Installation of cobrapy
All releases require Python 2.7+ or 3.4+ to be installed before proceeding. Mac OS X (10.7+) and Ubuntu ship with Python. Windows users without python can download and install python from the python website. Please note that though Anaconda and other python distributions may work with cobrapy, they are not explicitly supported (yet!).
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
- install pip.
- In a terminal, run
sudo pip install cobra
We highly recommend updating
pip beforehand (
pip install pip --upgrade).
The preferred installation method on Windows is also to use pip. The latest Windows installers for Python 2.7 and 3.4 include pip, so if you use those you will already have pip.
- In a terminal, run
C:\Python27\Scripts\pip.exe install cobra(you may need to adjust the path accordingly).
To install without pip, you will need to download and use the appropriate installer for your version of python from the python package index.
Installation for development
Get the detailed contribution instructions for contributing to cobrapy.
Installation of optional dependencies
On windows, these can downloaded from [this site] (http://www.lfd.uci.edu/~gohlke/pythonlibs/). On Mac/Linux, they can be installed using pip, or from the OS package manager (e.g brew, apt, yum).
- libsbml >= 5.10 to read/write SBML level 2
- Windows libsbml installer
sudo pip install python-libsbmlon Mac/Linux
- lxml to speed up read/write of SBML level 3 files.
- scipy >= 0.11 for MOMA and saving to *.mat files. - Windows scipy installer
- pytest and pytest-benchmark are required for testing
You can install all packages directly by
pip install "cobra[all]"
cobrapy uses optlang to interface the mathematical solvers used to optimize the created COBRA models, which at the time of writing
Testing your installation
While it is not a hard requirement for using cobrapy, you need pytest and pytest-benchmark to run its tests. First do
pip install pytest pytest-benchmark
or to install cobrapy directly with the test dependencies
pip install "cobra[test]"
Then start python and type the following into the Python shell
from cobra.test import test_all test_all()
You should see some skipped tests and expected failures, and the
function should return
0. If you see a value other than
0 please file
an issue report.