Installation

PyBEL is tested on both Python3 and legacy Python2 installations on Mac OS and Linux using Travis CI.

Warning

PyBEL is not thoroughly tested on Windows.

Installation

Easiest

Download the latest stable code from PyPI with:

$ python3 -m pip install pybel

Get the Latest

Download the most recent code from GitHub with:

$ python3 -m pip install git+https://github.com/pybel/pybel.git@develop

For Developers

Clone the repository from GitHub and install in editable mode with:

$ git clone https://github.com/pybel/pybel.git@develop
$ cd pybel
$ python3 -m pip install -e .

Caveats

  • PyBEL extends the networkx for its core data structure. Many of the graphical aspects of networkx depend on matplotlib, which is an optional dependency.
  • If HTMLlib5 is installed, the test that’s supposed to fail on a web page being missing actually tries to parse it as RDFa, and doesn’t fail. Disregard this.

Upgrading

During the current development cycle, programmatic access to the definition and graph caches might become unstable. If you have any problems working with the database, try removing it either by

  1. Running pybel manage remove (unix)
  2. Running python3 -m pybel manage remove (windows)
  3. Removing the folder ~/.pybel

PyBEL will build a new database and populate it on the next run.