title: Alembic does not make composite primary key
body: <p>I had a SQLAlchemy model like -</p>
  
  <pre><code>class UserFavPlace(db.Model):
      # This model stores the feedback from the user whether he has
      # faved a place or not
      __tablename__ = u'user_fav_places'
  
      id = db.Column(db.Integer, primary_key = True)
      public_place_id = db.Column(db.Integer, db.ForeignKey(u'public_places.id'))
      user_id = db.Column(db.Integer, db.ForeignKey(u'users.user_id'))
      fav = db.Column(db.Boolean)
      updated_time = db.Column(db.DateTime)
  
      place = relationship(u'PublicPlace', backref = u'user_fav_places')
      user = relationship(u'User', backref = u'user_fav_places')
  </code></pre>
  
  <p>And then I changed this model to the following - </p>
  
  <pre><code>class UserFavPlace(db.Model):
      # This model stores the feedback from the user whether he has
      # faved a place or not
      __tablename__ = u'user_fav_places'
  
      public_place_id = db.Column(db.Integer, db.ForeignKey(u'public_places.id'),
              primary_key = True)
      user_id = db.Column(db.Integer, db.ForeignKey(u'users.user_id'),
              primary_key = True)
      fav = db.Column(db.Boolean)
      updated_time = db.Column(db.DateTime)
  
      place = relationship(u'PublicPlace', backref = u'user_fav_places')
      user = relationship(u'User', backref = u'user_fav_places')
  </code></pre>
  
  <p>However, Alembic is not generating the correct upgrade and downgrade statements. Seems like it is not adding the newly introduced primary key constraints.</p>
  
  <pre><code>def upgrade():
      ### commands auto generated by Alembic - please adjust! ###
      op.drop_column('user_fav_places', 'id')
      ### end Alembic commands ###
  
  
  def downgrade():
      ### commands auto generated by Alembic - please adjust! ###
      op.add_column('user_fav_places', sa.Column('id', mysql.INTEGER(display_width=11), nullable=False))
      ### end Alembic commands ###
  </code></pre>
  
  <p>I am not sure on how to add this. </p>