Installation for Ubuntu 12.04¶

Required dependencies¶

First, be sure that your system is up-to-date:

$ sudo apt-get update
$ sudo apt-get upgrade

Then install the following packages:

$ sudo apt-get install python-dev python-numpy python-scipy python-matplotlib python-pip python-sympy gcc

The version of nibabel and nipy packages available in the Ubuntu 12.04 repositories are too old for PyHRF, install newer versions with:

$ pip install --user nibabel
$ pip install --user nipy

Optional dependencies¶

Install the following packages:

$ sudo apt-get install python-scikits-learn python-joblib python-pygraph python-pygraphviz python-PIL python-munkres python-paramiko

This dependency is too old on the packages system manager:

$ pip install --user sphinx

If you already installed sphinx with the package manager, add the flag --upgrade to the previous command

If you plan to use our specific viewer (pyhrf_viewer), run:

$ sudo apt-get install python-qt4

PyHRF Installation¶

Install package from PyPI. It is recommended to install the package in user mode (the --user option).

$ pip install --user pyhrf

If you install in user mode, you need to concatenate $HOME/.local/bin to your $PATH environment variable by adding the following to your $HOME/.bashrc file:

if [ -d "$HOME/.local/bin" ]; then
    PATH="$HOME/.local/bin:$PATH"
fi

Update your $PATH environment variable by sourcing your .bashrc file:

$ source ~/.bashrc

Then you can run the unit tests:

$ pyhrf_maketests

PyHRF update¶

To update the package, use pip:

$ pip install --upgrade --user pyhrf

PyHRF uninstallation¶

To remove pyhrf package, use pip:

$ pip uninstall pyhrf