[FIXES] Several fixes related to unicode literals

- Close #1655: fixes the References:: leftover in help() of interfaces
- Close #1644: fixes the parameterized paths generated with python 2
- All uses of repr and re-definitions of __repr__ have been revised
  (again, this is related to #1644, #1621, etc).

Author: oesteban

nipype/algorithms/modelgen.py

@@ -547,7 +547,7 @@ def _generate_design(self, infolist=None):
                     out = np.array([])
 
                 if out.size > 0:
-                    iflogger.debug('fname=%s, out=%s, nscans=%s', filename, out, repr(sum(nscans[0:i])))
+                    iflogger.debug('fname=%s, out=%s, nscans=%d', filename, out, sum(nscans[0:i]))
                     sumscans = out.astype(int) + sum(nscans[0:i])
 
                     if out.size == 1:

nipype/caching/memory.py

@@ -93,10 +93,9 @@ def __call__(self, **kwargs):
         return out
 
     def __repr__(self):
-        return '%s(%s.%s, base_dir=%s)' % (self.__class__.__name__,
-                                           self.interface.__module__,
-                                           self.interface.__name__,
-                                           self.base_dir)
+        return '{}({}.{}}, base_dir={})'.format(
+            self.__class__.__name__, self.interface.__module__, self.interface.__name__,
+            self.base_dir)
 
 ################################################################################
 # Memory manager: provide some tracking about what is computed when, to
@@ -302,5 +301,4 @@ def _clear_all_but(self, runs, warn=True):
                        job_names, warn=warn)
 
     def __repr__(self):
-        return '%s(base_dir=%s)' % (self.__class__.__name__,
-                                    self.base_dir)
+        return '{}(base_dir={})'.format(self.__class__.__name__, self.base_dir)

nipype/external/due.py

@@ -42,7 +42,7 @@ def nondecorating_decorator(func):
     cite = load = add = _donothing
 
     def __repr__(self):
-        return self.__class__.__name__ + '()'
+        return '{}()'.format(self.__class__.__name__)
 
 
 def _donothing_func(*args, **kwargs):

nipype/interfaces/base.py

@@ -72,7 +72,7 @@ def __init__(self, value):
         self.value = value
 
     def __str__(self):
-        return repr(self.value)
+        return '{}'.format(self.value)
 
 def _exists_in_path(cmd, environ):
     """
@@ -381,7 +381,7 @@ def __repr__(self):
         outstr = []
         for name, value in sorted(self.trait_get().items()):
             outstr.append('%s = %s' % (name, value))
-        return '\n' + '\n'.join(outstr) + '\n'
+        return '\n{}\n'.format('\n'.join(outstr))
 
     def _generate_handlers(self):
         """Find all traits with the 'xor' metadata and attach an event
@@ -808,10 +808,13 @@ def help(cls, returnhelp=False):
     def _refs_help(cls):
         """ Prints interface references.
         """
+        if not cls.references_:
+            return []
+
         helpstr = ['References::']
 
         for r in cls.references_:
-            helpstr += [repr(r['entry'])]
+            helpstr += ['{}'.format(r['entry'])]
 
         return helpstr
 

nipype/interfaces/fsl/dti.py

@@ -946,7 +946,7 @@ def _list_outputs(self):
             cwd, base_name = os.path.split(name)
             outputs['out_files'].append(self._gen_fname(
                 base_name, cwd=cwd,
-                suffix='_proj_seg_thr_' + repr(self.inputs.threshold)))
+                suffix='_proj_seg_thr_{}'.format(self.inputs.threshold)))
         return outputs
 
 

nipype/pipeline/engine/base.py

@@ -105,7 +105,7 @@ def __repr__(self):
         if self._hierarchy:
             return '.'.join((self._hierarchy, self._id))
         else:
-            return self._id
+            return '{}'.format(self._id)
 
     def save(self, filename=None):
         if filename is None:

nipype/pipeline/engine/nodes.py

@@ -205,20 +205,16 @@ def output_dir(self):
         if self._hierarchy:
             outputdir = op.join(outputdir, *self._hierarchy.split('.'))
         if self.parameterization:
+            params_str = ['{}'.format(p) for p in self.parameterization]
             if not str2bool(self.config['execution']['parameterize_dirs']):
-                param_dirs = [self._parameterization_dir(p) for p in
-                              self.parameterization]
-                outputdir = op.join(outputdir, *param_dirs)
-            else:
-                outputdir = op.join(outputdir, *self.parameterization)
+                params_str = [self._parameterization_dir(p) for p in params_str]
+            outputdir = op.join(outputdir, *params_str)
         return op.abspath(op.join(outputdir,
                                   self.name))
 
     def set_input(self, parameter, val):
         """ Set interface input value"""
-        logger.debug('setting nodelevel(%s) input %s = %s' % (str(self),
-                                                              parameter,
-                                                              str(val)))
+        logger.debug('setting nodelevel(%s) input %s = %s', self.name, parameter, val)
         setattr(self.inputs, parameter, deepcopy(val))
 
