ENH: Add new dwifslpreproc interface for MRtrix3

[axiezai]

Summary

Added new MRtrix3 dwifslpreproc interface.

Close #3276

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

• Added new interface at interfaces/mrtrix3/preprocess.py named DWIPreproc, interfaces with the newly updated dwifslpreproc command.
• make specs created new pytest
• All pytests for mrtrix3 interfaces passed

Acknowledgment

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

[axiezai]

Seems like the CI is failing at

Downloading standalone SPM ...
curl: (7) Failed to connect to www.fil.ion.ucl.ac.uk port 80: Connection timed out

[effigies]

I've restarted the CI...

[codecov]

Codecov Report

Merging #3278 (a1c43ad) into master (35b7927) will increase coverage by 0.04%.
The diff coverage is 75.00%.

@@            Coverage Diff             @@
##           master    #3278      +/-   ##
==========================================
+ Coverage   64.69%   64.73%   +0.04%     
==========================================
  Files         302      302              
  Lines       39837    39869      +32     
  Branches     5286     5288       +2     
==========================================
+ Hits        25773    25810      +37     
  Misses      12974    12974              
+ Partials     1090     1085       -5     

Flag	Coverage Δ
unittests	64.73% <75.00%> (+0.04%)	⬆️

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

Impacted Files	Coverage Δ
nipype/interfaces/mrtrix3/__init__.py	100.00% <ø> (ø)
nipype/interfaces/mrtrix3/preprocess.py	82.83% <75.00%> (-2.46%)	⬇️
nipype/pipeline/plugins/base.py	59.72% <0.00%> (+1.64%)	⬆️
nipype/pipeline/plugins/legacymultiproc.py	68.81% <0.00%> (+3.46%)	⬆️

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[effigies]

Thanks! This looks good overall. Some comments and at least one question.

[effigies]

Are these position arguments really necessary for all inputs?

[axiezai]

Not necessary, this was my lazy way of ensuring the interface command stayed consistent with the examples from the mrtrix documentation.

I think if position is left empty, the inputs appear right after dwifslpreproc? I was going for a format of dwifslpreproc in_file out_file -rpe_options -other_options to follow the examples here.

Is there a way to achieve that without specifying positions for everything?

[effigies]

If that's necessary, I think you could set position of 0 for in_file, 1 for out_file, 2 for rpe_options, and leave it unset for the rest. If it's not actually necessary for an option, I would personally leave it unset, because you're indicating to future maintainers that they need to be very particular about this.

[effigies]

Looks like you're going to need to re-make specs once you're done.

[effigies]

LGTM. Thanks!