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.. python-isal documentation master file, created by
sphinx-quickstart on Fri Sep 11 15:42:56 2020.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
=======================================
Welcome to python-isal's documentation!
=======================================
.. toctree::
:maxdepth: 2
:caption: Contents:
============
Introduction
============
.. include:: includes/README.rst
:start-after: .. introduction start
:end-before: .. introduction end
==========
Quickstart
==========
.. include:: includes/README.rst
:start-after: .. quickstart start
:end-before: .. quickstart end
============
Installation
============
Installation with pip
---------------------
::
pip install isal
Installation is supported on Linux, MacOS and Windows. On most platforms
wheels are provided.
The installation will include a staticallly linked version of ISA-L.
If a wheel is not provided for your system the
installation will build ISA-L first in a temporary directory. Please check the
`ISA-L homepage <https://github.com/intel/isa-l>`_ for the build requirements.
The latest development version of python-isal can be installed with::
pip install git+https://github.com/rhpvorderman/python-isal.git
This requires having the build requirements installed.
If you wish to link
dynamically against a version of libisal installed on your system use::
PYTHON_ISAL_LINK_DYNAMIC=true pip install isal --no-binary isal
ISA-L is available in numerous Linux distro's as well as on conda via the
conda-forge channel. Checkout the `ports documentation
<https://github.com/intel/isa-l/wiki/Ports--Repos>`_ on the ISA-L project wiki
to find out how to install it. It is important that the development headers
are also installed.
On Debian and Ubuntu the ISA-L libraries (including the development headers)
can be installed with::
sudo apt install libisal-dev
Installation via conda
----------------------
Python-isal can be installed via conda, for example using
the `miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ installer
with a properly setup `conda-forge
<https://conda-forge.org/docs/user/introduction.html#how-can-i-install-packages-from-conda-forge>`_
channel. When used with bioinformatics tools setting up `bioconda
<http://bioconda.github.io/user/install.html#install-conda>`_
provides a clear set of installation instructions for conda.
python-isal is available on conda-forge and can be installed with::
conda install python-isal
This will automatically install the ISA-L library dependency as well, since
it is available on conda-forge.
===========================================
python-isal as a dependency in your project
===========================================
.. include:: includes/README.rst
:start-after: .. dependency start
:end-before: .. dependency end
.. _differences-with-zlib-and-gzip-modules:
======================================
Differences with zlib and gzip modules
======================================
.. include:: includes/README.rst
:start-after: .. differences start
:end-before: .. differences end
============================
API Documentation: isal_zlib
============================
.. automodule:: isal.isal_zlib
:members:
.. autoclass:: Compress
:members:
.. autoclass:: Decompress
:members:
========================
API-documentation: igzip
========================
.. automodule:: isal.igzip
:members: compress, decompress, open, BadGzipFile, GzipFile, READ_BUFFER_SIZE
.. autoclass:: IGzipFile
:members:
:special-members: __init__
=================================
API-documentation: igzip_threaded
=================================
.. automodule:: isal.igzip_threaded
:members: open
============================
API Documentation: igzip_lib
============================
.. automodule:: isal.igzip_lib
:members: compress, decompress,
.. autoclass:: IgzipDecompressor
:members:
==========================
python -m isal.igzip usage
==========================
.. argparse::
:module: isal.igzip
:func: _argument_parser
:prog: python -m isal.igzip
============
Contributing
============
.. include:: includes/README.rst
:start-after: .. contributing start
:end-before: .. contributing end
===========
Development
===========
.. include:: includes/README.rst
:start-after: .. development start
:end-before: .. development end
================
Acknowledgements
================
.. include:: includes/README.rst
:start-after: .. acknowledgements start
:end-before: .. acknowledgements end
.. include:: includes/CHANGELOG.rst
|
