Merge remote-tracking branch 'upstream/master' into enh/denoise

* upstream/master:
  fix: fixes issue #1227 when install fails with pypi
  fix: decode bytes output when multiprocessing plugin is used with stdout/err
  fix: from make check

Author: satra

bin/nipype2boutiques

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 import sys

bin/nipype_cmd

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 import sys

bin/nipype_display_crash

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!python
 """Displays crash information from Nipype crash files. For certain crash files,
 one can rerun a failed node in a temp directory.
 

nipype/algorithms/tests/test_auto_TVTKBaseInterface.py

@@ -0,0 +1,16 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ...testing import assert_equal
+from ..mesh import TVTKBaseInterface
+
+
+def test_TVTKBaseInterface_inputs():
+    input_map = dict(ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    )
+    inputs = TVTKBaseInterface.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            yield assert_equal, getattr(inputs.traits()[key], metakey), value
+

nipype/interfaces/ants/tests/test_auto_Registration.py

@@ -44,6 +44,7 @@ def test_Registration_inputs():
     ),
     interpolation_parameters=dict(),
     invert_initial_moving_transform=dict(requires=['initial_moving_transform'],
+    usedefault=True,
     xor=['initial_moving_transform_com'],
     ),
     metric=dict(mandatory=True,

nipype/interfaces/base.py

@@ -1270,6 +1270,10 @@ def _process(drain=0):
         result['merged'] = [r[1] for r in temp]
     if output == 'allatonce':
         stdout, stderr = proc.communicate()
+        if stdout and isinstance(stdout, bytes):
+            stdout = stdout.decode()
+        if stderr and isinstance(stderr, bytes):
+            stderr = stderr.decode()
         result['stdout'] = str(stdout).split('\n')
         result['stderr'] = str(stderr).split('\n')
         result['merged'] = ''

nipype/interfaces/fsl/model.py

@@ -252,7 +252,7 @@ def _create_ev_files(
                                                               element=count,
                                                               ctype=ctype, val=val)
                         ev_txt += "\n"
-                        
+
                     for fconidx in ftest_idx:
                         fval=0
                         if con[0] in con_map.keys() and fconidx in con_map[con[0]]: