removing trailing spaces

nipype/algorithms/confounds.py

@@ -668,7 +668,7 @@ def compute_dvars(in_file, in_mask, remove_zerovariance=False):
         warnings.filterwarnings('error')
 
         # voxelwise standardization
-        diff_vx_stdz = func_diff / np.array([diff_sdhat] * func_diff.shape[-1]).T            
+        diff_vx_stdz = func_diff / np.array([diff_sdhat] * func_diff.shape[-1]).T
         dvars_vx_stdz = diff_vx_stdz.std(axis=0, ddof=1)
 
     return (dvars_stdz, dvars_nstd, dvars_vx_stdz)

nipype/algorithms/tests/test_compcor.py

@@ -16,7 +16,7 @@ class TestCompCor():
     filenames = {'functionalnii': 'compcorfunc.nii',
                  'masknii': 'compcormask.nii',
                  'components_file': None}
-    
+
     @pytest.fixture(autouse=True)
     def setup_class(self, tmpdir):
         # setup

nipype/algorithms/tests/test_mesh_ops.py

@@ -25,7 +25,7 @@ def test_ident_distances(tmpdir):
     dist_ident.inputs.out_file = os.path.join(tempdir, 'distance.npy')
     res = dist_ident.run()
     assert res.outputs.distance == 0.0
-    
+
     dist_ident.inputs.weighting = 'area'
     res = dist_ident.run()
     assert res.outputs.distance == 0.0
@@ -35,23 +35,23 @@ def test_ident_distances(tmpdir):
 def test_trans_distances(tmpdir):
     tempdir = str(tmpdir)
     os.chdir(tempdir)
-    
+
     from ...interfaces.vtkbase import tvtk
-    
+
     in_surf = example_data('surf01.vtk')
     warped_surf = os.path.join(tempdir, 'warped.vtk')
-    
+
     inc = np.array([0.7, 0.3, -0.2])
-    
+
     r1 = tvtk.PolyDataReader(file_name=in_surf)
     vtk1 = VTKInfo.vtk_output(r1)
     r1.update()
     vtk1.points = np.array(vtk1.points) + inc
-    
+
     writer = tvtk.PolyDataWriter(file_name=warped_surf)
     VTKInfo.configure_input_data(writer, vtk1)
     writer.write()
-    
+
     dist = m.ComputeMeshWarp()
     dist.inputs.surface1 = in_surf
     dist.inputs.surface2 = warped_surf
@@ -79,10 +79,10 @@ def test_meshwarpmaths(tmpdir):
 
 @pytest.mark.skipif(not VTKInfo.no_tvtk(), reason="tvtk is installed")
 def test_importerror():
-    with pytest.raises(ImportError): 
+    with pytest.raises(ImportError):
         m.ComputeMeshWarp()
 
-    with pytest.raises(ImportError): 
+    with pytest.raises(ImportError):
         m.WarpPoints()
 
     with pytest.raises(ImportError):

nipype/algorithms/tests/test_modelgen.py

@@ -152,8 +152,8 @@ def test_modelgen_sparse(tmpdir):
     assert len(res.outputs.session_info[0]['regress']) == 1
     s.inputs.use_temporal_deriv = True
     res = s.run()
-    
+
     assert len(res.outputs.session_info[0]['regress']) == 2
     npt.assert_almost_equal(res.outputs.session_info[0]['regress'][0]['val'][0], 0.016675298129743384)
     npt.assert_almost_equal(res.outputs.session_info[1]['regress'][1]['val'][5], 0.007671459162258378)
-    
+

nipype/algorithms/tests/test_overlap.py

@@ -26,7 +26,7 @@ def check_close(val1, val2):
     overlap.inputs.volume2 = in1
     res = overlap.run()
     check_close(res.outputs.jaccard, 1.0)
-    
+
     overlap = Overlap()
     overlap.inputs.volume1 = in1
     overlap.inputs.volume2 = in2

nipype/interfaces/freesurfer/tests/test_preprocess.py

@@ -58,7 +58,7 @@ def test_robustregister(create_files_in_directory):
     assert reg2.cmdline == ('mri_robust_register --halfdst %s_halfway.nii --lta foo.lta '
                             '--sat 3.0000 --mov %s --dst %s'
                             % (os.path.join(outdir, filelist[1][:-4]), filelist[0], filelist[1]))
-    
+
 
