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Merged
merged 15 commits into from
Jan 3, 2025
Merged
1 change: 1 addition & 0 deletions docs/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,7 @@ def skip_submodules(
"spec/v3": "https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html",
"license": "https://github.com/zarr-developers/zarr-python/blob/main/LICENSE.txt",
"tutorial": "user-guide",
"getting-started": "quickstart",
}

# The language for content autogenerated by Sphinx. Refer to documentation
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28 changes: 0 additions & 28 deletions docs/getting_started.rst

This file was deleted.

13 changes: 7 additions & 6 deletions docs/index.rst
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Expand Up @@ -8,7 +8,8 @@ Zarr-Python
:maxdepth: 1
:hidden:

getting_started
quickstart
installation
user-guide/index
api/index
release
Expand All @@ -34,20 +35,20 @@ Zarr is a file storage format for chunked, compressed, N-dimensional arrays base
.. grid-item-card::
:img-top: _static/index_getting_started.svg

Getting Started
^^^^^^^^^^^^^^^
Quick Start
^^^^^^^^^^^

New to Zarr? Check out the getting started guide. It contains an
New to Zarr? Check out the quick start guide. It contains a brief
introduction to Zarr's main concepts and links to additional tutorials.

+++

.. button-ref:: getting_started
.. button-ref:: quickstart
:expand:
:color: dark
:click-parent:

To the getting started guide
To the Quick Start

.. grid-item-card::
:img-top: _static/index_user_guide.svg
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186 changes: 186 additions & 0 deletions docs/quickstart.rst
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@@ -0,0 +1,186 @@
.. only:: doctest

>>> import shutil
>>> shutil.rmtree('data', ignore_errors=True)
>>>
>>> import numpy as np
>>> np.random.seed(0)

Quickstart
==========

Welcome to the Zarr-Python Quickstart guide! This page will help you get up and running with
the Zarr library in Python to efficiently manage and analyze multi-dimensional arrays.

Zarr is a powerful library for storage of n-dimensional arrays, supporting chunking,
compression, and various backends, making it a versatile choice for scientific and
large-scale data.

Installation
------------

Zarr requires Python 3.11 or higher. You can install it via `pip`:

.. code-block:: bash

pip install zarr

or `conda`:

.. code-block:: bash

conda install --channel conda-forge zarr

Creating an Array
-----------------

To get started, you can create a simple Zarr array::

>>> import zarr
>>> import numpy as np
>>>
>>> # Create a 2D Zarr array
>>> z = zarr.create_array(
... store="data/example-1.zarr",
... shape=(100, 100),
... chunks=(10, 10),
... dtype="f4"
... )
>>>
>>> # Assign data to the array
>>> z[:, :] = np.random.random((100, 100))
>>> z.info
Type : Array
Zarr format : 3
Data type : DataType.float32
Shape : (100, 100)
Chunk shape : (10, 10)
Order : C
Read-only : False
Store type : LocalStore
Codecs : [{'endian': <Endian.little: 'little'>}, {'level': 0, 'checksum': False}]
No. bytes : 40000 (39.1K)

Here, we created a 2D array of shape ``(100, 100)``, chunked into blocks of
``(10, 10)``, and filled it with random floating-point data. This array was
written to a ``LocalStore`` in the ``data/example-1.zarr`` directory.

Compression and Filters
~~~~~~~~~~~~~~~~~~~~~~~

Zarr supports data compression and filters. For example, to use Blosc compression::

>>> z = zarr.create_array(
... "data/example-3.zarr",
... mode="w", shape=(100, 100),
... chunks=(10, 10), dtype="f4",
... compressor=zarr.codecs.BloscCodec(cname="zstd", clevel=3, shuffle=zarr.codecs.BloscShuffle.SHUFFLE)
... )
>>> z[:, :] = np.random.random((100, 100))
>>>
>>> z.info
Type : Array
Zarr format : 3
Data type : DataType.float32
Shape : (100, 100)
Chunk shape : (10, 10)
Order : C
Read-only : False
Store type : LocalStore
Codecs : [{'endian': <Endian.little: 'little'>}, {'level': 0, 'checksum': False}]
No. bytes : 40000 (39.1K)

This compresses the data using the Zstandard codec with shuffle enabled for better compression.

Hierarchical Groups
-------------------

Zarr allows you to create hierarchical groups, similar to directories::

>>> # Create nested groups and add arrays
>>> root = zarr.group("data/example-2.zarr")
>>> foo = root.create_group(name="foo")
>>> bar = root.create_array(
... name="bar", shape=(100, 10), chunks=(10, 10)
... )
>>> spam = foo.create_array(name="spam", shape=(10,), dtype="i4")
>>>
>>> # Assign values
>>> bar[:, :] = np.random.random((100, 10))
>>> spam[:] = np.arange(10)
>>>
>>> # print the hierarchy
>>> root.tree()
/
└── foo
└── spam (10,) int32
<BLANKLINE>

This creates a group with two datasets: ``foo`` and ``bar``.

Persistent Storage
------------------

Zarr supports persistent storage to disk or cloud-compatible backends. While examples above
utilized a :class:`zarr.storage.LocalStore`, a number of other storage options are available.

Zarr integrates seamlessly with cloud object storage such as Amazon S3 and Google Cloud Storage
using external libraries like `s3fs <https://s3fs.readthedocs.io>`_ or
`gcsfs <https://gcsfs.readthedocs.io>`_::

>>> import s3fs # doctest: +SKIP
>>>
>>> z = zarr.create_array("s3://example-bucket/foo", mode="w", shape=(100, 100), chunks=(10, 10)) # doctest: +SKIP
>>> z[:, :] = np.random.random((100, 100)) # doctest: +SKIP

A single-file store can also be created using the the :class:`zarr.storage.ZipStore`::

>>> # Store the array in a ZIP file
>>> store = zarr.storage.ZipStore("data/example-3.zip", mode='w')
>>>
>>> z = zarr.create_array(
... store=store,
... mode="w",
... shape=(100, 100),
... chunks=(10, 10),
... dtype="f4"
... )
>>>
>>> # write to the array
>>> z[:, :] = np.random.random((100, 100))
>>>
>>> # the ZipStore must be explicitly closed
>>> store.close()

To open an existing array from a ZIP file::

>>> # Open the ZipStore in read-only mode
>>> store = zarr.storage.ZipStore("data/example-3.zip", read_only=True)
>>>
>>> z = zarr.open_array(store, mode='r')
>>>
>>> # read the data as a NumPy Array
>>> z[:]
array([[0.66734236, 0.15667458, 0.98720884, ..., 0.36229587, 0.67443246,
0.34315267],
[0.65787303, 0.9544212 , 0.4830079 , ..., 0.33097172, 0.60423803,
0.45621237],
[0.27632037, 0.9947008 , 0.42434934, ..., 0.94860053, 0.6226942 ,
0.6386924 ],
...,
[0.12854576, 0.934397 , 0.19524333, ..., 0.11838563, 0.4967675 ,
0.43074256],
[0.82029045, 0.4671437 , 0.8090906 , ..., 0.7814118 , 0.42650765,
0.95929915],
[0.4335856 , 0.7565437 , 0.7828931 , ..., 0.48119593, 0.66220033,
0.6652362 ]], shape=(100, 100), dtype=float32)

Read more about Zarr's storage options in the :ref:`User Guide <user-guide-storage>`.

Next Steps
----------

Now that you're familiar with the basics, explore the following resources:

- `User Guide <user-guide>`_
- `API Reference <api>`_
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