.. numcodecs documentation main file, created by
   sphinx-quickstart on Mon May  2 21:40:09 2016.


Numcodecs
=========

.. automodule:: numcodecs

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

Numcodecs depends on NumPy. It is generally best to `install NumPy
<https://numpy.org/install/>`_ first using whatever method is most
appropriate for you operating system and Python distribution.

Install from PyPI::

    $ pip install numcodecs

Alternatively, install via conda::

    $ conda install -c conda-forge numcodecs

Numcodecs includes a C extension providing integration with the Blosc_
library. Wheels are available for most platforms.

Installing a wheel or via conda will install a pre-compiled binary distribution.
However, if you have a newer CPU that supports the AVX2 instruction set (e.g.,
Intel Haswell, Broadwell or Skylake) then installing via pip is preferable,
because you can compile the Blosc library from source with optimisations
for AVX2.::

    $ pip install -v --no-cache-dir --no-binary numcodecs numcodecs

Note that if you compile the C extensions on a machine with AVX2 support
you probably then cannot use the same binaries on a machine without AVX2.

If you specifically want to disable AVX2 or SSE2 when compiling, you can use
the following environment variables::

    $ export DISABLE_NUMCODECS_AVX2=1
    $ export DISABLE_NUMCODECS_SSE2=1


To work with Numcodecs source code in development, clone the repository from GitHub
and then install in editable mode using `pip`.::

    $ git clone --recursive https://github.com/zarr-developers/numcodecs.git
    $ cd numcodecs
    $ pip install -e .[test,msgpack,zfpy]

Note: if you prefer to use the GitHub CLI ``gh`` you will need to append ``-- --recurse-submodules``
to the clone command to everything works properly.

To verify that Numcodecs has been fully installed (including the Blosc
extension) run the test suite::

    $ pytest -v

Contents
--------

.. toctree::
    :maxdepth: 2

    abc
    registry
    blosc
    lz4
    zfpy
    zstd
    zlib
    gzip
    bz2
    lzma
    delta
    fixedscaleoffset
    quantize
    bitround
    packbits
    categorize
    checksum32
    astype
    json
    pickles
    msgpacks
    vlen
    shuffle
    release
    contributing

Acknowledgments
---------------

The following people have contributed to the development of NumCodecs by contributing code,
documentation, code reviews, comments and/or ideas:

* :user:`Francesc Alted <FrancescAlted>`
* :user:`Prakhar Goel <newt0311>`
* :user:`Jerome Kelleher <jeromekelleher>`
* :user:`John Kirkham <jakirkham>`
* :user:`Alistair Miles <alimanfoo>`
* :user:`Jeff Reback <jreback>`
* :user:`Trevor Manz <manzt>`
* :user:`Grzegorz Bokota <Czaki>`
* :user:`Josh Moore <joshmoore>`
* :user:`Martin Durant <martindurant>`
* :user:`Paul Branson <pbranson>`

Numcodecs bundles the `c-blosc <https://github.com/Blosc/c-blosc>`_ library.

Development of this package is supported by the
`MRC Centre for Genomics and Global Health <https://www.sanger.ac.uk/collaboration/mrc-centre-genomics-and-global-health-cggh/>`_.

Indices and tables
------------------

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

.. _Blosc: https://www.blosc.org/
