FIX: Add informative error for interfaces that fail to return valid runtime object

[effigies]

Summary

If an interface has a _run_interface implementation that in some (or all) cases fails to return the passed runtime object, then the error you currently get is:

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 471, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 544, in run
    runtime.endTime = dt.isoformat(dt.utcnow())
AttributeError: 'NoneType' object has no attribute 'endTime'

Arising from this chunk of code:

nipype/nipype/interfaces/base/core.py

Lines 542 to 553 in 37f3781

	finally:
	# This needs to be done always
	runtime.endTime = dt.isoformat(dt.utcnow())
	timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)
	runtime.duration = (timediff.days * 86400 + timediff.seconds +
	timediff.microseconds / 1e6)
	results = InterfaceResult(
	interface,
	runtime,
	inputs=inputs,
	outputs=outputs,
	provenance=None)

This PR simply makes an absent runtime object raise a RuntimeError and give a likely cause.

Acknowledgment

• (Mandatory) I acknowledge that this contribution will be available under the Apache 2 license.

[effigies]

Any objections/suggestions here? I'll merge tomorrow AM if nobody minds.

[satra]

while we are at this, should we simply check for None, or actually check that the reserved keywords still exist.

[effigies]

Sorry, could you be more explicit?

[satra]

i.e. that these attributes are still present:

https://github.com/nipy/nipype/blob/master/nipype/interfaces/base/core.py#L492

[effigies]

The easiest way to do that without digging into private variables was to add a Bunch.keys() method. That alright?

[satra]

@effigies - that's fine with me, but for the moment could we keep that api private. ideally we will move away from Bunch to more standard Python objects in Py 3.x.

dict(bunch_var.items()) will return a dict that can be used as well.

so set(dict(bunch_var.items())) == set(dict(orig_runtime.items())) could also work as a check.

where orig_runtime is the pre-call runtime.

[effigies]

Switched to dictcopy, which already exists. We use it elsewhere in the file, so a replace-all when moving to a standard object will catch these additions.