fix: final touches to the PR

Close #2944. Close #2949.

Author: oesteban

nipype/caching/tests/test_memory.py

@@ -15,8 +15,7 @@ class SideEffectInterface(EngineTestInterface):
     def _run_interface(self, runtime):
         global nb_runs
         nb_runs += 1
-        runtime.returncode = 0
-        return runtime
+        return super(SideEffectInterface, self)._run_interface(runtime)
 
 
 def test_caching(tmpdir):

nipype/pipeline/engine/tests/test_base.py

@@ -20,19 +20,15 @@ class OutputSpec(nib.TraitedSpec):
     output1 = nib.traits.List(nib.traits.Int, desc='outputs')
 
 
-class EngineTestInterface(nib.BaseInterface):
+class EngineTestInterface(nib.SimpleInterface):
     input_spec = InputSpec
     output_spec = OutputSpec
 
     def _run_interface(self, runtime):
         runtime.returncode = 0
+        self._results['output1'] = [1, self.inputs.input1]
         return runtime
 
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs['output1'] = [1, self.inputs.input1]
-        return outputs
-
 
 @pytest.mark.parametrize(
     'name', ['valid1', 'valid_node', 'valid-node', 'ValidNode0'])

nipype/pipeline/engine/utils.py

@@ -32,7 +32,6 @@
     to_str,
     ensure_list,
     get_related_files,
-    FileNotFoundError,
     save_json,
     savepkl,
     write_rst_header,
@@ -41,9 +40,10 @@
 )
 from ...utils.misc import str2bool
 from ...utils.functions import create_function_from_source
-from ...interfaces.base.traits_extension import rebase_path_traits, resolve_path_traits
-from ...interfaces.base import (Bunch, CommandLine, isdefined, Undefined,
-                                InterfaceResult, traits)
+from ...interfaces.base.traits_extension import (
+    rebase_path_traits, resolve_path_traits, OutputMultiPath, isdefined, Undefined, traits)
+from ...interfaces.base.support import Bunch, InterfaceResult
+from ...interfaces.base import CommandLine
 from ...interfaces.utility import IdentityInterface
 from ...utils.provenance import ProvStore, pm, nipype_ns, get_id
 
@@ -240,7 +240,7 @@ def save_resultfile(result, cwd, name, rebase=True):
         return
 
     try:
-        outputs = result.outputs.trait_get()
+        output_names = result.outputs.copyable_trait_names()
     except AttributeError:
         logger.debug('Storing non-traited results, skipping rebase of paths')
         savepkl(resultsfile, result)
@@ -250,9 +250,12 @@ def save_resultfile(result, cwd, name, rebase=True):
     try:
         with indirectory(cwd):
             # All the magic to fix #2944 resides here:
-            for key, old in list(outputs.items()):
+            for key in output_names:
+                old = getattr(result.outputs, key)
                 if isdefined(old):
-                    old = result.outputs.trait(key).handler.get_value(result.outputs, key)
+                    if result.outputs.trait(key).is_trait_type(OutputMultiPath):
+                        old = result.outputs.trait(key).handler.get_value(
+                            result.outputs, key)
                     backup_traits[key] = old
                     val = rebase_path_traits(result.outputs.trait(key), old, cwd)
                     setattr(result.outputs, key, val)
@@ -317,8 +320,9 @@ def load_resultfile(path, name, resolve=True):
             logger.debug('Resolving paths in outputs loaded from results file.')
             for trait_name, old in list(outputs.items()):
                 if isdefined(old):
-                    old = result.outputs.trait(trait_name).handler.get_value(
-                        result.outputs, trait_name)
+                    if result.outputs.trait(trait_name).is_trait_type(OutputMultiPath):
+                        old = result.outputs.trait(trait_name).handler.get_value(
+                            result.outputs, trait_name)
                     value = resolve_path_traits(result.outputs.trait(trait_name), old, path)
                     setattr(result.outputs, trait_name, value)