Use absolute imports.

theano/compile/__init__.py

-import ops
-from ops import (
+from theano.compile.ops import (
         DeepCopyOp, deep_copy_op, register_deep_copy_op_c_code,
         ViewOp, view_op, register_view_op_c_code)
 
-import function_module
-from function_module import *
+from theano.compile.function_module import *
 
-import mode
-from mode import *
+from theano.compile.mode import *
 
-import io
-from io import *
+from theano.compile.io import *
 
-import builders
-from builders import *
+from theano.compile.builders import *
 
-import module
-from module import *
+from theano.compile.module import *
 
-import debugmode   # register DEBUG_MODE
-from debugmode import DebugMode
+from theano.compile.debugmode import DebugMode
 
-from monitormode import MonitorMode
+from theano.compile.monitormode import MonitorMode
 
-from profilemode import ProfileMode
+from theano.compile.profilemode import ProfileMode
 
 from theano.compile.sharedvalue import shared, shared_constructor, SharedVariable
 from theano.compile.pfunc import pfunc, Param, rebuild_collect_shared
 
-from function import function
+from theano.compile.function import function