cellml_converter.py and limpet_fe.py are not found

Question

i was trying to do the example number 6 (conversion of a cellMll model to a easyml) but when i typed this command: cellml_converter.py  luo_rudy_1994.cellml > luo_rudy_1994.model

i got this error: command not found

but the luo_rudy_1994.model file was created.

i typed the second command: limpet_fe.py luo_rudy_1994.model

i got this error: Use /usr/local/bin/limpet_fe.py <.model file> <path of imp_list.txt> <imp source dir> Build openCARP (LIMPET) C++ code from EasyML .model files

i do not understand what it is asking me to do if someone can explain me in my docker contener how can i reach this path (/usr/local/bin/limpet_fe.py <.model file> <path of imp_list.txt> <imp source dir>)

i found cellml_converter.py and limpet_fe.py in my docker flask container in this path: /openCARP/ physics/limpet/src/python

Answer 1

Hi Igniole,

Seeing that you mention flask I assume you are running carputilsGUI? carputilsGUI is supposed to be a tool for starters to run some of the examples in a web-based environment. Building new ionic models is not supported from the web-based GUI.

If you want to compile new ionic models, then installation from source is the best option: https://opencarp.org/download/installation

As you identified correctly, cellml_converter.py is located in the subfolder physics/limpet/src/python of the openCARP repository. Calling it with the full path will solve the issue. We've added this to the documentation of this example: https://git.opencarp.org/openCARP/experiments/-/commit/b06d51ea12f0688786be800dbf68a9ab2bf13750

A version of the luo_rudy_1994.model file is already shipped with the experiment, that's probably what you see. 

Also for limpet_fe.py, you need to provide the full path if the folder \$openCARProot/physics/limpet/src/python is not in your $PATH.

Cheers,

Axel