Ubuntu: Set up a virtual environment with IPython, numpy and pandas

So this is a much needed update for an earlier post on setting up a virtual environment. The original post was based on one I found technomilk-setup. My prior post is mofj-setup. Most of the time you read about setting up virtual environments, it is in the context of web development. But the same benefits hold for analysis and research software. You want to be able to reproduce results. It also increases security not to be adding all the unverified libraries with root level privileges. This post is a minor modification of the outstanding tutorial I have been using for the last few months. There are three reasons why this needs to be updated:

there is another version of python

it does not cover IPython

pythonbrew which managed the versions of python is longer maintained

I will repeat the steps here. First install the c libraries that python needs to function.

I use apt-get in ubuntu so type

cd ~

sudo apt-get install libsqlite3-dev libbz2-dev libxml2-dev libxslt-dev curl

Get a non-system version of python.

Then install the pyenv scripts from source. Here is the link for pyenv. Pyenv is in many ways more sophsticated than pythonbrew. It is written in bash not any particular version of python. The advantage is that it is not dependent on anything in the language itself. The disadvantage is that it is much harder to read the code and understand the nature of a bug. One important trick is to turn on the debug flag. As my advisor always used to tell me there was nothing more brain-dead than a shell, I have spent most of my time avoiding them. I use the Bourne Again Shell that comes with Ubuntu. The syntax is tricky because everything is a string. Variable definitions can’t have any spaces. There are some good tutorials which I will include later. For now, here are three links that can tell you the differences between bash and an interpreted language like Python.

python-bash

when-to-use

can-i-replace

I am assuming you have git installed. If not, git-tutorial is a good tutorial for installing git.

cd ~
git clone git://github.com/yyuu/pyenv.git .pyenv

Define environment variable PYENV_ROOT to point to the path where pyenv repo is cloned and add $PYENV_ROOT/bin to your $PATH for access to the pyenv command-line utility.

echo ‘export PYENV_ROOT=”$HOME/.pyenv”‘ >> ~/.bashrc
echo ‘export PATH=”$PYENV_ROOT/bin:$PATH”‘ >> ~/.bashrc

Add pyenv init to your shell to enable shims and autocompletion. Shims and binstubs are worth knowing about. You can read up on them understand-shims.

echo ‘eval “$(pyenv init -)”‘ >> ~/.bashrc

Restart your shell so the path changes take effect. You can now begin using pyenv.

exec $SHELL

Install Python versions into $PYENV_ROOT/versions. For example, to install Python 2.7.5, download and unpack the source, then run:

pyenv install 2.7.5
pyenv rehash

And now we have to tell the system to use this new version of python

pyenv local 2.7.5

Install virtualenv

We are going to do two tricky things we are going to install virtualenv in the version of python AND install the pyenv plugin virtualenv.

pip install virtualenv

and to install the pyenv plugin.

git clone git://github.com/yyuu/pyenv-virtualenv.git ~/.pyenv/plugins/pyenv-virtualenv

You are now ready to create a virtual environment in a non-system version of python. I don’t understand why this will not work if you are anywhere else.

pyenv virtualenv
pyenv virtualenv 2.7.5 no-more-drug-war

We can list all of the virtual environments. Change directory to the one you want to work in and in my case the virtual environment is no-more-drug-war:

pyenv activate no-more-drug-war:

We can list the virtualenvs:

#+BEGIN_SRC sh :exports code pyenv virtualenvs dssg (created from /usr) lc (created from /usr

no-more-drug-war (created from /usr)

scrp (created from /usr) seek (created from /usr) \#+END_SRC

To review, we can activate the virtual environment with the following command.

pyenv activate no-more-drug-war

You can deactivate the activate’d virtualenv by pyenv deactivate.

pyenv deactivate

So, in order to know what packages we have installed at any time, we install yolk.

pip install yolk

Do not type sudo! To see what it installed at any time:

yolk -l

A list of further packages for IPython are available here. Type these individually and they each may take a few minutes to install.

pip install jinja2

pip install pyzmq

pip install pygments

pip install tornado

pip install nose

pip install numpy

pip install scipy

pip install matplotlib

pip install pandas

pip install ipython

Turning it on and off

Now to get out of your virtual environment, just type

pyenv deactivate

To get back in, type:

pyenv activate no-more-drug-war

Good luck!

I will try to send a pull request to add some of this to pyenv and correct my question on stack overlfow.