From 052461d2a9ae2e04e23750fdcd38848e675e6e53 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 16 Jul 2019 14:55:28 -0700
Subject: [PATCH 01/10] ENH: Modify ``Directory`` and ``File`` traits to get
 along with pathlib

Closes #2959
---
 nipype/info.py                             |   1 +
 nipype/interfaces/base/specs.py            |  72 +--
 nipype/interfaces/base/support.py          |   2 +-
 nipype/interfaces/base/tests/test_specs.py |   9 +-
 nipype/interfaces/base/traits_extension.py | 498 ++++++++++++---------
 nipype/interfaces/io.py                    |  21 +-
 nipype/interfaces/spm/base.py              |  36 +-
 requirements.txt                           |   1 +
 8 files changed, 350 insertions(+), 290 deletions(-)

diff --git a/nipype/info.py b/nipype/info.py
index d4a5df9cac..75e9bae6d7 100644
--- a/nipype/info.py
+++ b/nipype/info.py
@@ -155,6 +155,7 @@ def get_nipype_gitversion():
     'packaging',
     'futures; python_version == "2.7"',
     'configparser; python_version <= "3.4"',
+    'pathlib2; python_version <= "3.4"',
 ]
 
 TESTS_REQUIRES = [
diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index dbbc816dc9..47fec9ad1d 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -19,19 +19,26 @@
 from builtins import str, bytes
 from packaging.version import Version
 
+from traits.trait_errors import TraitError
+from traits.trait_handlers import TraitDictObject, TraitListObject
 from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str
 from .traits_extension import (
     traits,
     Undefined,
     isdefined,
-    TraitError,
-    TraitDictObject,
-    TraitListObject,
     has_metadata,
 )
 
 from ... import config, __version__
 
+
+USING_PATHLIB2 = False
+try:
+    from pathlib import Path
+except ImportError:
+    from pathlib2 import Path  # noqa
+    USING_PATHLIB2 = True
+
 FLOAT_FORMAT = '{:.10f}'.format
 nipype_version = Version(__version__)
 
@@ -314,6 +321,39 @@ def __all__(self):
         return self.copyable_trait_names()
 
 
+def _deepcopypatch(self, memo):
+    """
+    Replace the ``__deepcopy__`` member with a traits-friendly implementation.
+
+    A bug in ``__deepcopy__`` for ``HasTraits`` results in weird cloning behaviors.
+    Occurs for all specs in Python<3 and only for DynamicTraitedSpec in Python>2.
+
+    """
+    id_self = id(self)
+    if id_self in memo:
+        return memo[id_self]
+    dup_dict = deepcopy(self.trait_get(), memo)
+    # access all keys
+    for key in self.copyable_trait_names():
+        if key in self.__dict__.keys():
+            _ = getattr(self, key)
+    # clone once
+    dup = self.clone_traits(memo=memo)
+    for key in self.copyable_trait_names():
+        try:
+            _ = getattr(dup, key)
+        except:
+            pass
+    # clone twice
+    dup = self.clone_traits(memo=memo)
+    dup.trait_set(**dup_dict)
+    return dup
+
+
+if USING_PATHLIB2:
+    BaseTraitedSpec.__deepcopy__ = _deepcopypatch
+
+
 class TraitedSpec(BaseTraitedSpec):
     """ Create a subclass with strict traits.
 
@@ -333,29 +373,9 @@ class DynamicTraitedSpec(BaseTraitedSpec):
     functioning well together.
     """
 
-    def __deepcopy__(self, memo):
-        """ bug in deepcopy for HasTraits results in weird cloning behavior for
-        added traits
-        """
-        id_self = id(self)
-        if id_self in memo:
-            return memo[id_self]
-        dup_dict = deepcopy(self.trait_get(), memo)
-        # access all keys
-        for key in self.copyable_trait_names():
-            if key in self.__dict__.keys():
-                _ = getattr(self, key)
-        # clone once
-        dup = self.clone_traits(memo=memo)
-        for key in self.copyable_trait_names():
-            try:
-                _ = getattr(dup, key)
-            except:
-                pass
-        # clone twice
-        dup = self.clone_traits(memo=memo)
-        dup.trait_set(**dup_dict)
-        return dup
+
+if not USING_PATHLIB2:
+    DynamicTraitedSpec.__deepcopy__ = _deepcopypatch
 
 
 class CommandLineInputSpec(BaseInterfaceInputSpec):
diff --git a/nipype/interfaces/base/support.py b/nipype/interfaces/base/support.py
index de9d46f61a..0fd1d27674 100644
--- a/nipype/interfaces/base/support.py
+++ b/nipype/interfaces/base/support.py
@@ -278,7 +278,7 @@ def _inputs_help(cls):
 
     >>> from nipype.interfaces.afni import GCOR
     >>> _inputs_help(GCOR)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
-    ['Inputs::', '', '\t[Mandatory]', '\tin_file: (an existing file name)', ...
+    ['Inputs::', '', '\t[Mandatory]', '\tin_file: (a pathlike object or string...
 
     """
     helpstr = ['Inputs::']
diff --git a/nipype/interfaces/base/tests/test_specs.py b/nipype/interfaces/base/tests/test_specs.py
index bab112e96d..b27daea6a8 100644
--- a/nipype/interfaces/base/tests/test_specs.py
+++ b/nipype/interfaces/base/tests/test_specs.py
@@ -2,9 +2,9 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from __future__ import print_function, unicode_literals
-from future import standard_library
 import os
 import warnings
+from future import standard_library
 
 import pytest
 
@@ -420,7 +420,8 @@ def test_ImageFile():
     # setup traits
     x.add_trait('nifti', nib.ImageFile(types=['nifti1', 'dicom']))
     x.add_trait('anytype', nib.ImageFile())
-    x.add_trait('newtype', nib.ImageFile(types=['nifti10']))
+    with pytest.raises(ValueError):
+        x.add_trait('newtype', nib.ImageFile(types=['nifti10']))
     x.add_trait('nocompress',
                 nib.ImageFile(types=['mgh'], allow_compressed=False))
 
@@ -428,10 +429,8 @@ def test_ImageFile():
         x.nifti = 'test.mgz'
     x.nifti = 'test.nii'
     x.anytype = 'test.xml'
-    with pytest.raises(AttributeError):
-        x.newtype = 'test.nii'
     with pytest.raises(nib.TraitError):
-        x.nocompress = 'test.nii.gz'
+        x.nocompress = 'test.mgz'
     x.nocompress = 'test.mgh'
 
 
diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py
index 7a464cc557..3538c4e27e 100644
--- a/nipype/interfaces/base/traits_extension.py
+++ b/nipype/interfaces/base/traits_extension.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
@@ -24,28 +23,72 @@
                         absolute_import)
 
 from builtins import str, bytes
-import os
 from collections import Sequence
 
 # perform all external trait imports here
 from traits import __version__ as traits_version
 import traits.api as traits
-from traits.trait_handlers import TraitDictObject, TraitListObject
-from traits.trait_errors import TraitError
-from traits.trait_base import _Undefined, class_of
+from traits.trait_handlers import TraitType, NoDefaultSpecified
+from traits.trait_base import _Undefined
 
-from traits.api import BaseUnicode
 from traits.api import Unicode
 from future import standard_library
 
+try:
+    from pathlib import Path
+except ImportError:
+    from pathlib2 import Path
+
+
 if traits_version < '3.7.0':
     raise ImportError('Traits version 3.7.0 or higher must be installed')
 
 standard_library.install_aliases()
 
+IMG_FORMATS = {
+    'afni': ('.HEAD', '.BRIK'),
+    'cifti2': ('.nii', '.nii.gz'),
+    'dicom': ('.dcm', '.IMA', '.tar', '.tar.gz'),
+    'gifti': ('.gii', '.gii.gz'),
+    'mgh': ('.mgh', '.mgz', '.mgh.gz'),
+    'nifti1': ('.nii', '.nii.gz', '.hdr', '.img', '.img.gz'),
+    'nifti2': ('.nii', '.nii.gz'),
+    'nrrd': ('.nrrd', '.nhdr'),
+}
+IMG_ZIP_FMT = set(['.nii.gz', 'tar.gz', '.gii.gz', '.mgz', '.mgh.gz', 'img.gz'])
+
+"""
+The functions that pop-up the Traits GUIs, edit_traits and
+configure_traits, were failing because all of our inputs default to
+Undefined deep and down in traits/ui/wx/list_editor.py it checks for
+the len() of the elements of the list.  The _Undefined class in traits
+does not define the __len__ method and would error.  I tried defining
+our own Undefined and even sublassing Undefined, but both of those
+failed with a TraitError in our initializer when we assign the
+Undefined to the inputs because of an incompatible type:
+
+TraitError: The 'vertical_gradient' trait of a BetInputSpec instance must be \
+a float, but a value of <undefined> <class 'nipype.interfaces.traits._Undefined'> was specified.
+
+So... in order to keep the same type but add the missing method, I
+monkey patched.
+"""
+
+
+def _length(self):
+    return 0
+
+
+##########################################################################
+# Apply monkeypatch here
+_Undefined.__len__ = _length
+##########################################################################
+
+Undefined = _Undefined()
+
 
 class Str(Unicode):
-    """Replacement for the default traits.Str based in bytes"""
+    """Replaces the default traits.Str based in bytes."""
 
 
 # Monkeypatch Str and DictStrStr for Python 2 compatibility
@@ -54,244 +97,254 @@ class Str(Unicode):
 traits.DictStrStr = DictStrStr
 
 
-class File(BaseUnicode):
-    """ Defines a trait whose value must be the name of a file.
-    """
+class BasePath(TraitType):
+    """Defines a trait whose value must be a valid filesystem path."""
 
     # A description of the type of value this trait accepts:
-    info_text = 'a file name'
-
-    def __init__(self,
-                 value='',
-                 filter=None,
-                 auto_set=False,
-                 entries=0,
-                 exists=False,
-                 **metadata):
-        """ Creates a File trait.
-
-        Parameters
-        ----------
-        value : string
-            The default value for the trait
-        filter : string
-            A wildcard string to filter filenames in the file dialog box used by
-            the attribute trait editor.
-        auto_set : boolean
-            Indicates whether the file editor updates the trait value after
-            every key stroke.
-        exists : boolean
-            Indicates whether the trait value must be an existing file or
-            not.
-
-        Default Value
-        -------------
-        *value* or ''
-        """
-        self.filter = filter
-        self.auto_set = auto_set
-        self.entries = entries
+    info_text = 'a pathlike object or string'
+    exists = False
+    pathlike = False
+    resolve = False
+    _is_file = False
+    _is_dir = False
+
+    def __init__(self, value=Undefined,
+                 exists=False, pathlike=False, resolve=False, **metadata):
+        """Create a BasePath trait."""
         self.exists = exists
+        self.resolve = resolve
+        self.pathlike = pathlike
+        if any((exists, self._is_file, self._is_dir)):
+            self.info_text += ' representing a'
+            if exists:
+                self.info_text += 'n existing'
+            if self._is_file:
+                self.info_text += ' file'
+            elif self._is_dir:
+                self.info_text += ' directory'
+            else:
+                self.info_text += ' file or directory'
 
-        if exists:
-            self.info_text = 'an existing file name'
+        super(BasePath, self).__init__(value, **metadata)
 
-        super(File, self).__init__(value, **metadata)
+    def validate(self, objekt, name, value, return_pathlike=False):
+        """Validate a value change."""
+        try:
+            value = Path('%s' % value)  # Use pathlib's validation
+        except Exception:
+            self.error(objekt, name, str(value))
 
