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

.. note::

    Wheels are provided for Linux and MacOS on x86-64 and NEON-enabled Arm platforms, 
    but other machines will have to build the wheel from the source distribution. 
    Building ``pyhmmer`` involves compiling HMMER3 and Easel, which requires a 
    C compiler to be available.

.. hint::

    Windows is not supported by HMMER, so it is not possible to build PyHMMER
    on Windows as the moment. Consider using a Python install inside the 
    `Windows Subsystem for Linux <https://learn.microsoft.com/en-us/windows/wsl/install>`_
    if you need PyHMMER on a Windows computer.


PyPi
^^^^

``pyhmmer`` 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/pyhmmer>`_.
It will install all dependencies then install ``pyhmmer`` either from a wheel if
one is available, or from source after compiling the Cython code :

.. code:: console

    $ pip install --user pyhmmer
    

Conda
^^^^^

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

.. code:: console

     $ conda install -c bioconda pyhmmer


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

A package recipe for Arch Linux can be found in the Arch User Repository
under the name `python-pyhmmer <https://aur.archlinux.org/packages/python-pyhmmer>`_.
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-pyhmmer


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 -Sy
    $ pacman -S python-pyhmmer


Piwheels
^^^^^^^^

PyHMMER works on Raspberry Pi computers (with NEON vectorization enabled), 
and pre-built wheels are compiled for `armv7l` on 
`piwheels <https://www.piwheels.org/project/pyhmmer/>`_.
Run the following command to install these instead of compiling from source:

.. code:: console

   $ pip3 install pyhmmer --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

    $ pip install -U git+https://github.com/althonos/pyhmmer

.. 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.


GitHub + ``setuptools``
^^^^^^^^^^^^^^^^^^^^^^^

If you do not want to use ``pip``, you can still clone the repository and
run the ``setup.py`` file manually, although you will need to install the
build dependencies (mainly `Cython <https://pypi.org/project/cython>`_):

.. code:: console

    $ git clone --recursive https://github.com/althonos/pyhmmer
    $ cd pyhmmer
    $ python setup.py build
    # python setup.py install

.. Danger::

    Installing packages without ``pip`` is strongly discouraged, as they can
    only be uninstalled manually, and may damage your system.