Then I go to Preferences/Preferences Native and observe that while the R path is correct
the one for python is empty. I write /usr/bin/python and select ok, but the ok button goes
greyed and nothing happens, the Preferences window stays there. Finally click Cancel (not greyed)
but the error remains there
You have to correct the other paths, too if the button stays grey. Only if all paths are valid in the preferences you can confirm the settings (platform default). If you are not interested in other applications simply select for them a valid path from your OS.
One note i've forgotten. To use native python you have to select the directory of python.
So e.g. /usr/bin
if the python interpreter is located there. Then you can start the native python shell in the Bio7 console.
If you would like to use the Jython/Python editor, too of Bio7 then go to the native preferences and enable the Execute Editor... option. This executes the source in your OS Python instead of the Bio7 bundled Jython interpreter.
The default paths are simply stored in the default preferences. I left the preference empty for python so that the user can select the appropriate python path (more important for Windows where python has no default location). In the next release i will set the default path for Linux and Mac to /usr/bin.