Linux (Debian/Ubuntu)
=====================
This section details how to install the Python version and the command line
version of Psignifit from a source download.
.. note::
Currently (Jun 2012) we provide experimental support for packages via
`Neurodebian <http://neuro.debian.net/>`_ for `all current releases of
Debian *and* Ubuntu
<http://neuro.debian.net/pkgs/python-pypsignifit.html>`_. If you have
configured the NeuroDebian repositories correctly, the following command
will install Psignifit3 for Python:
.. code-block:: console
$ sudo apt-get install python-pypsignifit
This option is the easiest route to getting python-psignifit installed.
.. note::
If you wish (or need) to install from source, first look at:
* `Obtaining the Sources`_
* `Installing Dependencies`_
And then continue to install the desired version:
* `Installing Psignifit for Python (python-psignifit)`_
Or:
* `Installing the Command Line Interface (cli)`_
.. note::
If you need to build the documentation on your local machine, you may want to
look at:
* `Building the documentation`_
Obtaining the Sources
---------------------
You will want to download the most recent version of psignifit from:
`<http://sourceforge.net/projects/psignifit/files/>`_. You will want the
``zip`` file, for example ``psignifit_3.0_beta.20120207.1.zip``.
Extract the file, and enter the directory by typing:
.. code-block:: console
$ unzip psignifit_3.0_beta.<date of the snapshot>.1.zip
$ cd psignifit_3.0_beta.<date of the snapshot>.1
replacing ``<date of the snapshot>`` by the date string in the file
name.
Installing Dependencies
-----------------------
If you are using `Debian <http://www.debian.org/>`_ or `Ubuntu
<http://www.ubuntu.com/>`_ the following packages need to be installed.
* ``make``
* ``gcc``
If you additionally wish to install the Python version, you must install:
* ``python``
* ``python-dev``
* ``python-numpy (provides python-numpy-dev)``
* ``python-scipy``
* ``python-matplotlib``
* ``python-nose``
* ``swig``
In order to check whether or not you have the packages already installed, type:
.. code-block:: console
$ aptitude search make gcc python python-dev \
python-numpy python-scipy python-matplotlib python-nose swig
Packages that are installed on your machine are listed with a leading ``<i>``
In order to install missing packages, type:
.. code-block:: console
$ sudo aptitude install make gcc python python-dev \
python-numpy python-scipy python-matplotlib python-nose
If you are using a different Linux distribution, please refer to the
documentation of that system for more information on how to install the required
software.
Installing Psignifit for Python (python-psignifit)
--------------------------------------------------
System-wide installation
~~~~~~~~~~~~~~~~~~~~~~~~
Installing system wide is simple, type:
.. code-block:: console
$ make install
as ``root`` and everything will be installed to the right place.
Install into a Custom Location
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you do not have root privileges, you can use the ``DESTDIR`` variable to
install into an alternative location, for example the directory
``psignifit-install`` in your home-directory:
.. code-block:: console
$ mkdir $HOME/psignifit-install
$ make DESTDIR=$HOME/psignifit-install install
The first command first creates the directory ``$HOME/psignifit-install``
where ``$HOME`` is automatically replaced by the name of your own
home-directory. The second command will install Psignifit into that directory.
To use psignifit from, you will also have to set the ``$PYTHONPATH`` and
``$LD_LIBRARY_PATH`` environment variables. Either invoke the Python
interpreter from the command line by typing:
.. code-block:: console
$ PYTHONPATH=psignifit-install/lib/python/ LD_LIBRARY_PATH=psignifit-install/usr/lib/ ipython
Or, you set the variables in your ``.bashrc`` (or equivalent) file
by adding the line:
.. code-block:: console
$ export PYTHONPATH=psignifit-install/lib/python/
$ export LD_LIBRARY_PATH=psignifit-install/usr/lib/
Testing your Installation
~~~~~~~~~~~~~~~~~~~~~~~~~
Open a Python interpreter and type:
.. code-block:: pycon
>>> import pypsignifit
>>> pypsignifit.version
...
If you can see a version string, such as ``snap-2011-10-28-59-gda5adc6`` you
installation was probably successful.
Installing the Command Line Interface (cli)
-------------------------------------------
System-wide installation
~~~~~~~~~~~~~~~~~~~~~~~~
Installing system wide is simple, type:
.. code-block:: console
$ make cli-install
as ``root`` and everything will be installed to the right place.
Install into a Custom Location
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If you do not have root privileges, you can use the ``DESTDIR`` variable to
install into an alternative location, for example the directory
``psignifit-install`` in your home-directory:
.. code-block:: console
$ mkdir $HOME/psignifit-install
$ make DESTDIR=$HOME/psignifit-install cli-install
The first command first creates the directory ``$HOME/psignifit-install``
where ``$HOME`` is automatically replaced by the name of your own
home-directory. The second command will install Psignifit into that directory.
Additionally you must add the installation directory to you ``$PATH``, by
typing:
.. code-block:: console
$ export PATH=$PATH:$HOME/psignifit-install/usr/bin
Or, for a more permanent solution and the above line to ``.bashrc`` (or
equivalent) file.
Testing your Installation
~~~~~~~~~~~~~~~~~~~~~~~~~
Now, you should be able to call:
.. code-block:: console
$ psignifit-mcmc -h
$ psignifit-diagnostics -h
$ psignifit-bootstrap -h
$ psignifit-mapestimate -h
And see some usage messages after each call.
Building the documentation
--------------------------
We recommend you to use the documentation we supply on the website. But in case
you would like to build it locally, you must first install the following
packages:
* ``python-sphinx``
* ``doxygen``
And then do:
.. code-block:: console
$ make doc
The documentation can be found in ``doc-html/``. Point your browser at
``doc-html/index.html`` to begin.