fix final errors and wrong imports

Author: oesteban

nipype/interfaces/base/__init__.py

@@ -9,17 +9,19 @@
 
 """
 from .core import (
-    BaseInterface, SimpleInterface, CommandLine, StdOutCommandLine,
+    Interface, BaseInterface, SimpleInterface,
+    CommandLine, StdOutCommandLine,
     MpiCommandLine, SEMLikeCommandLine, PackageInfo
 )
 
 from .specs import (
-    BaseTraitedSpec, BaseInterfaceInputSpec, CommandLineInputSpec,
+    BaseTraitedSpec, TraitedSpec, DynamicTraitedSpec,
+    BaseInterfaceInputSpec, CommandLineInputSpec,
 )
 
 from .traits_extension import (
     traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined,
     File, Directory, Str, DictStrStr, has_metadata, ImageFile,
     MultiPath, OutputMultiPath, InputMultiPath)
 
-from .support import load_template
+from .support import Bunch, InterfaceResult, load_template

nipype/interfaces/base/specs.py

@@ -316,6 +316,7 @@ class TraitedSpec(BaseTraitedSpec):
 
     This is used in 90% of the cases.
     """
+    _ = traits.Disallow
 
 
 class BaseInterfaceInputSpec(TraitedSpec):
@@ -354,7 +355,6 @@ def __deepcopy__(self, memo):
         dup = self.clone_traits(memo=memo)
         dup.trait_set(**dup_dict)
         return dup
-    _ = traits.Disallow
 
 
 class CommandLineInputSpec(BaseInterfaceInputSpec):

nipype/pipeline/engine/nodes.py

@@ -42,10 +42,10 @@
                                 copyfiles, fnames_presuffix, loadpkl,
                                 split_filename, load_json, savepkl,
                                 write_rst_header, write_rst_dict,
-                                write_rst_list, to_str)
+                                write_rst_list, to_str, md5)
 from ...interfaces.base import (traits, InputMultiPath, CommandLine,
                                 Undefined, TraitedSpec, DynamicTraitedSpec,
-                                Bunch, InterfaceResult, md5, Interface,
+                                Bunch, InterfaceResult, Interface,
                                 TraitDictObject, TraitListObject, isdefined)
 from .utils import (generate_expanded_graph, modify_paths,
                     export_graph, make_output_dir, write_workflow_prov,

nipype/pipeline/engine/workflows.py

@@ -41,10 +41,10 @@
 from ...utils.functions import (getsource, create_function_from_source)
 from ...interfaces.base import (traits, InputMultiPath, CommandLine,
                                 Undefined, TraitedSpec, DynamicTraitedSpec,
-                                Bunch, InterfaceResult, md5, Interface,
+                                Bunch, InterfaceResult, Interface,
                                 TraitDictObject, TraitListObject, isdefined)
 
-from ...utils.filemanip import (save_json, FileNotFoundError,
+from ...utils.filemanip import (save_json, FileNotFoundError, md5,
                                 filename_to_list, list_to_filename,
                                 copyfiles, fnames_presuffix, loadpkl,
                                 split_filename, load_json, savepkl,

nipype/utils/filemanip.py

@@ -24,8 +24,6 @@
 
 from .. import logging, config
 from .misc import is_container
-from ..interfaces.traits_extension import isdefined
-
 from future import standard_library
 standard_library.install_aliases()
 
@@ -181,7 +179,9 @@ def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True):
     pth, fname, ext = split_filename(fname)
     if not use_ext:
         ext = ''
-    if newpath and isdefined(newpath):
+
+    # Avoid cyclic references importing isdefined
+    if newpath and ('%s' % newpath) != '<undefined>':
         pth = os.path.abspath(newpath)
     return os.path.join(pth, prefix + fname + suffix + ext)