Building Tellurium Spyder

Binary installer for Tellurium Spyder is only available for Windows. For all other OSs, it is encouraged to install Tellurium Notebook or install through pip on Anaconda distros.

Windows version of Tellurium Spyder utilizes WinPython. If you are starting to configure Tellurium Spyder or wish to update WinPython, check Setting Up. If you are simply updating few packages, check Maintenance.

Setting Up

WinPython comes with either full Qt5 version or bare-bone Zero version for various Python distributions. Zero version is preferred because it is smaller and cleaner. We currently support Python 2.7 and 3.6 64-bit. Install corresponding WinPython installations. Copy settings folder to somewhere else and start installing packages listed under Required Packages using pip. Once this is done, follow the instruction below for both Python 2.7 and 3.6 versions of WinPython.

Manual Customizations

After adding specified packages, the following steps must be taken in either Windows or Mac version of Tellurium to ensure compatibility.

Spyder manual customization:

• Contents of tellurium/spyder_mod should be placed accordingly. Splash image from tellurium/spyder_mod/img_src must be placed in spyderlib/images. Also, some of the txt files (i.e. VERSION.txt) should be in tellurium site-packages folder, and the distribution should also contain tellurium-files.
• Make sure that the example files from rrPlugins are also in the tellurium-files folder.
• For import plugins, place following plugins in spyderplugins folder.
• For Network Viewer, get the latest release from here and place files accordingly.
• For Rate Law plugin, get the latest files from here. Put ratelawgui.py and ratelaw2_0_3.xml in spyderplugins/widgets, ratelaw.png in spyderplugins/images, and p_ratelaw.py in spyderplugins.

Required Packages

Following lists the bare minimum number of packages required for Tellurium Spyder.

• tellurium
• libroadrunner
• antimony
• rrplugins
• tesbml
• tesedml
• tenuml
• tecombine
• phrasedml
• netplotlib
• pySBOL
• sbml2matlab
• spyder
• jupyter
• ipywidgets
• bioservices
• numpy
• scipy
• sympy
• matplotlib
• pandas
• seaborn
• bokeh
• statsmodels
• plotly
• control
• simplesbml
• matplotlib2tikz
• lmfit
• cobra
• biopython
• spyder-ratelaw
• spyder-teimport
• spyder-opensbml

Building Binary Installers

Now that packages are installed and manual customization are configured, let's build installers. Binary installers are built using Inno Setup with ISSI.

Maintenance

In many cases, updating WinPython version is not necessary. If you already set up WinPython, simply update packages you wish to update using pip, re-build the installer and release.