FIX: revert E501 changes in doc description to please doctest

Author: miykael

nipype/interfaces/freesurfer/longitudinal.py

@@ -100,31 +100,22 @@ class RobustTemplate(FSCommandOpenMP):
     >>> template.inputs.no_iteration = True
     >>> template.inputs.subsample_threshold = 200
     >>> template.cmdline  #doctest:
-    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii
-        functional.nii --inittp 1 --noit --template mri_robust_template_out.mgz
-        --subsample 200'
+    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template mri_robust_template_out.mgz --subsample 200'
     >>> template.inputs.out_file = 'T1.nii'
     >>> template.cmdline  #doctest:
-    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii
-        functional.nii --inittp 1 --noit --template T1.nii --subsample 200'
+    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --subsample 200'
 
     >>> template.inputs.transform_outputs = ['structural.lta',
     ...                                      'functional.lta']
     >>> template.inputs.scaled_intensity_outputs = ['structural-iscale.txt',
     ...                                             'functional-iscale.txt']
     >>> template.cmdline    #doctest: +ELLIPSIS
-    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii
-        functional.nii --inittp 1 --noit --template T1.nii
-        --iscaleout .../structural-iscale.txt .../functional-iscale.txt
-        --subsample 200 --lta .../structural.lta .../functional.lta'
+    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --iscaleout .../structural-iscale.txt .../functional-iscale.txt --subsample 200 --lta .../structural.lta .../functional.lta'
 
     >>> template.inputs.transform_outputs = True
     >>> template.inputs.scaled_intensity_outputs = True
     >>> template.cmdline    #doctest: +ELLIPSIS
-    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii
-        functional.nii --inittp 1 --noit --template T1.nii
-        --iscaleout .../is1.txt .../is2.txt --subsample 200
-        --lta .../tp1.lta .../tp2.lta'
+    'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --iscaleout .../is1.txt .../is2.txt --subsample 200 --lta .../tp1.lta .../tp2.lta'
 
     >>> template.run()  #doctest: +SKIP
 
@@ -210,8 +201,7 @@ class FuseSegmentations(FSCommand):
     >>> fuse.inputs.in_segmentations_noCC = ['aseg.mgz', 'aseg.mgz']
     >>> fuse.inputs.in_norms = ['norm.mgz', 'norm.mgz', 'norm.mgz']
     >>> fuse.cmdline
-    'mri_fuse_segmentations -n norm.mgz -a aseg.mgz
-        -c aseg.mgz tp.long.A.template tp1 tp2'
+    'mri_fuse_segmentations -n norm.mgz -a aseg.mgz -c aseg.mgz tp.long.A.template tp1 tp2'
     """
 
     _cmd = 'mri_fuse_segmentations'

nipype/interfaces/fsl/dti.py

@@ -8,8 +8,7 @@
     Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(filepath,
-        '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 
 """
@@ -587,10 +586,7 @@ class ProbTrackX(FSLCommand):
     thsamples='merged_thsamples.nii', fsamples='merged_fsamples.nii', \
     phsamples='merged_phsamples.nii', out_dir='.')
     >>> pbx.cmdline
-    'probtrackx --forcedir -m mask.nii --mode=seedmask --nsamples=3 --nsteps=10
-        --opd --os2t --dir=. --samples=merged
-        --seed=MASK_average_thal_right.nii
-        --targetmasks=targets.txt --xfm=trans.mat'
+    'probtrackx --forcedir -m mask.nii --mode=seedmask --nsamples=3 --nsteps=10 --opd --os2t --dir=. --samples=merged --seed=MASK_average_thal_right.nii --targetmasks=targets.txt --xfm=trans.mat'
 
     """
 
@@ -788,8 +784,7 @@ class ProbTrackX2(ProbTrackX):
     >>> pbx2.inputs.n_samples = 3
     >>> pbx2.inputs.n_steps = 10
     >>> pbx2.cmdline
-    'probtrackx2 --forcedir -m nodif_brain_mask.nii.gz --nsamples=3 --nsteps=10
-        --opd --dir=. --samples=merged --seed=seed_source.nii.gz'
+    'probtrackx2 --forcedir -m nodif_brain_mask.nii.gz --nsamples=3 --nsteps=10 --opd --dir=. --samples=merged --seed=seed_source.nii.gz'
     """
     _cmd = 'probtrackx2'
     input_spec = ProbTrackX2InputSpec
@@ -988,8 +983,7 @@ class FindTheBiggest(FSLCommand):
 