-    def validate(self, object, name, value):
-        """ Validates that a specified value is valid for this trait."""
-        validated_value = super(File, self).validate(object, name, value)
-        if not self.exists:
-            return validated_value
-        elif os.path.isfile(value):
-            return validated_value
-        else:
-            raise TraitError(
-                args='The trait \'{}\' of {} instance is {}, but the path '
-                ' \'{}\' does not exist.'.format(name, class_of(object),
-                                                 self.info_text, value))
+        if self.exists:
+            if self.exists and not value.exists():
+                self.error(objekt, name, str(value))
+
+            if self._is_file and not value.is_file():
+                self.error(objekt, name, str(value))
+
+            if self._is_dir and not value.is_dir():
+                self.error(objekt, name, str(value))
+
+        if self.resolve:
+            try:
+                value = value.resolve(strict=self.exists)
+            except TypeError:
+                if self.exists:
+                    value = value.resolve()
+                elif not value.is_absolute():
+                    value = Path().resolve() / value
+
+        if not return_pathlike and not self.pathlike:
+            value = str(value)
+
+        return value
+
+    # def get_value(self, objekt, name, trait=None):
+    #     value = super(BasePath, self).get_value(objekt, name)
+    #     if value is Undefined:
+    #         return self.default_value
+
+    #     if self.pathlike:
+    #         return value
+    #     return str(value)
+
+
+class Directory(BasePath):
+    """
+    Defines a trait whose value must be a directory path.
+
+    Examples::
+
+    >>> from nipype.interfaces.base import Directory, TraitedSpec, TraitError
+    >>> class A(TraitedSpec):
+    ...     foo = Directory(exists=False)
+    >>> a = A()
+    >>> a.foo
+    <undefined>
+
+    >>> a.foo = '/some/made/out/path'
+    >>> a.foo
+    '/some/made/out/path'
+
+    >>> class A(TraitedSpec):
+    ...     foo = Directory(exists=False, resolve=True)
+    >>> a = A(foo='relative_dir')
+    >>> a.foo  # doctest: +ELLIPSIS
+    '.../relative_dir'
+
+    >>> class A(TraitedSpec):
+    ...     foo = Directory(exists=True, resolve=True)
+    >>> a = A()
+    >>> a.foo = 'relative_dir'  # doctest: +IGNORE_EXCEPTION_DETAIL
+    Traceback (most recent call last):
+    TraitError:
+
+    >>> from os import mkdir
+    >>> mkdir('relative_dir')
+    >>> a.foo = 'relative_dir'
+    >>> a.foo  # doctest: +ELLIPSIS
+    '.../relative_dir'
+
+    >>> class A(TraitedSpec):
+    ...     foo = Directory(exists=True, resolve=False)
+    >>> a = A(foo='relative_dir')
+    >>> a.foo
+    'relative_dir'
 
-        self.error(object, name, value)
 
+    >>> class A(TraitedSpec):
+    ...     foo = Directory('tmpdir')
+    >>> a = A()
+    >>> a.foo  # doctest: +ELLIPSIS
+    <undefined>
 
-# -------------------------------------------------------------------------------
-#  'Directory' trait
-# -------------------------------------------------------------------------------
 
+    >>> class A(TraitedSpec):
+    ...     foo = Directory('tmpdir', usedefault=True)
+    >>> a = A()
+    >>> a.foo  # doctest: +ELLIPSIS
+    'tmpdir'
 
-class Directory(BaseUnicode):
     """
-    Defines a trait whose value must be the name of a directory.
+
+    _is_dir = True
+
+
+class File(BasePath):
     """
+    Defines a trait whose value must be a file path.
 
-    # A description of the type of value this trait accepts:
-    info_text = 'a directory name'
-
-    def __init__(self,
-                 value='',
-                 auto_set=False,
-                 entries=0,
-                 exists=False,
-                 **metadata):
-        """ Creates a Directory trait.
-
-        Parameters
-        ----------
-        value : string
-            The default value for the trait
-        auto_set : boolean
-            Indicates whether the directory editor updates the trait value
-            after every key stroke.
-        exists : boolean
-            Indicates whether the trait value must be an existing directory or
-            not.
-
-        Default Value
-        -------------
-        *value* or ''
-        """
-        self.entries = entries
-        self.auto_set = auto_set
-        self.exists = exists
+    >>> from nipype.interfaces.base import File, TraitedSpec, TraitError
+    >>> class A(TraitedSpec):
+    ...     foo = File()
+    >>> a = A()
+    >>> a.foo
+    <undefined>
 
-        if exists:
-            self.info_text = 'an existing directory name'
+    >>> a.foo = '/some/made/out/path/to/file'
+    >>> a.foo
+    '/some/made/out/path/to/file'
 
-        super(Directory, self).__init__(value, **metadata)
+    >>> class A(TraitedSpec):
+    ...     foo = File(exists=False, resolve=True)
+    >>> a = A(foo='idontexist.txt')
+    >>> a.foo  # doctest: +ELLIPSIS
+    '.../idontexist.txt'
 
-    def validate(self, object, name, value):
-        """ Validates that a specified value is valid for this trait."""
-        if isinstance(value, (str, bytes)):
-            if not self.exists:
-                return value
-            if os.path.isdir(value):
-                return value
-            else:
-                raise TraitError(
-                    args='The trait \'{}\' of {} instance is {}, but the path '
-                    ' \'{}\' does not exist.'.format(name, class_of(object),
-                                                     self.info_text, value))
-
-        self.error(object, name, value)
-
-
-# lists of tuples
-# each element consists of :
-# - uncompressed (tuple[0]) extension
-# - compressed (tuple[1]) extension
-img_fmt_types = {
-    'nifti1': [('.nii', '.nii.gz'), (('.hdr', '.img'), ('.hdr', '.img.gz'))],
-    'mgh': [('.mgh', '.mgz'), ('.mgh', '.mgh.gz')],
-    'nifti2': [('.nii', '.nii.gz')],
-    'cifti2': [('.nii', '.nii.gz')],
-    'gifti': [('.gii', '.gii.gz')],
-    'dicom': [('.dcm', '.dcm'), ('.IMA', '.IMA'), ('.tar', '.tar.gz')],
-    'nrrd': [('.nrrd', 'nrrd'), ('nhdr', 'nhdr')],
-    'afni': [('.HEAD', '.HEAD'), ('.BRIK', '.BRIK')]
-}
+    >>> class A(TraitedSpec):
+    ...     foo = File(exists=True, resolve=True)
+    >>> a = A()
+    >>> a.foo = 'idontexist.txt'  # doctest: +IGNORE_EXCEPTION_DETAIL
+    Traceback (most recent call last):
+    TraitError:
 
+    >>> open('idoexist.txt', 'w').close()
+    >>> a.foo = 'idoexist.txt'
+    >>> a.foo  # doctest: +ELLIPSIS
+    '.../idoexist.txt'
 
