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Comment: Migrated to Confluence 5.3

The latest release of pyxnat in the Python Package Index (pypi) has a few bugs and missing features that get in the way of following the HCP-pyxnat tutorial. I strongly recommend using a Python virtual environment with our fork of pyxnat, which also includes some customizations for ConnectomeDB and the OHBM Hackathon.

To set up the virtual environment on Linux or Mac OS X:

  1. Make sure you have virtualenv in your python installation: look here for details.
  2. Create the virtual environment.

    Code Block
    titleCreating a Python virtual environment
    $ mkdir ~/ohbm-hcp
    $ cd ~/ohbm-hcp
    $ virtualenv pyxnat-env
  3. Source the virtual environment's activate script; you'll need to do this for any shell where you're using this virtual environment. The exact commands needed depend on which shell you use: the most common choices are bash (or sh, the original Bourne shell) or csh.

    Code Block
    titleSelecting the virtual environment (bash/sh)
    $ . pyxnat-env/bin/activate
    (pyxnat-env) $ 
    Code Block
    titleSelecting the virtual environment (csh)
    % source pyxnat-env/bin/activate.csh
    [pyxnat-env] %

    Note that your shell prompt now includes the name of the virtual environment (pyxnat-env).

  4. Install pyxnat into the virtual environment: 

    Code Block
    titleInstalling pyxnat
    (pyxnat-env) $ pip install git+git://
Aside for Python experts: since I work on pyxnat as well as with pyxnat, I usually clone the pyxnat source tree and run python develop instead. Unless you anticipate making changes to pyxnat itself, the above sequence seems less complicated.

Now that you have the virtual environment set up, you can cd to whatever directory you need; your PATH has been changed so that you'll be running the Python executable from the virtual environment, with the packages you've installed. If you rely on other non-standard-library Python packages, you'll need to install those into this virtual environment as well.

Remember you must source the activate script in every shell where you intend to use pyxnat. The easiest way to verify this is, before you run python, to make sure that the virtual environment name (pyxnat-env) appears in the shell prompt.