super(_open_file, self).__init__(open(name, mode)) PermissionError: [Errno 13] Permission denied: 'model/topo_based'

This error message indicates that the Python script is trying to access a file called "model/topo_based" but does not have the necessary permissions to do so. The most likely cause of this issue is that the file does not have read or write permissions for the user running the script.

To resolve this issue, you can try changing the permissions of the file by running the following command in the terminal:

chmod +rw model/topo_based

This will give read and write permissions to the file for the current user. Alternatively, you can try running the script with elevated permissions using the sudo command:

sudo python your_script.py

This will run the script as a superuser and should give it the necessary permissions to access the file. However, be cautious when using the sudo command as it can potentially cause security issues.