Installation

Install from PyPI

To install the latest stable version of BoolDog from PyPI, use the following command:

pip install booldog

Optionally, specify a version.

Optional dependencies

To install optional dependencies, use the following command:

pip install booldog[<optional-dependencies>]

Where <optional-dependences> is a comma-separated list of the following:

• sbml: for SBML support (requires python-libsbml)

• networks: for network analyses (requires networkx and igraph)

• graphviz: for more elaborate STG visualization (requires pygraphviz)

Or: * all: for all optional dependencies

For details see the pyproject.toml file in the repository.

Install from GitHub

Install directly:

pip install git+https://github.com/NIB-SI/BoolDog.git

Download and install:

git clone https://github.com/NIB-SI/BoolDog.git
cd BoolDog
pip install .

Tests

See https://github.com/NIB-SI/BoolDog/tree/main/tests.

Uninstall

pip uninstall booldog

Known installation issues

1. Pyeda not compiling on Windows

This is an issue with pip and pyeda: https://github.com/cjdrake/pyeda/issues/126.

There is a possible fix, not yet merged: https://github.com/cjdrake/pyeda/pull/153.

To solve, download the appropriate binary from Christophe Gohlke’s pythonlibs page, and run

pip install <downloaded.whl>

Then re-attempt BoolDog installation.