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

.. note::

    Wheels are provided for Windows, Linux and MacOS x86-64 platforms, as well as 
    Linux and MacOS Aarch64 platforms. Other machines will have to build the wheel 
    from the source distribution. Building ``pyjess`` involves compiling the 
    Jess code, which requires a C compiler to be available.


PyPi
^^^^

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

.. code:: console

	$ pip install --user pyjess

To install additional dependencies required for parsing mmCIF files in 
addition to PDB files, run instead:

.. code:: console

	$ pip install --user pyjess[cif]


Conda
^^^^^

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

.. code:: console

   $ conda install -c bioconda pyjess


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

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


.. 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-pyjess


Piwheels
^^^^^^^^

PyJess works on Raspberry Pi computers, and pre-built wheels are compiled 
for `armv7l` platforms on piwheels. Run the following command to install these 
instead of compiling from source:

.. code:: console

   $ pip3 install pyjess --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/pyjess
   $ pip install --user ./pyjess

.. 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 + ``installer``
^^^^^^^^^^^^^^^^^^^^^^

If you do not want to use ``pip``, you can still clone the repository and
run ``build`` 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/pyjess
   $ cd pyjess
   $ 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.