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FIX: Patch ApplyTransforms spec to permit identity in a chain #554

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Merged
merged 2 commits into from
Aug 14, 2020
Merged

FIX: Patch ApplyTransforms spec to permit identity in a chain #554

merged 2 commits into from
Aug 14, 2020

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effigies
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First step in addressing #553.

The current trait is:

    transforms = traits.Either(
        InputMultiPath(File(exists=True)),
        "identity",
        argstr="%s",
        mandatory=True,
        desc="transform files: will be applied in reverse order. For "
        "example, the last specified transform will be applied first.",
    )

This will deserve its own nipype patch, but let's not stand on ceremony, there.

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pull-assistant bot commented Aug 13, 2020 •
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Score: 1.00

Best reviewed: commit by commit

Optimal code review plan

     FIX: Patch ApplyTransforms spec to permit identity in a chain

     ENH: Handle "identity" values when arranging xfms

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@effigies effigies mentioned this pull request Aug 13, 2020
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codecov bot commented Aug 13, 2020 •
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Codecov Report

Merging #554 into master will increase coverage by 0.03%.
The diff coverage is 76.92%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #554      +/-   ##
==========================================
+ Coverage   64.59%   64.63%   +0.03%     
==========================================
  Files          44       44              
  Lines        5401     5403       +2     
  Branches      793      790       -3     
==========================================
+ Hits         3489     3492       +3     
+ Misses       1751     1750       -1     
  Partials      161      161
Flag Coverage Δ
#documentation 33.64% <76.92%> (+0.01%) ⬆️
#masks ?
#reportlettests 100.00% <ø> (ø)
#travis 59.79% <76.92%> (-0.02%) ⬇️
#unittests 48.26% <76.92%> (+<0.01%) ⬆️

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

Impacted Files Coverage Δ
niworkflows/interfaces/itk.py 38.34% <62.50%> (-0.89%) ⬇️
niworkflows/interfaces/fixes.py 55.55% <100.00%> (+2.61%) ⬆️
niworkflows/interfaces/images.py 66.14% <0.00%> (+0.17%) ⬆️
niworkflows/viz/utils.py 80.05% <0.00%> (+0.23%) ⬆️
niworkflows/interfaces/mni.py 42.52% <0.00%> (+0.24%) ⬆️
niworkflows/utils/bids.py 75.00% <0.00%> (+0.74%) ⬆️

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emdupre
emdupre approved these changes Aug 14, 2020
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This is green here and in nipreps/fmriprep#2239 ! I also confirmed locally that it fixes the toy example outlined in #553

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Thanks for the reviews, @emdupre and @mgxd. Merging to smooth the path for tomorrow.

@oesteban Please shout if you have concerns.

@effigies effigies merged commit 8e9b574 into nipreps:master Aug 14, 2020
@effigies effigies deleted the enh/multiapply-identity branch August 14, 2020 02:44
oesteban added a commit that referenced this pull request Aug 14, 2020
@oesteban
rel(1.3.0rc1): Update CHANGES [skip ci]
a08116e 
First release in the 1.3.x series. This release includes enhancements and bug-fixes
towards the release of the first LTS version of fMRIPrep.
PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces
have been deemed ready to upstream into Nipype, and several improvements regarding
multi-echo EPI are included.
With thanks to Basile Pinsard for contributions.

  * FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (#554)
  * FIX: Add dots to extensions in PyBIDS' config file (#548)
  * FIX: Segmentation plots aligned with cardinal axes (#544)
  * FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (#545)
  * FIX: Avoid diverting CIFTI dtype from original BOLD (#532)
  * ENH: Add ``smooth`` input to ``RegridToZooms`` (#549)
  * ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (#547)
  * ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (#408)
  * ENH: Numerical stability of EPI brain-masks using probabilistic prior (#485)
  * ENH: Add a pure-Python interface to resample to specific resolutions (#511)
  * MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (#550)
  * MAINT: Update to Python +3.6 (#541)
HippocampusGirl added a commit to HippocampusGirl/niworkflows that referenced this pull request Sep 29, 2020
@HippocampusGirl
Merge tag '1.3.0rc3' into halfpipe
88a51c8 
1.3.0rc3

First release in the 1.3.x series. This release includes enhancements and bug-fixes
towards the release of the first LTS version of fMRIPrep.
PyBIDS has been revised to use more recent versions, a series of ANTs' interfaces
have been deemed ready to upstream into Nipype, and several improvements regarding
multi-echo EPI are included.
With thanks to Basile Pinsard for contributions.

* FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (nipreps#554)
* FIX: Add dots to extensions in PyBIDS' config file (nipreps#548)
* FIX: Segmentation plots aligned with cardinal axes (nipreps#544)
* FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (nipreps#545)
* FIX: Avoid diverting CIFTI dtype from original BOLD (nipreps#532)
* ENH: Add ``smooth`` input to ``RegridToZooms`` (nipreps#549)
* ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (nipreps#547)
* ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (nipreps#408)
* ENH: Numerical stability of EPI brain-masks using probabilistic prior (nipreps#485)
* ENH: Add a pure-Python interface to resample to specific resolutions (nipreps#511)
* MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (nipreps#550)
* MAINT: Update to Python +3.6 (nipreps#541)
HippocampusGirl added a commit to HippocampusGirl/niworkflows that referenced this pull request Sep 29, 2020
@HippocampusGirl
Merge tag '1.3.0' into halfpipe
4a90e70 
1.3.0

First release in the 1.3.x series.
This release includes enhancements and bug-fixes towards the release of the first
LTS (*long-term support*) version of *fMRIPrep*.
*PyBIDS* has been revised to use more recent versions, a series of ANTs' interfaces
have been deemed ready to upstream into *Nipype*, and several improvements regarding
multi-echo EPI are included.
With thanks to Basile Pinsard for contributions.

* FIX: Patch ``ApplyTransforms`` spec to permit identity in a chain (nipreps#554)
* FIX: Add dots to extensions in PyBIDS' config file (nipreps#548)
* FIX: Segmentation plots aligned with cardinal axes (nipreps#544)
* FIX: Skip T1w file existence check if ``anat_derivatives`` are provided (nipreps#545)
* FIX: Avoid diverting CIFTI dtype from original BOLD (nipreps#532)
* ENH: Add ``smooth`` input to ``RegridToZooms`` (nipreps#549)
* ENH: Enable ``DerivativesDataSink`` to take multiple source files to derive entities (nipreps#547)
* ENH: Allow ``bold_reference_wf`` to accept multiple EPIs/SBRefs (nipreps#408)
* ENH: Numerical stability of EPI brain-masks using probabilistic prior (nipreps#485)
* ENH: Add a pure-Python interface to resample to specific resolutions (nipreps#511)
* MAINT: Upstream all bug-fixes in the 1.2.9 release
* MAINT: Finalize upstreaming of ANTs' interfaces to Nipype (nipreps#550)
* MAINT: Update to Python +3.6 (nipreps#541)
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@mgxd mgxd mgxd approved these changes

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