Zarr

-----

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

* Start stop for iterator (`islice()`)
By :user:`Sebastian Grill <yetyetanotherusername>`; :issue:`621`.

* Add capability to partially read and decompress chunks
By :user:`Andrew Fulton <andrewfulton9>`; :issue:`667`.

Bug fixes
~~~~~~~~~

* Make DirectoryStore __setitem__ resilient against antivirus file locking
By :user:`Eric Younkin <ericgyounkin>`; :issue:`698`.

* Compare test data's content generally
By :user:`John Kirkham <jakirkham>`; :issue:`436`.

* Fix dtype usage in zarr/meta.py
By :user:`Josh Moore <joshmoore>`; :issue:`700`.

* Fix FSStore key_seperator usage
By :user:`Josh Moore <joshmoore>`; :issue:`669`.

* Simplify text handling in DB Store
By :user:`John Kirkham <jakirkham>`; :issue:`670`.

* GitHub Actions migration
By :user:`Matthias Bussonnier <Carreau>`;
:issue:`641`, :issue:`671`, :issue:`674`, :issue:`676`, :issue:`677`, :issue:`678`,
:issue:`679`, :issue:`680`, :issue:`682`, :issue:`684`, :issue:`685`, :issue:`686`,
:issue:`687`, :issue:`695`, :issue:`706`.

.. _release_2.6.1:

-----

* Minor build fix
By :user:`Matthias Bussonnier <Carreau>`; :issue:`666`.

.. _release_2.6.0:

-----

This release of Zarr Python is the first release of Zarr to not support Python 3.5.

* End Python 3.5 support.
By :user:`Chris Barnes <clbarnes>`; :issue:`602`.

* Fix ``open_group/open_array`` to allow opening of read-only store with
``mode='r'`` :issue:`269`

* Add `Array` tests for FSStore.
By :user:`Andrew Fulton <andrewfulton9>`; :issue: `644`.

* fix a bug in which ``attrs`` would not be copied on the root when using ``copy_all``; :issue:`613`

* Fix ``FileNotFoundError`` with dask/s3fs :issue:`649`

* Fix flaky fixture in test_storage.py :issue:`652`

* Fix FSStore getitems fails with arrays that have a 0 length shape dimension :issue:`644`

* Use async to fetch/write result concurrently when possible. :issue:`536`, See `this comment
<https://github.com/zarr-developers/zarr-python/issues/536#issuecomment-721253094>`_ for some performance analysis
showing order of magnitude faster response in some benchmark.

See `this link <https://github.com/zarr-developers/zarr-python/milestone/11?closed=1>`_
for the full list of closed and merged PR tagged with the 2.6 milestone.

* Add ability to partially read and decompress arrays, see :issue:`667`. It is
only available to chunks stored using fsspec and using Blosc as a compressor.

For certain analysis case when only a small portion of chunks is needed it can
be advantageous to only access and decompress part of the chunks. Doing
partial read and decompression add high latency to many of the operation so
should be used only when the subset of the data is small compared to the full
chunks and is stored contiguously (that is to say either last dimensions for C
layout, firsts for F). Pass ``partial_decompress=True`` as argument when
creating an ``Array``, or when using ``open_array``. No option exists yet to
apply partial read and decompress on a per-operation basis.

.. _release_2.5.0:

-----

This release will be the last to support Python 3.5, next version of Zarr will be Python 3.6+.

* `DirectoryStore` now uses `os.scandir`, which should make listing large store
faster, :issue:`563`

* Remove a few remaining Python 2-isms.
By :user:`Poruri Sai Rahul <rahulporuri>`; :issue:`393`.

* Fix minor bug in `N5Store`.
By :user:`gsakkis`, :issue:`550`.

* Improve error message in Jupyter when trying to use the ``ipytree`` widget
without ``ipytree`` installed.
By :user:`Zain Patel <mzjp2>`; :issue:`537`

* Add typing information to many of the core functions :issue:`589`

* Explicitly close stores during testing.
By :user:`Elliott Sales de Andrade <QuLogic>`; :issue:`442`

* Many of the convenience functions to emit errors (``err_*`` from
``zarr.errors`` have been replaced by ``ValueError`` subclasses. The corresponding
``err_*`` function have been removed. :issue:`590`, :issue:`614`)

* Improve consistency of terminology regarding arrays and datasets in the
documentation.
By :user:`Josh Moore <joshmoore>`; :issue:`571`.

* Added support for generic URL opening by ``fsspec``, where the URLs have the
form "protocol://[server]/path" or can be chained URls with "::" separators.
The additional argument ``storage_options`` is passed to the backend, see
the ``fsspec`` docs.
By :user:`Martin Durant <martindurant>`; :issue:`546`

* Added support for fetching multiple items via ``getitems`` method of a
store, if it exists. This allows for concurrent fetching of data blocks
from stores that implement this; presently HTTP, S3, GCS. Currently only
applies to reading.
By :user:`Martin Durant <martindurant>`; :issue:`606`

* Efficient iteration expanded with option to pass start and stop index via
``array.islice``.
By :user:`Sebastian Grill <yetyetanotherusername>`, :issue:`615`.

.. _release_2.4.0:

-----

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

* Add key normalization option for ``DirectoryStore``, ``NestedDirectoryStore``,
``TempStore``, and ``N5Store``.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`459`.

* Add ``recurse`` keyword to ``Group.array_keys`` and ``Group.arrays`` methods.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`458`.

* Use uniform chunking for all dimensions when specifying ``chunks`` as an integer.
Also adds support for specifying ``-1`` to chunk across an entire dimension.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`456`.

* Rename ``DictStore`` to ``MemoryStore``.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`455`.

* Rewrite ``.tree()`` pretty representation to use ``ipytree``.
Allows it to work in both the Jupyter Notebook and JupyterLab.
By :user:`John Kirkham <jakirkham>`; :issue:`450`.

* Do not rename Blosc parameters in n5 backend and add `blocksize` parameter,
compatible with n5-blosc. By :user:`axtimwalde`, :issue:`485`.

* Update ``DirectoryStore`` to create files with more permissive permissions.
By :user:`Eduardo Gonzalez <eddienko>` and :user:`James Bourbeau <jrbourbeau>`; :issue:`493`

* Use ``math.ceil`` for scalars.
By :user:`John Kirkham <jakirkham>`; :issue:`500`.

* Ensure contiguous data using ``astype``.
By :user:`John Kirkham <jakirkham>`; :issue:`513`.

* Refactor out ``_tofile``/``_fromfile`` from ``DirectoryStore``.
By :user:`John Kirkham <jakirkham>`; :issue:`503`.

* Add ``__enter__``/``__exit__`` methods to ``Group`` for ``h5py.File`` compatibility.
By :user:`Chris Barnes <clbarnes>`; :issue:`509`.

Bug fixes
~~~~~~~~~

* Fix Sqlite Store Wrong Modification.
By :user:`Tommy Tran <potter420>`; :issue:`440`.

* Add intermediate step (using ``zipfile.ZipInfo`` object) to write
inside ``ZipStore`` to solve too restrictive permission issue.
By :user:`Raphael Dussin <raphaeldussin>`; :issue:`505`.

* Fix '/' prepend bug in ``ABSStore``.
By :user:`Shikhar Goenka <shikharsg>`; :issue:`525`.

Documentation
~~~~~~~~~~~~~
* Fix hyperlink in ``README.md``.
By :user:`Anderson Banihirwe <andersy005>`; :issue:`531`.

* Replace "nuimber" with "number".
By :user:`John Kirkham <jakirkham>`; :issue:`512`.

* Fix azure link rendering in tutorial.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`507`.

* Update ``README`` file to be more detailed.
By :user:`Zain Patel <mzjp2>`; :issue:`495`.

* Import blosc from numcodecs in tutorial.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`491`.

* Adds logo to docs.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`462`.

* Fix N5 link in tutorial.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`480`.

* Fix typo in code snippet.
By :user:`Joe Jevnik <llllllllll>`; :issue:`461`.

* Fix URLs to point to zarr-python
By :user:`John Kirkham <jakirkham>`; :issue:`453`.

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

* Add documentation build to CI.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`516`.

* Use ``ensure_ndarray`` in a few more places.
By :user:`John Kirkham <jakirkham>`; :issue:`506`.

* Support Python 3.8.
By :user:`John Kirkham <jakirkham>`; :issue:`499`.

* Require Numcodecs 0.6.4+ to use text handling functionality from it.
By :user:`John Kirkham <jakirkham>`; :issue:`497`.

* Updates tests to use ``pytest.importorskip``.
By :user:`James Bourbeau <jrbourbeau>`; :issue:`492`

* Removed support for Python 2.
By :user:`jhamman`; :issue:`393`, :issue:`470`.

* Upgrade dependencies in the test matrices and resolve a
compatibility issue with testing against the Azure Storage
Emulator. By :user:`alimanfoo`; :issue:`468`, :issue:`467`.

* Use ``unittest.mock`` on Python 3.
By :user:`Elliott Sales de Andrade <QuLogic>`; :issue:`426`.

* Drop ``decode`` from ``ConsolidatedMetadataStore``.
By :user:`John Kirkham <jakirkham>`; :issue:`452`.


.. _release_2.3.2:

-----

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

* Use ``scandir`` in ``DirectoryStore``'s ``getsize`` method.
By :user:`John Kirkham <jakirkham>`; :issue:`431`.

Bug fixes
~~~~~~~~~

* Add and use utility functions to simplify reading and writing JSON.
By :user:`John Kirkham <jakirkham>`; :issue:`429`, :issue:`430`.

* Fix ``collections``'s ``DeprecationWarning``\ s.
By :user:`John Kirkham <jakirkham>`; :issue:`432`.

* Fix tests on big endian machines.
By :user:`Elliott Sales de Andrade <QuLogic>`; :issue:`427`.


.. _release_2.3.1: