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:
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)
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.