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ENH: Add workbench.CiftiSmooth interface #2871

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merged 2 commits into from
Feb 6, 2019
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@mgxd mgxd commented Jan 31, 2019

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

  • Adds -cifti-smoothing command from wb_command

Acknowledgment

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

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Codecov Report

Merging #2871 into master will decrease coverage by 3.36%.
The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2871      +/-   ##
==========================================
- Coverage   67.49%   64.13%   -3.37%     
==========================================
  Files         342      341       -1     
  Lines       43562    43537      -25     
  Branches     5422     5419       -3     
==========================================
- Hits        29402    27922    -1480     
- Misses      13458    14543    +1085     
- Partials      702     1072     +370
Flag Coverage Δ
#smoketests ?
#unittests 64.13% <100%> (-0.79%) ⬇️
Impacted Files Coverage Δ
nipype/interfaces/workbench/__init__.py 100% <100%> (ø) ⬆️
nipype/interfaces/workbench/cifti.py 100% <100%> (ø)
nipype/interfaces/nilearn.py 40% <0%> (-56.67%) ⬇️
nipype/utils/spm_docs.py 25.92% <0%> (-44.45%) ⬇️
nipype/interfaces/freesurfer/base.py 50% <0%> (-30.51%) ⬇️
nipype/utils/logger.py 59.7% <0%> (-29.86%) ⬇️
nipype/algorithms/rapidart.py 35% <0%> (-29.42%) ⬇️
nipype/interfaces/spm/base.py 58.08% <0%> (-29.05%) ⬇️
nipype/utils/provenance.py 55.73% <0%> (-28.99%) ⬇️
nipype/interfaces/fsl/model.py 55.26% <0%> (-25.35%) ⬇️
... and 44 more

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LGTM. I have a question about the position metadata for flagged arguments.

desc="Specify the left surface to use")
left_corrected_areas = File(
exists=True,
position=6,
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Are all these flagged arguments truly positional?

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@effigies effigies changed the title enh: wb cifti-smoothing ENH: Add workbench.CiftiSmooth interface Feb 6, 2019
@effigies effigies added this to the 1.1.9 milestone Feb 6, 2019
@effigies effigies merged commit eaf4953 into nipy:master Feb 6, 2019
yarikoptic added a commit to yarikoptic/nipype that referenced this pull request Mar 15, 2019
1.1.9 (February 25, 2019)

Full changelog: https://github.com/nipy/nipype/milestone/30?closed=1

  * FIX: Make positional arguments to LaplacianThickness require previous argument (nipy#2848)
  * FIX: Import math and csv modules for bids_gen_info (nipy#2881)
  * FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (nipy#2739)
  * ENH: Allow afni.MaskTool to take multiple input files (nipy#2892)
  * ENH: Add flags dictionary input to spm.Level1Design (nipy#2861)
  * ENH: Threshold stddev once only in TSNR (nipy#2883)
  * ENH: Add workbench.CiftiSmooth interface (nipy#2871)
  * DOC: Replace initialism typo in comment with intended phrase (nipy#2875)
  * DOC: Fix typos in ANTs Registration input documentation (nipy#2869)

* tag '1.1.9': (34 commits)
  MNT: Update changelog
  MNT: Add Katherine Bottenhorn, Paul Mihai to Zenodo
  MNT: Add kchawla-pi to Zenodo, update mailmap and ordering
  add to zenodo
  MNT: Update zenodo ordering
  Update .zenodo.json
  afni utils.py - masktool - InputMultiPath for in_file argument
  MNT: Update .zenodo ordering
  MNT: Add Oliver Contier name to .zenodo.json
  Update nipype/interfaces/spm/model.py
  ENH: Add zenodo updating script
  MNT: Update mailmap to avoid renames in script
  MNT: Update .mailmap, .zenodo.json
  MNT: Version 1.1.9
  DOC: 1.1.9 changelog
  ENH: minor - compute non degenerate stddev map once
  BF: regenerated test_auto_LaplacianThickness using wonderfully long running tools/checkspecs.py
  TEST: Thorough test of LaplacianThickness requirement cascade
  FIX: Requires error text was backwards
  import math and csv modules for bids_gen_info
  ...
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3 participants