RF: Clean-up the BaseInterface run() function using context

[oesteban]

Python contexts seem the most appropriate pattern to follow.

Summary

Fixes # .

List of changes proposed in this PR (pull-request)

Acknowledgment

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

[codecov]

Codecov Report

Merging #3347 (24f2cbc) into master (0289137) will increase coverage by 0.02%.
The diff coverage is 82.50%.

@@            Coverage Diff             @@
##           master    #3347      +/-   ##
==========================================
+ Coverage   65.08%   65.11%   +0.02%     
==========================================
  Files         307      307              
  Lines       40362    40373      +11     
  Branches     5329     5326       -3     
==========================================
+ Hits        26270    26288      +18     
+ Misses      13019    13014       -5     
+ Partials     1073     1071       -2     

Flag	Coverage Δ
unittests	64.83% <82.50%> (+0.02%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
nipype/utils/profiler.py	22.27% <57.89%> (+3.88%)	⬆️
nipype/interfaces/base/support.py	80.93% <86.95%> (+1.39%)	⬆️
nipype/interfaces/base/core.py	88.17% <100.00%> (+2.69%)	⬆️

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[oesteban]

I've been noticing that under some (yet unknown) conditions, the node report after a crash will show definitely set inputs as undefined, and some errors that escape generating a crash file.

This PR, in collaboration with #3349, makes the flow of operations a bit more clear and makes the treatment of errors more reliable.

[oesteban]

To note, I have tested this and #3349 locally with fMRIPrep and dMRIPrep and they seem to work as expected.

[satra]

some things to discuss about exceptions.

[effigies]

LGTM too.