This guide provides instructions for how to get apsis running on your system. The guide is mainly targeted at Ubuntu/Debian and Mac OS users, However as a user of another linux based OS you should easily to be able to follow this guide with the methods used in your distro.
Since GPy requires Python 2, so does apsis.
Apsis requires the following python frameworks and their dependencies to be installed.
- numpy
- scipy
- sklearn
- gpY, versions >= 0.6.0
- matplotlib
Note
For apsis versions newer than December 2014 older GPy versions will no longer work. It has been developed and tested to work with GPy version 0.6.0.
Operating Systems
- developed on Ubuntu 14.04/Arch. Tested on Mac OS X Yosemite.
- most unix based operating systems for which the dependencies listed above are available should work.
- Currently, tests for Windows support is in progress.
apsis can easiest be installed using PIP by just executing
$ pip install apsis --pre
If the installation fails then you most likely do not have the appropriate non-python requirements for one of the packages installed above. These are a fortran compiler and a blas library (for scipy), libpng and libfreetpye (for matplotlib).
On a newly installed Ubuntu system (tested with 15.04), execute
$ sudo apt-get install python-pip python-dev gfortran libpng12-dev libfreetype6-dev libopenblas-dev
followed by the following pip commands:
$ pip install numpy $ pip install scipy $ pip install --pre apsis
The compilation of matplotlib and scipy have several non-python dependencies such as C and fortran compilers or linear algebra libraries. Also you should install pip
to install the newest versions of the python dependencies.
Tested on Ubuntu 14.04 the following command should give you what you need. If you run on another OS please check out the documentation of the listed prerequesites above for how to install them.
$ sudo apt-get install git build-essential python-pip gfortran libopenblas-dev liblapack-dev libfreetype6-dev libpng12-dev python-dev
You need to update your python version to a later version than the one distributed with your OS.
Installation works easy when using homebrew package manager, please see the homebrew page for how to install it.
http://brew.sh/
When homebrew is installed follow these instructions.
Install another and up to date Python distribution.
$ brew install python $ brew linkapps python
Install pip
$ brew install pip $ brew linkapps pip
Make sure you have
pip
and the non-python prerequisites for the libraries listed above installed on your systemInstall numpy.
$ pip install --upgrade numpy
Install scikit learn.
$ pip install --upgrade scikit-learn
Install matplotlib.
$ pip install --upgrade matplotlib
Install gpY. It will also install the required scipy version for you.
$ pip install --upgrade gpy==0.6.0
You can find the current dev version on github.. To be ready to use you need to
Pull the code repository
$ git clone https://github.com/FrederikDiehl/apsis.git
Set the PYTHONPATH environment variable to include the apsis- and apsis_client folders
$ export PYTHONPATH=[WHEREVER]/apsis/code
Finally run the test suite to see if everything works alright:
$ cd apsis/code/apsis $ nosetests
Which should print something like
$ nosetests . ---------------------------------------------------------------------- Ran XX tests in YYs OK