-class ImageFile(File):
-    """ Defines a trait of specific neuroimaging files """
-
-    def __init__(self,
-                 value='',
-                 filter=None,
-                 auto_set=False,
-                 entries=0,
-                 exists=False,
-                 types=[],
-                 allow_compressed=True,
-                 **metadata):
-        """ Trait handles neuroimaging files.
-
-        Parameters
-        ----------
-        types : list
-            Strings of file format types accepted
-        compressed : boolean
-            Indicates whether the file format can compressed
-        """
-        self.types = types
-        self.allow_compressed = allow_compressed
-        super(ImageFile, self).__init__(value, filter, auto_set, entries,
-                                        exists, **metadata)
-
-    def info(self):
-        existing = 'n existing' if self.exists else ''
-        comma = ',' if self.exists and not self.allow_compressed else ''
-        uncompressed = ' uncompressed' if not self.allow_compressed else ''
-        with_ext = ' (valid extensions: [{}])'.format(
-            ', '.join(self.grab_exts())) if self.types else ''
-        return 'a{existing}{comma}{uncompressed} file{with_ext}'.format(
-            existing=existing, comma=comma, uncompressed=uncompressed,
-            with_ext=with_ext)
-
-    def grab_exts(self):
-        # TODO: file type validation
-        exts = []
-        for fmt in self.types:
-            if fmt in img_fmt_types:
-                exts.extend(
-                    sum([[u for u in y[0]]
-                         if isinstance(y[0], tuple) else [y[0]]
-                         for y in img_fmt_types[fmt]], []))
-                if self.allow_compressed:
-                    exts.extend(
-                        sum([[u for u in y[-1]]
-                             if isinstance(y[-1], tuple) else [y[-1]]
-                             for y in img_fmt_types[fmt]], []))
-            else:
-                raise AttributeError(
-                    'Information has not been added for format'
-                    ' type {} yet. Supported formats include: '
-                    '{}'.format(fmt, ', '.join(img_fmt_types.keys())))
-        return list(set(exts))
-
-    def validate(self, object, name, value):
-        """ Validates that a specified value is valid for this trait.
-        """
-        validated_value = super(ImageFile, self).validate(object, name, value)
-        if validated_value and self.types:
-            _exts = self.grab_exts()
-            if not any(validated_value.endswith(x) for x in _exts):
-                raise TraitError(
-                    args="{} is not included in allowed types: {}".format(
-                        validated_value, ', '.join(_exts)))
-        return validated_value
+    >>> class A(TraitedSpec):
+    ...     foo = File('idoexist.txt')
+    >>> a = A()
+    >>> a.foo
+    <undefined>
 
+    >>> class A(TraitedSpec):
+    ...     foo = File('idoexist.txt', usedefault=True)
+    >>> a = A()
+    >>> a.foo
+    'idoexist.txt'
 
-"""
-The functions that pop-up the Traits GUIs, edit_traits and
-configure_traits, were failing because all of our inputs default to
-Undefined deep and down in traits/ui/wx/list_editor.py it checks for
-the len() of the elements of the list.  The _Undefined class in traits
-does not define the __len__ method and would error.  I tried defining
-our own Undefined and even sublassing Undefined, but both of those
-failed with a TraitError in our initializer when we assign the
-Undefined to the inputs because of an incompatible type:
+    >>> class A(TraitedSpec):
+    ...     foo = File(exists=True, resolve=True, extensions=['.txt', 'txt.gz'])
+    >>> a = A()
+    >>> a.foo = 'idoexist.badtxt'  # doctest: +IGNORE_EXCEPTION_DETAIL
+    Traceback (most recent call last):
+    TraitError:
 
-TraitError: The 'vertical_gradient' trait of a BetInputSpec instance must be a float, but a value of <undefined> <class 'nipype.interfaces.traits._Undefined'> was specified.
+    >>> a.foo = 'idoexist.txt'
+    >>> a.foo  # doctest: +ELLIPSIS
+    '.../idoexist.txt'
 
-So... in order to keep the same type but add the missing method, I
-monkey patched.
-"""
+    """
 
+    _is_file = True
+    _exts = None
 
-def length(self):
-    return 0
+    def __init__(self, value=NoDefaultSpecified, exists=False, pathlike=False,
+                 resolve=False, allow_compressed=True, extensions=None, **metadata):
+        """Create a File trait."""
+        if extensions is not None:
+            if isinstance(extensions, (bytes, str)):
+                extensions = [extensions]
 
+            if allow_compressed is False:
+                extensions = list(set(extensions) - IMG_ZIP_FMT)
 
-##########################################################################
-# Apply monkeypatch here
-_Undefined.__len__ = length
-##########################################################################
+            self._exts = sorted(set(['.%s' % ext if not ext.startswith('.') else ext
+                                     for ext in extensions]))
 
-Undefined = _Undefined()
+        super(File, self).__init__(value=value, exists=exists,
+                                   pathlike=pathlike, resolve=resolve, **metadata)
+
+    def validate(self, objekt, name, value, return_pathlike=False):
+        """Validate a value change."""
+        value = super(File, self).validate(objekt, name, value, return_pathlike=True)
+        if self._exts:
+            ext = ''.join(value.suffixes)
+            if ext not in self._exts:
+                self.error(objekt, name, str(value))
+
+        if not return_pathlike and not self.pathlike:
+            value = str(value)
+
+        return value
 
 
-def isdefined(object):
-    return not isinstance(object, _Undefined)
+class ImageFile(File):
+    """Defines a trait whose value must be a known neuroimaging file."""
+
+    def __init__(self, value=NoDefaultSpecified, exists=False,
+                 pathlike=False, resolve=False, types=None, **metadata):
+        """Create an ImageFile trait."""
+        extensions = None
+        if types is not None:
+            if isinstance(types, (bytes, str)):
+                types = [types]
+
+            if set(types) - set(IMG_FORMATS.keys()):
+                invalid = set(types) - set(IMG_FORMATS.keys())
+                raise ValueError("""\
+Unknown value(s) %s for metadata type of an ImageFile input.\
+""" % ', '.join(['"%s"' % t for t in invalid]))
+            extensions = [ext for t in types for ext in IMG_FORMATS[t]]
+
+        super(ImageFile, self).__init__(
+            value=value, exists=exists, extensions=extensions,
+            pathlike=pathlike, resolve=resolve, **metadata)
+
+
+def isdefined(objekt):
+    return not isinstance(objekt, _Undefined)
 
 
 def has_metadata(trait, metadata, value=None, recursive=True):
@@ -319,7 +372,7 @@ class MultiObject(traits.List):
     """ Abstract class - shared functionality of input and output MultiObject
     """
 
-    def validate(self, object, name, value):
+    def validate(self, objekt, name, value):
 
