fix: store undefined by default so that xor checks don't trip

[satra]

No description provided.

[codecov-io]

Codecov Report

Merging #1903 into master will decrease coverage by 0.58%.
The diff coverage is 0%.

@@            Coverage Diff             @@
##           master    #1903      +/-   ##
==========================================
- Coverage   72.92%   72.33%   -0.59%     
==========================================
  Files        1061     1060       -1     
  Lines       53784    53635     -149     
  Branches     7738     7736       -2     
==========================================
- Hits        39221    38799     -422     
- Misses      13349    13599     +250     
- Partials     1214     1237      +23

Flag	Coverage Δ
#smoketests	72.33% <0%> (-0.59%)	⬇️
#unittests	70.38% <0%> (ø)	⬆️

Impacted Files	Coverage Δ
nipype/scripts/utils.py	40.42% <0%> (-0.88%)	⬇️
nipype/interfaces/spm/model.py	41.76% <0%> (-29.98%)	⬇️
nipype/interfaces/spm/preprocess.py	55.93% <0%> (-13.01%)	⬇️
nipype/algorithms/modelgen.py	67.28% <0%> (-6.08%)	⬇️
nipype/utils/provenance.py	84.91% <0%> (-3.94%)	⬇️
nipype/workflows/fmri/spm/preprocess.py	68.68% <0%> (-3.04%)	⬇️
nipype/interfaces/fsl/utils.py	70.26% <0%> (-2.39%)	⬇️
nipype/interfaces/spm/base.py	82.6% <0%> (-1.82%)	⬇️
nipype/interfaces/utility/base.py	89.47% <0%> (-1.17%)	⬇️
nipype/utils/misc.py	85.82% <0%> (-0.79%)	⬇️
... and 6 more

---

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[codecov-io]

Codecov Report

Merging #1903 into master will increase coverage by <.01%.
The diff coverage is 0%.

@@            Coverage Diff             @@
##           master    #1903      +/-   ##
==========================================
+ Coverage   72.92%   72.93%   +<.01%     
==========================================
  Files        1061     1061              
  Lines       53784    53771      -13     
  Branches     7738     7736       -2     
==========================================
- Hits        39221    39216       -5     
+ Misses      13349    13341       -8     
  Partials     1214     1214

Flag	Coverage Δ
#smoketests	72.93% <0%> (ø)	⬆️
#unittests	70.38% <0%> (ø)	⬆️

Impacted Files	Coverage Δ
nipype/scripts/utils.py	39.58% <0%> (-1.73%)	⬇️
nipype/algorithms/modelgen.py	73.36% <0%> (ø)	⬆️
...ype/interfaces/tests/test_auto_FreeSurferSource.py	100% <0%> (ø)	⬆️
.../interfaces/freesurfer/tests/test_auto_ReconAll.py	100% <0%> (ø)	⬆️
nipype/interfaces/io.py	50.93% <0%> (ø)	⬆️
nipype/interfaces/base.py	84.38% <0%> (+0.18%)	⬆️
nipype/interfaces/fsl/epi.py	65.96% <0%> (+0.41%)	⬆️

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[satra]

@chrisfilo - quick review? this will allow running things like:

nipypecli run nipype.interfaces.fsl BET somefile.nii

[chrisgorgo]

Seems to be working:

root@19bad2d1679b:/scratch# nipypecli run nipype.interfaces.fsl BET /data/sub-0051323_task-rest_run-1_bold_avg.nii.gz
setting function inputs

args = <undefined>
center = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
frac = <undefined>
functional = <undefined>
ignore_exception = False
in_file = /data/sub-0051323_task-rest_run-1_bold_avg.nii.gz
mask = <undefined>
mesh = <undefined>
no_output = <undefined>
out_file = <undefined>
outline = <undefined>
output_type = NIFTI_GZ
padding = <undefined>
radius = <undefined>
reduce_bias = <undefined>
remove_eyes = <undefined>
robust = <undefined>
skull = <undefined>
surfaces = <undefined>
t2_guided = <undefined>
terminal_output = stream
threshold = <undefined>
vertical_gradient = <undefined>


inskull_mask_file = <undefined>
inskull_mesh_file = <undefined>
mask_file = <undefined>
meshfile = <undefined>
out_file = /scratch/sub-0051323_task-rest_run-1_bold_avg_brain.nii.gz
outline_file = <undefined>
outskin_mask_file = <undefined>
outskin_mesh_file = <undefined>
outskull_mask_file = <undefined>
outskull_mesh_file = <undefined>
skull_mask_file = <undefined>