fix: deprecation warning does not reset trait to Undefined - will set new value

Author: satra

nipype/interfaces/base.py

@@ -268,6 +268,7 @@ def __init__(self, interface, runtime, inputs=None, outputs=None):
     def version(self):
         return self._version
 
+
 class BaseTraitedSpec(traits.HasTraits):
     """Provide a few methods necessary to support nipype interface api
 
@@ -374,7 +375,6 @@ def _deprecated_warn(self, obj, name, old, new):
                                   self.__class__.__name__.split('InputSpec')[0])
             msg2 = ('Will be removed or raise an error as of release %s') % \
                                                            trait_spec.deprecated
-            self.trait_set(trait_change_notify=False, **{'%s' % name: Undefined})
             if trait_spec.new_name:
                 if trait_spec.new_name not in self.copyable_trait_names():
                     raise TraitError(msg1 + ' Replacement trait %s not found' %
@@ -387,7 +387,12 @@ def _deprecated_warn(self, obj, name, old, new):
                 raise TraitError(msg)
             else:
                 warn(msg)
-
+                if trait_spec.new_name:
+                    warn('Unsetting %s and setting %s.' % (name,
+                                                           trait_spec.new_name))
+                    self.trait_set(trait_change_notify=False,
+                                   **{'%s' % name: Undefined,
+                                      '%s' % trait_spec.new_name: new})
 
     def _hash_infile(self, adict, key):
         """ Inject file hashes into adict[key]"""

nipype/interfaces/tests/test_base.py

@@ -139,7 +139,7 @@ class DeprecationSpec1(nib.TraitedSpec):
     set_foo = lambda : setattr(spec_instance, 'foo', 1)
     yield assert_raises, nib.TraitError, set_foo
     class DeprecationSpec1numeric(nib.TraitedSpec):
-        foo = nib.traits.Int(deprecated=0.1)
+        foo = nib.traits.Int(deprecated='0.1')
     spec_instance = DeprecationSpec1numeric()
     set_foo = lambda : setattr(spec_instance, 'foo', 1)
     yield assert_raises, nib.TraitError, set_foo
@@ -158,6 +158,18 @@ class DeprecationSpec3(nib.TraitedSpec):
     except nib.TraitError:
         not_raised = False
     yield assert_true, not_raised
+    class DeprecationSpec3(nib.TraitedSpec):
+        foo = nib.traits.Int(deprecated='1000', new_name='bar')
+        bar = nib.traits.Int()
+    spec_instance = DeprecationSpec3()
+    not_raised = True
+    try:
+        spec_instance.foo = 1
+    except nib.TraitError:
+        not_raised = False
+    yield assert_true, not_raised
+    yield assert_equal, spec_instance.foo, Undefined
+    yield assert_equal, spec_instance.bar, 1
 
 def checknose():
     """check version of nose for known incompatability"""