         # want to treat range and other sequences (except str) as list
         if not isinstance(value, (str, bytes)) and isinstance(
@@ -338,12 +391,12 @@ def validate(self, object, name, value):
                 not isinstance(inner_trait.trait_type, InputMultiObject) and
                 not isinstance(value[0], list)):
             newvalue = [value]
-        value = super(MultiObject, self).validate(object, name, newvalue)
+        value = super(MultiObject, self).validate(objekt, name, newvalue)
 
         if value:
             return value
 
-        self.error(object, name, value)
+        self.error(objekt, name, value)
 
 
 class OutputMultiObject(MultiObject):
@@ -379,8 +432,8 @@ class OutputMultiObject(MultiObject):
 
     """
 
-    def get(self, object, name):
-        value = self.get_value(object, name)
+    def get(self, objekt, name):
+        value = self.get_value(objekt, name)
         if len(value) == 0:
             return Undefined
         elif len(value) == 1:
@@ -388,8 +441,8 @@ def get(self, object, name):
         else:
             return value
 
-    def set(self, object, name, value):
-        self.set_value(object, name, value)
+    def set(self, objekt, name, value):
+        self.set_value(objekt, name, value)
 
 
 class InputMultiObject(MultiObject):
@@ -425,5 +478,6 @@ class InputMultiObject(MultiObject):
     """
     pass
 
+
 InputMultiPath = InputMultiObject
 OutputMultiPath = OutputMultiObject
diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
index 60e8b6fafc..4b9afd1ce1 100644
--- a/nipype/interfaces/io.py
+++ b/nipype/interfaces/io.py
@@ -1024,15 +1024,18 @@ def _list_outputs(self):
     def s3tolocal(self, s3path, bkt):
         import boto
         # path formatting
-        if not os.path.split(self.inputs.local_directory)[1] == '':
-            self.inputs.local_directory += '/'
-        if not os.path.split(self.inputs.bucket_path)[1] == '':
-            self.inputs.bucket_path += '/'
-        if self.inputs.template[0] == '/':
-            self.inputs.template = self.inputs.template[1:]
-
-        localpath = s3path.replace(self.inputs.bucket_path,
-                                   self.inputs.local_directory)
+        local_directory = str(self.inputs.local_directory)
+        bucket_path = str(self.inputs.bucket_path)
+        template = str(self.inputs.template)
+        if not os.path.split(local_directory)[1] == '':
+            local_directory += '/'
+        if not os.path.split(bucket_path)[1] == '':
+            bucket_path += '/'
+        if template[0] == '/':
+            template = template[1:]
+
+        localpath = s3path.replace(bucket_path,
+                                   local_directory)
         localdir = os.path.split(localpath)[0]
         if not os.path.exists(localdir):
             os.makedirs(localdir)
diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py
index fd93dfc522..bbabbf42ba 100644
--- a/nipype/interfaces/spm/base.py
+++ b/nipype/interfaces/spm/base.py
@@ -32,6 +32,7 @@
 from ..base import (BaseInterface, traits, isdefined, InputMultiPath,
                     BaseInterfaceInputSpec, Directory, Undefined, ImageFile,
                     PackageInfo)
+from ..base.traits_extension import NoDefaultSpecified
 from ..matlab import MatlabCommand
 from ...external.due import due, Doi, BibTeX
 
@@ -597,30 +598,11 @@ def _make_matlab_command(self, contents, postscript=None):
 
 
 class ImageFileSPM(ImageFile):
-    """
-    Defines an ImageFile trait specific to SPM interfaces.
-    """
-
-    def __init__(self,
-                 value='',
-                 filter=None,
-                 auto_set=False,
-                 entries=0,
-                 exists=False,
-                 types=['nifti1', 'nifti2'],
-                 allow_compressed=False,
-                 **metadata):
-        """ Trait handles neuroimaging files.
-
-        Parameters
-        ----------
-        types : list
-            Strings of file format types accepted
-        compressed : boolean
-            Indicates whether the file format can compressed
-        """
-        self.types = types
-        self.allow_compressed = allow_compressed
-        super(ImageFileSPM,
-              self).__init__(value, filter, auto_set, entries, exists, types,
-                             allow_compressed, **metadata)
+    """Defines a trait whose value must be a NIfTI file."""
+
+    def __init__(self, value=NoDefaultSpecified, exists=False,
+                 pathlike=False, resolve=False, **metadata):
+        """Create an ImageFileSPM trait."""
+        super(ImageFileSPM, self).__init__(
+            value=value, exists=exists, types=['nifti1', 'nifti2'],
+            pathlike=pathlike, resolve=resolve, **metadata)
diff --git a/requirements.txt b/requirements.txt
index 0d951f49c0..a5cd2d8cd9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -11,6 +11,7 @@ neurdflib
 click>=6.6.0
 funcsigs
 configparser
+pathlib2
 pydotplus
 pydot>=1.2.3
 packaging

From b76860dd068466c4a0ede3bf75df68f37591d8e9 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 16 Jul 2019 15:06:16 -0700
Subject: [PATCH 02/10] sty: better placement of imports from enthought.traits

---
 nipype/interfaces/base/__init__.py | 5 ++++-
 nipype/interfaces/base/core.py     | 3 ++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/base/__init__.py b/nipype/interfaces/base/__init__.py
index 2284c1763a..30d44db56a 100644
--- a/nipype/interfaces/base/__init__.py
+++ b/nipype/interfaces/base/__init__.py
@@ -8,6 +8,9 @@
 This module defines the API of all nipype interfaces.
 
 """
+from traits.trait_handlers import TraitDictObject, TraitListObject
+from traits.trait_errors import TraitError
+
 from .core import (Interface, BaseInterface, SimpleInterface, CommandLine,
                    StdOutCommandLine, MpiCommandLine, SEMLikeCommandLine,
                    LibraryBaseInterface, PackageInfo)
@@ -17,7 +20,7 @@
                     StdOutCommandLineInputSpec)
 
 from .traits_extension import (
-    traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined,
+    traits, Undefined, isdefined,
     File, Directory, Str, DictStrStr, has_metadata, ImageFile,
     OutputMultiObject, InputMultiObject,
     OutputMultiPath, InputMultiPath)
diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
index 77ab6cf398..0011c925dd 100644
--- a/nipype/interfaces/base/core.py
+++ b/nipype/interfaces/base/core.py
@@ -27,6 +27,7 @@
 import simplejson as json
 from dateutil.parser import parse as parseutc
 from future import standard_library
+from traits.trait_errors import TraitError
 
 from ... import config, logging, LooseVersion
 from ...utils.provenance import write_provenance
@@ -37,7 +38,7 @@
 
 from ...external.due import due
 
-from .traits_extension import traits, isdefined, TraitError
+from .traits_extension import traits, isdefined
 from .specs import (BaseInterfaceInputSpec, CommandLineInputSpec,
                     StdOutCommandLineInputSpec, MpiCommandLineInputSpec,
                     get_filecopy_info)

From e993a7f1ad4d518a4a3b1391882aaf2a5de90c52 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 16 Jul 2019 17:47:15 -0700
Subject: [PATCH 03/10] enh(filemanip): Solidify a patched version of
 ``pathlib.Path`` for internal consumption.

