Unfortunately there are some manual steps in the installation process.

First (assuming you are using OS X and Homebrew) install ZeroMQ and gfortran:

$ brew install zeromq
$ brew install gfortran

Create an isolated virtualenv called 'lab-md-analysis' and activate it:

$ python vendor/virtualenv.py lab-md-analysis
$ source lab-md-analysis/bin/activate

It is necessary to install readline by hand using easy_install instead of pip, and matplotlib must be installed after pip install -r requirements.txt

(lab-md-analysis)$ easy_install readline
(lab-md-analysis)$ pip install -r requirements.txt
(lab-md-analysis)$ pip install matplotlib

(You may also find that it's necessary to remove scipy from requirements.txt and install it via pip install scipy at the end.)

Once the smoke test passes, install the lab repo:

$ npm install

(optionally)

$ npm link <path to local installation of lab repo>

(lab-md-analysis)$ ipython --pylab
...
In [1]: x = randn(100000)

In [2]: hist(x, 100)

You should see a histogram approximating a normal distribution.

Some data from the constrained random walk of the center of mass of the Lab molecular dynamics simulation is in data/. Once you have done the install steps above, to plot this data, run ./plot-cm-random-walk.py in the root of this repository to generate the figure; open figure/cm-random-walk.png to view the figure.

You may find that you need Python 2.7 installed.