Installation

PySCeSToolbox is compatible with Mac OS X, Linux, and Windows. Operating system-specific instructions are discussed in the sections below. We have made special effort to provide as detailed instructions as possible, assuming a clean installation of each operating system prior to installation of PySCeSToolbox, and relatively limited knowledge of Python. If further assistance is required, please contact the developers.

Abbreviated requirements

PySCeSToolbox has a number of requirements that must be met before installation can take place. Fortunately most requirements, save for a few exceptions (as discussed in the operating system-specific sections), will be taken care of automatically during installation. An abbreviated list of requirements follows:

Windows

Windows requires the manual installation of Python 2.7, PySCeS and Maxima. Installation was tested on Windows 8 and 10.

Python

For Windows users (especially those unfamiliar with Python) we recommend using the Anaconda Python distribution (https://www.continuum.io/downloads#windows). This is a low fuss solution that will install Python on you system together with many of the packages necessary for running PySCeSToolbox. Download the appropriate Python 2.7 package from the download page (most probably the 64bit edition) and follow the instructions of the installation wizard.

PySCeS

After installing Anaconda, download and install the latest PySCeS binary package from break http://pysces.sourceforge.net/download.html. PySCeS can also be built from source (for more details see the instructions given at the provided URL).

Maxima

Maxima is necessary for generating control coefficient expressions using SymCA. The latest version of Maxima can be downloaded and installed from the Windows download page at http://maxima.sourceforge.net/download.html.

Windows might also require the path to maxima.bat to be defined in the psctb_config.ini file (found at C:\Pysces\psctb_config.ini by default). The default path included in psctb_config.ini is set as C:\Program Files?\Maxima?\bin\maxima.bat, where the question marks are wildcards (since the specific path will depend on the version of Maxima). If Maxima has been installed to a user specified directory, the correct path to the maxima.bat file must be specified here.

PySCeSToolbox

Now you are ready to install PySCeSToolbox. In the Anaconda Command Prompt (Start –> Anaconda Command Prompt), simply type in and execute the command:

pip install pyscestoolbox

As previously mentioned, this will automatically download both PySCeSToolbox and any outstanding requirements.

Enabling widgets

If you are running the Jupyter notebook for the first time, or if you have not yet enabled the notebook widgets you may need to run the following command:

jupyter nbextension enable --py --sys-prefix widgetsnbextension

We also recommend running the following two commands to enable the ModelGraph functionality of PySCeSToolbox. Rerunning this command may be necessary when updating/reinstalling PySCeSToolbox.

jupyter nbextension install --py --user d3networkx_psctb
jupyter nbextension enable --py --user d3networkx_psctb

Mac OS X (MacOS)

Mac OS X requires the manual installation of PySCeS and Maxima. While OS X comes pre-installed with Python 2.7 we still recommend installing a Python distribution such as Anaconda as it will take care of many of the SciPy stack requirements. Installation was tested on MacOS Sierra.

Python

One of the most simple ways to get Python on your system is to install the Anaconda Python distribution (https://www.continuum.io/downloads#macos). Download either of the Python 2.7 installers from the download page and follow the provided instructions.

PySCeS

Currently the only options for installing PySCeS on OS X are to either build it from source (see http://pysces.sourceforge.net/download.html) or to install it with pip via the command:

pip install pysces

Both cases requires the xcode command line tools and the gfortran compiler to be present on the system. The xcode command line tools can be installed by running:

sudo xcode-select --install

in the terminal and following the instructions given in the resulting popup (the full xcode package is not required. Gfortran dmg’s for your particular version of OS X (or MacOS) can downloaded and installed from http://gcc.gnu.org/wiki/GFortranBinaries.

Once the appropriate compilers are present the actual PySCeS install may be skipped as PySCeS will be installed automatically when PySCeSToolbox is installed.

Maxima

Maxima is necessary for generating control coefficient expressions using SymCA. The latest version of Maxima can be downloaded and installed from the MacOS download page at http://maxima.sourceforge.net/download.html. We recommend the VTK version of Maxima.

After downloading and installing the Maxima dmg, the following lines must be added to your .bash_profile file:

export M_PREFIX=/Applications/Maxima.app/Contents/Resources/opt
export PYTHONPATH=${M_PREFIX/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/:$PYTHONPATH
export MANPATH=${M_PREFIX/share/man:$MANPATH
export PATH=${M_PREFIX/bin:$PATH
alias maxima=rmaxima

PySCeSToolbox

Now you are ready to install PySCeSToolbox. In the Terminal (or iTerm) simply type in and execute the command:

pip install pyscestoolbox

As previously mentioned, this will automatically download both PySCeSToolbox and any outstanding requirements.

Note

You may encounter an error during the installation of PySCeSToolbox relating to the removal of temporary files on OS X or MacOS. This does not impact on the functioning of PySCeSToolbox at all, and we mean to address this bug in the future.

Enabling widgets

If you are running the Jupyter notebook for the first time, or if you have not yet enabled the notebook widgets you may need to run the following command:

jupyter nbextension enable --py --sys-prefix widgetsnbextension

We also recommend running the following two commands to enable the ModelGraph functionality of PySCeSToolbox. Rerunning this command may be necessary when updating/reinstalling PySCeSToolbox.

jupyter nbextension install --py --user d3networkx_psctb
jupyter nbextension enable --py --user d3networkx_psctb

Linux

Linux requires the manual installation Maxima and PySCeS. Most Linux systems come pre-installed with Python 2.7, however a Python distribution such as Anaconda may be used instead. Installation was tested on Ubuntu 16.04.

Python

We assume that your system comes with Python 2.7 and with pip (necessary for installing Python packages that are not available in your OS’s repositories). Pip may be installed from your OS’s repositories or by following the instructions found at https://pip.pypa.io/en/stable/installing/.

PySCeS

Currently the only options for installing PySCeS on Linux are to build it from source (see http://pysces.sourceforge.net/download.html) or to install it with the command:

pip install pysces

Both cases require the gcc, g++, and gfortran compilers to be present on the system. These compilers are most probably available from your OS’s repositories.

Once the appropriate compilers are present the actual PySCeS install may be skipped as PySCeS will be installed automatically when PySCeSToolbox is installed.

Maxima

Maxima is necessary for generating control coefficient expressions using SymCA. Maxima can be installed from your repositories, if available, otherwise the latest packages can be downloaded from the Linux link at http://maxima.sourceforge.net/download.html.

PySCeSToolbox

Now you are ready to install PySCeSToolbox. In the terminal simply type in and execute the command:

pip install pyscestoolbox

Enabling widgets

If you are running the Jupyter notebook for the first time, or if you have not yet enabled the notebook widgets you may need to run the following command:

jupyter nbextension enable --py --sys-prefix widgetsnbextension

We also recommend running the following two commands to enable the ModelGraph functionality of PySCeSToolbox. Rerunning this command may be necessary when updating/reinstalling PySCeSToolbox.

jupyter nbextension install --py --user d3networkx_psctb
jupyter nbextension enable --py --user d3networkx_psctb