changing Node._output_dir to realpath

[djarecka]

I changed abspath to realpath in Node._output_dir to fix problems with temporary directories on OSX. abspath gives /var/... and realpath returns /private/var.... In clean_working_directory we had needed_files that used /private/var/... and cwd used /var/..., so many files were removed.

I'm not sure if this is the best place to change the path, I can do it also in clean_working_directory, if for any reason we should keep abspath in _output_dir.

There is a chance that this will solve the general issue from #2395. For now it fixed all tests from heudiconv, so should also solve this issue

[codecov-io]

Codecov Report

Merging #2639 into master will decrease coverage by 3.54%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #2639      +/-   ##
==========================================
- Coverage    67.6%   64.06%   -3.55%     
==========================================
  Files         340      338       -2     
  Lines       43003    42952      -51     
  Branches     5321     5318       -3     
==========================================
- Hits        29073    27516    -1557     
- Misses      13231    14383    +1152     
- Partials      699     1053     +354

Flag	Coverage Δ
#smoketests	?
#unittests	64.06% <100%> (-1%)	⬇️

Impacted Files	Coverage Δ
nipype/pipeline/engine/nodes.py	77.52% <100%> (-6.78%)	⬇️
nipype/interfaces/nilearn.py	40% <0%> (-56.67%)	⬇️
nipype/utils/spm_docs.py	25.92% <0%> (-44.45%)	⬇️
nipype/interfaces/nitime/analysis.py	43.15% <0%> (-36.85%)	⬇️
nipype/interfaces/freesurfer/base.py	49.59% <0%> (-30.9%)	⬇️
nipype/utils/logger.py	59.7% <0%> (-29.86%)	⬇️
nipype/algorithms/rapidart.py	35.39% <0%> (-29.21%)	⬇️
nipype/interfaces/spm/base.py	58.41% <0%> (-29.05%)	⬇️
nipype/utils/provenance.py	55.73% <0%> (-28.99%)	⬇️
nipype/interfaces/fsl/model.py	55.26% <0%> (-25.35%)	⬇️
... and 45 more

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[mgxd]

@djarecka are unused outputs still removed within a workflow (by default)? if so, i'm good with this change - nice catch

[djarecka]

@mgxd - yes, unused output is still removed, you can check that you don't have all dcm files at the end. My changes just ensure that we run walk_files using path that is a realpath and not an abspath.

Dcm2niix that we were testing yesterday uses abspath in out_file, but fnam contains ., so abspath is equivalent to realpath.

I hope that we don't have interfaces that return abspath that is different than realpath in output (this might lead to similar problems). If we notice any new problems, I'd suggest adding realpath in File class: here and here (and similar changes in Directory and ImageFile).

[mgxd]

OK, let's merge this and see!