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RF: Derive MRIsExpand from FSSurfaceCommand #1963

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Merged
merged 5 commits into from
Apr 24, 2017

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effigies
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This change takes advantage of work in #1948 to handle some common quirks in FreeSurfer commands that write surface files.

Some doc fixes and a minor update to FSSurfaceCommand to not push absolute paths at that stage (consistent with how MRIsExpand._associated_file worked).

@tsalo I made a couple changes to MRIsCombine, if you'd have a look. It's mostly docs, but I also moved the out_file description into _list_outputs, just because it didn't really need the machinery of _associated_file. I can revert these if you prefer.

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codecov-io commented Apr 21, 2017

Codecov Report

Merging #1963 into master will increase coverage by 0.1%.
The diff coverage is 89.79%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master    #1963     +/-   ##
=========================================
+ Coverage   72.52%   72.63%   +0.1%     
=========================================
  Files        1070     1070             
  Lines       54389    54407     +18     
  Branches     7858     7858             
=========================================
+ Hits        39447    39517     +70     
+ Misses      13715    13659     -56     
- Partials     1227     1231      +4
Flag Coverage Δ
#smoketests 72.63% <89.79%> (+0.1%) ⬆️
#unittests 70.18% <89.79%> (+0.1%) ⬆️
Impacted Files Coverage Δ
...nterfaces/freesurfer/tests/test_auto_MRIsExpand.py 85.71% <ø> (ø) ⬆️
nipype/interfaces/freesurfer/tests/test_utils.py 96.87% <100%> (+0.87%) ⬆️
nipype/interfaces/freesurfer/base.py 73.68% <100%> (+6.76%) ⬆️
...terfaces/freesurfer/tests/test_FSSurfaceCommand.py 100% <100%> (ø)
nipype/interfaces/freesurfer/utils.py 63.19% <28.57%> (+1.05%) ⬆️
nipype/interfaces/io.py 52.55% <0%> (+1.94%) ⬆️

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@effigies
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Added tests for FSSurfaceCommand and MRIsExpand. Not for MRIsCombine. In the process realized there was an option that shouldn't be enabled.

@satra satra merged commit 6c23846 into nipy:master Apr 24, 2017
@effigies effigies deleted the ref/mris_expand branch April 24, 2017 15:10
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3 participants