STYLE: fixed inconsistencies

[che85]

While looking through some code I noticed some inconsistencies and a lot of unused code

• inconsistent number of lines between methods
• typos
• equality comparison against None with == instead if 'is' or 'is not': http://jaredgrubb.blogspot.com/2009/04/python-is-none-vs-none.html
• trailing semicolons
• general python code best practices
• mutable value as list or dictionary in a default value for an argument
• removed unused code