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

.. caution::

    Windows is not supported by Infernal, so it is not possible to build 
    PyInfernal 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 PyInfernal on a Windows computer.


PyPi
^^^^

``pyinfernal`` 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 ``pyinfernal`` either from a wheel if
one is available, or from source after compiling the Cython code :

.. code:: console

    $ pip install --user pyinfernal

.. 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 ``pyinfernal`` involves compiling Infernal, which requires a 
    C compiler to be available.


.. Conda
.. ^^^^^

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

.. .. code:: console

..      $ conda install -c bioconda pyinfernal


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

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


.. 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-pyinfernal


.. Piwheels
.. ^^^^^^^^

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

.. .. code:: console

..    $ pip3 install pyinfernal --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/pyinfernal

.. 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 + ``build``
^^^^^^^^^^^^^^^^^^

If you do not want to use ``pip``, you can still clone the repository and
use ``build`` and ``installer`` manually:

.. code:: console

    $ git clone --recursive https://github.com/althonos/pyinfernal
    $ cd pyinfernal
    $ python -m build .
    # python -m installer dist/*.whl

.. Danger::

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