RF: Drop to_str, makedirs compatibility functions

Author: effigies

nipype/interfaces/base/specs.py

@@ -15,7 +15,7 @@
 from warnings import warn
 from packaging.version import Version
 
-from ...utils.filemanip import md5, hash_infile, hash_timestamp, to_str
+from ...utils.filemanip import md5, hash_infile, hash_timestamp
 from .traits_extension import (
     traits,
     Undefined,
@@ -251,7 +251,7 @@ def get_hashval(self, hash_method=None):
                                       True,
                                       hash_method=hash_method,
                                       hash_files=hash_files)))
-        return list_withhash, md5(to_str(list_nofilename).encode()).hexdigest()
+        return list_withhash, md5(str(list_nofilename).encode()).hexdigest()
 
     def _get_sorteddict(self,
                         objekt,

nipype/interfaces/base/support.py

@@ -14,7 +14,7 @@
 
 from ... import logging
 from ...utils.misc import is_container
-from ...utils.filemanip import md5, to_str, hash_infile
+from ...utils.filemanip import md5, hash_infile
 iflogger = logging.getLogger('nipype.interface')
 
 HELP_LINEWIDTH = 70
@@ -161,7 +161,7 @@ def _get_bunch_hash(self):
         # Sort the items of the dictionary, before hashing the string
         # representation so we get a predictable order of the
         # dictionary.
-        sorted_dict = to_str(sorted(dict_nofilename.items()))
+        sorted_dict = str(sorted(dict_nofilename.items()))
         return dict_withhash, md5(sorted_dict.encode()).hexdigest()
 
     def _repr_pretty_(self, p, cycle):

nipype/pipeline/engine/nodes.py

@@ -21,8 +21,8 @@
 from ...utils.misc import flatten, unflatten, str2bool, dict_diff
 from ...utils.filemanip import (md5, FileNotFoundError, ensure_list,
                                 simplify_list, copyfiles, fnames_presuffix,
-                                loadpkl, split_filename, load_json, makedirs,
-                                emptydirs, savepkl, to_str, indirectory)
+                                loadpkl, split_filename, load_json,
+                                emptydirs, savepkl, indirectory)
 
 from ...interfaces.base import (traits, InputMultiPath, CommandLine, Undefined,
                                 DynamicTraitedSpec, Bunch, InterfaceResult,
@@ -267,7 +267,7 @@ def output_dir(self):
     def set_input(self, parameter, val):
         """Set interface input value"""
         logger.debug('[Node] %s - setting input %s = %s', self.name, parameter,
-                     to_str(val))
+                     str(val))
         setattr(self.inputs, parameter, deepcopy(val))
 
     def get_output(self, parameter):
@@ -453,7 +453,7 @@ def run(self, updatehash=False):
                 os.remove(filename)
 
         # Make sure outdir is created
-        makedirs(outdir, exist_ok=True)
+        os.makedirs(outdir, exist_ok=True)
 
         # Store runtime-hashfile, pre-execution report, the node and the inputs set.
         _save_hashfile(hashfile_unfinished, self._hashed_inputs)
@@ -663,7 +663,7 @@ def _copyfiles_to_wd(self, execute=True, linksonly=False):
         if execute and linksonly:
             olddir = outdir
             outdir = op.join(outdir, '_tempinput')
-            makedirs(outdir, exist_ok=True)
+            os.makedirs(outdir, exist_ok=True)
 
         for info in filecopy_info:
             files = self.inputs.trait_get().get(info['key'])
@@ -1019,13 +1019,13 @@ def set_input(self, parameter, val):
         Set interface input value or nodewrapper attribute
         Priority goes to interface.
         """
-        logger.debug('setting nodelevel(%s) input %s = %s', to_str(self),
-                     parameter, to_str(val))
+        logger.debug('setting nodelevel(%s) input %s = %s', str(self),
+                     parameter, str(val))
         self._set_mapnode_input(parameter, deepcopy(val))
 
     def _set_mapnode_input(self, name, newvalue):
-        logger.debug('setting mapnode(%s) input: %s -> %s', to_str(self), name,
-                     to_str(newvalue))
+        logger.debug('setting mapnode(%s) input: %s -> %s', str(self), name,
+                     str(newvalue))
         if name in self.iterfield:
             setattr(self._inputs, name, newvalue)
         else:

nipype/pipeline/engine/utils.py

@@ -21,9 +21,7 @@
 from ... import logging, config, LooseVersion
 from ...utils.filemanip import (
     relpath,
-    makedirs,
     fname_presuffix,
-    to_str,
     ensure_list,
     get_related_files,
     FileNotFoundError,
@@ -117,7 +115,7 @@ def write_report(node, report_type=None, is_mapnode=False):
     cwd = node.output_dir()
     report_dir = os.path.join(cwd, '_report')
     report_file = os.path.join(report_dir, 'report.rst')
-    makedirs(report_dir, exist_ok=True)
+    os.makedirs(report_dir, exist_ok=True)
 
     logger.debug('[Node] Writing %s-exec report to "%s"', report_type[:-4],
                  report_file)
@@ -627,7 +625,7 @@ def _get_valid_pathstr(pathstr):
     Replaces: ',' -> '.'
     """
     if not isinstance(pathstr, (str, bytes)):
-        pathstr = to_str(pathstr)
+        pathstr = str(pathstr)
     pathstr = pathstr.replace(os.sep, '..')
     pathstr = re.sub(r'''[][ (){}?:<>#!|"';]''', '', pathstr)
     pathstr = pathstr.replace(',', '.')
@@ -1355,7 +1353,7 @@ def export_graph(graph_in,
     if base_dir is None:
         base_dir = os.getcwd()
 
-    makedirs(base_dir, exist_ok=True)
+    os.makedirs(base_dir, exist_ok=True)
     out_dot = fname_presuffix(
         dotfilename, suffix='_detailed.dot', use_ext=False, newpath=base_dir)
     _write_detailed_dot(graph, out_dot)

nipype/pipeline/engine/workflows.py

@@ -22,7 +22,7 @@
 
 from ...interfaces.base import (traits, TraitedSpec, TraitDictObject,
                                 TraitListObject)
-from ...utils.filemanip import save_json, makedirs, to_str
+from ...utils.filemanip import save_json
 from .utils import (generate_expanded_graph, export_graph, write_workflow_prov,
                     write_workflow_resources, format_dot, topological_sort,
                     get_print_name, merge_dict, format_node)
@@ -218,12 +218,12 @@ def connect(self, *args, **kwargs):
             edge_data = self._graph.get_edge_data(srcnode, destnode, None)
             if edge_data:
                 logger.debug('(%s, %s): Edge data exists: %s', srcnode,
-                             destnode, to_str(edge_data))
+                             destnode, str(edge_data))
                 for data in connects:
                     if data not in edge_data['connect']:
                         edge_data['connect'].append(data)
                     if disconnect:
-                        logger.debug('Removing connection: %s', to_str(data))
+                        logger.debug('Removing connection: %s', str(data))
                         edge_data['connect'].remove(data)
                 if edge_data['connect']:
                     self._graph.add_edges_from([(srcnode, destnode,
@@ -240,7 +240,7 @@ def connect(self, *args, **kwargs):
                 })])
             edge_data = self._graph.get_edge_data(srcnode, destnode)
             logger.debug('(%s, %s): new edge data: %s', srcnode, destnode,
-                         to_str(edge_data))
+                         str(edge_data))
 
     def disconnect(self, *args):
         """Disconnect nodes
@@ -256,7 +256,7 @@ def disconnect(self, *args):
 
         for srcnode, dstnode, conn in connection_list:
             logger.debug('disconnect(): %s->%s %s', srcnode, dstnode,
-                         to_str(conn))
+                         str(conn))
             if self in [srcnode, dstnode]:
                 raise IOError(
                     'Workflow connect cannot contain itself as node: src[%s] '
@@ -277,10 +277,10 @@ def disconnect(self, *args):
                     # idx = ed_conns.index(edge)
                     remove.append((edge[0], edge[1]))
 
-            logger.debug('disconnect(): remove list %s', to_str(remove))
+            logger.debug('disconnect(): remove list %s', str(remove))
             for el in remove:
                 edge_data['connect'].remove(el)
-                logger.debug('disconnect(): removed connection %s', to_str(el))
+                logger.debug('disconnect(): removed connection %s', str(el))
 
