fix final errors and wrong imports

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)