make check-before-commit

Author: oesteban

Makefile

@@ -56,14 +56,14 @@ inplace:
 	$(PYTHON) setup.py build_ext -i
 
 test-code: in
-	$(NOSETESTS) -s nipype --with-doctest
+	$(NOSETESTS) -s nipype --with-doctest --with-doctest-ignore-unicode
 
 test-doc:
-	$(NOSETESTS) -s --with-doctest --doctest-tests --doctest-extension=rst \
+	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --doctest-tests --doctest-extension=rst \
 	--doctest-fixtures=_fixture doc/
 
 test-coverage: clean-tests in
-	$(NOSETESTS) -s --with-doctest --with-coverage --cover-package=nipype \
+	$(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --with-coverage --cover-package=nipype \
 	--config=.coveragerc
 
 test: clean test-code

doc/sphinxext/numpy_ext/docscrape.py

@@ -2,7 +2,6 @@
 """Extract reference documentation from the NumPy source tree.
 
 """
-
 from __future__ import print_function
 from future import standard_library
 standard_library.install_aliases()
@@ -14,7 +13,7 @@
 import pydoc
 from warnings import warn
 
-from six import StringIO
+from io import StringIO
 
 
 class Reader(object):

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -1,12 +1,12 @@
 # -*- coding: utf-8 -*-
-from __future__ import absolute_import
+from __future__ import absolute_import, unicode_literals
+from builtins import str, bytes
 import re
 import inspect
 import textwrap
 import pydoc
 import sphinx
 from .docscrape import NumpyDocString, FunctionDoc, ClassDoc
-from six import string_types
 
 
 class SphinxDocString(NumpyDocString):
@@ -147,7 +147,7 @@ def _str_references(self):
         out = []
         if self['References']:
             out += self._str_header('References')
-            if isinstance(self['References'], string_types):
+            if isinstance(self['References'], (str, bytes)):
                 self['References'] = [self['References']]
             out.extend(self['References'])
             out += ['']

examples/fmri_ants_openfmri.py

@@ -11,9 +11,8 @@
 
     python fmri_ants_openfmri.py --datasetdir ds107
 """
-
-from __future__ import division
-from builtins import range
+from __future__ import division, unicode_literals
+from builtins import range, str, bytes
 
 from nipype import config
 config.enable_provenance()
@@ -26,7 +25,6 @@
 import nipype.algorithms.modelgen as model
 import nipype.algorithms.rapidart as ra
 from nipype.algorithms.misc import TSNR
-from six import string_types
 from nipype.interfaces.c3 import C3dAffineTool
 import nipype.interfaces.io as nio
 import nipype.interfaces.utility as niu
@@ -774,7 +772,7 @@ def get_contrasts(contrast_file, task_id, conds):
     def check_behav_list(behav, run_id, conds):
         import numpy as np
         num_conds = len(conds)
-        if isinstance(behav, string_types):
+        if isinstance(behav, (str, bytes)):
             behav = [behav]
         behav_array = np.array(behav).flatten()
         num_elements = behav_array.shape[0]

examples/fmri_openfmri.py

@@ -12,9 +12,8 @@
     python fmri_openfmri.py --datasetdir ds107
 """
 
-from __future__ import division
-from __future__ import unicode_literals
-from builtins import open, range
+from __future__ import division, unicode_literals
+from builtins import open, range, str, bytes
 
 from glob import glob
 import os
@@ -25,7 +24,6 @@
 import nipype.interfaces.fsl as fsl
 import nipype.interfaces.io as nio
 import nipype.interfaces.utility as niu
-from six import string_types
 from nipype.workflows.fmri.fsl import (create_featreg_preproc,
                                        create_modelfit_workflow,
                                        create_fixed_effects_flow,
@@ -242,7 +240,7 @@ def get_contrasts(contrast_file, task_id, conds):
 
     def check_behav_list(behav):
         out_behav = []
-        if isinstance(behav, string_types):
+        if isinstance(behav, (str, bytes)):
             behav = [behav]
         for val in behav:
             if not isinstance(val, list):

nipype/algorithms/tests/test_auto_SpecifyModel.py

@@ -5,7 +5,7 @@
 
 def test_SpecifyModel_inputs():
     input_map = dict(event_files=dict(mandatory=True,
-    xor=['subject_info', 'event_files'],
+    xor=[u'subject_info', u'event_files'],
     ),
     functional_runs=dict(copyfile=False,
     mandatory=True,
@@ -22,7 +22,7 @@ def test_SpecifyModel_inputs():
     realignment_parameters=dict(copyfile=False,
     ),
     subject_info=dict(mandatory=True,
-    xor=['subject_info', 'event_files'],
+    xor=[u'subject_info', u'event_files'],
     ),
     time_repetition=dict(mandatory=True,
     ),

nipype/algorithms/tests/test_auto_SpecifySPMModel.py

@@ -7,7 +7,7 @@ def test_SpecifySPMModel_inputs():
     input_map = dict(concatenate_runs=dict(usedefault=True,
     ),
     event_files=dict(mandatory=True,
-    xor=['subject_info', 'event_files'],
+    xor=[u'subject_info', u'event_files'],
     ),
     functional_runs=dict(copyfile=False,
     mandatory=True,
@@ -26,7 +26,7 @@ def test_SpecifySPMModel_inputs():
     realignment_parameters=dict(copyfile=False,
     ),
     subject_info=dict(mandatory=True,
-    xor=['subject_info', 'event_files'],
+    xor=[u'subject_info', u'event_files'],
     ),
     time_repetition=dict(mandatory=True,
     ),

nipype/algorithms/tests/test_auto_SpecifySparseModel.py

@@ -5,7 +5,7 @@
 
 def test_SpecifySparseModel_inputs():
     input_map = dict(event_files=dict(mandatory=True,
-    xor=['subject_info', 'event_files'],
+    xor=[u'subject_info', u'event_files'],
     ),
     functional_runs=dict(copyfile=False,
     mandatory=True,
@@ -30,13 +30,13 @@ def test_SpecifySparseModel_inputs():
     stimuli_as_impulses=dict(usedefault=True,
     ),
     subject_info=dict(mandatory=True,
-    xor=['subject_info', 'event_files'],
+    xor=[u'subject_info', u'event_files'],
     ),
     time_acquisition=dict(mandatory=True,
     ),
     time_repetition=dict(mandatory=True,
     ),
-    use_temporal_deriv=dict(requires=['model_hrf'],
+    use_temporal_deriv=dict(requires=[u'model_hrf'],
     ),
     volumes_in_cluster=dict(usedefault=True,
     ),

nipype/interfaces/afni/tests/test_auto_AFNICommand.py

@@ -13,7 +13,7 @@ def test_AFNICommand_inputs():
     usedefault=True,
     ),
     out_file=dict(argstr='-prefix %s',
-    name_source=['in_file'],
+    name_source=[u'in_file'],
     name_template='%s_afni',
     ),
     outputtype=dict(),

nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py

@@ -26,7 +26,7 @@ def test_BlurToFWHM_inputs():
     mask=dict(argstr='-blurmaster %s',
     ),
     out_file=dict(argstr='-prefix %s',
-    name_source=['in_file'],
+    name_source=[u'in_file'],
     name_template='%s_afni',
     ),
     outputtype=dict(),