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 for all current releases of Debian *and* Ubuntu. If you have configured the NeuroDebian repositories correctly, the following command will install Psignifit3 for Python:
$ 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:
And then continue to install the desired version:
Or:
Note
If you need to build the documentation on your local machine, you may want to look at:
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:
$ 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 or Ubuntu 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:
$ 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:
$ 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:
$ 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:
$ 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:
$ 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:
$ export PYTHONPATH=psignifit-install/lib/python/
$ export LD_LIBRARY_PATH=psignifit-install/usr/lib/
Testing your Installation¶
Open a Python interpreter and type:
>>> 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:
$ 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:
$ 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:
$ 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:
$ 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:
$ make doc
The documentation can be found in doc-html/. Point your browser at doc-html/index.html to begin.
