Zarr

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3.0.0beta

for a record of changes included in this release.

Dependency Changes
~~~~~~~~~~~~~~~~~~

* fsspec was moved from a required dependency to an optional one. Users should install
fsspec and any relevant implementations (e.g. s3fs) before using the ``RemoteStore``.
By :user:`Joe Hamman <jhamman>` :issue:`2391`.


.. release_3.0.0-alpha:

3.0.0alpha

for a record of changes included in this release.

Enhancements
~~~~~~~~~~~~

* Implement listing of the sub-arrays and sub-groups for a V3 ``Group``.
By :user:`Davis Bennett <d-v-b>` :issue:`1726`.

* Bootstrap v3 branch with zarrita.
By :user:`Joe Hamman <jhamman>` :issue:`1584`.

* Extensible codecs for V3.
By :user:`Norman Rzepka <normanrz>` :issue:`1588`.

* Don't import from tests.
By :user:`Davis Bennett <d-v-b>` :issue:`1601`.

* Listable V3 Stores.
By :user:`Joe Hamman <jhamman>` :issue:`1634`.

* Codecs without array metadata.
By :user:`Norman Rzepka <normanrz>` :issue:`1632`.

* fix sync group class methods.
By :user:`Joe Hamman <jhamman>` :issue:`1652`.

* implement eq for LocalStore.
By :user:`Charoula Kyriakides <Charoula-Kyriakides>` :issue:`1792`.

* V3 reorg.
By :user:`Joe Hamman <jhamman>` :issue:`1809`.

* [v3] Sync with futures.
By :user:`Davis Bennett <d-v-b>` :issue:`1804`.

* implement group.members.
By :user:`Davis Bennett <d-v-b>` :issue:`1726`.

* Remove implicit groups.
By :user:`Joe Hamman <jhamman>` :issue:`1827`.

* feature(store): ``list_*`` -> AsyncGenerators.
By :user:`Joe Hamman <jhamman>` :issue:`1844`.

* Test codec entrypoints.
By :user:`Norman Rzepka <normanrz>` :issue:`1835`.

* Remove extra v3 sync module.
By :user:`Max Jones <maxrjones>` :issue:`1856`.

* Use donfig for V3 configuration.
By :user:`Max Jones <maxrjones>` :issue:`1655`.

* groundwork for V3 group tests.
By :user:`Davis Bennett <d-v-b>` :issue:`1743`.

* [v3] First step to generalizes ndarray and bytes.
By :user:`Mads R. B. Kristensen <madsbk>` :issue:`1826`.

* Reworked codec pipelines.
By :user:`Norman Rzepka <normanrz>` :issue:`1670`.

* Followup on codecs.
By :user:`Norman Rzepka <normanrz>` :issue:`1889`.

* Protocols for Buffer and NDBuffer.
By :user:`Mads R. B. Kristensen <madsbk>` :issue:`1899`.

* [V3] Expand store tests.
By :user:`Davis Bennett <d-v-b>` :issue:`1900`.

* [v3] Feature: Store open mode.
By :user:`Joe Hamman <jhamman>` :issue:`1911`.

* fix(types): Group.info -> NotImplementedError.
By :user:`Joe Hamman <jhamman>` :issue:`1936`.

* feature(typing): add py.typed file to package root.
By :user:`Joe Hamman <jhamman>` :issue:`1935`.

* Support all indexing variants.
By :user:`Norman Rzepka <normanrz>` :issue:`1917`.

* Feature: group and array name properties.
By :user:`Joe Hamman <jhamman>` :issue:`1940`.

* implement .chunks on v3 arrays.
By :user:`Ryan Abernathey <rabernat>` :issue:`1929`.

* Fixes bug in transpose.
By :user:`Norman Rzepka <normanrz>` :issue:`1949`.

* Buffer Prototype Argument.
By :user:`Mads R. B. Kristensen <madsbk>` :issue:`1910`.

* Feature: Top level V3 API.
By :user:`Joe Hamman <jhamman>` :issue:`1884`.

* Basic working FsspecStore.
By :user:`Martin Durant <martindurant>`; :issue:`1785`.

Typing
~~~~~~

* Resolve Mypy errors in v3 branch.
By :user:`Daniel Jahn <DahnJ>` :issue:`1692`.

* Allow dmypy to be run on v3 branch.
By :user:`David Stansby <dstansby>` :issue:`1780`.

* Remove unused typing ignore comments.
By :user:`David Stansby <dstansby>` :issue:`1781`.

* Check untyped defs on v3.
By :user:`David Stansby <dstansby>` :issue:`1784`.

* [v3] Enable some more strict mypy options.
By :user:`David Stansby <dstansby>` :issue:`1793`.

* [v3] Disallow generic Any typing.
By :user:`David Stansby <dstansby>` :issue:`1794`.

* Disallow incomplete type definitions.
By :user:`David Stansby <dstansby>` :issue:`1814`.

* Disallow untyped calls.
By :user:`David Stansby <dstansby>` :issue:`1811`.

* Fix some untyped calls.
By :user:`David Stansby <dstansby>` :issue:`1865`.

* Disallow untyped defs.
By :user:`David Stansby <dstansby>` :issue:`1834`.

* Add more typing to zarr.group.
By :user:`David Stansby <dstansby>` :issue:`1870`.

* Fix any generics in zarr.array.
By :user:`David Stansby <dstansby>` :issue:`1861`.

* Remove some unused mypy overrides.
By :user:`David Stansby <dstansby>` :issue:`1894`.

* Finish typing zarr.metadata.
By :user:`David Stansby <dstansby>` :issue:`1880`.

* Disallow implicit re-exports.
By :user:`David Stansby <dstansby>` :issue:`1908`.

* Make typing strict.
By :user:`David Stansby <dstansby>` :issue:`1879`.

* Enable extra mypy error codes.
By :user:`David Stansby <dstansby>` :issue:`1909`.

* Enable warn_unreachable for mypy.
By :user:`David Stansby <dstansby>` :issue:`1937`.

* Fix final typing errors.
By :user:`David Stansby <dstansby>` :issue:`1939`.

Maintenance
~~~~~~~~~~~

* Remedy a situation where ``zarr-python`` was importing ``DummyStorageTransformer`` from the test suite.
The dependency relationship is now reversed: the test suite imports this class from ``zarr-python``.
By :user:`Davis Bennett <d-v-b>` :issue:`1601`.

* [V3] Update minimum supported Python and Numpy versions.
By :user:`Joe Hamman <jhamman>` :issue:`1638`

* use src layout and use hatch for packaging.
By :user:`Davis Bennett <d-v-b>` :issue:`1592`.

* temporarily disable mypy in v3 directory.
By :user:`Joe Hamman <jhamman>` :issue:`1649`.

* create hatch test env.
By :user:`Ryan Abernathey <rabernat>` :issue:`1650`.

* removed unused environments and workflows.
By :user:`Ryan Abernathey <rabernat>` :issue:`1651`.

* Add env variables to sprint setup instructions.
By :user:`Max Jones <maxrjones>` :issue:`1654`.

* Add test matrix for V3.
By :user:`Max Jones <maxrjones>` :issue:`1656`.

* Remove attrs.
By :user:`Davis Bennett <d-v-b>` :issue:`1660`.

* Specify hatch envs using GitHub actions matrix for v3 tests.
By :user:`Max Jones <maxrjones>` :issue:`1728`.

* black -> ruff format + cleanup.
By :user:`Saransh Chopra <Saransh-cpp>` :issue:`1639`.

* Remove old v3.
By :user:`Davis Bennett <d-v-b>` :issue:`1742`.

* V3 update pre commit.
By :user:`Joe Hamman <jhamman>` :issue:`1808`.

* remove windows testing on v3 branch.
By :user:`Joe Hamman <jhamman>` :issue:`1817`.

* fix: add mypy to test dependencies.
By :user:`Davis Bennett <d-v-b>` :issue:`1789`.

* chore(ci): add numpy 2 release candidate to test matrix.
By :user:`Joe Hamman <jhamman>` :issue:`1828`.

* fix dependencies.
By :user:`Norman Rzepka <normanrz>` :issue:`1840`.

* Add pytest to mypy dependencies.
By :user:`David Stansby <dstansby>` :issue:`1846`.

* chore(pre-commit): update pre-commit versions and remove attrs dep mypy section.
By :user:`Joe Hamman <jhamman>` :issue:`1848`.

* Enable some ruff rules (RUF) and fix issues.
By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1869`.

* Configure Ruff to apply flake8-bugbear/isort/pyupgrade.
By :user:`Norman Rzepka <normanrz>` :issue:`1890`.

