removing ignore_exception=True from CommandLine call (ignore_exception is deprecated)

Author: djarecka

nipype/interfaces/afni/base.py

@@ -87,7 +87,6 @@ def standard_image(img_name):
         Could be made more fancy to allow for more relocatability'''
         clout = CommandLine(
             'which afni',
-            ignore_exception=True,
             resource_monitor=False,
             terminal_output='allatonce').run()
         if clout.runtime.returncode is not 0:

nipype/pipeline/plugins/condor.py

@@ -54,7 +54,7 @@ def _is_pending(self, taskid):
         # check condor cluster
         oldlevel = iflogger.level
         iflogger.setLevel(logging.getLevelName('CRITICAL'))
-        result = cmd.run(ignore_exception=True)
+        result = cmd.run()
         iflogger.setLevel(oldlevel)
         if result.runtime.stdout.count('\n%d' % taskid):
             return True

nipype/pipeline/plugins/lsf.py

@@ -54,7 +54,7 @@ def _is_pending(self, taskid):
         # check lsf task
         oldlevel = iflogger.level
         iflogger.setLevel(logging.getLevelName('CRITICAL'))
-        result = cmd.run(ignore_exception=True)
+        result = cmd.run()
         iflogger.setLevel(oldlevel)
         # logger.debug(result.runtime.stdout)
         if 'DONE' in result.runtime.stdout or 'EXIT' in result.runtime.stdout:

nipype/pipeline/plugins/pbs.py

@@ -52,8 +52,7 @@ def _is_pending(self, taskid):
         result = CommandLine('qstat -f {}'.format(taskid),
                              environ=dict(os.environ),
                              terminal_output='file_split',
-                             resource_monitor=False,
-                             ignore_exception=True).run()
+                             resource_monitor=False).run()
 
         stdout = result.runtime.stdout
         stderr = result.runtime.stderr