ENH: Modify Directory and File traits to get along with pathlib

Closes nipy#2959

Author: oesteban

nipype/info.py

@@ -147,6 +147,7 @@ def get_nipype_gitversion():
     'numpy>=%s ; python_version >= "3.7"' % NUMPY_MIN_VERSION_37,
     'numpy>=%s,!=%s ; python_version == "2.7"' % (NUMPY_MIN_VERSION, NUMPY_BAD_VERSION_27),
     'packaging',
+    'pathlib2; python_version <= "3.4"',
     'prov>=%s' % PROV_VERSION,
     'pydot>=%s' % PYDOT_MIN_VERSION,
     'pydotplus',

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):

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::']

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
 
@@ -420,18 +420,17 @@ 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))
 
     with pytest.raises(nib.TraitError):
         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'