Thanks Simon for your replay.
when I'm removing the FK definition from the Column - The tables are being 
built as they should - the ptoblem is when i try to perform a join I'm 
getting the following error:

Can't find any foreign key relationships between 'Signals' and 'Clips'.

and this is the code:

return engine.query(func.count(signals_table.Signals.sig_value)).\ filter(
signals_table.Signals.message_id == msg_id).\ filter(signals_table.Signals.
signal_id == sig_id).\ filter(func.format(signals_table.Signals.sig_value, 2
) == func.format(sig_val, 2)).\ first()[0]


and this is the definition of the class Clips:
 from datetime import datetime from sqlalchemy import * from sqlalchemy.orm 
import relationship from BaseCoverRuns import Base class Clips(Base): 
__table_args__ = { 'mysql_engine': 'MyISAM', 'mysql_charset': 'utf8' } 
__tablename__ = 'Clips' id = Column(Integer, autoincrement=True, primary_key
=True) clip_name = Column(String(255)) def get_table_orm_def(self): return 
self.__table__ def __init__(self, clip_name=None): self.clip_name = 
clip_name def __repr__(self): return "<Clips ('%s')>" % (self.clip_name) 

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