roll back testsetup blocks, some encoding fixes

Author: oesteban

nipype/interfaces/utility/base.py

@@ -4,14 +4,12 @@
 """
 Various utilities
 
-   Change directory to provide relative paths for doctests
-
-   .. testsetup::
-      import os
-      filepath = os.path.dirname( os.path.realpath( __file__ ) )
-      datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-      os.chdir(datadir)
-
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname(os.path.realpath(__file__))
+    >>> datadir = os.path.realpath(os.path.join(filepath,
+    ...                            '../../testing/data'))
+    >>> os.chdir(datadir)
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import
@@ -27,7 +25,7 @@
 
 from ..base import (traits, TraitedSpec, DynamicTraitedSpec, File,
                     Undefined, isdefined, OutputMultiPath, InputMultiPath,
-                    BaseInterface, BaseInterfaceInputSpec)
+                    BaseInterface, BaseInterfaceInputSpec, Str)
 from ..io import IOBase, add_traits
 from ...utils.filemanip import filename_to_list, copyfile, split_filename
 
@@ -158,11 +156,10 @@ class RenameInputSpec(DynamicTraitedSpec):
     in_file = File(exists=True, mandatory=True, desc="file to rename")
     keep_ext = traits.Bool(desc=("Keep in_file extension, replace "
                                  "non-extension component of name"))
-    format_string = traits.String(mandatory=True,
-                                  desc=("Python formatting string for output "
-                                        "template"))
-    parse_string = traits.String(desc=("Python regexp parse string to define "
-                                       "replacement inputs"))
+    format_string = Str(mandatory=True,
+                        desc="Python formatting string for output template")
+    parse_string = Str(desc="Python regexp parse string to define "
+                            "replacement inputs")
     use_fullpath = traits.Bool(False, usedefault=True,
                                desc="Use full path as input to regex parser")
 
@@ -186,6 +183,7 @@ class Rename(IOBase):
 
     Examples
     --------
+
     >>> from nipype.interfaces.utility import Rename
     >>> rename1 = Rename()
     >>> rename1.inputs.in_file = "zstat1.nii.gz"

nipype/interfaces/utility/csv.py

@@ -3,14 +3,12 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """CSV Handling utilities
 
-   Change directory to provide relative paths for doctests
-
-   .. testsetup::
-      import os
-      filepath = os.path.dirname( os.path.realpath( __file__ ) )
-      datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-      os.chdir(datadir)
-
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname(os.path.realpath(__file__))
+    >>> datadir = os.path.realpath(os.path.join(filepath,
+    ...                            '../../testing/data'))
+    >>> os.chdir(datadir)
 
 """
 from __future__ import print_function, division, unicode_literals, absolute_import

nipype/interfaces/utility/wrappers.py

@@ -3,13 +3,12 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Various utilities
 
-   Change directory to provide relative paths for doctests
-
-   .. testsetup::
-      import os
-      filepath = os.path.dirname( os.path.realpath( __file__ ) )
-      datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
-      os.chdir(datadir)
+    Change directory to provide relative paths for doctests
+    >>> import os
+    >>> filepath = os.path.dirname(os.path.realpath(__file__))
+    >>> datadir = os.path.realpath(os.path.join(filepath,
+    ...                            '../../testing/data'))
+    >>> os.chdir(datadir)
 
 
 """
@@ -18,6 +17,7 @@
 from future import standard_library
 standard_library.install_aliases()
 
+from builtins import str, bytes
 
 from nipype import logging
 from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, runtime_profile,