Installation

BayesPy is a Python 3 package and it can be installed from PyPI or the latest development version from GitHub. The instructions below explain how to set up the system by installing required packages, how to install BayesPy and how to compile this documentation yourself. However, if these instructions contain errors or some relevant details are missing, please file a bug report at https://github.com/bayespy/bayespy/issues.

Installing BayesPy

BayesPy can be installed easily by using Pip if the system has been properly set up. If you have problems with the following methods, see the following section for some help on installing the requirements. For instance, a bug in recent versions of h5py and pip may require you to install some of the requirements manually.

For users

First, you may want to set up a virtual environment. Using virtual environment is optional but recommended. To create and activate a new virtual environment, run (in the folder in which you want to create the environment):

virtualenv -p python3 --system-site-packages ENV
source ENV/bin/activate

The latest release of BayesPy can be installed from PyPI simply as

pip install bayespy

If you want to install the latest development version of BayesPy, use GitHub instead:

pip install git+https://github.com/bayespy/[email protected]

For developers

If you want to install the development version of BayesPy in such a way that you can easily edit the package, follow these instructions. Get the git repository:

git clone https://github.com/bayespy/bayespy.git
cd bayespy

Create and activate a new virtual environment (optional but recommended):

virtualenv -p python3 --system-site-packages ENV
source ENV/bin/activate

Install BayesPy in editable mode:

pip install -e .

Checking installation

If you have problems installing BayesPy, read the next section for more details. It is recommended to run the unit tests in order to check that BayesPy is working properly. Thus, install Nose and run the unit tests:

pip install nose
nosetests bayespy

Installing requirements

BayesPy requires Python 3.3 (or later) and the following packages:

  • NumPy (>=1.10.0),
  • SciPy (>=0.13.0)
  • matplotlib (>=1.2)
  • h5py

Ideally, Pip should install the necessary requirements and a manual installation of these dependencies is not required. However, there are several reasons why the installation of these dependencies needs to be done manually in some cases. Thus, this section tries to give some details on how to set up your system. A proper installation of the dependencies for Python 3 can be a bit tricky and you may refer to http://www.scipy.org/install.html for more detailed instructions about the SciPy stack. Detailed instructions on installing recent SciPy stack for various platforms is out of the scope of these instructions, but we provide some general guidance here. There are basically three ways to install the dependencies:

  1. Install a Python distribution which includes the packages. For Windows, Mac and Linux, there are several Python distributions which include all the necessary packages: http://www.scipy.org/install.html#scientific-python-distributions. For instance, you may try Anaconda or Enthought.

  2. Install the packages using the system package manager. On Linux, the packages might be called something like python-scipy or scipy. However, it is possible that these system packages are not recent enough for BayesPy.

  3. Install the packages using Pip:

    pip install "distribute>=0.6.28"
    pip install "numpy>=1.10.0" "scipy>=0.13.0" "matplotlib>=1.2" h5py
    

    This also makes sure you have recent enough version of Distribute (required by Matplotlib). However, this installation method may require that the system has some libraries needed for compiling (e.g., C compiler, Python development files, BLAS/LAPACK). For instance, on Ubuntu (>= 12.10), you may install the required system libraries for each package as:

    sudo apt-get build-dep python3-numpy
    sudo apt-get build-dep python3-scipy
    sudo apt-get build-dep python3-matplotlib
    sudo apt-get build-dep python-h5py
    

    Then installation using Pip should work.

Compiling documentation

This documentation can be found at http://bayespy.org/ in HTML and PDF formats. The documentation source files are also readable as such in reStructuredText format in doc/source/ directory. It is possible to compile the documentation into HTML or PDF yourself. In order to compile the documentation, Sphinx is required and a few extensions for it. Those can be installed as:

pip install "sphinx>=1.2.3" sphinxcontrib-tikz sphinxcontrib-bayesnet sphinxcontrib-bibtex "numpydoc>=0.5"

Or you can simply install BayesPy with doc extra, which will take care of installing the required dependencies:

pip install bayespy[doc]

In order to visualize graphical models in HTML, you need to have ImageMagick or Netpbm installed. The documentation can be compiled to HTML and PDF by running the following commands in the doc directory:

make html
make latexpdf

You can also run doctest to test code snippets in the documentation:

make doctest

or in the docstrings:

nosetests --with-doctest --doctest-options="+ELLIPSIS" bayespy