     >>> from nipype.interfaces import fsl
     >>> ldir = ['seeds_to_M1.nii', 'seeds_to_M2.nii']
-    >>> fBig = fsl.FindTheBiggest(in_files=ldir,
-        out_file='biggestSegmentation')
+    >>> fBig = fsl.FindTheBiggest(in_files=ldir, out_file='biggestSegmentation')
     >>> fBig.cmdline
     'find_the_biggest seeds_to_M1.nii seeds_to_M2.nii biggestSegmentation'
 

nipype/interfaces/fsl/maths.py

@@ -8,8 +8,7 @@
     Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(
-            os.path.join(filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 """
 from __future__ import (print_function, division, unicode_literals,
@@ -442,8 +441,7 @@ class MultiImageMaths(MathsCommand):
     >>> maths.inputs.operand_files = ["functional2.nii", "functional3.nii"]
     >>> maths.inputs.out_file = "functional4.nii"
     >>> maths.cmdline
-    'fslmaths functional.nii -add functional2.nii -mul -1 -div functional3.nii
-    functional4.nii'
+    'fslmaths functional.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii'
 
     """
     input_spec = MultiImageMathsInput

nipype/interfaces/minc/base.py

@@ -109,8 +109,7 @@ def aggregate_filename(files, new_suffix):
     --------
 
     >>> from nipype.interfaces.minc.base import aggregate_filename
-    >>> f = aggregate_filename(['/tmp/foo1.mnc', '/tmp/foo2.mnc',
-                                '/tmp/foo3.mnc'], 'averaged')
+    >>> f = aggregate_filename(['/tmp/foo1.mnc', '/tmp/foo2.mnc', '/tmp/foo3.mnc'], 'averaged')
     >>> os.path.split(f)[1] # This has a full path, so just check the filename.
     'foo_averaged.mnc'
 

nipype/interfaces/niftyseg/em.py

@@ -128,8 +128,7 @@ class EM(NiftySegCommand):
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.no_prior = 4
     >>> node.cmdline
-    'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz -out im1_em.nii.gz
-    -out_outlier im1_outlier_em.nii.gz'
+    'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz -out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
 
     """
     _cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')

nipype/interfaces/niftyseg/label_fusion.py

@@ -148,8 +148,7 @@ class LabelFusion(NiftySegCommand):
     >>> node.inputs.template_num = 2
     >>> node.inputs.classifier_type = 'STEPS'
     >>> node.cmdline
-    'seg_LabFusion -in im1.nii -STEPS 2.000000 2 im2.nii im3.nii
-    -out im1_steps.nii'
+    'seg_LabFusion -in im1.nii -STEPS 2.000000 2 im2.nii im3.nii -out im1_steps.nii'
 
     """
     _cmd = get_custom_path('seg_LabFusion', env_dir='NIFTYSEGDIR')

nipype/interfaces/nipy/utils.py

@@ -3,8 +3,7 @@
     Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(
-        os.path.join(filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 
 """

nipype/interfaces/vista/vista.py

@@ -5,8 +5,7 @@
     Change directory to provide relative paths for doctests
     >>> import os
     >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
-    >>> datadir = os.path.realpath(os.path.join(
-        filepath, '../../testing/data'))
+    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
     >>> os.chdir(datadir)
 
 """

nipype/utils/filemanip.py

@@ -177,8 +177,7 @@ def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True):
     '/tmp/prefoopost.nii.gz'
 
     >>> from nipype.interfaces.base import Undefined
-    >>> fname_presuffix(fname, 'pre', 'post', Undefined) == fname_presuffix(
-        fname, 'pre', 'post')
+    >>> fname_presuffix(fname, 'pre', 'post', Undefined) == fname_presuffix(fname, 'pre', 'post')
     True
 
     """