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Author: pre-commit-ci[bot]

nipype-auto-conv/specs/interfaces/accuracy_tester.yaml

@@ -5,10 +5,10 @@
 #
 # Docs
 # ----
-# 
+#
 # Test the accuracy of an existing training dataset on a set of hand-labelled subjects.
 # Note: This may or may not be working. Couldn't presently not confirm because fix fails on this (even outside of nipype) without leaving an error msg.
-# 
+#
 task_name: AccuracyTester
 nipype_name: AccuracyTester
 nipype_module: nipype.interfaces.fsl.fix
@@ -76,8 +76,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/apply_mask.yaml

@@ -84,8 +84,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/apply_topup.yaml

@@ -5,18 +5,18 @@
 #
 # Docs
 # ----
-# 
+#
 # Interface for FSL topup, a tool for estimating and correcting
 # susceptibility induced distortions.
 # `General reference
 # <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ApplytopupUsersGuide>`_
 # and `use example
 # <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup>`_.
-# 
-# 
+#
+#
 # Examples
 # --------
-# 
+#
 # >>> from nipype.interfaces.fsl import ApplyTOPUP
 # >>> applytopup = ApplyTOPUP()
 # >>> applytopup.inputs.in_files = ["epi.nii", "epi_rev.nii"]
@@ -27,8 +27,8 @@
 # >>> applytopup.cmdline # doctest: +ELLIPSIS
 # 'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii --inindex=1,2 --topup=topup --out=epi_corrected.nii.gz'
 # >>> res = applytopup.run() # doctest: +SKIP
-# 
-# 
+#
+#
 task_name: ApplyTOPUP
 nipype_name: ApplyTOPUP
 nipype_module: nipype.interfaces.fsl.epi
@@ -114,8 +114,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true
@@ -138,8 +138,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/apply_warp.yaml

@@ -6,7 +6,7 @@
 # Docs
 # ----
 # FSL's applywarp wrapper to apply the results of a FNIRT registration
-# 
+#
 # Examples
 # --------
 # >>> from nipype.interfaces import fsl
@@ -16,9 +16,9 @@
 # >>> aw.inputs.ref_file = example_data('mni.nii')
 # >>> aw.inputs.field_file = 'my_coefficients_filed.nii' #doctest: +SKIP
 # >>> res = aw.run() #doctest: +SKIP
-# 
-# 
-# 
+#
+#
+#
 task_name: ApplyWarp
 nipype_name: ApplyWarp
 nipype_module: nipype.interfaces.fsl.preprocess
@@ -119,8 +119,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/apply_xfm.yaml

@@ -7,13 +7,13 @@
 # ----
 # Currently just a light wrapper around FLIRT,
 # with no modifications
-# 
+#
 # ApplyXFM is used to apply an existing transform to an image
-# 
-# 
+#
+#
 # Examples
 # --------
-# 
+#
 # >>> import nipype.interfaces.fsl as fsl
 # >>> from nipype.testing import example_data
 # >>> applyxfm = fsl.preprocess.ApplyXFM()
@@ -23,8 +23,8 @@
 # >>> applyxfm.inputs.reference = example_data('mni.nii')
 # >>> applyxfm.inputs.apply_xfm = True
 # >>> result = applyxfm.run() # doctest: +SKIP
-# 
-# 
+#
+#
 task_name: ApplyXFM
 nipype_name: ApplyXFM
 nipype_module: nipype.interfaces.fsl.preprocess
@@ -208,8 +208,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/ar1_image.yaml

@@ -7,8 +7,8 @@
 # ----
 # Use fslmaths to generate an AR1 coefficient image across a
 # given dimension. (Should use -odt float and probably demean first)
-# 
-# 
+#
+#
 task_name: AR1Image
 nipype_name: AR1Image
 nipype_module: nipype.interfaces.fsl.maths
@@ -85,8 +85,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/av_scale.yaml

@@ -6,16 +6,16 @@
 # Docs
 # ----
 # Use FSL avscale command to extract info from mat file output of FLIRT
-# 
+#
 # Examples
 # --------
-# 
+#
 # >>> avscale = AvScale()
 # >>> avscale.inputs.mat_file = 'flirt.mat'
 # >>> res = avscale.run()  # doctest: +SKIP
-# 
-# 
-# 
+#
+#
+#
 task_name: AvScale
 nipype_name: AvScale
 nipype_module: nipype.interfaces.fsl.utils
@@ -68,7 +68,7 @@ tests:
   # dict[str, str] - values to provide to inputs fields in the task initialisation
   # (if not specified, will try to choose a sensible value)
     all_param:
-    # type=bool|default=False: 
+    # type=bool|default=False:
     mat_file:
     # type=file|default=<undefined>: mat file to read
     ref_file:
@@ -85,8 +85,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/b0_calc.yaml

@@ -5,24 +5,24 @@
 #
 # Docs
 # ----
-# 
+#
 # B0 inhomogeneities occur at interfaces of materials with different magnetic susceptibilities,
 # such as tissue-air interfaces. These differences lead to distortion in the local magnetic field,
 # as Maxwell’s equations need to be satisfied. An example of B0 inhomogneity is the first volume
 # of the 4D volume ```$FSLDIR/data/possum/b0_ppm.nii.gz```.
-# 
+#
 # Examples
 # --------
-# 
+#
 # >>> from nipype.interfaces.fsl import B0Calc
 # >>> b0calc = B0Calc()
 # >>> b0calc.inputs.in_file = 'tissue+air_map.nii'
 # >>> b0calc.inputs.z_b0 = 3.0
 # >>> b0calc.inputs.output_type = "NIFTI_GZ"
 # >>> b0calc.cmdline
 # 'b0calc -i tissue+air_map.nii -o tissue+air_map_b0field.nii.gz --chi0=4.000000e-07 -d -9.450000e-06 --extendboundary=1.00 --b0x=0.00 --gx=0.0000 --b0y=0.00 --gy=0.0000 --b0=3.00 --gz=0.0000'
-# 
-# 
+#
+#
 task_name: B0Calc
 nipype_name: B0Calc
 nipype_module: nipype.interfaces.fsl.possum
@@ -112,8 +112,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true
@@ -134,8 +134,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true

nipype-auto-conv/specs/interfaces/bedpostx5.yaml

@@ -5,30 +5,30 @@
 #
 # Docs
 # ----
-# 
+#
 # BEDPOSTX stands for Bayesian Estimation of Diffusion Parameters Obtained
 # using Sampling Techniques. The X stands for modelling Crossing Fibres.
 # bedpostx runs Markov Chain Monte Carlo sampling to build up distributions
 # on diffusion parameters at each voxel. It creates all the files necessary
 # for running probabilistic tractography. For an overview of the modelling
 # carried out within bedpostx see this `technical report
 # <http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/index.html>`_.
-# 
-# 
+#
+#
 # .. note:: Consider using
 #   :func:`niflow.nipype1.workflows.fsl.dmri.create_bedpostx_pipeline` instead.
-# 
-# 
+#
+#
 # Example
 # -------
-# 
+#
 # >>> from nipype.interfaces import fsl
 # >>> bedp = fsl.BEDPOSTX5(bvecs='bvecs', bvals='bvals', dwi='diffusion.nii',
 # ...                     mask='mask.nii', n_fibres=1)
 # >>> bedp.cmdline
 # 'bedpostx bedpostx -b 0 --burnin_noard=0 --forcedir -n 1 -j 5000 -s 1 --updateproposalevery=40'
-# 
-# 
+#
+#
 task_name: BEDPOSTX5
 nipype_name: BEDPOSTX5
 nipype_module: nipype.interfaces.fsl.dti
@@ -52,7 +52,7 @@ inputs:
     grad_dev: generic/file
     # type=file|default=<undefined>: grad_dev file, if gradnonlin, -g is True
     logdir: generic/directory
-    # type=directory|default=<undefined>: 
+    # type=directory|default=<undefined>:
     mask: medimage/nifti1
     # type=file|default=<undefined>: bet binary mask file
     out_dir: generic/directory
@@ -113,7 +113,7 @@ tests:
     bvals:
     # type=file|default=<undefined>: b values file
     logdir:
-    # type=directory|default=<undefined>: 
+    # type=directory|default=<undefined>:
     n_fibres:
     # type=range|default=2: Maximum number of fibres to fit in each voxel
     model:
@@ -172,8 +172,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true
@@ -200,8 +200,8 @@ tests:
   # be terminated before they complete for time-saving reasons, and therefore
   # these values will be ignored, when running in CI
   timeout: 10
-  # int - the value to set for the timeout in the generated test, 
-  # after which the test will be considered to have been initialised 
+  # int - the value to set for the timeout in the generated test,
+  # after which the test will be considered to have been initialised
   # successfully. Set to 0 to disable the timeout (warning, this could
   # lead to the unittests taking a very long time to complete)
   xfail: true