Get the Latest¶
Download the most recent code from GitHub with:
$ python3 -m pip install git+https://github.com/pybel/pybel.git@develop
setup.py makes use of the
extras_require argument of
setuptools.setup() in order to make some heavy
packages that support special features of PyBEL optional to install, in order to make the installation more lean by
default. A single extra can be installed from PyPI like
python3 -m pip install -e pybel[ndex] or multiple can
be installed using a list like
python3 -m pip install -e pybel[ndex,owl]. Likewise, for developer installation,
extras can be installed in editable mode with
python3 -m pip install -e .[ndex] or multiple can be installed
using a list like
python3 -m pip install -e .[ndex,owl]. The avaliable extras are:
ndex2 supports download and upload to the Network Data Exchange.
This extra installs support for Artifactory and enables many of the functions in
This extra installs support for using OWL ontologies as namespaces via the
onto2nx package. In the future,
this extra will include other wrappers around packages like
obonet for OBO support.
This extension installs the
py2neo package to support upload and download to Neo4j databases.
This extra installs support for
indra, the integrated network dynamical reasoner and assembler. Because it also
represents biology in BEL-like statements, many statements from PyBEL can be converted to INDRA, and visa-versa. This
package also enables the import of BioPAX, SBML, and SBGN into BEL.
- PyBEL extends the
networkxfor its core data structure. Many of the graphical aspects of
matplotlib, which is an optional dependency.
HTMLlib5is 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.
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 with one of the following commands:
pybel manage drop(unix)
python3 -m pybel manage drop(windows)
- Removing the folder
PyBEL will build a new database and populate it on the next run.