Basic installation

Use pip to install cameo from PyPI.

$ pip install cameo

In case you downloaded or cloned the source code from GitHub or your own fork, you can run the following to install cameo for development.

$ pip install -e <path-to-cameo-repo>  # recommended

You might need to run these commands with administrative privileges if you’re not using a virtual environment (using sudo for example). Please check the documentation for further details.

Setting up a virtual environment first

We highly recommended installing cameo inside a virtual environment (virtualenv). virtualenvwrapper tremendously simplifies using virtualenv and can easily be installed using virtualenv-burrito. Once you installed virtualenv and virtualenvwrapper, run

$ mkvirtualenv cameo  # or whatever you'd like to call your virtual environment
$ workon cameo

and then continue with the installation instructions described below.

Alternatively you can use conda if you are an Anaconda user (there is no conda recipe for cameo though so you’ll still need to install it using pip). Do the following to create a virtual environment and get some of the heavier dependencies out of the way.

$ conda create -y -n cameo3.4 python=3.4 lxml scipy pandas numexpr matplotlib

Then follow the basic installation instructions described below.

Soft dependencies

The following soft dependencies can be installed all at once using

$ pip install cameo[all]

or individually by specifying individual categories of dependencies. For example

$ pip install cameo[test, sbml, ...]

The following categories are available:

'docs': ['Sphinx>=1.3.5', 'numpydoc>=0.5'],
'plotly': ['plotly>=4.12.0'],
'bokeh': ['bokeh<=0.12.1'],
'jupyter': ['jupyter>=1.0.0', 'ipywidgets>=4.1.1'],
'test': ['pytest', 'pytest-cov', 'pytest-benchmark'],
'parallel': ['redis>=2.10.5', 'ipyparallel>=5.0.1'],
'sbml': ['python-libsbml>=5.13.0', 'lxml>=3.6.0']

Working with jupyter lab

Both plotly and escher require additional steps to work with jupyter lab. For escher (based on escher-readme):

$ jupyter labextension install @jupyter-widgets/jupyterlab-manager
$ python -m jupyter labextension install escher

For plotly (based on plotly-docs), identify your version of plotly:

$ pip freeze | grep plotly  # e.g. 4.14.3
$ python -m jupyter labextension install jupyterlab-plotly@4.14.3