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.
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 :
$ pip install --user pyjess
To install additional dependencies required for parsing mmCIF files in addition to PDB files, run instead:
$ pip install --user pyjess[cif]
Conda#
PyJess is also available as a recipe
in the bioconda channel. To install, simply
use the conda installer:
$ 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. It will always match the latest release from PyPI.
Steps to install on ArchLinux depend on your AUR helper
(yaourt, aura, yay, etc.). For aura, you’ll need to run:
$ aura -A 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:
$ pip3 install pyjess --extra-index-url https://www.piwheels.org/simple
Check the piwheels documentation 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):
$ 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):
$ 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.