Installation
============

.. note::

    Wheels are provided for Linux and OSX x86-64, but other machines will
    have to build the wheel from the source distribution. Building ``pyfastani``
    involves compiling fastANI, which requires a C++ compiler to be available
    on the local machine.


PyPi
^^^^

``pyfastani`` is hosted on GitHub, but the easiest way to install it is to download
the latest release from its `PyPi repository <https://pypi.python.org/pypi/pyfastani>`_.
It will install all dependencies then install ``pyfastani`` either from a wheel if
one is available, or from source after compiling the Cython code :

.. code:: console

   $ pip install --user pyfastani


Conda
^^^^^

`pyfastani` is also available as a `recipe <https://anaconda.org/bioconda/pyfastani>`_
in the `bioconda <https://bioconda.github.io/>`_ channel. To install, simply
use the ``conda`` installer:

.. code:: console

   $ conda install -c bioconda pyfastani


Arch User Repository
^^^^^^^^^^^^^^^^^^^^

A package recipe for Arch Linux can be found in the Arch User Repository
under the name `python-pyfastani <https://aur.archlinux.org/packages/python-pyfastani>`_.
It will always match the latest release from PyPI.

Steps to install on ArchLinux depend on your `AUR helper <https://wiki.archlinux.org/title/AUR_helpers>`_
(``yaourt``, ``aura``, ``yay``, etc.). For ``aura``, you'll need to run:

.. code:: console

    $ aura -A python-pyfastani


BioArchLinux
^^^^^^^^^^^^

The `BioArchLinux <https://bioarchlinux.org>`_ project provides pre-compiled packages
based on the AUR recipe. Add the BioArchLinux package repository to ``/etc/pacman.conf``:

.. code:: ini

    [bioarchlinux]
    Server = https://repo.bioarchlinux.org/$arch

Then install the latest version of the package and its dependencies with ``pacman``:

.. code:: console

    $ pacman -S python-pyfastani


Piwheels
^^^^^^^^

PyFastANI works on Raspberry Pi platforms (with NEON vectorization enabled!), and 
pre-built wheels are made available for `armv7l` platforms. Run the following 
command to install them instead of compiling from source:

.. code:: console

   $ pip3 install pyfastani --extra-index-url https://www.piwheels.org/simple

Check the `piwheels documentation <https://www.piwheels.org/faq.html>`_ for 
more information.



GitHub + ``pip``
^^^^^^^^^^^^^^^^

If, for any reason, you prefer to download the library from GitHub, you can clone
the repository and install the repository by running (with the admin rights):

.. code:: console

   $ git clone --recursive https://github.com/althonos/pyfastani
   $ pip install --user ./pyfastani

.. caution::

    Keep in mind this will install always try to install the latest commit,
    which may not even build, so consider using a versioned release instead.