There is an open bug in pyramid_mako, which causes that Pyramid doesn't reload templates. Downgrade your pyramid_mako to 0.3.1 version, i.e. point exact version in setup.py
:
requires = [
'pyramid',
'pyramid_mako==0.3.1',
'pyramid_debugtoolbar',
'pyramid_tm',
'SQLAlchemy',
'transaction',
'zope.sqlalchemy',
'waitress',
]
As for changes in *.py, there is a solution in comments of your question.