These installation instructions are for a general Linux system but should work with minor changes on other OSes (Windows, MacOS, etc..). They assume that most software will be installed in $HOME/local.
I find the easiest way to install Python packages is into a virtual environment created by virtualenv. If you do not have administrator privileges or even if you do, then virtualenv is a good way to manage what Python packages you install. These installation instructions are based on this method, although you could easily adapt them to install straight into your machine’s Python environment. If not using virtualenv I recommend using pip or failing that easy_install or the standard Python method of downloading a tarball, unpacking it and installing with:
python setup.py install
pybool relies on the following third-party softwares. Many of these can probably be installed using your operating system’s package manager which should be more straight-forward.
Python 2.5 or newer. Development has been done on Python 2.6 but it should work on Python 2.5 and Python 2.7. It should not be difficult to get pybool working on Python 3 but it may not work out of the box. If installing on a Linux system with a package manager you will need the development package that contains the Python header files, for example the python-dev package on Ubuntu.
A tool to create virtual Python environments called virtualenv. Please see the installation instructions on its website. You can install pybool without using virtualenv but you will need to adapt these instructions somewhat.
A C++ compiler to compile the core C++ algorithm. All development has been done with GCC 4.4.3 and 4.6.3 but other versions and compilers should work.
The Boost C++ libraries: I have used version 1.45 although other versions should work. Following the commands given at the Boost website is straightforward, e.g.:
./bootstrap.sh --help
./bootstrap.sh --prefix=$HOME/local
./bjam --with-python --prefix=$HOME/local install release
should install the boost Python library and the necessary headers. Once they are installed, you will need to update your LD_LIBRARY_PATH environment variable, e.g.:
export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH
so that the shared objects can be found at runtime.
GraphViz tools: These are used to generate the network diagrams. In particular neato must be in your PATH.
The following softwares are optional
Create a virtual environment to install pybool and its dependencies into:
virtualenv --system-site-packages $HOME/local/pybool-env
If you are using a C shell then activate the environment with:
source $HOME/local/pybool-env/bin/activate
or if you are using a bash shell:
. $HOME/local/pybool-env/bin/activate
If you are using something else then look at the instructions at virtualenv. Every time you want to run pybool you will need to activate its environment in this way.
If you haven’t already, download the pybool source distribution, unpack it somewhere and change into the top level directory.
This Python package uses aksetup for installation, which means that installation should be easy and quick. Try:
./configure.py --help
to examine the possible options. By the way, if a configuration option says several ok, then you may specify several values, separated by commas. Depending on where the boost libraries are installed on your system, something like the following should work:
./configure.py --boost-inc-dir=$HOME/local/include --boost-lib-dir=$HOME/local/lib
python setup.py build
python setup.py install
Configuration is obtained from files in this order (local, user, global):
$PACKAGEDIR/siteconf.py
$HOME/.aksetup-defaults.py
/etc/aksetup-defaults.py
Once you’ve run configure, you can copy options from your siteconf.py file to one of these files, and you won’t ever have to configure them again manually. In fact, you may pass the options --update-user and --update-global to configure, and it will automatically update these files for you. This is particularly handy if you want to perform an unattended or automatic installation via easy_install.
To check that pybool has been successfully installed, change to an empty directory and try running the following command:
python -c "import pybool.cNetwork"
If you see any errors such as:
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: libboost_python.so.1.45.0: cannot open shared object file: No such file or directory
you probably have not updated your LD_LIBRARY_PATH successfully.
The next step is to use the tutorial on how to use pybool. Enjoy!