============ Installation ============ Basic installation ================== .. include:: ../README.rst :start-after: installation-start :end-before: installation-end 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 .. code-block:: guess $ mkvirtualenv cameo # or whatever you'd like to call your virtual environment $ workon cameo and then continue with the installation instructions described above. 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. .. code-block:: guess $ conda create -y -n cameo3.4 python=3.4 lxml scipy pandas numexpr matplotlib Then follow the basic installation instructions described above. Soft dependencies ================= The following soft dependencies can be installed all at once using .. code-block:: guess $ pip install cameo[all] or individually by specifying individual categories of dependencies. For example .. code-block:: guess $ pip install cameo[test, sbml, ...] The following categories are available:: 'docs': ['Sphinx>=1.3.5', 'numpydoc>=0.5'], 'plotly': ['plotly>=1.9.6'], 'bokeh': ['bokeh<=0.12.1'], 'jupyter': ['jupyter>=1.0.0', 'ipywidgets>=4.1.1'], 'test': ['pytest', 'pytest-cov'], 'parallel': ['redis>=2.10.5', 'ipyparallel>=5.0.1'], 'sbml': ['python-libsbml>=5.13.0', 'lxml>=3.6.0'] .. _optlang: https://github.com/biosustain/optlang .. _virtualenv-burrito: https://github.com/brainsik/virtualenv-burrito .. _virtualenv: https://pypi.python.org/pypi/virtualenv .. _virtualenvwrapper: https://pypi.python.org/pypi/virtualenvwrapper