 @pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed")
 def test_fitmsparams(create_files_in_directory):

nipype/interfaces/fsl/tests/test_base.py

@@ -9,7 +9,7 @@
 
 import pytest
 
-@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") 
+@pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_fslversion():
     ver = fsl.Info.version()
     ver = ver.split('.')
@@ -27,8 +27,8 @@ def test_outputtype_to_ext():
     for ftype, ext in fsl.Info.ftypes.items():
         res = fsl.Info.output_type_to_ext(ftype)
         assert res == ext
-        
-    with pytest.raises(KeyError): 
+
+    with pytest.raises(KeyError):
         fsl.Info.output_type_to_ext('JUNK')
 
 
@@ -60,11 +60,11 @@ def test_FSLCommand2():
 
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
-@pytest.mark.parametrize("args, desired_name", 
-                         [({},   {"file": 'foo.nii.gz'}), # just the filename 
-                          ({"suffix": '_brain'}, {"file": 'foo_brain.nii.gz'}), # filename with suffix 
-                          ({"suffix": '_brain', "cwd": '/data'}, 
-                           {"dir": '/data', "file": 'foo_brain.nii.gz'}), # filename with suffix and working directory 
+@pytest.mark.parametrize("args, desired_name",
+                         [({},   {"file": 'foo.nii.gz'}), # just the filename
+                          ({"suffix": '_brain'}, {"file": 'foo_brain.nii.gz'}), # filename with suffix
+                          ({"suffix": '_brain', "cwd": '/data'},
+                           {"dir": '/data', "file": 'foo_brain.nii.gz'}), # filename with suffix and working directory
                           ({"suffix": '_brain.mat', "change_ext": False}, {"file": 'foo_brain.mat'}) # filename with suffix and no file extension change
                           ])
 def test_gen_fname(args, desired_name):

nipype/interfaces/fsl/tests/test_dti.py

@@ -70,7 +70,7 @@ def test_dtifit2(create_files_in_directory):
                                                                        filelist[1])
 
 
-@pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code") 
+@pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code")
 def test_randomise2():
 
     rand = fsl.Randomise()
@@ -79,7 +79,7 @@ def test_randomise2():
     assert rand.cmd == 'randomise'
 
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         rand.run()
 
     # .inputs based parameters setting
@@ -155,7 +155,7 @@ def test_Randomise_parallel():
     assert rand.cmd == 'randomise_parallel'
 
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         rand.run()
 
     # .inputs based parameters setting
@@ -269,7 +269,7 @@ def test_Vec_reg():
     assert vrg.cmd == 'vecreg'
 
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         vrg.run()
 
     # .inputs based parameters setting
@@ -330,7 +330,7 @@ def test_Find_the_biggest():
     assert fbg.cmd == 'find_the_biggest'
 
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         fbg.run()
 
     # .inputs based parameters setting
@@ -355,12 +355,12 @@ def test_tbss_skeleton(create_files_in_directory):
     skeletor = fsl.TractSkeleton()
 
     files, newdir = create_files_in_directory
-    
+
     # Test the underlying command
     assert skeletor.cmd == "tbss_skeleton"
 
     # It shouldn't run yet
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         skeletor.run()
 
     # Test the most basic way to use it
@@ -379,7 +379,7 @@ def test_tbss_skeleton(create_files_in_directory):
     bones = fsl.TractSkeleton(in_file="a.nii", project_data=True)
 
     # This should error
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         bones.run()
 
     # But we can set what we need

nipype/interfaces/fsl/tests/test_epi.py

@@ -47,7 +47,7 @@ def test_eddy_correct2(create_files_in_directory):
     assert eddy.cmd == 'eddy_correct'
 
     # test raising error with mandatory args absent
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         eddy.run()
 
     # .inputs based parameters setting

nipype/interfaces/fsl/tests/test_maths.py

@@ -49,7 +49,7 @@ def create_files_in_directory(request):
         nb.save(nb.Nifti1Image(img, np.eye(4), hdr),
                 os.path.join(testdir, f))
 
-    out_ext = Info.output_type_to_ext(Info.output_type()) 
+    out_ext = Info.output_type_to_ext(Info.output_type())
 
     def fin():
         if os.path.exists(testdir):
@@ -186,7 +186,7 @@ def test_meanimage(create_files_in_directory):
     meaner = fsl.MeanImage(in_file="a.nii")
     assert meaner.cmdline == "fslmaths a.nii -Tmean %s" % os.path.join(testdir, "a_mean%s" % out_ext)
 
-    
+
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 def test_stdimage(create_files_in_directory):
     files, testdir, out_ext = create_files_in_directory
@@ -209,7 +209,7 @@ def test_stdimage(create_files_in_directory):
     # Test the auto naming
     stder = fsl.StdImage(in_file="a.nii")
     #NOTE_dj, FAIL: this is failing (even the original version of the test with pytest)
-    #NOTE_dj: not sure if this should pass, it uses cmdline from interface.base.CommandLine 
+    #NOTE_dj: not sure if this should pass, it uses cmdline from interface.base.CommandLine
     #assert stder.cmdline == "fslmaths a.nii -Tstd %s"%os.path.join(testdir, "a_std.nii")
 
