fix: make sure stdout/stderr are of python version's string type.

Author: Ben Cipollini

nipype/interfaces/base.py

@@ -1212,7 +1212,7 @@ def run_command(runtime, output=None, timeout=0.01, redirect_x=False):
     if output == 'file':
         errfile = os.path.join(runtime.cwd, 'stderr.nipype')
         outfile = os.path.join(runtime.cwd, 'stdout.nipype')
-        stderr = open(errfile, 'wt')
+        stderr = open(errfile, 'wt')  # t=='text'===default
         stdout = open(outfile, 'wt')
 
         proc = subprocess.Popen(cmdline,
@@ -1263,8 +1263,8 @@ def _process(drain=0):
         result['merged'] = [r[1] for r in temp]
     if output == 'allatonce':
         stdout, stderr = proc.communicate()
-        result['stdout'] = stdout.decode().split('\n')
-        result['stderr'] = stderr.decode().split('\n')
+        result['stdout'] = str(stdout).split('\n')
+        result['stderr'] = str(stderr).split('\n')
         result['merged'] = ''
     if output == 'file':
         ret_code = proc.wait()

nipype/interfaces/tests/test_base.py

@@ -621,6 +621,7 @@ def test_CommandLine_output():
     ci.inputs.terminal_output = 'file'
     res = ci.run()
     yield assert_true, 'stdout.nipype' in res.runtime.stdout
+    yield assert_equal, type(res.runtime.stdout), type('hi')
     ci = nib.CommandLine(command='ls -l')
     ci.inputs.terminal_output = 'none'
     res = ci.run()