clean up previous execution of examples

Author: oesteban

nipype/pipeline/engine/nodes.py

@@ -528,6 +528,10 @@ def _load_resultfile(self, cwd):
             pkl_file = gzip.open(resultsoutputfile, 'rb')
             try:
                 result = pickle.load(pkl_file)
+            except UnicodeDecodeError:
+                # Was this pickle created with Python 2.x?
+                pickle.load(pkl_file, fix_imports=True, encoding='utf-8')
+                logger.warn('Successfully loaded pickle in compatibility mode')
             except (traits.TraitError, AttributeError, ImportError) as err:
                 if isinstance(err, (AttributeError, ImportError)):
                     attribute_error = True

nipype/utils/filemanip.py

@@ -470,17 +470,21 @@ def loadpkl(infile):
     if infile.endswith('pklz'):
         pkl_file = gzip.open(infile, 'rb')
     else:
-        pkl_file = open(infile)
-    return pickle.load(pkl_file)
+        pkl_file = open(infile, 'rb')
+
+    try:
+        unpkl = pickle.load(pkl_file)
+    except UnicodeDecodeError:
+        unpkl = pickle.load(pkl_file, fix_imports=True, encoding='utf-8')
+    return unpkl
 
 
 def savepkl(filename, record):
-    content = pickle.dumps(record)
     if filename.endswith('pklz'):
         pkl_file = gzip.open(filename, 'wb')
     else:
         pkl_file = open(filename, 'wb')
-    pkl_file.write(content.encode())
+    pickle.dump(record, pkl_file)
     pkl_file.close()
 
 rst_levels = ['=', '-', '~', '+']

tools/run_examples.py

@@ -6,7 +6,7 @@
 from multiprocessing import cpu_count
 
 
-def run_examples(example, pipelines, data_path, plugin=None):
+def run_examples(example, pipelines, data_path, plugin=None, rm_base_dir=True):
     from nipype import config
     from nipype.interfaces.base import CommandLine
 
@@ -27,6 +27,10 @@ def run_examples(example, pipelines, data_path, plugin=None):
         wf = getattr(sys.modules[example], pipeline)
         wf.base_dir = os.path.join(os.getcwd(), 'output', example, plugin)
 
+        results_dir = os.path.join(wf.base_dir, wf.name)
+        if rm_base_dir and os.path.exists(results_dir):
+            rmtree(results_dir)
+
         # Handle a logging directory
         log_dir = os.path.join(os.getcwd(), 'logs', example)
         if not os.path.exists(log_dir):