---
 nipype/interfaces/base/specs.py            | 10 +----
 nipype/interfaces/base/traits_extension.py | 24 +----------
 nipype/utils/filemanip.py                  | 47 +++++++++++++++++++++-
 nipype/utils/tests/test_filemanip.py       | 19 ++++++++-
 4 files changed, 67 insertions(+), 33 deletions(-)

diff --git a/nipype/interfaces/base/specs.py b/nipype/interfaces/base/specs.py
index 47fec9ad1d..fb0f3295f0 100644
--- a/nipype/interfaces/base/specs.py
+++ b/nipype/interfaces/base/specs.py
@@ -21,7 +21,8 @@
 
 from traits.trait_errors import TraitError
 from traits.trait_handlers import TraitDictObject, TraitListObject
-from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str
+from ...utils.filemanip import (
+    md5, hash_infile, hash_timestamp, to_str, USING_PATHLIB2)
 from .traits_extension import (
     traits,
     Undefined,
@@ -32,13 +33,6 @@
 from ... import config, __version__
 
 
-USING_PATHLIB2 = False
-try:
-    from pathlib import Path
-except ImportError:
-    from pathlib2 import Path  # noqa
-    USING_PATHLIB2 = True
-
 FLOAT_FORMAT = '{:.10f}'.format
 nipype_version = Version(__version__)
 
diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py
index 3538c4e27e..ce4c43e4cc 100644
--- a/nipype/interfaces/base/traits_extension.py
+++ b/nipype/interfaces/base/traits_extension.py
@@ -34,10 +34,7 @@
 from traits.api import Unicode
 from future import standard_library
 
-try:
-    from pathlib import Path
-except ImportError:
-    from pathlib2 import Path
+from ...utils.filemanip import Path
 
 
 if traits_version < '3.7.0':
@@ -145,35 +142,18 @@ def validate(self, objekt, name, value, return_pathlike=False):
                 self.error(objekt, name, str(value))
 
         if self.resolve:
-            try:
-                value = value.resolve(strict=self.exists)
-            except TypeError:
-                if self.exists:
-                    value = value.resolve()
-                elif not value.is_absolute():
-                    value = Path().resolve() / value
+            value = value.resolve(strict=self.exists)
 
         if not return_pathlike and not self.pathlike:
             value = str(value)
 
         return value
 
-    # def get_value(self, objekt, name, trait=None):
-    #     value = super(BasePath, self).get_value(objekt, name)
-    #     if value is Undefined:
-    #         return self.default_value
-
-    #     if self.pathlike:
-    #         return value
-    #     return str(value)
-
 
 class Directory(BasePath):
     """
     Defines a trait whose value must be a directory path.
 
-    Examples::
-
     >>> from nipype.interfaces.base import Directory, TraitedSpec, TraitError
     >>> class A(TraitedSpec):
     ...     foo = Directory(exists=False)
diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index d8a65a6712..3012fd6e56 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -21,7 +21,6 @@
 import contextlib
 import posixpath
 import simplejson as json
-import numpy as np
 
 from builtins import str, bytes, open
 
@@ -40,8 +39,52 @@
 
 PY3 = sys.version_info[0] >= 3
 
-class FileNotFoundError(Exception):
+
+class FileNotFoundError(OSError):
+    """Defines the expception for Python 2."""
+
+    def __init__(self, path):
+        """Initialize the exception."""
+        super(FileNotFoundError, self).__init__(
+            2, 'No such file or directory', '%s' % path)
+
+
+USING_PATHLIB2 = False
+USING_PATHLIB_PATCHED = False
+try:
+    from pathlib import Path
+except ImportError:
+    from pathlib2 import Path
+    USING_PATHLIB2 = True
+
+try:
+    Path('/invented/file/path').resolve(strict=True)
+except TypeError:
+    def _patch_resolve(self, strict=False):
+        """Add the argument strict to signature in Python>3,<3.6."""
+        resolved = Path().old_resolve() / self
+
+        if strict and not resolved.exists():
+            raise FileNotFoundError(resolved)
+        return resolved
+
+    Path.old_resolve = Path.resolve
+    Path.resolve = _patch_resolve
+    USING_PATHLIB_PATCHED = True
+except FileNotFoundError:
     pass
+except OSError:
+    def _patch_resolve(self, strict=False):
+        """Add the argument strict to signature for pathlib2."""
+        try:
+            resolved = self.old_resolve(strict=strict)
+        except OSError:
+            raise FileNotFoundError(self.old_resolve())
+
+        return resolved
+
+    Path.old_resolve = Path.resolve
+    Path.resolve = _patch_resolve
 
 
 def split_filename(fname):
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
index b9a413d557..5d064a3817 100644
--- a/nipype/utils/tests/test_filemanip.py
+++ b/nipype/utils/tests/test_filemanip.py
@@ -16,7 +16,7 @@
     check_forhash, _parse_mount_table, _cifs_table, on_cifs, copyfile,
     copyfiles, ensure_list, simplify_list, check_depends,
     split_filename, get_related_files, indirectory,
-    loadpkl, loadcrash, savepkl)
+    loadpkl, loadcrash, savepkl, FileNotFoundError, Path)
 
 
 def _ignore_atime(stat):
@@ -570,3 +570,20 @@ def test_unversioned_pklization(tmpdir):
     with pytest.raises(Exception):
         with mock.patch('nipype.utils.tests.test_filemanip.Pickled', PickledBreaker):
             loadpkl('./pickled.pkz', versioning=True)
+
+
+def test_Path_strict_resolve(tmpdir):
+    """Check the monkeypatch to test strict resolution of Path."""
+    tmpdir.chdir()
+
+    # Default strict=False should work out out of the box
+    testfile = Path('somefile.txt')
+    assert '%s/somefile.txt' % tmpdir == '%s' % testfile.resolve()
+
+    # Switching to strict=True must raise FileNotFoundError (also in Python2)
+    with pytest.raises(FileNotFoundError):
+        testfile.resolve(strict=True)
+
+    # If the file is created, it should not raise
+    testfile.write_text('')
+    assert '%s/somefile.txt' % tmpdir == '%s' % testfile.resolve(strict=True)

