multiple fixes for python 3 compatibility

- added from __future__ import ... to all files
- removed dependency on six
- cleaned up imports
- used only relative explicit imports

Author: oesteban

build_docs.py

@@ -8,7 +8,7 @@
 
     python setup.py build_sphinx
 """
-from __future__ import print_function, unicode_literals
+from __future__ import print_function, division, unicode_literals, absolute_import
 from builtins import open, str
 
 # Standard library imports

nipype/__init__.py

@@ -1,29 +1,28 @@
 # -*- 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:
-from __future__ import absolute_import
+from __future__ import print_function, division, unicode_literals, absolute_import
 
 import os
+from distutils.version import LooseVersion
 
 from .info import (LONG_DESCRIPTION as __doc__,
                    URL as __url__,
                    STATUS as __status__,
                    __version__)
 from .utils.config import NipypeConfig
-config = NipypeConfig()
-from .utils.logger import Logging
-logging = Logging(config)
-
-from distutils.version import LooseVersion
-
 from .fixes.numpy.testing import nosetester
+from .utils.logger import Logging
 
 try:
     import faulthandler
     faulthandler.enable()
-except (ImportError,IOError) as e:
+except (ImportError, IOError) as e:
     pass
 
+config = NipypeConfig()
+logging = Logging(config)
+
 
 class _NoseTester(nosetester.NoseTester):
     """ Subclass numpy's NoseTester to add doctests by default

nipype/algorithms/icc.py

@@ -1,13 +1,13 @@
 # -*- coding: utf-8 -*-
-from __future__ import division
+from __future__ import print_function, division, unicode_literals, absolute_import
 from builtins import range
+import os
+import numpy as np
 from numpy import ones, kron, mean, eye, hstack, dot, tile
+import nibabel as nb
 from scipy.linalg import pinv
 from ..interfaces.base import BaseInterfaceInputSpec, TraitedSpec, \
     BaseInterface, traits, File
-import nibabel as nb
-import numpy as np
-import os
 
 
 class ICCInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/mesh.py

@@ -12,16 +12,14 @@
     >>> os.chdir(datadir)
 
 """
-from __future__ import division
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import zip, str, bytes
 
 import os.path as op
 import numpy as np
 from numpy import linalg as nla
 
-from builtins import zip
-
 from .. import logging
-from six import string_types
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
                                BaseInterfaceInputSpec)
 from ..interfaces.vtkbase import tvtk
@@ -325,7 +323,7 @@ def _run_interface(self, runtime):
         operator = self.inputs.operator
         opfield = np.ones_like(points1)
 
-        if isinstance(operator, string_types):
+        if isinstance(operator, (str, bytes)):
             r2 = tvtk.PolyDataReader(file_name=self.inputs.surface2)
             vtk2 = VTKInfo.vtk_output(r2)
             r2.update()

nipype/algorithms/metrics.py

@@ -12,9 +12,8 @@
     >>> os.chdir(datadir)
 
 '''
-from __future__ import division
-from builtins import zip
-from builtins import range
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import zip, range
 
 import os
 import os.path as op

nipype/algorithms/misc.py

@@ -11,12 +11,8 @@
     >>> os.chdir(datadir)
 
 '''
-from __future__ import print_function
-from __future__ import absolute_import
-from __future__ import division
-from builtins import str
-from builtins import zip
-from builtins import range
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import str, zip, range
 from future.utils import raise_from
 
 import os
@@ -30,17 +26,15 @@
 import scipy.io as sio
 import itertools
 import scipy.stats as stats
-
-from nipype import logging
-
 import warnings
 
+from .. import logging
 from . import metrics as nam
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
                                InputMultiPath, OutputMultiPath,
                                BaseInterfaceInputSpec, isdefined,
                                DynamicTraitedSpec, Undefined)
-from nipype.utils.filemanip import fname_presuffix, split_filename
+from ..utils.filemanip import fname_presuffix, split_filename
 iflogger = logging.getLogger('interface')
 
