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First, I am not familiar with PyCharm.
I do all my calibre debugging with print statements. Yes, very old fashioned but it works, often better than stepping with an IDE. Add the print statements, restart calibre, voila. When working on a plugin I use a script to install the plugin (which is the plugin's source) then start calibre in debug mode.
This technique also lets you "instrument" base calibre if you are having some trouble with an API, assuming you are running from source.
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