Getting Started

Initialising and Startup

1. Install OpenCOR

Download and install OpenCOR version 0.8.1 from this link. I recommend installing with zip/tarball in a directory where you have access and edit rights, such as ~/Desktop.

2. Clone the project

If you have not worked with git and GitHub, firstly download and install git, and then open the terminal and navigate (with terminal in Linux/Mac or gitbash in Windows) to a directory where you want the repository to be. Then write these commands to clone the project on your pc:

git clone https://github.com/FinbarArgus/OpenCOR_python_tutorial.git

Directory Definition

In this tutorial, we define the working_dir as the directory where the tutorial has been cloned. For example, on our computer, this directory is as below:

[working_dir]: ~/Documents/git_projects/OpenCOR_python_tutorial

Also, the OpenCOR directory is needed for installing the necessary python libraries, which we defined as the OpenCOR_dir, e.g.:

[OpenCOR_dir]: ~/Desktop/OpenCOR-0-8-1-Linux/

Setting up your python path

Open [working_dir]/opencor_pythonshell_path.sh file and change the opencor_pythonshell_path to the directory of pythonshell in the OpenCOR_dir:

Linux and Mac

    opencor_pythonshell_path=`<OpenCOR_dir>/pythonshell`.

Windows

    opencor_pythonshell_path=`C:\<OpenCOR_dir>\pythonshell.bat`.

Note that the windows path conventions need to be used with C: and "\ rather than "/".

IDE Note

If you want to use an IDE such as vscode, you have to set your python path to the same as the opencor_pythonshell_path above.

If you're on Windows, we recommend using an IDE and setting the path. If instead, you want to use the bash script on Windows, you should download gitbash from here.

Running

Now to run, you can do the following from terminal (or run the run_tutorial.py script from an IDE with the python path set to the opencor_pythonshell_path)

./run_tutorial_bash.sh