 

nipype/algorithms/modelgen.py

@@ -18,9 +18,8 @@
    >>> os.chdir(datadir)
 
 """
-
-from __future__ import division
-from builtins import range
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import range, str, bytes
 
 from copy import deepcopy
 import os
@@ -29,7 +28,6 @@
 import numpy as np
 from scipy.special import gammaln
 
-from six import string_types
 from ..interfaces.base import (BaseInterface, TraitedSpec, InputMultiPath,
                                traits, File, Bunch, BaseInterfaceInputSpec,
                                isdefined)
@@ -458,7 +456,7 @@ def _concatenate_info(self, infolist):
         for i, f in enumerate(self.inputs.functional_runs):
             if isinstance(f, list):
                 numscans = len(f)
-            elif isinstance(f, string_types):
+            elif isinstance(f, (str, bytes)):
                 img = load(f)
                 numscans = img.shape[3]
             else:

nipype/algorithms/rapidart.py

@@ -18,10 +18,8 @@
    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
    >>> os.chdir(datadir)
 """
-
-from __future__ import division
-from __future__ import unicode_literals
-from builtins import open, range
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open, range, str, bytes
 
 import os
 from copy import deepcopy
@@ -31,7 +29,6 @@
 from scipy import signal
 import scipy.io as sio
 
-from six import string_types
 from ..interfaces.base import (BaseInterface, traits, InputMultiPath,
                                OutputMultiPath, TraitedSpec, File,
                                BaseInterfaceInputSpec, isdefined)
@@ -283,7 +280,7 @@ def _get_output_filenames(self, motionfile, output_dir):
         output_dir: string
             output directory in which the files will be generated
         """
-        if isinstance(motionfile, string_types):
+        if isinstance(motionfile, (str, bytes)):
             infile = motionfile
         elif isinstance(motionfile, list):
             infile = motionfile[0]
@@ -354,7 +351,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
             cwd = os.getcwd()
 
         # read in functional image
-        if isinstance(imgfile, string_types):
+        if isinstance(imgfile, (str, bytes)):
             nim = load(imgfile)
         elif isinstance(imgfile, list):
             if len(imgfile) == 1:

nipype/caching/memory.py

@@ -9,8 +9,7 @@
    >>> datadir = os.path.realpath(os.path.join(filepath, '../testing/data'))
    >>> os.chdir(datadir)
 """
-
-from __future__ import print_function
+from __future__ import print_function, division, unicode_literals, absolute_import
 from builtins import object
 
 import os

nipype/external/portalocker.py

@@ -49,9 +49,8 @@
 Version: $Id: portalocker.py 5474 2008-05-16 20:53:50Z lowell $
 
 '''
-from __future__ import print_function
-from __future__ import absolute_import
-
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open
 
 __all__ = [
     'lock',
@@ -132,11 +131,9 @@ def unlock(file):
 
     log = open('log.txt', 'a+')
     portalocker.lock(log, portalocker.LOCK_EX)
-
     timestamp = strftime('%m/%d/%Y %H:%M:%S\n', localtime(time()))
     log.write(timestamp)
 
     print('Wrote lines. Hit enter to release lock.')
     dummy = sys.stdin.readline()
-
     log.close()

nipype/fixes/numpy/testing/nosetester.py

@@ -5,16 +5,12 @@
 This module implements ``test()`` and ``bench()`` functions for NumPy modules.
 
 """
-
-from __future__ import print_function
-from __future__ import absolute_import
-from builtins import object
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import object, str, bytes
 
 import os
 import sys
 
-from six import string_types
-
 
 def get_package_name(filepath):
     """
@@ -177,7 +173,7 @@ def _test_argv(self, label, verbose, extra_argv):
         '''
         argv = [__file__, self.package_path, '-s']
         if label and label != 'full':
-            if not isinstance(label, string_types):
+            if not isinstance(label, (str, bytes)):
                 raise TypeError('Selection label should be a string')
             if label == 'fast':
                 label = 'not slow'

nipype/info.py

@@ -2,6 +2,7 @@
 settings in setup.py, the nipy top-level docstring, and for building the
 docs.  In setup.py in particular, we exec this file, so it cannot import nipy
 """
+from __future__ import print_function, division, unicode_literals, absolute_import
 