From 06ba99f6722f5a224e8ffaa71ac8ae3b2957ef1c Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 16 Jul 2019 18:34:52 -0700
Subject: [PATCH 04/10] fix(py2/34): address compatibility issues

---
 nipype/interfaces/base/traits_extension.py | 9 ++++++---
 nipype/utils/filemanip.py                  | 4 ++--
 nipype/utils/tests/test_filemanip.py       | 2 +-
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py
index ce4c43e4cc..652ca5f772 100644
--- a/nipype/interfaces/base/traits_extension.py
+++ b/nipype/interfaces/base/traits_extension.py
@@ -33,9 +33,10 @@
 
 from traits.api import Unicode
 from future import standard_library
+from ...utils.filemanip import Path, USING_PATHLIB2
 
-from ...utils.filemanip import Path
-
+if USING_PATHLIB2:
+    from future.types.newstr import newstr
 
 if traits_version < '3.7.0':
     raise ImportError('Traits version 3.7.0 or higher must be installed')
@@ -127,7 +128,9 @@ def __init__(self, value=Undefined,
     def validate(self, objekt, name, value, return_pathlike=False):
         """Validate a value change."""
         try:
-            value = Path('%s' % value)  # Use pathlib's validation
+            if USING_PATHLIB2 and isinstance(value, newstr):
+                value = '%s' % value  # pathlib2 doesn't like newstr
+            value = Path(value)  # Use pathlib's validation
         except Exception:
             self.error(objekt, name, str(value))
 
diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index 3012fd6e56..7403671a48 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -41,7 +41,7 @@
 
 
 class FileNotFoundError(OSError):
-    """Defines the expception for Python 2."""
+    """Defines the exception for Python 2."""
 
     def __init__(self, path):
         """Initialize the exception."""
@@ -75,7 +75,7 @@ def _patch_resolve(self, strict=False):
     pass
 except OSError:
     def _patch_resolve(self, strict=False):
-        """Add the argument strict to signature for pathlib2."""
+        """Raise FileNotFoundError instead of OSError with pathlib2."""
         try:
             resolved = self.old_resolve(strict=strict)
         except OSError:
diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py
index 5d064a3817..7eaa8b9c86 100644
--- a/nipype/utils/tests/test_filemanip.py
+++ b/nipype/utils/tests/test_filemanip.py
@@ -585,5 +585,5 @@ def test_Path_strict_resolve(tmpdir):
         testfile.resolve(strict=True)
 
     # If the file is created, it should not raise
-    testfile.write_text('')
+    open('somefile.txt', 'w').close()
     assert '%s/somefile.txt' % tmpdir == '%s' % testfile.resolve(strict=True)

From 5e69e7a552c34ff5f0ba1e608c4af2cdd897baae Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 17 Jul 2019 06:50:33 -0700
Subject: [PATCH 05/10] Update nipype/interfaces/spm/base.py [skip ci]

Co-Authored-By: Satrajit Ghosh <satrajit.ghosh@gmail.com>
---
 nipype/interfaces/spm/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py
index bbabbf42ba..98d53b761b 100644
--- a/nipype/interfaces/spm/base.py
+++ b/nipype/interfaces/spm/base.py
@@ -604,5 +604,5 @@ def __init__(self, value=NoDefaultSpecified, exists=False,
                  pathlike=False, resolve=False, **metadata):
         """Create an ImageFileSPM trait."""
         super(ImageFileSPM, self).__init__(
-            value=value, exists=exists, types=['nifti1', 'nifti2'],
+            value=value, exists=exists, types=['nifti1', 'nifti2'], allow_compressed=False,
             pathlike=pathlike, resolve=resolve, **metadata)

From 523a21e5dbfc4bcff60f6f8a2e43dc3649857ace Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 17 Jul 2019 06:54:31 -0700
Subject: [PATCH 06/10] Update nipype/interfaces/base/traits_extension.py [skip
 ci]

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/base/traits_extension.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py
index 652ca5f772..cf1b3353c2 100644
--- a/nipype/interfaces/base/traits_extension.py
+++ b/nipype/interfaces/base/traits_extension.py
@@ -135,7 +135,7 @@ def validate(self, objekt, name, value, return_pathlike=False):
             self.error(objekt, name, str(value))
 
         if self.exists:
-            if self.exists and not value.exists():
+            if not value.exists():
                 self.error(objekt, name, str(value))
 
             if self._is_file and not value.is_file():

From c1d1151bd20d1ab109bda7965b35c72e20054f37 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 17 Jul 2019 08:02:15 -0700
Subject: [PATCH 07/10] fix: make info_text of ``BasePath``s a property
 (@effigies' suggestion)

---
 nipype/interfaces/base/traits_extension.py | 28 ++++++++++++----------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py
index cf1b3353c2..4d3538fd41 100644
--- a/nipype/interfaces/base/traits_extension.py
+++ b/nipype/interfaces/base/traits_extension.py
@@ -99,30 +99,34 @@ class BasePath(TraitType):
     """Defines a trait whose value must be a valid filesystem path."""
 
     # A description of the type of value this trait accepts:
-    info_text = 'a pathlike object or string'
     exists = False
     pathlike = False
     resolve = False
     _is_file = False
     _is_dir = False
 
+    @property
+    def info_text(self):
+        """Create the trait's general description."""
+        info_text = 'a pathlike object or string'
+        if any((self.exists, self._is_file, self._is_dir)):
+            info_text += ' representing a'
+            if self.exists:
+                info_text += 'n existing'
+            if self._is_file:
+                info_text += ' file'
+            elif self._is_dir:
+                info_text += ' directory'
+            else:
+                info_text += ' file or directory'
+        return info_text
+
     def __init__(self, value=Undefined,
                  exists=False, pathlike=False, resolve=False, **metadata):
         """Create a BasePath trait."""
         self.exists = exists
         self.resolve = resolve
         self.pathlike = pathlike
-        if any((exists, self._is_file, self._is_dir)):
-            self.info_text += ' representing a'
-            if exists:
-                self.info_text += 'n existing'
-            if self._is_file:
-                self.info_text += ' file'
-            elif self._is_dir:
-                self.info_text += ' directory'
-            else:
-                self.info_text += ' file or directory'
-
         super(BasePath, self).__init__(value, **metadata)
 
     def validate(self, objekt, name, value, return_pathlike=False):

