Merge pull request #2617 from mgxd/fix/win

fix: avoid closing file descriptors on windows

Author: effigies

nipype/interfaces/base/core.py

@@ -775,7 +775,7 @@ def run_command(runtime, output=None, timeout=0.01):
         shell=True,
         cwd=runtime.cwd,
         env=env,
-        close_fds=True,
+        close_fds=(not sys.platform.startswith('win')),
     )
 
     result = {

nipype/utils/filemanip.py

@@ -38,6 +38,7 @@
     ('.BRIK', '.HEAD'),
 ]
 
+PY3 = sys.version_info[0] >= 3
 
 class FileNotFoundError(Exception):
     pass
@@ -877,12 +878,18 @@ def canonicalize_env(env):
     if os.name != 'nt':
         return env
 
+    # convert unicode to string for python 2
+    if not PY3:
+        from future.utils import bytes_to_native_str
     out_env = {}
     for key, val in env.items():
         if not isinstance(key, bytes):
             key = key.encode('utf-8')
         if not isinstance(val, bytes):
             val = val.encode('utf-8')
+        if not PY3:
+            key = bytes_to_native_str(key)
+            val = bytes_to_native_str(val)
         out_env[key] = val
     return out_env