Installation¶

Base requirements¶

Python 3.7 (64-bit)
networkx==2.3
python-libsbml==5.18.0
numpy==1.16.4
sympy==1.4
scipy==1.4.1
matplotlib==3.1.1
plotnine==0.6.0

MacOS and Windows¶

antimony==2.11.0
rrplugins==1.2.2
libroadrunner==1.5.2.1

Creating a Virtual Environment¶

The preferred way to use CRNT4SBML is through a virtual environment. A virtual environment for Python is a self-contained directory tree. This environment can have a particular version of Python and Python packages. This is very helpful as it allows one to use different versions of Python and Python packages without their install conflicting with already installed versions. Here we will give a brief description of creating a virtual environment for CRNT4SBML using virtualenv. To begin we first obtain virtualenv through a pip install:

$ pip install virtualenv

Once virtualenv is installed, download the latest 64-bit version of Python 3.7 (be sure to take note of the download location). Next we will create a directory to hold all of the virtual environments that we may create called “python_environments”:

$ mkdir python_environments

Now that we have virtualenv and Python version 3.7, we can create the virtual environment crnt4sbml_env in the directory python_environments as follows:

$ cd python_environments
$ virtualenv -p /path/to/python/3.7/interpreter crnt4sbml_env

The flag “-p” tells virtualenv to create an environment using a specific Python interpreter. If a standard download of Python was followed, then “/path/to/python/3.7/interpreter” can be replaced with “/usr/local/bin/python3.7” on MacOS and Linux, and “C:\Users\your_user_name\AppData\Local \Programs\Python\Python37\python.exe” on Windows. One can now see a directory called “crnt4sbml_env” is created in the directory python_environments.

We can now activate this environment as follows:

On MacOS and Linux:

$ source /path/to/python_environments/crnt4sbml_env/bin/activate

On Windows:

$ path\to\crnt4sbml_env\Scripts\activate

Note, in case you are using PowerShell, make sure its policy is updated by executing command as administrator Set-ExecutionPolicy RemoteSigned. On the command line one should now see “(crnt4sbml_env)” on the left side of the command line, which indicates that one is now working in the virtual environment.

Stable Release¶

Once the environment is activated, one can now install CRNT4SBML as follows:

On MacOS:

$ pip install crnt4sbml[MacOS]

On Windows:

$ pip install crnt4sbml[Windows]

On Linux (numerical continuation is unavailable for Linux):

$ pip install crnt4sbml[Linux]

note that this will install crnt4sbml in the virtual environment crnt4sbml_env. One can only use crnt4sbml within this environment. If one wants to stop using the virtual environment, the following command can be used:

$ deactivate

“(base)” should show up on the left of the command line. One can then use the environment by using the “source” command above.

Working Version¶

The current working version of crnt4sbml can be downloaded from the Github repo.