replaced str with basestring in instance checks to support unicode strings

Author: belevtsoff

doc/sphinxext/numpy_ext/docscrape_sphinx.py

@@ -140,7 +140,7 @@ def _str_references(self):
         out = []
         if self['References']:
             out += self._str_header('References')
-            if isinstance(self['References'], str):
+            if isinstance(self['References'], basestring):
                 self['References'] = [self['References']]
             out.extend(self['References'])
             out += ['']

nipype/algorithms/modelgen.py

@@ -422,7 +422,7 @@ def _concatenate_info(self, infolist):
         for i, f in enumerate(self.inputs.functional_runs):
             if isinstance(f, list):
                 numscans = len(f)
-            elif isinstance(f, str):
+            elif isinstance(f, basestring):
                 img = load(f)
                 numscans = img.get_shape()[3]
             else:

nipype/algorithms/rapidart.py

@@ -279,7 +279,7 @@ def _get_output_filenames(self, motionfile, output_dir):
         output_dir: string
             output directory in which the files will be generated
         """
-        if isinstance(motionfile, str):
+        if isinstance(motionfile, basestring):
             infile = motionfile
         elif isinstance(motionfile, list):
             infile = motionfile[0]
@@ -350,7 +350,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None):
             cwd = os.getcwd()
 
         # read in functional image
-        if isinstance(imgfile, str):
+        if isinstance(imgfile, basestring):
             nim = load(imgfile)
         elif isinstance(imgfile, list):
             if len(imgfile) == 1:

nipype/interfaces/base.py

@@ -541,7 +541,7 @@ def _get_sorteddict(self, object, dictwithhash=False, hash_method=None,
                 out = tuple(out)
         else:
             if isdefined(object):
-                if (hash_files and isinstance(object, str) and
+                if (hash_files and isinstance(object, basestring) and
                         os.path.isfile(object)):
                     if hash_method is None:
                         hash_method = config.get('execution', 'hash_method')
@@ -984,7 +984,7 @@ def run(self, **inputs):
             else:
                 inputs_str = ''
 
-            if len(e.args) == 1 and isinstance(e.args[0], str):
+            if len(e.args) == 1 and isinstance(e.args[0], basestring):
                 e.args = (e.args[0] + " ".join([message, inputs_str]),)
             else:
                 e.args += (message, )

nipype/interfaces/dcmstack.py

@@ -109,7 +109,7 @@ class DcmStack(NiftiGeneratorBase):
     output_spec = DcmStackOutputSpec
 
     def _get_filelist(self, trait_input):
-        if isinstance(trait_input, str):
+        if isinstance(trait_input, basestring):
             if path.isdir(trait_input):
                 return glob(path.join(trait_input, '*.dcm'))
             else:
@@ -334,7 +334,7 @@ def _run_interface(self, runtime):
               ]
         if self.inputs.sort_order:
             sort_order = self.inputs.sort_order
-            if isinstance(sort_order, str):
+            if isinstance(sort_order, basestring):
                 sort_order = [sort_order]
             nws.sort(key=make_key_func(sort_order))
         if self.inputs.merge_dim == traits.Undefined:

nipype/interfaces/io.py

@@ -520,7 +520,7 @@ def _list_outputs(self):
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
-                    if isinstance(arg, str) and hasattr(self.inputs, arg):
+                    if isinstance(arg, basestring) and hasattr(self.inputs, arg):
                         arg = getattr(self.inputs, arg)
                     if isinstance(arg, list):
                         if (maxlen > 1) and (len(arg) != maxlen):
@@ -531,7 +531,7 @@ def _list_outputs(self):
                 for i in range(maxlen):
                     argtuple = []
                     for arg in arglist:
-                        if isinstance(arg, str) and hasattr(self.inputs, arg):
+                        if isinstance(arg, basestring) and hasattr(self.inputs, arg):
                             arg = getattr(self.inputs, arg)
                         if isinstance(arg, list):
                             argtuple.append(arg[i])
@@ -786,7 +786,7 @@ def _match_path(self, target_path):
 
