switched to six.string_types for string type checks

Author: belevtsoff

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -1,6 +1,7 @@
 import re, inspect, textwrap, pydoc
 import sphinx
 from docscrape import NumpyDocString, FunctionDoc, ClassDoc
+from nipype.external import six
 
 class SphinxDocString(NumpyDocString):
     def __init__(self, docstring, config={}):
@@ -140,7 +141,7 @@ def _str_references(self):
         out = []
         if self['References']:
             out += self._str_header('References')
-            if isinstance(self['References'], basestring):
+            if isinstance(self['References'], six.string_types):
                 self['References'] = [self['References']]
             out.extend(self['References'])
             out += ['']

examples/fmri_ants_openfmri.py

@@ -14,6 +14,8 @@
 
 from nipype import config
 config.enable_provenance()
+from nipype.external import six
+
 
 from glob import glob
 import os
@@ -443,7 +445,7 @@ def get_contrasts(contrast_file, task_id, conds):
 
     def check_behav_list(behav):
         out_behav = []
-        if isinstance(behav, basestring):
+        if isinstance(behav, six.string_types):
             behav = [behav]
         for val in behav:
             if not isinstance(val, list):

examples/fmri_openfmri.py

@@ -14,6 +14,7 @@
 
 from nipype import config
 config.enable_provenance()
+from nipype.external import six
 
 from glob import glob
 import os
@@ -237,7 +238,7 @@ def get_contrasts(contrast_file, task_id, conds):
 
     def check_behav_list(behav):
         out_behav = []
-        if isinstance(behav, basestring):
+        if isinstance(behav, six.string_types):
             behav = [behav]
         for val in behav:
             if not isinstance(val, list):

nipype/algorithms/modelgen.py

@@ -30,6 +30,7 @@
                                     isdefined)
 from nipype.utils.filemanip import filename_to_list
 from .. import config, logging
+from nipype.external import six
 iflogger = logging.getLogger('interface')
 
 def gcd(a, b):
@@ -422,7 +423,7 @@ def _concatenate_info(self, infolist):
         for i, f in enumerate(self.inputs.functional_runs):
             if isinstance(f, list):
                 numscans = len(f)
-            elif isinstance(f, basestring):
+            elif isinstance(f, six.string_types):
                 img = load(f)
                 numscans = img.get_shape()[3]
             else:

nipype/algorithms/rapidart.py

@@ -26,6 +26,7 @@
 import numpy as np
 from scipy import signal
 import scipy.io as sio
+from nipype.external import six
 
 from ..interfaces.base import (BaseInterface, traits, InputMultiPath,
                                     OutputMultiPath, TraitedSpec, File,
@@ -279,7 +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, basestring):
+        if isinstance(motionfile, six.string_types):
             infile = motionfile
         elif isinstance(motionfile, list):
             infile = motionfile[0]
@@ -350,7 +351,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
             cwd = os.getcwd()
 
         # read in functional image
-        if isinstance(imgfile, basestring):
+        if isinstance(imgfile, six.string_types):
             nim = load(imgfile)
         elif isinstance(imgfile, list):
             if len(imgfile) == 1:

nipype/external/provcopy.py

@@ -17,6 +17,7 @@
 import dateutil.parser
 import collections
 from collections import defaultdict
+import six
 
 try:
     from rdflib.term import URIRef, BNode
@@ -187,7 +188,7 @@ def _parse_xsd_dateTime(s):
 
 
 def _ensure_datetime(time):
-    if isinstance(time, basestring):
+    if isinstance(time, six.string_types):
         return _parse_xsd_dateTime(time)
     else:
         return time
@@ -232,12 +233,12 @@ def parse_xsd_types(value, datatype):
 
 
 def _ensure_multiline_string_triple_quoted(s):
-    format_str = u'"""%s"""' if isinstance(s, basestring) and '\n' in s else u'"%s"'
+    format_str = u'"""%s"""' if isinstance(s, six.string_types) and '\n' in s else u'"%s"'
     return format_str % s
 
 
 def encoding_PROV_N_value(value):
-    if isinstance(value, basestring):
+    if isinstance(value, six.string_types):
         return _ensure_multiline_string_triple_quoted(value)
     elif isinstance(value, datetime.datetime):
         return value.isoformat()
@@ -536,7 +537,7 @@ def _auto_literal_conversion(self, literal):
         if isinstance(literal, URIRef):
             return literal
 
