Merge remote-tracking branch 'upstream/master' into maint/reorder-deps

Author: oesteban

docker/generate_dockerfiles.sh

@@ -52,8 +52,8 @@ do
   esac
 done
 
-# neurodocker version 0.5.0
-NEURODOCKER_IMAGE="kaczmarj/neurodocker:0.5.0"
+# neurodocker version 0.4.1-22-g7c44e01
+NEURODOCKER_IMAGE="kaczmarj/neurodocker:master@sha256:858632a7533cac100f70932749b4cfc77fc40f667f41fca208f406215cff8a27"
 # neurodebian:stretch-non-free pulled on September 19, 2018
 BASE_IMAGE="neurodebian:stretch-non-free@sha256:7cd978427d7ad215834fee221d0536ed7825b3cddebc481eba2d792dfc2f7332"
 
@@ -88,6 +88,7 @@ function generate_main_dockerfile() {
           OMP_NUM_THREADS=1 \
     --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \
     --user neuro \
+    --workdir /home/neuro \
     --miniconda create_env=neuro \
                 conda_install='python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}
                                libxml2 libxslt matplotlib mkl "numpy!=1.16.0" paramiko

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/__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)

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)

nipype/interfaces/base/specs.py

@@ -19,19 +19,20 @@
 from builtins import str, bytes
 from packaging.version import Version
 
-from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str
+from traits.trait_errors import TraitError
+from traits.trait_handlers import TraitDictObject, TraitListObject
+from ...utils.filemanip import (
+    md5, hash_infile, hash_timestamp, to_str, USING_PATHLIB2)
 from .traits_extension import (
     traits,
     Undefined,
     isdefined,
-    TraitError,
-    TraitDictObject,
-    TraitListObject,
     has_metadata,
 )
 
 from ... import config, __version__
 
+
 FLOAT_FORMAT = '{:.10f}'.format
 nipype_version = Version(__version__)
 
@@ -314,6 +315,39 @@ 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 +367,9 @@ 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'