             if not edge_data['connect']:
                 self._graph.remove_edge(srcnode, dstnode)
@@ -410,7 +410,7 @@ def write_graph(self,
                     base_dir = op.join(base_dir, self.name)
             else:
                 base_dir = os.getcwd()
-        base_dir = makedirs(base_dir, exist_ok=True)
+        base_dir = os.makedirs(base_dir, exist_ok=True)
         if graph2use in ['hierarchical', 'colored']:
             if self.name[:1].isdigit():  # these graphs break if int
                 raise ValueError('{} graph failed, workflow name cannot begin '
@@ -576,7 +576,7 @@ def run(self, plugin=None, plugin_args=None, updatehash=False):
         flatgraph = self._create_flat_graph()
         self.config = merge_dict(deepcopy(config._sections), self.config)
         logger.info('Workflow %s settings: %s', self.name,
-                    to_str(sorted(self.config)))
+                    str(sorted(self.config)))
         self._set_needed_outputs(flatgraph)
         execgraph = generate_expanded_graph(deepcopy(flatgraph))
         for index, node in enumerate(execgraph.nodes()):
@@ -609,7 +609,7 @@ def _write_report_info(self, workingdir, name, graph):
         if workingdir is None:
             workingdir = os.getcwd()
         report_dir = op.join(workingdir, name)
-        makedirs(report_dir, exist_ok=True)
+        os.makedirs(report_dir, exist_ok=True)
         shutil.copyfile(
             op.join(op.dirname(__file__), 'report_template.html'),
             op.join(report_dir, 'index.html'))
@@ -821,7 +821,7 @@ def _set_node_input(self, node, param, source, sourceinfo):
             newval = dict(val)
         if isinstance(val, TraitListObject):
             newval = val[:]
-        logger.debug('setting node input: %s->%s', param, to_str(newval))
+        logger.debug('setting node input: %s->%s', param, str(newval))
         node.set_input(param, deepcopy(newval))
 
     def _get_all_nodes(self):
@@ -881,9 +881,9 @@ def _generate_flatgraph(self):
                 # dj: added list() for networkx ver.2
                 for u, _, d in list(
                         self._graph.in_edges(nbunch=node, data=True)):
-                    logger.debug('in: connections-> %s', to_str(d['connect']))
+                    logger.debug('in: connections-> %s', str(d['connect']))
                     for cd in deepcopy(d['connect']):
-                        logger.debug("in: %s", to_str(cd))
+                        logger.debug("in: %s", str(cd))
                         dstnode = node._get_parameter_node(cd[1], subtype='in')
                         srcnode = u
                         srcout = cd[0]
@@ -896,9 +896,9 @@ def _generate_flatgraph(self):
                 # dj: for ver 2 use list(out_edges)
                 for _, v, d in list(
                         self._graph.out_edges(nbunch=node, data=True)):
-                    logger.debug('out: connections-> %s', to_str(d['connect']))
+                    logger.debug('out: connections-> %s', str(d['connect']))
                     for cd in deepcopy(d['connect']):
-                        logger.debug("out: %s", to_str(cd))
+                        logger.debug("out: %s", str(cd))
                         dstnode = v
                         if isinstance(cd[0], tuple):
                             parameter = cd[0][0]

nipype/pipeline/plugins/tools.py

@@ -12,7 +12,7 @@
 from traceback import format_exception
 
 from ... import logging
-from ...utils.filemanip import savepkl, crash2txt, makedirs
+from ...utils.filemanip import savepkl, crash2txt
 
 logger = logging.getLogger('nipype.workflow')
 
@@ -42,7 +42,7 @@ def report_crash(node, traceback=None, hostname=None):
                                        str(uuid.uuid4()))
     crashdir = node.config['execution'].get('crashdump_dir', os.getcwd())
 
-    makedirs(crashdir, exist_ok=True)
+    os.makedirs(crashdir, exist_ok=True)
     crashfile = os.path.join(crashdir, crashfile)
 
     if node.config['execution']['crashfile_format'].lower() in ['text', 'txt']:

nipype/utils/filemanip.py

@@ -86,14 +86,6 @@ def split_filename(fname):
     return pth, fname, ext
 
 
-def to_str(value):
-    """
-    Manipulates ordered dicts before they are hashed (Py2/3 compat.)
-
-    """
-    return str(value)
-
-
 def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True):
     """Manipulates path and name of input filename
 
@@ -711,31 +703,6 @@ def dist_is_editable(dist):
     return False
 
 
-def makedirs(path, exist_ok=False):
-    """
-    Create path, if it doesn't exist.
-
-    Parameters
-    ----------
-    path : output directory to create
-
-    """
-    if not exist_ok:  # The old makedirs
-        os.makedirs(path)
-        return path
-
-    # this odd approach deals with concurrent directory cureation
-    if not op.exists(op.abspath(path)):
-        fmlogger.debug("Creating directory %s", path)
-        try:
-            os.makedirs(path)
-        except OSError:
-            fmlogger.debug("Problem creating directory %s", path)
-            if not op.exists(path):
-                raise OSError('Could not create directory %s' % path)
-    return path
-
-
 def emptydirs(path, noexist_ok=False):
     """
     Empty an existing directory, without deleting it. Do not
@@ -769,7 +736,7 @@ def emptydirs(path, noexist_ok=False):
         else:
             raise ex
 
-    makedirs(path)
+    os.makedirs(path)
 
 
 def which(cmd, env=None, pathext=None):