-        if isinstance(literal, basestring):
+        if isinstance(literal, six.string_types):
             return unicode(literal)
 
         if isinstance(literal, Literal) and literal.has_no_langtag():
@@ -1568,7 +1569,7 @@ def _decode_JSON_container(self, jc):
                          key=lambda tuple_rec: tuple_rec[0])
 
         record_map = {}
-        _parse_attr_value = lambda value: record_map[value] if (isinstance(value, basestring) and value in record_map) else self._decode_json_representation(value)
+        _parse_attr_value = lambda value: record_map[value] if (isinstance(value, six.string_types) and value in record_map) else self._decode_json_representation(value)
         #  Create all the records before setting their attributes
         for (record_type, identifier, content) in records:
             if record_type == PROV_REC_BUNDLE:

nipype/fixes/numpy/testing/nosetester.py

@@ -6,6 +6,7 @@
 """
 import os
 import sys
+from nipype.external import six
 
 def get_package_name(filepath):
     """
@@ -166,7 +167,7 @@ def _test_argv(self, label, verbose, extra_argv):
         '''
         argv = [__file__, self.package_path, '-s']
         if label and label != 'full':
-            if not isinstance(label, basestring):
+            if not isinstance(label, six.string_types):
                 raise TypeError('Selection label should be a string')
             if label == 'fast':
                 label = 'not slow'

nipype/interfaces/base.py

@@ -24,6 +24,7 @@
 from datetime import datetime as dt
 from dateutil.parser import parse as parseutc
 from warnings import warn
+from nipype.external import six
 
 
 from .traits_extension import (traits, Undefined, TraitDictObject,
@@ -541,7 +542,7 @@ def _get_sorteddict(self, object, dictwithhash=False, hash_method=None,
                 out = tuple(out)
         else:
             if isdefined(object):
-                if (hash_files and isinstance(object, basestring) and
+                if (hash_files and isinstance(object, six.string_types) and
                         os.path.isfile(object)):
                     if hash_method is None:
                         hash_method = config.get('execution', 'hash_method')
@@ -984,7 +985,7 @@ def run(self, **inputs):
             else:
                 inputs_str = ''
 
-            if len(e.args) == 1 and isinstance(e.args[0], basestring):
+            if len(e.args) == 1 and isinstance(e.args[0], six.string_types):
                 e.args = (e.args[0] + " ".join([message, inputs_str]),)
             else:
                 e.args += (message, )

nipype/interfaces/dcmstack.py

@@ -23,6 +23,7 @@
 import nibabel as nb
 from nipype.interfaces.traits_extension import isdefined, Undefined
 import imghdr
+from nipype.external import six
 
 have_dcmstack = True
 try:
@@ -109,7 +110,7 @@ class DcmStack(NiftiGeneratorBase):
     output_spec = DcmStackOutputSpec
 
     def _get_filelist(self, trait_input):
-        if isinstance(trait_input, basestring):
+        if isinstance(trait_input, six.string_types):
             if path.isdir(trait_input):
                 return glob(path.join(trait_input, '*.dcm'))
             else:
@@ -334,7 +335,7 @@ def _run_interface(self, runtime):
               ]
         if self.inputs.sort_order:
             sort_order = self.inputs.sort_order
-            if isinstance(sort_order, basestring):
+            if isinstance(sort_order, six.string_types):
                 sort_order = [sort_order]
             nws.sort(key=make_key_func(sort_order))
         if self.inputs.merge_dim == traits.Undefined:

nipype/interfaces/io.py

@@ -30,6 +30,7 @@
 
 import sqlite3
 from nipype.utils.misc import human_order_sorted
+from nipype.external import six
 
 try:
     import pyxnat
@@ -520,7 +521,7 @@ def _list_outputs(self):
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
-                    if isinstance(arg, basestring) and hasattr(self.inputs, arg):
+                    if isinstance(arg, six.string_types) and hasattr(self.inputs, arg):
                         arg = getattr(self.inputs, arg)
                     if isinstance(arg, list):
                         if (maxlen > 1) and (len(arg) != maxlen):
@@ -531,7 +532,7 @@ def _list_outputs(self):
                 for i in range(maxlen):
                     argtuple = []
                     for arg in arglist:
-                        if isinstance(arg, basestring) and hasattr(self.inputs, arg):
+                        if isinstance(arg, six.string_types) and hasattr(self.inputs, arg):
                             arg = getattr(self.inputs, arg)
                         if isinstance(arg, list):
                             argtuple.append(arg[i])
@@ -786,7 +787,7 @@ def _match_path(self, target_path):
 
     def _run_interface(self, runtime):
         #Prepare some of the inputs
-        if isinstance(self.inputs.root_paths, basestring):
+        if isinstance(self.inputs.root_paths, six.string_types):
             self.inputs.root_paths = [self.inputs.root_paths]
         self.match_regex = re.compile(self.inputs.match_regex)
         if self.inputs.max_depth is Undefined:
@@ -1155,7 +1156,7 @@ def _list_outputs(self):
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
-                    if isinstance(arg, basestring) and hasattr(self.inputs, arg):
+                    if isinstance(arg, six.string_types) and hasattr(self.inputs, arg):
                         arg = getattr(self.inputs, arg)
                     if isinstance(arg, list):
                         if (maxlen > 1) and (len(arg) != maxlen):
@@ -1168,7 +1169,7 @@ def _list_outputs(self):
                 for i in range(maxlen):
                     argtuple = []
                     for arg in arglist:
-                        if isinstance(arg, basestring) and \
+                        if isinstance(arg, six.string_types) and \
                                 hasattr(self.inputs, arg):
                             arg = getattr(self.inputs, arg)
                         if isinstance(arg, list):
@@ -1725,7 +1726,7 @@ def _list_outputs(self):
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
-                    if isinstance(arg, basestring) and hasattr(self.inputs, arg):
+                    if isinstance(arg, six.string_types) and hasattr(self.inputs, arg):
                         arg = getattr(self.inputs, arg)
                     if isinstance(arg, list):
                         if (maxlen > 1) and (len(arg) != maxlen):
@@ -1736,7 +1737,7 @@ def _list_outputs(self):
                 for i in range(maxlen):
                     argtuple = []
                     for arg in arglist:
-                        if isinstance(arg, basestring) and hasattr(self.inputs, arg):
+                        if isinstance(arg, six.string_types) and hasattr(self.inputs, arg):
                             arg = getattr(self.inputs, arg)
                         if isinstance(arg, list):
                             argtuple.append(arg[i])

nipype/interfaces/mne/base.py

@@ -4,6 +4,7 @@
 import glob
 from nipype.interfaces.freesurfer.base import FSCommand, FSTraitedSpec
 from nipype.utils.filemanip import list_to_filename
+from nipype.external import six
 import logging
 
 logging.basicConfig()
@@ -89,7 +90,7 @@ def _list_outputs(self):
                         out_files = []
                         for value in value_list:
                             out_files.append(op.abspath(value))
-                    elif isinstance(value_list, basestring):
+                    elif isinstance(value_list, six.string_types):
                         out_files = op.abspath(value_list)
                     else:
                         raise TypeError