     def _run_interface(self, runtime):
         #Prepare some of the inputs
-        if isinstance(self.inputs.root_paths, str):
+        if isinstance(self.inputs.root_paths, basestring):
             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 +1155,7 @@ def _list_outputs(self):
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
-                    if isinstance(arg, str) and hasattr(self.inputs, arg):
+                    if isinstance(arg, basestring) and hasattr(self.inputs, arg):
                         arg = getattr(self.inputs, arg)
                     if isinstance(arg, list):
                         if (maxlen > 1) and (len(arg) != maxlen):
@@ -1168,7 +1168,7 @@ def _list_outputs(self):
                 for i in range(maxlen):
                     argtuple = []
                     for arg in arglist:
-                        if isinstance(arg, str) and \
+                        if isinstance(arg, basestring) and \
                                 hasattr(self.inputs, arg):
                             arg = getattr(self.inputs, arg)
                         if isinstance(arg, list):
@@ -1725,7 +1725,7 @@ def _list_outputs(self):
             for argnum, arglist in enumerate(args):
                 maxlen = 1
                 for arg in arglist:
-                    if isinstance(arg, str) and hasattr(self.inputs, arg):
+                    if isinstance(arg, basestring) and hasattr(self.inputs, arg):
                         arg = getattr(self.inputs, arg)
                     if isinstance(arg, list):
                         if (maxlen > 1) and (len(arg) != maxlen):
@@ -1736,7 +1736,7 @@ def _list_outputs(self):
                 for i in range(maxlen):
                     argtuple = []
                     for arg in arglist:
-                        if isinstance(arg, str) and hasattr(self.inputs, arg):
+                        if isinstance(arg, basestring) and hasattr(self.inputs, arg):
                             arg = getattr(self.inputs, arg)
                         if isinstance(arg, list):
                             argtuple.append(arg[i])

nipype/interfaces/mne/base.py

@@ -89,7 +89,7 @@ def _list_outputs(self):
                         out_files = []
                         for value in value_list:
                             out_files.append(op.abspath(value))
-                    elif isinstance(value_list, str):
+                    elif isinstance(value_list, basestring):
                         out_files = op.abspath(value_list)
                     else:
                         raise TypeError

nipype/interfaces/nipy/model.py

@@ -80,7 +80,7 @@ def _run_interface(self, runtime):
         session_info = self.inputs.session_info
 
         functional_runs = self.inputs.session_info[0]['scans']
-        if isinstance(functional_runs, str):
+        if isinstance(functional_runs, basestring):
             functional_runs = [functional_runs]
         nii = nb.load(functional_runs[0])
         data = nii.get_data()

nipype/interfaces/slicer/generate_classes.py

@@ -47,7 +47,7 @@ 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, str) or isinstance(v, unicode):
+        if isinstance(v, basestring) or isinstance(v, unicode):
             module_name = k.lower()
             class_name = k
             class_code = v
@@ -57,7 +57,7 @@ def crawl_code_struct(code_struct, package_dir):
             l1 = {}
             l2 = {}
             for key in v.keys():
-                if (isinstance(v[key], str) or isinstance(v[key], unicode)):
+                if (isinstance(v[key], basestring) or isinstance(v[key], unicode)):
                     l1[key] = v[key]
                 else:
                     l2[key] = v[key]
@@ -313,7 +313,7 @@ def grab_xml(module, launcher):
 def parse_params(params):
     list = []
     for key, value in params.iteritems():
-        if isinstance(value, str) or isinstance(value, unicode):
+        if isinstance(value, basestring) or isinstance(value, unicode):
             list.append('%s="%s"' % (key, value.replace('"', "'")))
         else:
             list.append('%s=%s' % (key, value))

nipype/interfaces/spm/base.py

@@ -416,7 +416,7 @@ def _generate_job(self, prefix='', contents=None):
                     if isinstance(val, np.ndarray):
                         jobstring += self._generate_job(prefix=None,
                                                         contents=val)
-                    elif isinstance(val, str):
+                    elif isinstance(val, basestring):
                         jobstring += '\'%s\';...\n' % (val)
                     else:
                         jobstring += '%s;...\n' % str(val)
@@ -431,7 +431,7 @@ def _generate_job(self, prefix='', contents=None):
                         jobstring += self._generate_job(newprefix,
                                                         val[field])
             return jobstring
-        if isinstance(contents, str):
+        if isinstance(contents, basestring):
             jobstring += "%s = '%s';\n" % (prefix, contents)
             return jobstring
         jobstring += "%s = %s;\n" % (prefix, str(contents))

nipype/interfaces/spm/model.py

@@ -196,7 +196,7 @@ 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, str):
+            if isinstance(val, basestring):
                 return {'%s' % val: 1}
             else:
                 return val

nipype/interfaces/utility.py

@@ -386,7 +386,7 @@ def __init__(self, input_names, output_names, function=None, imports=None,
                     raise Exception('Interface Function does not accept ' \
                                     'function objects defined interactively ' \
                                     'in a python session')
-            elif isinstance(function, str):
+            elif isinstance(function, basestring):
                 self.inputs.function_str = dumps(function)
             else:
                 raise Exception('Unknown type of function')
@@ -404,7 +404,7 @@ def _set_function_string(self, obj, name, old, new):
         if name == 'function_str':
             if hasattr(new, '__call__'):
                 function_source = getsource(new)
-            elif isinstance(new, str):
+            elif isinstance(new, basestring):
                 function_source = dumps(new)
             self.inputs.trait_set(trait_change_notify=False,
                                   **{'%s' % name: function_source})

