LSFPlugin sets ignore_exception=True on line 57 of lsf.py plugin causing workflow to crash due to deprecation

[mattfeld]

The _is_pending function in the LSFPlugin when running the command sets the ignore_exception=True on line 57. See below:

def _is_pending(self, taskid):
        """LSF lists a status of 'PEND' when a job has been submitted but is
        waiting to be picked up, and 'RUN' when it is actively being processed.
        But _is_pending should return True until a job has finished and is
        ready to be checked for completeness. So return True if status is
        either 'PEND' or 'RUN'"""
        cmd = CommandLine(
            'bjobs', resource_monitor=False, terminal_output='allatonce')
        cmd.inputs.args = '%d' % taskid
        # check lsf task
        oldlevel = iflogger.level
        iflogger.setLevel(logging.getLevelName('CRITICAL'))
        result = cmd.run(ignore_exception=True)
        iflogger.setLevel(oldlevel)
        # logger.debug(result.runtime.stdout)
        if 'DONE' in result.runtime.stdout or 'EXIT' in result.runtime.stdout:
            return False
        else:
            return True

This results in workflows not executing with newer versions of nipype (I'm using version 1.0.1) exiting with the following error:

TraitError: Input ignore_exception in interface CommandLine is deprecated. Will be removed or raise an error as of release 1.0.0

I removed ignore_exception=True from my copy of nipype and was able to execute the workflow with no problems.

[mgxd]

@mattfeld you could add it into the cmd as well

cmd = CommandLine(
            'bjobs', resource_monitor=False, terminal_output='allatonce', ignore_exception=True)

Would you like to submit a PR for this fix?

[mattfeld]

@mgxd I'd be happy to submit a PR for this fix. Do you think it would be more appropriate to add it into the cmd or remove it out right result = cmd.run()?

[mgxd]

I'd suggest adding it to the command to retain the previous behavior

[djarecka]

@mattfeld - could you please check if you're having problems with the current version. My PR hopefully solved also this issue.