 
@@ -248,7 +248,7 @@ def test_smooth(create_files_in_directory):
     assert smoother.cmd == "fslmaths"
 
     # Test that smoothing kernel is mandatory
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         smoother.run()
 
     # Test smoothing kernels
@@ -276,7 +276,7 @@ def test_mask(create_files_in_directory):
     assert masker.cmd == "fslmaths"
 
     # Test that the mask image is mandatory
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         masker.run()
 
     # Test setting the mask image
@@ -299,7 +299,7 @@ def test_dilation(create_files_in_directory):
     assert diller.cmd == "fslmaths"
 
     # Test that the dilation operation is mandatory
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         diller.run()
 
     # Test the different dilation operations
@@ -361,7 +361,7 @@ def test_spatial_filter(create_files_in_directory):
     assert filter.cmd == "fslmaths"
 
     # Test that it fails without an operation
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         filter.run()
 
     # Test the different operations
@@ -385,7 +385,7 @@ def test_unarymaths(create_files_in_directory):
     assert maths.cmd == "fslmaths"
 
     # Test that it fails without an operation
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         maths.run()
 
     # Test the different operations
@@ -488,4 +488,4 @@ def test_tempfilt(create_files_in_directory):
         "fslmaths a.nii -bptf 64.000000 -1.000000 %s" % os.path.join(testdir, "a_filt%s" % out_ext)
 
 
-            
+

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -30,7 +30,7 @@ def setup_infile(request):
     tmp_dir = tempfile.mkdtemp()
     tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
     open(tmp_infile, 'w')
-    
+
     def fin():
         shutil.rmtree(tmp_dir)
 
@@ -50,7 +50,7 @@ def test_bet(setup_infile):
     assert better.cmd == 'bet'
 
     # Test raising error with mandatory args absent
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         better.run()
 
     # Test generated outfile name
@@ -68,7 +68,7 @@ def test_bet(setup_infile):
     # infile foo.nii doesn't exist
     def func():
         better.run(in_file='foo2.nii', out_file='bar.nii')
-    with pytest.raises(TraitError): 
+    with pytest.raises(TraitError):
         func()
 
     # Our options and some test values for them
@@ -100,7 +100,7 @@ def func():
         better.inputs.in_file = tmp_infile
         realcmd = ' '.join([better.cmd, tmp_infile, outpath, settings[0]])
         assert better.cmdline == realcmd
-    
+
 # test fast
 
 
@@ -196,7 +196,7 @@ def setup_flirt(request):
     tmpdir = tempfile.mkdtemp()
     _, infile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
     _, reffile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
-    
+
     def teardown_flirt():
         shutil.rmtree(tmpdir)
 
@@ -234,11 +234,11 @@ def test_flirt(setup_flirt):
 
     flirter = fsl.FLIRT()
     # infile not specified
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         flirter.run()
     flirter.inputs.in_file = infile
     # reference not specified
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         flirter.run()
     flirter.inputs.reference = reffile
     # Generate outfile and outmatrix
@@ -415,7 +415,7 @@ def test_fnirt(setup_flirt):
 
     # Test ValueError is raised when missing mandatory args
     fnirt = fsl.FNIRT()
-    with pytest.raises(ValueError): 
+    with pytest.raises(ValueError):
         fnirt.run()
     fnirt.inputs.in_file = infile
     fnirt.inputs.ref_file = reffile
@@ -507,7 +507,7 @@ def test_applywarp(setup_flirt):
                                         settings[0])
         assert awarp.cmdline == realcmd
 
-   
+
 @pytest.fixture(scope="module")
 def setup_fugue(request):
     import nibabel as nb
@@ -528,7 +528,7 @@ def teardown_fugue():
 
 @pytest.mark.skipif(no_fsl(), reason="fsl is not installed")
 @pytest.mark.parametrize("attr, out_file", [
-        ({"save_unmasked_fmap":True, "fmap_in_file":"infile", "mask_file":"infile", "output_type":"NIFTI_GZ"}, 
+        ({"save_unmasked_fmap":True, "fmap_in_file":"infile", "mask_file":"infile", "output_type":"NIFTI_GZ"},
          'fmap_out_file'),
         ({"save_unmasked_shift":True, "fmap_in_file":"infile", "dwell_time":1.e-3, "mask_file":"infile", "output_type": "NIFTI_GZ"},
          "shift_out_file"),