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python-isal

.. introduction start

Faster zlib and gzip compatible compression and decompression
by providing Python bindings for the ISA-L library.

This package provides Python bindings for the ISA-L <https://github.com/intel/isa-l>_ library. The Intel(R) Intelligent Storage
Acceleration Library (ISA-L) implements several key algorithms in assembly language <https://en.wikipedia.org/wiki/Assembly_language>_. This includes
a variety of functions to provide zlib/gzip-compatible compression.

python-isal provides the bindings by offering four modules:

isal_zlib: A drop-in replacement for the zlib module that uses ISA-L to
accelerate its performance.
igzip: A drop-in replacement for the gzip module that uses isal_zlib
instead of zlib to perform its compression and checksum tasks, which
improves performance.
igzip_threaded offers an open function which returns buffered read
or write streams that can be used to read and write large files while
escaping the GIL using one or multiple threads. This functionality only
works for streaming, seeking is not supported.
igzip_lib: Provides compression functions which have full access to the
API of ISA-L's compression functions.

isal_zlib and igzip are almost fully compatible with zlib and
gzip from the Python standard library. There are some minor differences
see: differences-with-zlib-and-gzip-modules_.

.. introduction end

Quickstart

.. quickstart start

The python-isal modules can be imported as follows

.. code-block:: python

from isal import isal_zlib
from isal import igzip
from isal import igzip_lib

isal_zlib and igzip are meant to be used as drop in replacements so
their api and functions are the same as the stdlib's modules. Except where
ISA-L does not support the same calls as zlib (See differences below).

A full API documentation can be found on our readthedocs page <https://python-isal.readthedocs.io>_.

python -m isal.igzip implements a simple gzip-like command line
application (just like python -m gzip). Full usage documentation can be
found on our readthedocs page <https://python-isal.readthedocs.io>_.

.. quickstart end

Installation

with pip: pip install isal
with conda: conda install python-isal

Installation is supported on Linux, Windows and MacOS. For more advanced
installation options check the documentation <https://python-isal.readthedocs.io/en/stable/index.html#installation>_.

python-isal as a dependency in your project

.. dependency start

Python-isal supports a limited amount of platforms for which wheels have been
made available. To prevent your users from running into issues when installing
your project please list a python-isal dependency as follows.

setup.cfg::

install_requires =
    isal; platform.machine == "x86_64" or platform.machine == "AMD64" or platform.machine == "aarch64"

setup.py::

extras_require={
    ":platform.machine == 'x86_64' or platform.machine == 'AMD64' or platform.machine == 'aarch64'": ['isal']
},

.. dependency end

.. _differences-with-zlib-and-gzip-modules:

Differences with zlib and gzip modules

.. differences start

Compression level 0 in zlib and gzip means no compression, while
in isal_zlib and igzip this is the lowest compression level.
This is a design choice that was inherited from the ISA-L library.
Compression levels range from 0 to 3, not 1 to 9. isal_zlib.Z_DEFAULT_COMPRESSION
has been aliased to isal_zlib.ISAL_DEFAULT_COMPRESSION (2).
isal_zlib only supports NO_FLUSH, SYNC_FLUSH, FULL_FLUSH and
FINISH_FLUSH. Other flush modes are not supported and will raise errors.
zlib.Z_DEFAULT_STRATEGY, zlib.Z_RLE etc. are exposed as
isal_zlib.Z_DEFAULT_STRATEGY, isal_zlib.Z_RLE etc. for compatibility
reasons. However, isal_zlib only supports a default strategy and will
give warnings when other strategies are used.
zlib supports different memory levels from 1 to 9 (with 8 default).
isal_zlib supports memory levels smallest, small, medium, large and
largest. These have been mapped to levels 1, 2-3, 4-6, 7-8 and 9. So
isal_zlib can be used with zlib compatible memory levels.
igzip.open returns a class IGzipFile instead of GzipFile. Since
the compression levels are not compatible, a difference in naming was chosen
to reflect this. igzip.GzipFile does exist as an alias of
igzip.IGzipFile for compatibility reasons.
igzip._GzipReader has been rewritten in C. Since this is a private member
it should not affect compatibility, but it may cause some issues for
instances where this code is used directly. If such issues should occur,
please report them so the compatibility issues can be fixed.

.. differences end

Contributing

.. contributing start

Please make a PR or issue if you feel anything can be improved. Bug reports
are also very welcome. Please report them on the github issue tracker <https://github.com/rhpvorderman/python-isal/issues>_.

.. contributing end

Development

.. development start

The repository needs to be cloned recursively to make sure the
ISA-L <https://github.com/intel/isa-l>_ repository is checked out:
git clone --recursive https://github.com/pycompression/python-isal.git. If
the repository is already checked out you can use git submodule update --init.

Patches should be made on a feature branch. To run the testing install tox
with pip install tox and run the commands tox -e lint and
tox. That will run most of the testing that is also performed by the CI.
For changes to the documentation run tox -e docs. For changes to the C
code please also run tox -e asan to check for memory leaks. This requires
libasan to be installed.

Building requires the
ISA-L build requirements <https://github.com/intel/isa-l?tab=readme-ov-file#building-isa-l>_
as well.

.. development end

Acknowledgements

.. acknowledgements start

This project builds upon the software and experience of many. Many thanks to:

The ISA-L contributors <https://github.com/intel/isa-l/graphs/contributors>_ for making ISA-L.
Special thanks to @gbtucker for always being especially helpful and
responsive.
The Cython contributors <https://github.com/cython/cython/graphs/contributors>_ for making it easy
to create an extension and helping a novice get start with pointer addresses.
The CPython contributors <https://github.com/python/cpython/graphs/contributors>_.
Python-isal mimicks zlibmodule.c and gzip.py from the standard
library to make it easier for python users to adopt it.
@marcelm <https://github.com/marcelm>_ for taking a chance on this project
and make it a dependency for his xopen <https://github.com/pycompression/xopen>_ and by extension cutadapt <https://github.com/marcelm/cutadapt>_ projects. This gave python-isal its
first users who used python-isal in production.
Mark Adler (@madler) for the excellent comments in his pigz code which made
it very easy to replicate the behaviour for writing gzip with multiple
threads using the threading and isal_zlib modules. Another thanks
for his permissive license, which allowed the crc32_combine code to be
included in the project. (ISA-L does not provide a crc32_combine function,
unlike zlib.) And yet another thanks to Mark Adler and also for
Jean-loup Gailly for creating the gzip format which is very heavily used
in bioinformatics. Without that, I would have never written this library
from which I have learned so much.
The github actions team <https://github.com/orgs/actions/people>_ for
creating the actions CI service that enables building and testing on all
three major operating systems.
@animalize <https://github.com/animalize>_ for explaining how to test and
build python-isal for ARM 64-bit platforms.
And last but not least: everyone who submitted a bug report or a feature
request. These make the project better!

Python-isal would not have been possible without you!

.. acknowledgements end

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