fixing python 2 compatibility

Author: oesteban

nipype/interfaces/base.py

@@ -1832,10 +1832,12 @@ def _parse_inputs(self, skip=None):
             if skip and name in skip:
                 continue
             value = getattr(self.inputs, name)
-            if spec.genfile or spec.name_source:
+            if spec.name_source:
                 value = self._filename_from_source(name)
-                if not isdefined(value):
+            elif spec.genfile:
+                if not isdefined(value) or value is None:
                     value = self._gen_filename(name)
+
             if not isdefined(value):
                 continue
             arg = self._format_arg(name, spec, value)

nipype/interfaces/fsl/base.py

@@ -31,9 +31,11 @@
 from glob import glob
 import os
 
+from ... import logging
 from ...utils.filemanip import fname_presuffix
 from ..base import traits, isdefined, CommandLine, CommandLineInputSpec
 
+LOGGER = logging.getLogger('interface')
 
 
 class Info(object):
@@ -110,8 +112,8 @@ def output_type(cls):
         try:
             return os.environ['FSLOUTPUTTYPE']
         except KeyError:
-            warnings.warn(('FSL environment variables not set. setting output '
-                           'type to NIFTI'))
+            LOGGER.warn('FSLOUTPUTTYPE environment variable is not set. '
+                        'Setting FSLOUTPUTTYPE=NIFTI')
             return 'NIFTI'
 
     @staticmethod

nipype/interfaces/fsl/dti.py

@@ -16,6 +16,7 @@
 from builtins import range
 
 import os
+import warnings
 
 from ...utils.filemanip import fname_presuffix, split_filename, copyfile
 from ..base import (TraitedSpec, isdefined, File, Directory,

nipype/interfaces/fsl/epi.py

@@ -17,6 +17,7 @@
 import os
 import numpy as np
 import nibabel as nib
+import warnings
 
 from ...utils.filemanip import split_filename
 from ..base import (traits, TraitedSpec, InputMultiPath, File,

nipype/interfaces/meshfix.py

@@ -128,7 +128,7 @@ def _list_outputs(self):
         return outputs
 
     def _gen_filename(self, name):
-        if name is 'out_filename':
+        if name == 'out_filename':
             return self._gen_outfilename()
         else:
             return None

nipype/interfaces/traits_extension.py

@@ -33,7 +33,7 @@
 from traits.api import BaseUnicode
 from traits.api import Unicode
 
-DictStrStr = traits.Dict(str, str)
+DictStrStr = traits.Dict(str, (bytes, str))
 Str = Unicode
 
 class BaseFile(BaseUnicode):

nipype/pipeline/engine/base.py

@@ -24,8 +24,8 @@
 import re
 import numpy as np
 from ... import logging
+from ...interfaces.base import DynamicTraitedSpec
 from ...utils.filemanip import loadpkl, savepkl
-from ..interfaces.base import DynamicTraitedSpec
 
 logger = logging.getLogger('workflow')
 

nipype/pipeline/engine/nodes.py

@@ -46,7 +46,8 @@
 from ...interfaces.base import (traits, InputMultiPath, CommandLine,
                                 Undefined, TraitedSpec, DynamicTraitedSpec,
                                 Bunch, InterfaceResult, md5, Interface,
-                                TraitDictObject, TraitListObject, isdefined)
+                                TraitDictObject, TraitListObject, isdefined,
+                                runtime_profile)
 from .utils import (generate_expanded_graph, modify_paths,
                     export_graph, make_output_dir, write_workflow_prov,
                     clean_working_directory, format_dot, topological_sort,

nipype/utils/tests/test_cmd.py

@@ -26,6 +26,7 @@ def capture_sys_output():
 
 
 class TestNipypeCMD(unittest.TestCase):
+    maxDiff = None
 
     def test_main_returns_2_on_empty(self):
         with self.assertRaises(SystemExit) as cm:
@@ -113,13 +114,13 @@ def test_run_4d_realign_without_arguments(self):
                                                        in_file [in_file ...]
                                                        tr"""
 
-        if PY2:
+        if PY3:
             error_message += """
-nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
+nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: the following arguments are required: in_file, tr
 """
-        elif PY3:
+        else:
             error_message += """
-nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: the following arguments are required: in_file, tr
+nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments
 """
 
         self.assertEqual(stderr.getvalue(), error_message)

nipype/workflows/dmri/fsl/tests/test_dti.py

@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+from __future__ import unicode_literals, print_function, absolute_import
 import os
 
 from nipype.testing import skipif