Hi Adrian it is a good point the one you make, but perhaps it is time to 
consider how this is handled by Spyder...

I think we could add an 'override pep8 settings' option by Spyder settings 
where they apply. I do not think they are so many options that we can not 
handle it in an efficient way.

So if you want to change some stuff and want pep8 to follow this setting 
you modified manually in the preferences then clicking on this new option 
should do the trick

Happy new year!

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