nipype/interfaces/nipy/model.py

@@ -3,6 +3,7 @@
 
 import nibabel as nb
 import numpy as np
+from nipype.external import six
 
 
 from ...utils.misc import package_check
@@ -80,7 +81,7 @@ def _run_interface(self, runtime):
         session_info = self.inputs.session_info
 
         functional_runs = self.inputs.session_info[0]['scans']
-        if isinstance(functional_runs, basestring):
+        if isinstance(functional_runs, six.string_types):
             functional_runs = [functional_runs]
         nii = nb.load(functional_runs[0])
         data = nii.get_data()

nipype/interfaces/slicer/generate_classes.py

@@ -7,6 +7,7 @@
 import subprocess
 import os
 from shutil import rmtree
+from nipype.external import six
 
 import keyword
 python_keywords = keyword.kwlist  # If c++ SEM module uses one of these key words as a command line parameter, we need to modify variable
@@ -47,7 +48,7 @@ def add_class_to_package(class_codes, class_names, module_name, package_dir):
 def crawl_code_struct(code_struct, package_dir):
     subpackages = []
     for k, v in code_struct.iteritems():
-        if isinstance(v, basestring) or isinstance(v, unicode):
+        if isinstance(v, six.string_types) or isinstance(v, unicode):
             module_name = k.lower()
             class_name = k
             class_code = v
@@ -57,7 +58,7 @@ def crawl_code_struct(code_struct, package_dir):
             l1 = {}
             l2 = {}
             for key in v.keys():
-                if (isinstance(v[key], basestring) or isinstance(v[key], unicode)):
+                if (isinstance(v[key], six.string_types) or isinstance(v[key], unicode)):
                     l1[key] = v[key]
                 else:
                     l2[key] = v[key]
@@ -313,7 +314,7 @@ def grab_xml(module, launcher):
 def parse_params(params):
     list = []
     for key, value in params.iteritems():
-        if isinstance(value, basestring) or isinstance(value, unicode):
+        if isinstance(value, six.string_types) or isinstance(value, unicode):
             list.append('%s="%s"' % (key, value.replace('"', "'")))
         else:
             list.append('%s=%s' % (key, value))

nipype/interfaces/spm/base.py

@@ -24,6 +24,7 @@
 from nibabel import load
 import numpy as np
 from scipy.io import savemat
+from nipype.external import six
 
 # Local imports
 from ..base import (BaseInterface, traits, isdefined, InputMultiPath,
@@ -416,7 +417,7 @@ def _generate_job(self, prefix='', contents=None):
                     if isinstance(val, np.ndarray):
                         jobstring += self._generate_job(prefix=None,
                                                         contents=val)
-                    elif isinstance(val, basestring):
+                    elif isinstance(val, six.string_types):
                         jobstring += '\'%s\';...\n' % (val)
                     else:
                         jobstring += '%s;...\n' % str(val)
@@ -431,7 +432,7 @@ def _generate_job(self, prefix='', contents=None):
                         jobstring += self._generate_job(newprefix,
                                                         val[field])
             return jobstring
-        if isinstance(contents, basestring):
+        if isinstance(contents, six.string_types):
             jobstring += "%s = '%s';\n" % (prefix, contents)
             return jobstring
         jobstring += "%s = %s;\n" % (prefix, str(contents))

nipype/interfaces/spm/model.py

@@ -20,6 +20,7 @@
 # Third-party imports
 import numpy as np
 import scipy.io as sio
+from nipype.external import six
 
 # Local imports
 from nipype.interfaces.base import (Bunch, traits, TraitedSpec, File, Directory,
@@ -196,7 +197,7 @@ def _format_arg(self, opt, spec, val):
         if opt == 'spm_mat_file':
             return np.array([str(val)], dtype=object)
         if opt == 'estimation_method':
-            if isinstance(val, basestring):
+            if isinstance(val, six.string_types):
                 return {'%s' % val: 1}
             else:
                 return val