make linker=py use the theano flag allow_gc. It don't change the default.

theano/compile/mode.py

@@ -64,13 +64,13 @@ def check_equal(x, y):
 # Mode, it will be used as the key to retrieve the real linker in this
 # dictionary
 predefined_linkers = {
-    'py': gof.PerformLinker(),
-    'c': gof.CLinker(),
-    'c|py': gof.OpWiseCLinker(),
+    'py': gof.PerformLinker(),  # Use allow_gc Theano flag
+    'c': gof.CLinker(),  # Don't support gc. so don't check allow_gc
+    'c|py': gof.OpWiseCLinker(),  # Use allow_gc Theano flag
     'c|py_nogc': gof.OpWiseCLinker(allow_gc=False),
-    'c&py': gof.DualLinker(checker=check_equal),
-    'vm': gof.vm.VM_Linker(use_cloop=False),
-    'cvm': gof.vm.VM_Linker(use_cloop=True),
+    'c&py': gof.DualLinker(checker=check_equal),  # Deprecated
+    'vm': gof.vm.VM_Linker(use_cloop=False),  # Use allow_gc Theano flag
+    'cvm': gof.vm.VM_Linker(use_cloop=True),  # Use allow_gc Theano flag
     'vm_nogc': gof.vm.VM_Linker(allow_gc=False, use_cloop=False),
     'cvm_nogc': gof.vm.VM_Linker(allow_gc=False, use_cloop=True),
     }

theano/gof/link.py

 """WRITEME"""
+import theano
 from theano.gof import utils
 from theano.gof import graph
 from theano.gof.type import Type
@@ -419,8 +420,9 @@ class PerformLinker(LocalLinker):
     the L{FunctionGraph} in the order given by L{Linker.schedule}.
     """
 
-    def __init__(self, allow_gc=True, schedule=None):
-        #TODO: set allow_gc = True by default, when it works with the OpWiseCLinker
+    def __init__(self, allow_gc=None, schedule=None):
+        if allow_gc is None:
+            allow_gc = theano.config.allow_gc
         self.fgraph = None
         self.allow_gc = allow_gc
         if schedule: