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[WIP/ENH] Adds a new interface for AFNI's 3dMEMA command #2953

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JesseyWright
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Following Nipype's guidelines to write new interfaces.

Summary

Adds a new AFNI interface

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

Acknowledgment

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

Jessey Wright added 2 commits July 2, 2019 10:35
@oesteban oesteban changed the title [WIP/ENH] Adds a new interface for AFNI's 3dMema command [WIP/ENH] Adds a new interface for AFNI's 3dMEMA command Jul 2, 2019
@oesteban oesteban force-pushed the enh/add-3dMema-interface branch from 0bf3fb3 to 1a28ec3 Compare August 24, 2019 03:20
@oesteban
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@JesseyWright I have added a couple of full-examples. Please have a look. Still working on this interface, but I could use some help writing more of those:

first, some commands preceded with >>> , which get you to a certain state.
second, call interface_object.cmdline
third, a string that will be tested against the outcome of calculating the command line in the current state.

sorry for the short message, writing from SFO.

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codecov bot commented Aug 24, 2019

Codecov Report

Merging #2953 into master will decrease coverage by 0.01%.
The diff coverage is 60.29%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2953      +/-   ##
==========================================
- Coverage   64.24%   64.22%   -0.02%     
==========================================
  Files         342      342              
  Lines       43692    43752      +60     
  Branches     5453     5463      +10     
==========================================
+ Hits        28068    28101      +33     
- Misses      14545    14571      +26     
- Partials     1079     1080       +1
Flag Coverage Δ
#unittests 64.22% <60.29%> (-0.02%) ⬇️
Impacted Files Coverage Δ
nipype/interfaces/base/core.py 84.01% <60%> (-0.33%) ⬇️
nipype/interfaces/afni/model.py 79.48% <60.31%> (-7.45%) ⬇️

Continue to review full report at Codecov.

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Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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codecov bot commented Aug 24, 2019

Codecov Report

Merging #2953 into master will decrease coverage by 3.27%.
The diff coverage is 60.29%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2953      +/-   ##
==========================================
- Coverage    67.5%   64.22%   -3.28%     
==========================================
  Files         344      342       -2     
  Lines       44039    43752     -287     
  Branches     5554     5463      -91     
==========================================
- Hits        29727    28101    -1626     
- Misses      13560    14571    +1011     
- Partials      752     1080     +328
Flag Coverage Δ
#smoketests ?
#unittests 64.22% <60.29%> (-0.73%) ⬇️
Impacted Files Coverage Δ
nipype/interfaces/base/core.py 84.01% <60%> (-2.98%) ⬇️
nipype/interfaces/afni/model.py 79.48% <60.31%> (-2.48%) ⬇️
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%> (-29.01%) ⬇️
nipype/utils/provenance.py 55.73% <0%> (-28.35%) ⬇️
nipype/interfaces/fsl/model.py 55.26% <0%> (-25.35%) ⬇️
... and 56 more

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codecov bot commented Aug 24, 2019

Codecov Report

Merging #2953 into master will decrease coverage by 3.34%.
The diff coverage is 87.23%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master    #2953      +/-   ##
==========================================
- Coverage    67.5%   64.15%   -3.35%     
==========================================
  Files         344      342       -2     
  Lines       44039    44045       +6     
  Branches     5554     5561       +7     
==========================================
- Hits        29727    28256    -1471     
- Misses      13560    14667    +1107     
- Partials      752     1122     +370
Flag Coverage Δ
#smoketests ?
#unittests 64.15% <87.23%> (-0.8%) ⬇️
Impacted Files Coverage Δ
nipype/interfaces/afni/__init__.py 100% <100%> (ø) ⬆️
nipype/interfaces/base/core.py 84.13% <75%> (-2.86%) ⬇️
nipype/interfaces/afni/model.py 75.88% <88.09%> (-6.07%) ⬇️
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 57.94% <0%> (-29.14%) ⬇️
nipype/utils/provenance.py 55.73% <0%> (-28.35%) ⬇️
... and 45 more

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@effigies effigies added this to the 1.2.2 milestone Aug 30, 2019
@oesteban
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@JesseyWright I've finished the inputs and their tests. I believe this should be functional. However, this will fail when composing the outputs - could you find some data to test this on?

@oesteban oesteban modified the milestones: 1.2.2, 1.3.0, 1.2.3 Sep 5, 2019
@oesteban oesteban modified the milestones: 1.2.3, 1.3.0 Sep 13, 2019
@effigies effigies modified the milestones: 1.3.0, 1.4.0 Nov 11, 2019
@effigies effigies modified the milestones: 1.4.0, 1.5.0 Dec 14, 2019
@effigies effigies mentioned this pull request Feb 23, 2020
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This pull request is "orphaned," which means it has been deemed to be abandoned by its original author. Orphaned pull requests have not been rejected, and we hope that if a user sees one that will meet their needs with a little work, that they will fork it and open a new pull request (or, in the case of the original author, reopen the original PR).

We ask that all adopted PRs be updated to merge or rebase the current master. If you would like to adopt a PR and need help getting started, any of a number of contributors will be happy to help.

@effigies effigies closed this Feb 23, 2020
@effigies effigies removed this from the 1.5.0 milestone May 27, 2020
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3 participants