deprecated traits in BaseInterfaceInputSpec and CommandLineInputSpec

[djarecka]

Summary

we have two traits that are marked ad deprecated='1.0.0' in interfaces/base/specs.py:

• ignore_exception in BaseInterface
• terminal_output in CommandLine

At the same time we're using these traits in some plugins, e.g. here and it leads to errors

I'm not sure why we wanted to deprecate these traits, and if we still want to do it now, or we want to set a different nipype version.

Related to #2508

[effigies]

Yeah, I think we should remove those. I believe the justification for deprecation was that they were more properly attributes of an interface or node, rather than inputs.

[effigies]

I'm actually a little surprised that these aren't throwing errors in our tests as of 1.0. And to be clear, I think we should remove them ASAP. Setting 1.0.3 milestone.

[djarecka]

I didn't check everything carefully, but there are not in all plugins, and I don't think we test e.g. condor plugin

[djarecka]

I can remove ignore_exception=True from condor, lsf and pbs; terminal_output is set in couple more places.

[effigies]

Seems reasonable.