `8.1.2` | `8.1.3` |
| [setuptools-scm](https://github.com/pypa/setuptools_scm) | `8.0.4` | `8.1.0` |
| [pytest](https://github.com/pytest-dev/pytest) | `8.1.1` | `8.3.2` |
| [lmdb](https://github.com/jnwatson/py-lmdb) | `1.4.1` | `1.5.1` |
| [redis](https://github.com/redis/redis-py) | `5.0.4` | `5.0.8` |
| [pymongo](https://github.com/mongodb/mongo-python-driver) | `4.6.3` | `4.8.0` |



Updates `numpy` from 1.26.4 to 2.0.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v1.26.4...v2.0.1)

Updates `ipywidgets` from 8.1.2 to 8.1.3
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.2...8.1.3)

Updates `setuptools-scm` from 8.0.4 to 8.1.0
- [Release notes](https://github.com/pypa/setuptools_scm/releases)
- [Changelog](https://github.com/pypa/setuptools_scm/blob/main/CHANGELOG.md)
- [Commits](https://github.com/pypa/setuptools_scm/compare/v8.0.4...v8.1.0)

Updates `pytest` from 8.1.1 to 8.3.2
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.1.1...8.3.2)

Updates `lmdb` from 1.4.1 to 1.5.1
- [Changelog](https://github.com/jnwatson/py-lmdb/blob/master/ChangeLog)
- [Commits](https://github.com/jnwatson/py-lmdb/compare/py-lmdb_1.4.1...py-lmdb_1.5.1)

Updates `redis` from 5.0.4 to 5.0.8
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.4...v5.0.8)

Updates `pymongo` from 4.6.3 to 4.8.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.6.3...4.8.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:development
  update-type: version-update:semver-major
  dependency-group: requirements
- dependency-name: ipywidgets
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
- dependency-name: setuptools-scm
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
- dependency-name: lmdb
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
- dependency-name: redis
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
- dependency-name: pymongo
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump the actions group with 2 updates (#2087)

Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).


Updates `actions/setup-python` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.0...v5.1.1)

Updates `pypa/gh-action-pypi-publish` from 1.8.14 to 1.9.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.14...v1.9.0)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [v2] Drop support for Python 3.9 (#2074)

* Drop support for Python 3.9

* Ignore B905 ruff rule

* Fix release notes

* Fix Array.__array__ for numpy 2.1 (#2106)

* Fix Array.__array__ for numpy 2.1

* Add changelog

* Depend on np.array for array coercions

* Bump test version of numcodecs (#2114)

* Bump test version of numcodecs

* Fix test for numcodecs 0.13

* fix: numpy 1.24 compat for Array.__array__ (#2123)

* Deprecate N5Store (#2103)

* deprecate(n5): add deprecation warning to N5Store

* also deprecate N5FSStore

* docs

* fix doc

* Run tests on numpy 1.23 (#2124)

* Bump the requirements group across 1 directory with 3 updates (#2129)

Bumps the requirements group with 3 updates in the / directory: [numpy](https://github.com/numpy/numpy), [ipywidgets](https://github.com/jupyter-widgets/ipywidgets) and [azure-storage-blob](https://github.com/Azure/azure-sdk-for-python).


Updates `numpy` from 2.0.1 to 2.1.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.0.1...v2.1.0)

Updates `ipywidgets` from 8.1.3 to 8.1.5
- [Release notes](https://github.com/jupyter-widgets/ipywidgets/releases)
- [Commits](https://github.com/jupyter-widgets/ipywidgets/compare/8.1.3...8.1.5)

Updates `azure-storage-blob` from 12.16.0 to 12.21.0
- [Release notes](https://github.com/Azure/azure-sdk-for-python/releases)
- [Changelog](https://github.com/Azure/azure-sdk-for-python/blob/main/doc/esrp_release.md)
- [Commits](https://github.com/Azure/azure-sdk-for-python/compare/azure-storage-blob_12.16.0...azure-storage-blob_12.21.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
- dependency-name: ipywidgets
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
- dependency-name: azure-storage-blob
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* chore: bump minimum numpy version to 1.24 (#2127)

* chore: bump minimum version to 1.24

* Update .github/workflows/python-package.yml

* Remove un-needed package installs in CI (#2095)

* Bump the actions group with 2 updates (#2146)

Bumps the actions group with 2 updates: [actions/setup-python](https://github.com/actions/setup-python) and [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).


Updates `actions/setup-python` from 5.1.1 to 5.2.0
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5.1.1...v5.2.0)

Updates `pypa/gh-action-pypi-publish` from 1.9.0 to 1.10.0
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.9.0...v1.10.0)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump numpy from 2.1.0 to 2.1.1 in the requirements group (#2151)

Bumps the requirements group with 1 update: [numpy](https://github.com/numpy/numpy).


Updates `numpy` from 2.1.0 to 2.1.1
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.0...v2.1.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* chore(docs): update release notes ahead of 2.18.4 (#2152)

* Bump pypa/gh-action-pypi-publish from 1.10.0 to 1.10.1 in the actions group (#2161)

Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).


Updates `pypa/gh-action-pypi-publish` from 1.10.0 to 1.10.1
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.0...v1.10.1)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [docs] remove primary sidebar from tutorial (#2142)

* remove primary sidebar from tutorial

* lint

* Bump pytest from 8.3.2 to 8.3.3 in the requirements group (#2172)

Bumps the requirements group with 1 update: [pytest](https://github.com/pytest-dev/pytest).