From 6c3858ab81c6d375a53050cb89c896f94c86b916 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 17 Jul 2019 08:07:35 -0700
Subject: [PATCH 08/10] fix: remove pathlike metadata as it wasn't useful

---
 nipype/interfaces/base/traits_extension.py | 21 +++++++++------------
 nipype/interfaces/spm/base.py              |  7 +++----
 2 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/nipype/interfaces/base/traits_extension.py b/nipype/interfaces/base/traits_extension.py
index 4d3538fd41..de215beb96 100644
--- a/nipype/interfaces/base/traits_extension.py
+++ b/nipype/interfaces/base/traits_extension.py
@@ -100,7 +100,6 @@ class BasePath(TraitType):
 
     # A description of the type of value this trait accepts:
     exists = False
-    pathlike = False
     resolve = False
     _is_file = False
     _is_dir = False
@@ -121,12 +120,10 @@ def info_text(self):
                 info_text += ' file or directory'
         return info_text
 
-    def __init__(self, value=Undefined,
-                 exists=False, pathlike=False, resolve=False, **metadata):
+    def __init__(self, value=Undefined, exists=False, resolve=False, **metadata):
         """Create a BasePath trait."""
         self.exists = exists
         self.resolve = resolve
-        self.pathlike = pathlike
         super(BasePath, self).__init__(value, **metadata)
 
     def validate(self, objekt, name, value, return_pathlike=False):
@@ -151,7 +148,7 @@ def validate(self, objekt, name, value, return_pathlike=False):
         if self.resolve:
             value = value.resolve(strict=self.exists)
 
-        if not return_pathlike and not self.pathlike:
+        if not return_pathlike:
             value = str(value)
 
         return value
@@ -277,8 +274,8 @@ class File(BasePath):
     _is_file = True
     _exts = None
 
-    def __init__(self, value=NoDefaultSpecified, exists=False, pathlike=False,
-                 resolve=False, allow_compressed=True, extensions=None, **metadata):
+    def __init__(self, value=NoDefaultSpecified, exists=False, resolve=False,
+                 allow_compressed=True, extensions=None, **metadata):
         """Create a File trait."""
         if extensions is not None:
             if isinstance(extensions, (bytes, str)):
@@ -290,8 +287,8 @@ def __init__(self, value=NoDefaultSpecified, exists=False, pathlike=False,
             self._exts = sorted(set(['.%s' % ext if not ext.startswith('.') else ext
                                      for ext in extensions]))
 
-        super(File, self).__init__(value=value, exists=exists,
-                                   pathlike=pathlike, resolve=resolve, **metadata)
+        super(File, self).__init__(value=value, exists=exists, resolve=resolve,
+                                   extensions=self._exts, **metadata)
 
     def validate(self, objekt, name, value, return_pathlike=False):
         """Validate a value change."""
@@ -301,7 +298,7 @@ def validate(self, objekt, name, value, return_pathlike=False):
             if ext not in self._exts:
                 self.error(objekt, name, str(value))
 
-        if not return_pathlike and not self.pathlike:
+        if not return_pathlike:
             value = str(value)
 
         return value
@@ -311,7 +308,7 @@ class ImageFile(File):
     """Defines a trait whose value must be a known neuroimaging file."""
 
     def __init__(self, value=NoDefaultSpecified, exists=False,
-                 pathlike=False, resolve=False, types=None, **metadata):
+                 resolve=False, types=None, **metadata):
         """Create an ImageFile trait."""
         extensions = None
         if types is not None:
@@ -327,7 +324,7 @@ def __init__(self, value=NoDefaultSpecified, exists=False,
 
         super(ImageFile, self).__init__(
             value=value, exists=exists, extensions=extensions,
-            pathlike=pathlike, resolve=resolve, **metadata)
+            resolve=resolve, **metadata)
 
 
 def isdefined(objekt):
diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py
index 98d53b761b..fda02d40f1 100644
--- a/nipype/interfaces/spm/base.py
+++ b/nipype/interfaces/spm/base.py
@@ -600,9 +600,8 @@ def _make_matlab_command(self, contents, postscript=None):
 class ImageFileSPM(ImageFile):
     """Defines a trait whose value must be a NIfTI file."""
 
-    def __init__(self, value=NoDefaultSpecified, exists=False,
-                 pathlike=False, resolve=False, **metadata):
+    def __init__(self, value=NoDefaultSpecified, exists=False, resolve=False, **metadata):
         """Create an ImageFileSPM trait."""
         super(ImageFileSPM, self).__init__(
-            value=value, exists=exists, types=['nifti1', 'nifti2'], allow_compressed=False,
-            pathlike=pathlike, resolve=resolve, **metadata)
+            value=value, exists=exists, types=['nifti1', 'nifti2'],
+            allow_compressed=False, resolve=resolve, **metadata)

From 66c0f9b1ae83f0646ae71b913ef2991938ea21bb Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 17 Jul 2019 08:09:06 -0700
Subject: [PATCH 09/10] fix: remove unused ``USING_PATHLIB_PATCHED``

---
 nipype/utils/filemanip.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index 7403671a48..edf23532f5 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -50,7 +50,6 @@ def __init__(self, path):
 
 
 USING_PATHLIB2 = False
-USING_PATHLIB_PATCHED = False
 try:
     from pathlib import Path
 except ImportError:
@@ -70,7 +69,6 @@ def _patch_resolve(self, strict=False):
 
     Path.old_resolve = Path.resolve
     Path.resolve = _patch_resolve
-    USING_PATHLIB_PATCHED = True
 except FileNotFoundError:
     pass
 except OSError:

From d42db563bd11dadc2a38b8550f43677c0d22fb28 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 17 Jul 2019 08:10:08 -0700
Subject: [PATCH 10/10] sty: make codacy happy (Redefining built-in
 'FileNotFoundError')

---
 nipype/utils/filemanip.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py
index edf23532f5..e19563ed54 100644
--- a/nipype/utils/filemanip.py
+++ b/nipype/utils/filemanip.py
@@ -40,7 +40,7 @@
 PY3 = sys.version_info[0] >= 3
 
 
-class FileNotFoundError(OSError):
+class FileNotFoundError(OSError):  # noqa
     """Defines the exception for Python 2."""
 
     def __init__(self, path):