     def get_output(self, parameter):
@@ -278,7 +274,7 @@ def run(self, updatehash=False):
             self._get_inputs()
             self._got_inputs = True
         outdir = self.output_dir()
-        logger.info("Executing node %s in dir: %s" % (self._id, outdir))
+        logger.info("Executing node %s in dir: %s", self._id, outdir)
         if op.exists(outdir):
             logger.debug(os.listdir(outdir))
         hash_info = self.hash_exists(updatehash=updatehash)
@@ -301,25 +297,19 @@ def run(self, updatehash=False):
                           len(glob(json_unfinished_pat)) == 0)
             if need_rerun:
                 logger.debug("Rerunning node")
-                logger.debug(("updatehash = %s, "
-                              "self.overwrite = %s, "
-                              "self._interface.always_run = %s, "
-                              "os.path.exists(%s) = %s, "
-                              "hash_method = %s") %
-                             (str(updatehash),
-                              str(self.overwrite),
-                              str(self._interface.always_run),
-                              hashfile,
-                              str(op.exists(hashfile)),
-                              self.config['execution']['hash_method'].lower()))
+                logger.debug(
+                    "updatehash = %s, self.overwrite = %s, self._interface.always_run = %s, "
+                    "os.path.exists(%s) = %s, hash_method = %s", updatehash, self.overwrite,
+                    self._interface.always_run, hashfile, op.exists(hashfile),
+                    self.config['execution']['hash_method'].lower())
                 log_debug = config.get('logging', 'workflow_level') == 'DEBUG'
                 if log_debug and not op.exists(hashfile):
                     exp_hash_paths = glob(json_pat)
                     if len(exp_hash_paths) == 1:
                         split_out = split_filename(exp_hash_paths[0])
                         exp_hash_file_base = split_out[1]
                         exp_hash = exp_hash_file_base[len('_0x'):]
-                        logger.debug("Previous node hash = %s" % exp_hash)
+                        logger.debug("Previous node hash = %s", exp_hash)
                         try:
                             prev_inputs = load_json(exp_hash_paths[0])
                         except:
@@ -343,26 +333,26 @@ def run(self, updatehash=False):
                              self._interface.can_resume) and not
                          isinstance(self, MapNode))
             if rm_outdir:
-                logger.debug("Removing old %s and its contents" % outdir)
+                logger.debug("Removing old %s and its contents", outdir)
                 try:
                     rmtree(outdir)
                 except OSError as ex:
                     outdircont = os.listdir(outdir)
                     if ((ex.errno == errno.ENOTEMPTY) and (len(outdircont) == 0)):
-                        logger.warn(('An exception was raised trying to remove old %s, '
-                                     'but the path seems empty. Is it an NFS mount?. '
-                                     'Passing the exception.') % outdir)
+                        logger.warn(
+                            'An exception was raised trying to remove old %s, but the path '
+                            'seems empty. Is it an NFS mount?. Passing the exception.', outdir)
                     elif ((ex.errno == errno.ENOTEMPTY) and (len(outdircont) != 0)):
-                        logger.debug(('Folder contents (%d items): '
-                                      '%s') % (len(outdircont), outdircont))
+                        logger.debug(
+                            'Folder contents (%d items): %s', len(outdircont), outdircont)
                         raise ex
                     else:
                         raise ex
 
             else:
-                logger.debug(("%s found and can_resume is True or Node is a "
-                              "MapNode - resuming execution") %
-                             hashfile_unfinished)
+                logger.debug(
+                    "%s found and can_resume is True or Node is a MapNode - resuming execution",
+                    hashfile_unfinished)
                 if isinstance(self, MapNode):
                     # remove old json files
                     for filename in glob(op.join(outdir, '_0x*.json')):

nipype/pipeline/engine/utils.py

@@ -1060,12 +1060,12 @@ def make_output_dir(outdir):
     # this odd approach deals with concurrent directory cureation
     try:
         if not os.path.exists(os.path.abspath(outdir)):
-            logger.debug("Creating %s" % outdir)
+            logger.debug("Creating %s", outdir)
             os.makedirs(outdir)
     except OSError:
-            logger.debug("Problem creating %s" % outdir)
+            logger.debug("Problem creating %s", outdir)
             if not os.path.exists(outdir):
-               raise OSError('Could not create %s'%outdir)
+               raise OSError('Could not create %s', outdir)
     return outdir
 
 

nipype/pipeline/plugins/sge.py

@@ -51,12 +51,10 @@ def __init__(self, job_num, job_queue_state, job_time, job_queue_name, job_slots
         self._qsub_command_line = qsub_command_line
 
     def __repr__(self):
-        return str(self._job_num).ljust(8) \
-            + str(self._job_queue_state).ljust(12) \
-            + str(self._job_slots).ljust(3) \
-            + time.strftime("%Y-%m-%dT%H:%M:%S", time.gmtime(self._job_time)).ljust(20) \
-            + str(self._job_queue_name).ljust(8) \
-            + str(self._qsub_command_line)
+        return '{:<8d}{:12}{:<3d}{:20}{:8}{}'.format(
+            self._job_num, self._queue_state, self._job_slots,
+            time.strftime("%Y-%m-%dT%H:%M:%S", time.gmtime(self._job_time)),
+            self._job_queue_name, self._qsub_command_line)
 
     def is_initializing(self):
         return self._job_queue_state == "initializing"

nipype/utils/filemanip.py

@@ -111,7 +111,7 @@ def encode_dict_py27(value):
         nels = len(value)
         for i, v in enumerate(value):
             venc = encode_dict_py27(v)
-            if venc.startswith("u'") or venc.startswith('u"'):
+            if venc.startswith(("u'", 'u"')):
                 venc = venc[1:]
             retval += venc
 
@@ -124,7 +124,7 @@ def encode_dict_py27(value):
         return retval
 
     retval = repr(value).decode()
-    if retval.startswith("u'") or retval.startswith('u"'):
+    if retval.startswith(("u'", 'u"')):
         retval = retval[1:]
     return retval