FIX: Use raw strings for regular expressions

Author: effigies

nipype/interfaces/afni/utils.py

@@ -213,9 +213,9 @@ class Autobox(AFNICommand):
     def aggregate_outputs(self, runtime=None, needed_outputs=None):
         outputs = super(Autobox, self).aggregate_outputs(
             runtime, needed_outputs)
-        pattern = 'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+)  '\
-                  'y=(?P<y_min>-?\d+)\.\.(?P<y_max>-?\d+)  '\
-                  'z=(?P<z_min>-?\d+)\.\.(?P<z_max>-?\d+)'
+        pattern = r'x=(?P<x_min>-?\d+)\.\.(?P<x_max>-?\d+)  '\
+                  r'y=(?P<y_min>-?\d+)\.\.(?P<y_max>-?\d+)  '\
+                  r'z=(?P<z_min>-?\d+)\.\.(?P<z_max>-?\d+)'
         for line in runtime.stderr.split('\n'):
             m = re.search(pattern, line)
             if m:

nipype/interfaces/diffusion_toolkit/dti.py

@@ -94,7 +94,7 @@ class DTIRecon(CommandLine):
     def _create_gradient_matrix(self, bvecs_file, bvals_file):
         _gradient_matrix_file = 'gradient_matrix.txt'
         with open(bvals_file) as fbvals:
-            bvals = [val for val in re.split('\s+', fbvals.readline().strip())]
+            bvals = [val for val in re.split(r'\s+', fbvals.readline().strip())]
         with open(bvecs_file) as fbvecs:
           bvecs_x = fbvecs.readline().split()
           bvecs_y = fbvecs.readline().split()

nipype/interfaces/fsl/utils.py

@@ -858,18 +858,18 @@ def _run_interface(self, runtime):
         runtime = super(AvScale, self)._run_interface(runtime)
 
         expr = re.compile(
-            'Rotation\ &\ Translation\ Matrix:\n(?P<rot_tran_mat>[0-9\.\ \n-]+)[\s\n]*'
-            '(Rotation\ Angles\ \(x,y,z\)\ \[rads\]\ =\ (?P<rot_angles>[0-9\.\ -]+))?[\s\n]*'
-            '(Translations\ \(x,y,z\)\ \[mm\]\ =\ (?P<translations>[0-9\.\ -]+))?[\s\n]*'
-            'Scales\ \(x,y,z\)\ =\ (?P<scales>[0-9\.\ -]+)[\s\n]*'
-            'Skews\ \(xy,xz,yz\)\ =\ (?P<skews>[0-9\.\ -]+)[\s\n]*'
-            'Average\ scaling\ =\ (?P<avg_scaling>[0-9\.-]+)[\s\n]*'
-            'Determinant\ =\ (?P<determinant>[0-9\.-]+)[\s\n]*'
-            'Left-Right\ orientation:\ (?P<lr_orientation>[A-Za-z]+)[\s\n]*'
-            'Forward\ half\ transform\ =[\s]*\n'
-            '(?P<fwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*'
-            'Backward\ half\ transform\ =[\s]*\n'
-            '(?P<bwd_half_xfm>[0-9\.\ \n-]+)[\s\n]*')
+            r'Rotation & Translation Matrix:\n(?P<rot_tran_mat>[0-9\. \n-]+)[\s\n]*'
+            r'(Rotation Angles \(x,y,z\) \[rads\] = (?P<rot_angles>[0-9\. -]+))?[\s\n]*'
+            r'(Translations \(x,y,z\) \[mm\] = (?P<translations>[0-9\. -]+))?[\s\n]*'
+            r'Scales \(x,y,z\) = (?P<scales>[0-9\. -]+)[\s\n]*'
+            r'Skews \(xy,xz,yz\) = (?P<skews>[0-9\. -]+)[\s\n]*'
+            r'Average scaling = (?P<avg_scaling>[0-9\.-]+)[\s\n]*'
+            r'Determinant = (?P<determinant>[0-9\.-]+)[\s\n]*'
+            r'Left-Right orientation: (?P<lr_orientation>[A-Za-z]+)[\s\n]*'
+            r'Forward half transform =[\s]*\n'
+            r'(?P<fwd_half_xfm>[0-9\. \n-]+)[\s\n]*'
+            r'Backward half transform =[\s]*\n'
+            r'(?P<bwd_half_xfm>[0-9\. \n-]+)[\s\n]*')
         out = expr.search(runtime.stdout).groupdict()
         outputs = {}
         outputs['rotation_translation_matrix'] = [[

nipype/interfaces/image.py

@@ -43,8 +43,8 @@ class Rescale(SimpleInterface):
     Examples
     --------
 
-    To use a high-resolution T1w image as a registration target for a T2\*
-    image, it may be useful to invert the T1w image and rescale to the T2\*
+    To use a high-resolution T1w image as a registration target for a T2\\*
+    image, it may be useful to invert the T1w image and rescale to the T2\\*
     range.
     Using the 1st and 99th percentiles may reduce the impact of outlier
     voxels.

nipype/interfaces/io.py

@@ -1466,7 +1466,7 @@ class DataFinder(IOBase):
     >>> from nipype.interfaces.io import DataFinder
     >>> df = DataFinder()
     >>> df.inputs.root_paths = '.'
-    >>> df.inputs.match_regex = '.+/(?P<series_dir>.+(qT1|ep2d_fid_T1).+)/(?P<basename>.+)\.nii.gz'
+    >>> df.inputs.match_regex = r'.+/(?P<series_dir>.+(qT1|ep2d_fid_T1).+)/(?P<basename>.+)\.nii.gz'
     >>> result = df.run() # doctest: +SKIP
     >>> result.outputs.out_paths  # doctest: +SKIP
     ['./027-ep2d_fid_T1_Gd4/acquisition.nii.gz',

nipype/interfaces/tests/test_io.py

@@ -524,7 +524,7 @@ def test_datafinder_unpack(tmpdir):
 
     df = nio.DataFinder()
     df.inputs.root_paths = outdir
-    df.inputs.match_regex = '.+/(?P<basename>.+)\.txt'
+    df.inputs.match_regex = rb'.+/(?P<basename>.+)\.txt'
     df.inputs.unpack_single = True
     result = df.run()
     print(result.outputs.out_paths)

nipype/interfaces/utility/base.py

@@ -254,7 +254,7 @@ class Rename(SimpleInterface, IOBase):
 
     >>> rename3 = Rename(format_string="%(subject_id)s_%(seq)s_run%(run)02d.nii")
     >>> rename3.inputs.in_file = os.path.join(datadir, "func_epi_1_1.nii")
-    >>> rename3.inputs.parse_string = "func_(?P<seq>\w*)_.*"
+    >>> rename3.inputs.parse_string = r"func_(?P<seq>\w*)_.*"
     >>> rename3.inputs.subject_id = "subj_201"
     >>> rename3.inputs.run = 2
     >>> res = rename3.run()          # doctest: +SKIP