Installation¶
PySCeSToolbox is compatible with macOS, 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:
- A Python 3.x installation (Python 3.6 or higher is recommended)
- The full SciPy Stack (see http://scipy.org/install.html).
- PySCeS (see http://pysces.sourceforge.net)
- Maxima (see http://maxima.sourceforge.net)
- Jupyter Notebook (jupyter-core version in the 4.x.x series)
Windows¶
Windows requires the manual installation of Python 3.x, PySCeS and Maxima. Installation was tested on Windows 10.
Python¶
For Windows 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 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.
If you prefer more fine-grained control it is also possible to install Python
from Python.org (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.
PySCeS¶
If you installed Anaconda, PySCeS can be installed by opening a command prompt in an Anaconda environment (Python 3.6 or 3.7) and executing the command:
conda install -c sbmlteam -c pysces pysces
If you installed Python from Python.org directly, open a Windows Command
Prompt, verify that the Python paths are set up correctly by checking the
pip
version and install PySCeS by executing:
pip -V
pip install pysces
Currently Python versions 3.6-3.8 are supported with a pip install.
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.
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.
PySCeSToolbox¶
Now you are ready to install PySCeSToolbox. If you are using Anaconda, open
up the Anaconda Command Prompt (Start –> Anaconda Command Prompt), else
open up the Windows Command Prompt if you installed PySCeS with pip
. In the
command prompt, type in and execute the command:
pip install pyscestoolbox
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
macOS (Mac OS X)¶
macOS requires the manual installation of PySCeS and Maxima. While OS X comes pre-installed with Python 2.7, Python 3.x is needed and we 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 High Sierra.
Python¶
One of the easiest ways to get Python on your system is to install the Anaconda Python distribution (https://www.anaconda.com/products/individual#Downloads). Download either of the Python 3.7 installers for macOS from the download page and follow the provided instructions.
If you prefer more fine-grained control, there are other options such as installing directly from Python.org (https://www.python.org/downloads/mac-osx/), or installing Homebrew and then installing Python 3.7 with Homebrew. These are advanced options for experienced users, and if you are starting out, we recommend Anaconda!
PySCeS¶
Binary packages are available for Anaconda, and binary wheels are available for
direct installation with pip
. Depending on your Python installation (see
above), the process is similar to the Windows install.
For Anaconda:
conda install -c sbmlteam -c pysces pysces
For a pip
based install (Python versions 3.6-3.8 are supported):
pip install pysces
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. If you are using Anaconda, open
up a terminal in the Anaconda environment where PySCeS is installed. For
pip
based installations, just open up a Terminal. Execute the command:
pip install pyscestoolbox
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 a version of Python 3.x or it is available from the distribution repositories. However, a Python distribution such as Anaconda may be used instead. Installation was tested on Ubuntu 18.04.
Python¶
We assume that your system comes with Python 3.x (versions 3.6-3.8 are
recommended) and with pip
(necessary for
installing Python packages that are not available in your OS’s repositories).
In case pip
is not yet installed, it may be installed from your OS’s
repositories or by following the instructions found at
https://pip.pypa.io/en/stable/installing/.
If you prefer Anaconda, Linux installers are available here.
PySCeS¶
Binary packages are available for Anaconda, and binary wheels are available for
direct installation with pip
. Depending on your Python installation (see
above), the process is similar to the Windows and macOS installs.
For Anaconda:
conda install -c sbmlteam -c pysces pysces
For a pip
based install (Python versions 3.6-3.8 are supported):
pip install pysces
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. Open a terminal in the environment where you installed PySCeS (i.e. Anaconda environment or the native Python environment of your OS), and 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