Updates `pytest` from 8.3.2 to 8.3.3
- [Release notes](https://github.com/pytest-dev/pytest/releases)
- [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest/compare/8.3.2...8.3.3)

---
updated-dependencies:
- dependency-name: pytest
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump pypa/gh-action-pypi-publish in the actions group (#2220)

Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).


Updates `pypa/gh-action-pypi-publish` from 1.10.1 to 1.10.2
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.1...v1.10.2)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update TEAM.md (#2227)

* Bump the requirements group across 1 directory with 3 updates (#2284)

Bumps the requirements group with 3 updates in the / directory: [redis](https://github.com/redis/redis-py), [pymongo](https://github.com/mongodb/mongo-python-driver) and [h5py](https://github.com/h5py/h5py).


Updates `redis` from 5.0.8 to 5.1.0
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.0.8...v5.1.0)

Updates `pymongo` from 4.8.0 to 4.10.0
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.8.0...4.10.0)

Updates `h5py` from 3.11.0 to 3.12.1
- [Release notes](https://github.com/h5py/h5py/releases)
- [Changelog](https://github.com/h5py/h5py/blob/master/docs/release_guide.rst)
- [Commits](https://github.com/h5py/h5py/compare/3.11.0...3.12.1)

---
updated-dependencies:
- dependency-name: redis
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
- dependency-name: pymongo
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
- dependency-name: h5py
  dependency-type: direct:development
  update-type: version-update:semver-minor
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump pymongo from 4.10.0 to 4.10.1 in the requirements group (#2288)

Bumps the requirements group with 1 update: [pymongo](https://github.com/mongodb/mongo-python-driver).


Updates `pymongo` from 4.10.0 to 4.10.1
- [Release notes](https://github.com/mongodb/mongo-python-driver/releases)
- [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst)
- [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.10.0...4.10.1)

---
updated-dependencies:
- dependency-name: pymongo
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Fix low contrast box titles (#2287) (#2292)

* Bump pypa/gh-action-pypi-publish in the actions group (#2304)

Bumps the actions group with 1 update: [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish).


Updates `pypa/gh-action-pypi-publish` from 1.10.2 to 1.10.3
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.10.2...v1.10.3)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: actions
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump the requirements group with 2 updates (#2303)

Bumps the requirements group with 2 updates: [numpy](https://github.com/numpy/numpy) and [redis](https://github.com/redis/redis-py).


Updates `numpy` from 2.1.1 to 2.1.2
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](https://github.com/numpy/numpy/compare/v2.1.1...v2.1.2)

Updates `redis` from 5.1.0 to 5.1.1
- [Release notes](https://github.com/redis/redis-py/releases)
- [Changelog](https://github.com/redis/redis-py/blob/master/CHANGES)
- [Commits](https://github.com/redis/redis-py/compare/v5.1.0...v5.1.1)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
- dependency-name: redis
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump numcodecs from 0.13.0 to 0.13.1 in the requirements group (#2326)

Bumps the requirements group with 1 update: [numcodecs](https://github.com/zarr-developers/numcodecs).


Updates `numcodecs` from 0.13.0 to 0.13.1
- [Release notes](https://github.com/zarr-developers/numcodecs/releases)
- [Changelog](https://github.com/zarr-developers/numcodecs/blob/main/docs/release.rst)
- [Commits](https://github.com/zarr-developers/numcodecs/compare/v0.13.0...v0.13.1)

---
updated-dependencies:
- dependency-name: numcodecs
  dependency-type: direct:development
  update-type: version-update:semver-patch
  dependency-group: requirements
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* remove zarr.types from v2

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Janick Martinez Esturo <janick@jme.pub>
Co-authored-by: David Stansby <dstansby@gmail.com>
Co-authored-by: Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>
Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>
Co-authored-by: Josh Moore <josh@openmicroscopy.org>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: jakirkham <jakirkham@gmail.com>
Co-authored-by: Jeff Peck <jeffrey.peck@10xgenomics.com>
Co-authored-by: Norman Rzepka <code@normanrz.com>
Co-authored-by: Sanket Verma <svsanketverma5@gmail.com>
Co-authored-by: Hood Chatham <roberthoodchatham@gmail.com>
Co-authored-by: Wei Ouyang <oeway007@gmail.com>
Co-authored-by: Daniel Jahn (dahn) <dahnjahn@gmail.com>
Co-authored-by: Deepak Cherian <dcherian@users.noreply.github.com>
Co-authored-by: Ian Carroll <carroll.ian@gmail.com>
Co-authored-by: Martin Durant <martin.durant@alumni.utoronto.ca>
Co-authored-by: Ryan Abernathey <ryan.abernathey@gmail.com>
Co-authored-by: Jonny Saunders <sneakers-the-rat@protonmail.com>
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@joshmoore joshmoore joshmoore left review comments

@normanrz normanrz normanrz approved these changes

@d-v-b d-v-b Awaiting requested review from d-v-b

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V3 Affects the v3 branch
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Zarr-Python - 3.0
Status: Done
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2.18.0
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[v3] Deprecate stores that we don't expect to include in v3
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@jhamman @joshmoore @normanrz