nipype/pipeline/engine.py

@@ -361,7 +361,7 @@ def connect(self, *args, **kwargs):
                         # handles the case that source is specified
                         # with a function
                         sourcename = source[0]
-                    elif isinstance(source, str):
+                    elif isinstance(source, basestring):
                         sourcename = source
                     else:
                         raise Exception(('Unknown source specification in '
@@ -382,7 +382,7 @@ def connect(self, *args, **kwargs):
         # turn functions into strings
         for srcnode, destnode, connects in connection_list:
             for idx, (src, dest) in enumerate(connects):
-                if isinstance(src, tuple) and not isinstance(src[1], str):
+                if isinstance(src, tuple) and not isinstance(src[1], basestring):
                     function_source = getsource(src[1])
                     connects[idx] = ((src[0], function_source, src[2:]), dest)
 
@@ -896,7 +896,7 @@ def _set_input(self, object, name, newvalue):
 
     def _set_node_input(self, node, param, source, sourceinfo):
         """Set inputs of a node given the edge connection"""
-        if isinstance(sourceinfo, str):
+        if isinstance(sourceinfo, basestring):
             val = source.get_output(sourceinfo)
         elif isinstance(sourceinfo, tuple):
             if callable(sourceinfo[1]):
@@ -1841,7 +1841,7 @@ def __init__(self, interface, name, joinsource, joinfield=None,
         if not joinfield:
             # default is the interface fields
             joinfield = self._interface.inputs.copyable_trait_names()
-        elif isinstance(joinfield, str):
+        elif isinstance(joinfield, basestring):
             joinfield = [joinfield]
         self.joinfield = joinfield
         """the fields to join"""
@@ -2047,7 +2047,7 @@ def __init__(self, interface, iterfield, name, serial=False, **kwargs):
 
 
         super(MapNode, self).__init__(interface, name, **kwargs)
-        if isinstance(iterfield, str):
+        if isinstance(iterfield, basestring):
             iterfield = [iterfield]
         self.iterfield = iterfield
         self._inputs = self._create_dynamic_traits(self._interface.inputs,

nipype/pipeline/utils.py

@@ -103,7 +103,7 @@ def modify_paths(object, relative=True, basedir=None):
             out = tuple(out)
     else:
         if isdefined(object):
-            if isinstance(object, str) and os.path.isfile(object):
+            if isinstance(object, basestring) and os.path.isfile(object):
                 if relative:
                     if config.getboolean('execution', 'use_relative_paths'):
                         out = relpath(object, start=basedir)
@@ -186,7 +186,7 @@ def _write_detailed_dot(graph, dotfilename):
         inports = []
         for u, v, d in graph.in_edges_iter(nbunch=n, data=True):
             for cd in d['connect']:
-                if isinstance(cd[0], str):
+                if isinstance(cd[0], basestring):
                     outport = cd[0]
                 else:
                     outport = cd[0][0]
@@ -206,7 +206,7 @@ def _write_detailed_dot(graph, dotfilename):
         outports = []
         for u, v, d in graph.out_edges_iter(nbunch=n, data=True):
             for cd in d['connect']:
-                if isinstance(cd[0], str):
+                if isinstance(cd[0], basestring):
                     outport = cd[0]
                 else:
                     outport = cd[0][0]
@@ -607,7 +607,7 @@ def generate_expanded_graph(graph_in):
             # the itersource is a (node name, fields) tuple
             src_name, src_fields = inode.itersource
             # convert a single field to a list
-            if isinstance(src_fields, str):
+            if isinstance(src_fields, basestring):
                 src_fields = [src_fields]
             # find the unique iterable source node in the graph
             try:
@@ -789,7 +789,7 @@ def _standardize_iterables(node):
     if node.synchronize:
         if len(iterables) == 2:
             first, last = iterables
-            if all((isinstance(item, str) and item in fields
+            if all((isinstance(item, basestring) and item in fields
                     for item in first)):
                 iterables = _transpose_iterables(first, last)
 

nipype/utils/docparse.py

@@ -277,7 +277,7 @@ def _parse_doc(doc, style=['--']):
     # individual flag/option.
     doclist = doc.split('\n')
     optmap = {}
-    if isinstance(style,str):
+    if isinstance(style,basestring):
         style = [style]
     for line in doclist:
         linelist = line.split()

nipype/utils/provenance.py

@@ -94,7 +94,7 @@ def _get_sorteddict(object, dictwithhash=False):
         if isinstance(object, tuple):
             out = tuple(out)
     else:
-        if isinstance(object, str) and os.path.isfile(object):
+        if isinstance(object, basestring) and os.path.isfile(object):
             hash = hash_infile(object)
             if dictwithhash:
                 out = (object, hash)