* chore(ci): remove mypy from test action in favor of pre-commit action.
By :user:`Joe Hamman <jhamman>` :issue:`1887`.

* Enable ruff/flake8-raise rules (RSE) and fix issues.
By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1872`.

* Apply assorted ruff/refurb rules (FURB).
By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1873`.

* Enable ruff/flake8-implicit-str-concat rules (ISC) and fix issues.
By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1868`.

* Add numpy to mypy pre-commit check env.
By :user:`David Stansby <dstansby>` :issue:`1893`.

* remove fixture files from src.
By :user:`Davis Bennett <d-v-b>` :issue:`1897`.

* Fix list of packages in mypy pre-commit environment.
By :user:`David Stansby <dstansby>` :issue:`1907`.

* Run sphinx directly on readthedocs.
By :user:`David Stansby <dstansby>` :issue:`1919`.

* Apply preview ruff rules.
By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1942`.

* Enable and apply ruff rule RUF009.
By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1941`.

Documentation
~~~~~~~~~~~~~

* Specify docs hatch env for v3 branch.
By :user:`Max Jones <maxrjones>` :issue:`1655`.

* Development installation/contributing docs updates.
By :user:`Alden Keefe Sampson <aldenks>` :issue:`1643`.

* chore: update project settings per scientific python repo-review.
By :user:`Joe Hamman <jhamman>` :issue:`1863`.

* doc: update release notes for 3.0.0.alpha.
By :user:`Joe Hamman <jhamman>` :issue:`1959`.

.. _release_2.18.3:

2.18.3

------

Enhancements
~~~~~~~~~~~~
* Added support for creating a copy of data when converting a `zarr.Array`
to a numpy array.
By :user:`David Stansby <dstansby>` (:issue:`2106`) and
:user:`Joe Hamman <jhamman>` (:issue:`2123`).

Maintenance
~~~~~~~~~~~
* Removed support for Python 3.9.
By :user:`David Stansby <dstansby>` (:issue:`2074`).

* Fix a regression when using orthogonal indexing with a scalar.
By :user:`Deepak Cherian <dcherian>` :issue:`1931`

* Added compatibility with NumPy 2.1.
By :user:`David Stansby <dstansby>`

* Bump minimum NumPy version to 1.24.
:user:`Joe Hamman <jhamman>` (:issue:`2127`).

Deprecations
~~~~~~~~~~~~

* Deprecate :class:`zarr.n5.N5Store` and :class:`zarr.n5.N5FSStore`. These
stores are slated to be removed in Zarr Python 3.0.
By :user:`Joe Hamman <jhamman>` :issue:`2085`.

.. _release_2.18.2:

2.18.2

------

Enhancements
~~~~~~~~~~~~

* Add Zstd codec to old V3 code path.
By :user:`Ryan Abernathey <rabernat>`

.. _release_2.18.1:

2.18.1

------

Maintenance
~~~~~~~~~~~
* Fix a regression when getting or setting a single value from arrays with size-1 chunks.
By :user:`Deepak Cherian <dcherian>` :issue:`1874`

.. _release_2.18.0:

2.18.0

------

Enhancements
~~~~~~~~~~~~
* Performance improvement for reading and writing chunks if any of the dimensions is size 1.
By :user:`Deepak Cherian <dcherian>` :issue:`1730`.

Maintenance
~~~~~~~~~~~
* Enable ruff/bugbear rules (B) and fix issues.
By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1702`.

* Minor updates to use `np.inf` instead of `np.PINF` / `np.NINF` in preparation for NumPy 2.0.0 release.
By :user:`Joe Hamman <jhamman>` :issue:`1842`.

Deprecations
~~~~~~~~~~~~

* Deprecate experimental v3 support by issuing a `FutureWarning`.
Also updated docs to warn about using the experimental v3 version.
By :user:`Joe Hamman <jhamman>` :issue:`1802` and :issue:`1807`.

* Deprecate the following stores: :class:`zarr.storage.DBMStore`, :class:`zarr.storage.LMDBStore`,
:class:`zarr.storage.SQLiteStore`, :class:`zarr.storage.MongoDBStore`, :class:`zarr.storage.RedisStore`,
and :class:`zarr.storage.ABSStore`. These stores are slated to be removed from Zarr-Python in version 3.0.
By :user:`Joe Hamman <jhamman>` :issue:`1801`.

.. _release_2.17.2:

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