Merge pull request #1966 from mgxd/enh/clean-dir

ENH: Add ``--clean-workdir`` argument

Author: oesteban

fmriprep/cli/run.py

@@ -244,6 +244,9 @@ def get_parser():
     g_other = parser.add_argument_group('Other options')
     g_other.add_argument('-w', '--work-dir', action='store', type=Path, default=Path('work'),
                          help='path where intermediate results should be stored')
+    g_other.add_argument('--clean-workdir', action='store_true', default=False,
+                         help='Clears working directory of contents. Use of this flag is not'
+                              'recommended when running concurrent processes of fMRIPrep.')
     g_other.add_argument(
         '--resource-monitor', action='store_true', default=False,
         help='enable Nipype\'s resource monitoring to keep track of memory and CPU usage')
@@ -508,6 +511,12 @@ def build_workflow(opts, retval):
     output_dir = opts.output_dir.resolve()
     work_dir = opts.work_dir.resolve()
 
+    if opts.clean_workdir:
+        from niworkflows.utils.misc import clean_directory
+        build_log.log("Clearing previous fMRIPrep working directory: %s" % work_dir)
+        if not clean_directory(work_dir):
+            build_log.warning("Could not clear all contents of working directory: %s" % work_dir)
+
     retval['return_code'] = 1
     retval['workflow'] = None
     retval['bids_dir'] = str(bids_dir)

setup.cfg

@@ -24,7 +24,7 @@ install_requires =
     nibabel ~= 3.0.0rc1
     nipype >=1.3.1
     nitime
-    niworkflows ~= 1.1.3
+    niworkflows ~= 1.1.5
     numpy
     pandas
     psutil >=5.4