Merge pull request #612 from effigies/makedir

RF: Replace make_folder with os.makedirs(exist_ok=True)

Author: effigies

fmriprep/cli/run.py

@@ -7,6 +7,7 @@
 """
 from __future__ import absolute_import, division, print_function, unicode_literals
 
+import os
 import os.path as op
 import glob
 import sys
@@ -160,7 +161,6 @@ def main():
 def create_workflow(opts):
     """Build workflow"""
     import logging
-    from fmriprep.utils import make_folder
     from fmriprep.viz.reports import run_reports
     from fmriprep.workflows.base import init_fmriprep_wf
 
@@ -183,10 +183,9 @@ def create_workflow(opts):
     run_uuid = strftime('%Y%m%d-%H%M%S_') + str(uuid.uuid4())
 
     # Check and create output and working directories
-    # Using make_folder to prevent https://github.com/poldracklab/mriqc/issues/111
-    make_folder(output_dir)
-    make_folder(opts.work_dir)
-    make_folder(log_dir)
+    os.makedirs(output_dir, exist_ok=True)
+    os.makedirs(opts.work_dir, exist_ok=True)
+    os.makedirs(log_dir, exist_ok=True)
 
     ncfg.update_config({
         'logging': {'log_directory': log_dir, 'log_to_file': True},

fmriprep/interfaces/bids.py

@@ -23,7 +23,6 @@
 from builtins import str, bytes
 
 from niworkflows.interfaces.base import SimpleInterface
-from fmriprep.utils.misc import make_folder
 
 LOGGER = logging.getLogger('interface')
 BIDS_NAME = re.compile(
@@ -138,7 +137,7 @@ def _run_interface(self, runtime):
 
         out_path = op.join(base_directory, out_path)
 
-        make_folder(out_path)
+        os.makedirs(out_path, exist_ok=True)
 
         base_fname = op.join(out_path, fname)
 
@@ -235,7 +234,7 @@ class BIDSFreeSurferDir(SimpleInterface):
     def _run_interface(self, runtime):
         subjects_dir = os.path.join(self.inputs.derivatives,
                                     self.inputs.subjects_dir)
-        make_folder(subjects_dir)
+        os.makedirs(subjects_dir, exist_ok=True)
         self._results['subjects_dir'] = subjects_dir
 
         spaces = list(self.inputs.spaces)

fmriprep/utils/__init__.py

@@ -2,4 +2,4 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-from .misc import collect_bids_data, make_folder
+from .misc import collect_bids_data

fmriprep/utils/misc.py

@@ -5,8 +5,6 @@
 from __future__ import print_function, division, absolute_import, unicode_literals
 
 import copy
-import os
-from errno import EEXIST
 
 from bids.grabbids import BIDSLayout
 
@@ -44,15 +42,6 @@ def _first(inlist):
     return sorted(inlist)[0]
 
 
-def make_folder(folder):
-    try:
-        os.makedirs(folder)
-    except OSError as exc:
-        if exc.errno == EEXIST:
-            pass
-    return folder
-
-
 def collect_bids_data(dataset, subject, task=None, session=None, run=None):
     subject = str(subject)
     if subject.startswith('sub-'):