use new makedirs

Author: oesteban

nipype/pipeline/engine/nodes.py

@@ -684,7 +684,7 @@ def _copyfiles_to_wd(self, outdir, execute, linksonly=False):
             if execute and linksonly:
                 olddir = outdir
                 outdir = op.join(outdir, '_tempinput')
-                os.makedirs(outdir)
+                makedirs(outdir, exist_ok=True)
             for info in self._interface._get_filecopy_info():
                 files = self.inputs.get().get(info['key'])
                 if not isdefined(files):
@@ -725,8 +725,8 @@ def write_report(self, report_type=None, cwd=None):
             return
         report_dir = op.join(cwd, '_report')
         report_file = op.join(report_dir, 'report.rst')
-        if not op.exists(report_dir):
-            os.makedirs(report_dir)
+        makedirs(report_dir, exist_ok=True)
+
         if report_type == 'preexec':
             logger.debug('writing pre-exec report to %s', report_file)
             fp = open(report_file, 'wt')

nipype/pipeline/engine/utils.py

@@ -24,8 +24,9 @@
 import numpy as np
 import networkx as nx
 
-from ...utils.filemanip import (fname_presuffix, FileNotFoundError, to_str,
-                                filename_to_list, get_related_files)
+from ...utils.filemanip import (
+    makedirs, fname_presuffix, to_str,
+    filename_to_list, get_related_files)
 from ...utils.misc import str2bool
 from ...utils.functions import create_function_from_source
 from ...interfaces.base import (CommandLine, isdefined, Undefined,
@@ -195,7 +196,7 @@ def modify_paths(object, relative=True, basedir=None):
                 else:
                     out = os.path.abspath(os.path.join(basedir, object))
                 if not os.path.exists(out):
-                    raise FileNotFoundError('File %s not found' % out)
+                    raise IOError('File %s not found' % out)
             else:
                 out = object
     return out
@@ -1013,8 +1014,8 @@ def export_graph(graph_in, base_dir=None, show=False, use_execgraph=False,
         logger.debug('using input graph')
     if base_dir is None:
         base_dir = os.getcwd()
-    if not os.path.exists(base_dir):
-        os.makedirs(base_dir)
+
+    makedirs(base_dir, exist_ok=True)
     outfname = fname_presuffix(dotfilename,
                                suffix='_detailed.dot',
                                use_ext=False,

nipype/pipeline/engine/workflows.py

@@ -413,7 +413,7 @@ def write_graph(self, dotfilename='graph.dot', graph2use='hierarchical',
                     base_dir = op.join(base_dir, self.name)
             else:
                 base_dir = os.getcwd()
-        base_dir = makedirs(base_dir)
+        base_dir = 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 '
@@ -599,8 +599,7 @@ def _write_report_info(self, workingdir, name, graph):
         if workingdir is None:
             workingdir = os.getcwd()
         report_dir = op.join(workingdir, name)
-        if not op.exists(report_dir):
-            os.makedirs(report_dir)
+        makedirs(report_dir, exist_ok=True)
         shutil.copyfile(op.join(op.dirname(__file__),
                                 'report_template.html'),
                         op.join(report_dir, 'index.html'))

nipype/pipeline/plugins/tools.py

@@ -15,7 +15,7 @@
 from traceback import format_exception
 
 from ... import logging
-from ...utils.filemanip import savepkl, crash2txt
+from ...utils.filemanip import savepkl, crash2txt, makedirs
 
 logger = logging.getLogger('workflow')
 
@@ -42,8 +42,7 @@ def report_crash(node, traceback=None, hostname=None):
         timeofcrash, login_name, name, str(uuid.uuid4()))
     crashdir = node.config['execution'].get('crashdump_dir', os.getcwd())
 
-    if not os.path.exists(crashdir):
-        os.makedirs(crashdir)
+    makedirs(crashdir, exist_ok=True)
     crashfile = os.path.join(crashdir, crashfile)
 
     if node.config['execution']['crashfile_format'].lower() in ['text', 'txt']: