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Cleaning up is good, but be aware that the GUI in calibre uses layouts and styles and the styles vary on every platform calibre is run, so doing pixel level adjustments is not always a good idea, they might make it look nicer on one platform and break it on others.
Pydev should offer you those kinds of features, but note that since python is dynamic it isn't always possible to do method resolution like it is in C/C++.
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