INSTALL.rst

Installation of COBRApy

For installation help, please use the Google Group. For usage instructions, please see the documentation.

We only test against Python 3.6+, however, Python 3.4 or higher and even 2.7 should work mostly. For Windows users and possibly also Mac OS users, we recommend using the Anaconda Python distribution.

Stable version installation

COBRApy can be installed with any recent installation of pip. Instructions for several operating systems are below:

Mac OS X or Linux

1. We highly recommend that you create a Python virtual environment.
2. Install COBRApy when an environment is active by running pip install cobra in the terminal.

Microsoft Windows

If you heed our recommendation to use Anaconda, you can open an Anaconda shell and install COBRApy from the bioconda channel. Soon it should also be available from the conda-forge channel.

conda install -c bioconda cobra

Installation for development

Get the detailed contribution instructions for contributing to COBRApy.

Solvers

COBRApy uses optlang to interface the mathematical solvers used to optimize the created COBRA models. At the time of writing the supported solvers are:

• ILOG/CPLEX (available with Academic and Commercial licenses)
• Gurobi
• GLPK which is automatically installed as swiglpk