Instead of invoking Popen, use CommandLine

CommandLine already uses the default encoding to decode the
stdout/stderr of the command, so take advantage of that functionality
rather than re-implementing.

First try was to implement decoding pattern seen elsewhere - then I
changed my mind and used a CommandLine object from the interfaces.base
module.

First Attempt
-------------

Decode the stderr using the default encoding

* Fixes TypeError bug for PBS jobs running on python3.x
* Fixes issue #1959

Second Attempt
--------------

Use the nipype CommandLine class instead of Popen

Remove unused modules

Ignore exceptions in qstat CommandLine call.

Author: gjcooper

nipype/pipeline/plugins/pbs.py

@@ -6,7 +6,6 @@
 
 import os
 from time import sleep
-import subprocess
 
 from ...interfaces.base import CommandLine
 from .base import (SGELikeBatchManagerBase, logger, iflogger, logging)
@@ -46,13 +45,12 @@ def __init__(self, **kwargs):
         super(PBSPlugin, self).__init__(template, **kwargs)
 
     def _is_pending(self, taskid):
-        #  subprocess.Popen requires taskid to be a string
-        proc = subprocess.Popen(["qstat", str(taskid)],
-                                stdout=subprocess.PIPE,
-                                stderr=subprocess.PIPE)
-        _, e = proc.communicate()
+        result = CommandLine('qstat {}'.format(taskid),
+                             environ=dict(os.environ),
+                             terminal_output='allatonce',
+                             ignore_exception=True).run()
         errmsg = 'Unknown Job Id'  # %s' % taskid
-        return errmsg not in e
+        return errmsg not in result.runtime.stderr
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine('qsub', environ=dict(os.environ),