test passing locally

Author: oesteban

nipype/interfaces/base/__init__.py

@@ -17,11 +17,15 @@
 from .specs import (
     BaseTraitedSpec, TraitedSpec, DynamicTraitedSpec,
     BaseInterfaceInputSpec, CommandLineInputSpec,
+    StdOutCommandLineInputSpec
 )
 
 from .traits_extension import (
     traits, Undefined, TraitDictObject, TraitListObject, TraitError, isdefined,
     File, Directory, Str, DictStrStr, has_metadata, ImageFile,
     MultiPath, OutputMultiPath, InputMultiPath)
 
-from .support import Bunch, InterfaceResult, load_template
+from .support import (
+    Bunch, InterfaceResult, load_template,
+    NipypeInterfaceError
+)

nipype/interfaces/base/core.py

@@ -440,7 +440,7 @@ def run(self, **inputs):
         results :  an InterfaceResult object containing a copy of the instance
         that was executed, provenance information and, if successful, results
         """
-        from ..utils.profiler import ResourceMonitor
+        from ...utils.profiler import ResourceMonitor
 
         enable_rm = config.resource_monitor and self.resource_monitor
         force_raise = not getattr(self.inputs, 'ignore_exception', False)
@@ -624,6 +624,7 @@ class SimpleInterface(BaseInterface):
 
     .. testsetup::
 
+    >>> from .specs import TraitedSpec
     >>> tmp = getfixture('tmpdir')
     >>> old = tmp.chdir() # changing to a temporary directory
 

nipype/interfaces/base/traits_extension.py

@@ -395,7 +395,7 @@ class OutputMultiPath(MultiPath):
 
     XXX This needs to be vetted by somebody who understands traits
 
-    >>> from nipype.interfaces.base import OutputMultiPath
+    >>> from nipype.interfaces.base import OutputMultiPath, TraitedSpec
     >>> class A(TraitedSpec):
     ...     foo = OutputMultiPath(File(exists=False))
     >>> a = A()
@@ -440,7 +440,7 @@ class InputMultiPath(MultiPath):
 
     XXX This needs to be vetted by somebody who understands traits
 
-    >>> from nipype.interfaces.base import InputMultiPath
+    >>> from nipype.interfaces.base import InputMultiPath, TraitedSpec
     >>> class A(TraitedSpec):
     ...     foo = InputMultiPath(File(exists=False))
     >>> a = A()

nipype/interfaces/brainsuite/brainsuite.py

@@ -5,7 +5,7 @@
 import re as regex
 
 from ..base import TraitedSpec, CommandLineInputSpec, CommandLine, File, traits, isdefined
-from ..traits_extension import str
+
 
 """This script provides interfaces for BrainSuite command line tools.
 Please see brainsuite.org for more information.
@@ -902,7 +902,7 @@ class SVRegInputSpec(CommandLineInputSpec):
              'Cortical Surface Extraction Sequence'
     )
     dataSinkDelay = traits.List(
-        str, argstr='%s',
+        traits.Str, argstr='%s',
         desc='Connect datasink out_file to dataSinkDelay to delay execution of SVReg '
              'until dataSink has finished sinking CSE outputs.'
              'For use with parallel processing workflows including Brainsuites Cortical '
@@ -1087,7 +1087,7 @@ class BDPInputSpec(CommandLineInputSpec):
              'bvec and .bval files can be used instead (see diffusionGradientFile and bValueFile). '
     )
     BVecBValPair = traits.List(
-        str, minlen=2, maxlen=2, mandatory=True, position=-1, xor=['bMatrixFile'],
+        traits.Str, minlen=2, maxlen=2, mandatory=True, position=-1, xor=['bMatrixFile'],
         argstr='--bvec %s --bval %s',
         desc='Must input a list containing first the BVector file, then the BValue file (both must be absolute paths)\n'
              'Example: bdp.inputs.BVecBValPair = [\'/directory/subdir/prefix.dwi.bvec\', \'/directory/subdir/prefix.dwi.bval\'] '
@@ -1100,7 +1100,7 @@ class BDPInputSpec(CommandLineInputSpec):
              'usually has an extension of .bvec '
     )
     dataSinkDelay = traits.List(
-        str, argstr='%s',
+        traits.Str, argstr='%s',
         desc='For use in parallel processing workflows including Brainsuite Cortical '
              'Surface Extraction sequence. Connect datasink out_file to dataSinkDelay '
              'to delay execution of BDP until dataSink has finished sinking outputs. '

nipype/interfaces/dcmstack.py

@@ -19,10 +19,12 @@
 import nibabel as nb
 import imghdr
 
-from .base import (TraitedSpec, DynamicTraitedSpec,
-                   InputMultiPath, File, Directory,
-                   traits, BaseInterface)
-from .traits_extension import isdefined, Undefined
+from .base import (
+    TraitedSpec, DynamicTraitedSpec,
+    InputMultiPath, File, Directory,
+    traits, BaseInterface,
+    isdefined, Undefined
+)
 from ..utils import NUMPY_MMAP
 
 

nipype/interfaces/fsl/fix.py

@@ -64,21 +64,24 @@
     OutputMultiPath,
     BaseInterface,
     BaseInterfaceInputSpec,
-    traits
+    traits,
+    Directory,
+    File,
+    isdefined
 )
-from ..traits_extension import Directory, File, isdefined
 import os
 
 
 class TrainingSetCreatorInputSpec(BaseInterfaceInputSpec):
     mel_icas_in = InputMultiPath(Directory(exists=True), copyfile=False,
-                              desc='Melodic output directories',
-                              argstr='%s', position=-1)
+                                 desc='Melodic output directories',
+                                 argstr='%s', position=-1)
+
 
 class TrainingSetCreatorOutputSpec(TraitedSpec):
     mel_icas_out = OutputMultiPath(Directory(exists=True), copyfile=False,
-                              desc='Hand labels for noise vs signal',
-                              argstr='%s', position=-1)
+                                   desc='Hand labels for noise vs signal',
+                                   argstr='%s', position=-1)
 
 
 class TrainingSetCreator(BaseInterface):

nipype/interfaces/fsl/model.py

@@ -2185,9 +2185,10 @@ def load_template(name):
     template : string.Template
 
     """
-    full_fname = os.path.join(os.path.dirname(__file__),
-                              'script_templates', name)
-    template_file = open(full_fname)
-    template = Template(template_file.read())
-    template_file.close()
+    from pkg_resources import resource_filename as pkgrf
+    full_fname = pkgrf('nipype',
+                       os.path.join('script_templates', name))
+    with open(full_fname) as template_file:
+        template = Template(template_file.read())
+
     return template

nipype/interfaces/mrtrix/tracking.py

@@ -15,8 +15,10 @@
 import os.path as op
 
 from ...utils.filemanip import split_filename
-from ..base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File
-from ..traits_extension import isdefined
+from ..base import (
+    CommandLineInputSpec, CommandLine, traits, TraitedSpec, File,
+    isdefined
+)
 
 
 class FilterTracksInputSpec(CommandLineInputSpec):

nipype/interfaces/mrtrix3/base.py

@@ -14,8 +14,7 @@
 from __future__ import print_function, division, unicode_literals, absolute_import
 
 from ... import logging
-from ..traits_extension import isdefined
-from ..base import (CommandLineInputSpec, CommandLine, traits, File)
+from ..base import (CommandLineInputSpec, CommandLine, traits, File, isdefined)
 iflogger = logging.getLogger('interface')
 
 

nipype/interfaces/mrtrix3/connectivity.py

@@ -16,8 +16,7 @@
 import os
 import os.path as op
 
-from ..traits_extension import isdefined
-from ..base import (CommandLineInputSpec, traits, TraitedSpec, File)
+from ..base import (CommandLineInputSpec, traits, TraitedSpec, File, isdefined)
 from .base import MRTrix3Base