Installation

PySCeSToolbox is compatible with macOS, Linux, and Windows, and can be installed either with conda in an Anaconda environment, or with pip in an existing Python environment. 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.

Below follow abbreviated requirements, installation instructions for conda and pip, as well as operating system-specific instructions for setting up Maxima.

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:

Installation on Anaconda

For most users (especially those unfamiliar with Python) we recommend using the Anaconda Python distribution (https://www.anaconda.com/products/individual#Downloads). This is a low fuss solution available for all three operating systems that will install Python on you system together with many of the packages necessary for running PySCeSToolbox. Download the appropriate Python 3.7 package from the download page (most probably the 64bit edition) and follow the instructions of the installation wizard.

Virtual environments

Virtual environments are a great way to keep package dependencies separate from your system files. It is highly recommended to install PyscesToolbox into a separate environment, which first must be created (here we create an environment called pysces). It is recommended to use a Python version >=3.6 (here we use Python 3.7). After creation, activate the environment:

(base) $ conda create -n pysces python=3.7
(base) $ conda activate pysces

Then install PyscesToolbox:

(pysces) $ conda install -c pysces -c sbmlteam pyscestoolbox

Be sure to specify the pysces and sbmlteam channels in the command line as above, otherwise some of the packages won’t be found. The required Python dependencies will be installed automatically. For Maxima, refer to the operating system-specific instructions below.

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:

(pysces) $ jupyter nbextension enable --py --sys-prefix widgetsnbextension

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

(pysces) $ jupyter nbextension install --py --user d3networkx_psctb
(pysces) $ jupyter nbextension enable --py --user d3networkx_psctb

Alternative: direct pip-based install

First be sure to have Python 3 and pip installed. Pip is a useful Python package management system.

On Debian and Ubuntu-like Linux systems these can be installed with the following terminal commands:

$ sudo apt install python3
$ sudo apt install python3-pip

Other Linux distributions will also have Python 3 and pip available in their repositories.

On Windows, download Python from https://www.python.org/downloads/windows; be sure to install pip as well when prompted by the installer, and add the Python directories to the system PATH. You can verify that the Python paths are set up correctly by checking the pip version in a Windows Command Prompt:

> pip -V

On macOS you can install Python directly from https://www.python.org/downloads/mac-osx, or by installing Homebrew and then installing Python 3 with Homebrew. Both come with pip available.

Note

While most Linux distributions come pre-installed with a version of Python 3, the options for Windows and macOS detailed above are more advanced and for experienced users, who prefer fine-grained control. If you are starting out, we strongly recommend using Anaconda!

Virtual environments

Again it is highly recommended to install PyscesToolbox into a separate virtual environment. There are several options for setting up your working environment. We will use virtualenvwrapper, which works out of the box on Linux and macOS. On Windows, virtualenvwrapper can be used under an MSYS environment in a native Windows Python installation. Alternatively, you can use virtualenvwrapper-win. This will take care of managing your virtual environments by maintaining a separate Python site-directory for you.

Install virtualenvwrapper using pip. On Linux and MacOS:

$ sudo -H pip install virtualenv
$ sudo -H pip install virtualenvwrapper

On Windows in a Python command prompt:

> pip install virtualenv
> pip install virtualenvwrapper-win

Make a new virtual environment for working with PyscesToolbox (e.g. pysces), and specify that it use Python 3 (we used Python 3.7):

$ mkvirtualenv -p /path/to/your/python3.7 pysces

The new virtual environment will be activated automatically, and this will be indicated in the shell prompt, e.g.:

(pysces) $

If you are not yet familiar with virtual environments we recommend you survey the basic commands (https://virtualenvwrapper.readthedocs.io/en/latest/) before continuing.

The PyscesToolbox code and its dependencies can now be installed directly from PyPI into your virtual environment using pip.

(pysces) $ pip install pyscestoolbox

As for the conda-based install, the required Python dependencies will be installed automatically. For Maxima, refer to the operating system-specific instructions below.

Enabling widgets

Refer to the Anaconda-based install.

Maxima

Maxima is necessary for generating control coefficient expressions using SymCA. Below we provide operating-specific instructions for setting up Maxima.

Windows

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 %USERPROFILE%\Pysces\psctb_config.ini by default, or in C:\Pysces for older PySCeS versions.

Note

As of PySCeS version 0.9.8 the default location of configuration and model files moved from C:\Pysces to %USERPROFILE%\Pysces, i.e. typically C:\Users\<username>\Pysces, to bring the Windows installation more in line with the macOS and Linux installations. Refer to the PySCeS 0.9.8 release notes for more information.

The default path included in psctb_config.ini is set as C:\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.

macOS (Mac OS X)

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 or .zshrc file (depending on which shell you use):

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

Linux

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.