 
 # nipype version information.  An empty _version_extra corresponds to a

nipype/interfaces/__init__.py

@@ -6,8 +6,7 @@
 
 Requires Packages to be installed
 """
-
-from __future__ import absolute_import
+from __future__ import print_function, division, unicode_literals, absolute_import
 __docformat__ = 'restructuredtext'
 
 from .io import DataGrabber, DataSink, SelectFiles

nipype/interfaces/afni/base.py

@@ -2,11 +2,12 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Provide interface to AFNI commands."""
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import object, str, bytes
+from future.utils import raise_from
 
 import os
 from sys import platform
-from builtins import object
-from future.utils import raise_from
 
 from ... import logging
 from ...utils.filemanip import split_filename

nipype/interfaces/afni/preprocess.py

@@ -9,21 +9,20 @@
     >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 """
-from __future__ import unicode_literals
-from builtins import open
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import open, str, bytes
 
 import os
 import os.path as op
 import re
 import numpy as np
-from six import string_types
 
-from nipype.utils.filemanip import (load_json, save_json, split_filename)
-from nipype.interfaces.base import (
+from ...utils.filemanip import (load_json, save_json, split_filename)
+from ..base import (
     CommandLineInputSpec, CommandLine, Directory, TraitedSpec,
     traits, isdefined, File, InputMultiPath, Undefined)
 
-from nipype.interfaces.afni.base import (
+from .base import (
     AFNICommandBase, AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec,
     Info, no_afni)
 
@@ -2856,7 +2855,7 @@ def _format_arg(self, name, trait_spec, value):
                     return None
             elif isinstance(value, tuple):
                 return trait_spec.argstr + ' %s %f' % value
-            elif isinstance(value, string_types):
+            elif isinstance(value, (str, bytes)):
                 return trait_spec.argstr + ' ' + value
         return super(FWHMx, self)._format_arg(name, trait_spec, value)
 
@@ -2878,7 +2877,7 @@ def _list_outputs(self):
             sout = tuple(sout[0])
 
             outputs['out_acf'] = op.abspath('3dFWHMx.1D')
-            if isinstance(self.inputs.acf, string_types):
+            if isinstance(self.inputs.acf, (str, bytes)):
                 outputs['out_acf'] = op.abspath(self.inputs.acf)
 
         outputs['fwhm'] = tuple(sout)

nipype/interfaces/afni/svm.py

@@ -9,19 +9,10 @@
     >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 """
-import os
-import re
-
-from ..base import (Directory, TraitedSpec,
-                    traits, isdefined, File, InputMultiPath, Undefined)
-from ...utils.filemanip import (load_json, save_json, split_filename)
-from nipype.utils.filemanip import fname_presuffix
-from .base import AFNICommand, AFNICommandInputSpec,\
-    AFNICommandOutputSpec
-from nipype.interfaces.base import CommandLineInputSpec, CommandLine,\
-    OutputMultiPath
-
-from warnings import warn
+from __future__ import print_function, division, unicode_literals, absolute_import
+
+from ..base import TraitedSpec, traits, File
+from .base import AFNICommand, AFNICommandInputSpec, AFNICommandOutputSpec
 
 
 class SVMTrainInputSpec(AFNICommandInputSpec):

nipype/interfaces/ants/base.py

@@ -2,12 +2,11 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """The ants module provides basic functions for interfacing with ANTS tools."""
-
+from __future__ import print_function, division, unicode_literals, absolute_import
+from builtins import str
 # Local imports
-from ..base import (CommandLine, CommandLineInputSpec, traits,
-                    isdefined)
-
 from ... import logging
+from ..base import CommandLine, CommandLineInputSpec, traits, isdefined
 logger = logging.getLogger('interface')
 
 # -Using -1 gives primary responsibilty to ITKv4 to do the correct