Sphinx automodule: how to reference classes in same module?

Don't know if I understand the problem but this works flawlessly to me with autodoc, as per Cross-referencing Python objects

class FlowDirection(GeneralTable):
    '''
    Heat Flow Direction

    :cvar int id: database primary key
    :cvar unicode name: name 
    '''
    def __repr__(self):
        return u'<FlowDirection {0} instance at {1}>'.format(
                self.name, hex(id(self))).encode('utf-8')

    def __unicode__(self):
        return self.name

class AirCavityRes(GeneralTable):
    '''
    Air Cavity :term:`thermal resistance`

    :cvar flow_direction: heat flow direction
        (see :class:`FlowDirection`)
    :cvar int id: database primary key
    :cvar int if_fd: database foreign key to :class:`FlowDirection`
    :cvar float res: :term:`thermal resistance`
    :cvar float thick: thickness
    '''
    def __repr__(self):
        return u'<AirCavityRes {0} instance at {1}>'.format(
                self.res, hex(id(self)))

You can reference a class like this:

class B(object):
    """docs for B with reference to :class:`.A`"""
    pass

Sphinx will intelligently try and figure out what you're referencing. If there are multiple classes with the name A, you might get a warning, but it should pick up the one in the current module.