Merge pull request #836 from DimitriPapadopoulos/pyupgrade

STY: Use f-strings where possible

Author: effigies

niworkflows/anat/ants.py

@@ -716,15 +716,11 @@ def init_atropos_wf(
     me_7_2 = pe.Node(ImageMath(operation='ME', op2='5'), name='22_me_7_2')
 
     # De-pad
-    depad_mask = pe.Node(
-        ImageMath(operation='PadImage', op2='-%d' % padding), name='23_depad_mask'
-    )
-    depad_segm = pe.Node(
-        ImageMath(operation='PadImage', op2='-%d' % padding), name='24_depad_segm'
-    )
-    depad_gm = pe.Node(ImageMath(operation='PadImage', op2='-%d' % padding), name='25_depad_gm')
-    depad_wm = pe.Node(ImageMath(operation='PadImage', op2='-%d' % padding), name='26_depad_wm')
-    depad_csf = pe.Node(ImageMath(operation='PadImage', op2='-%d' % padding), name='27_depad_csf')
+    depad_mask = pe.Node(ImageMath(operation='PadImage', op2=f'-{padding}'), name='23_depad_mask')
+    depad_segm = pe.Node(ImageMath(operation='PadImage', op2=f'-{padding}'), name='24_depad_segm')
+    depad_gm = pe.Node(ImageMath(operation='PadImage', op2=f'-{padding}'), name='25_depad_gm')
+    depad_wm = pe.Node(ImageMath(operation='PadImage', op2=f'-{padding}'), name='26_depad_wm')
+    depad_csf = pe.Node(ImageMath(operation='PadImage', op2=f'-{padding}'), name='27_depad_csf')
 
     msk_conform = pe.Node(niu.Function(function=_conform_mask), name='msk_conform')
     merge_tpms = pe.Node(niu.Merge(in_segmentation_model[0]), name='merge_tpms')
@@ -1052,7 +1048,7 @@ def _select_labels(in_segm, labels):
     for label in labels:
         newnii = nii.__class__(np.uint8(label_data == label), nii.affine, nii.header)
         newnii.set_data_dtype('uint8')
-        out_file = fname_presuffix(in_segm, suffix='_class-%02d' % label, newpath=cwd)
+        out_file = fname_presuffix(in_segm, suffix=f'_class-{label:02d}', newpath=cwd)
         newnii.to_filename(out_file)
         out_files.append(out_file)
     return out_files

niworkflows/interfaces/itk.py

@@ -182,7 +182,7 @@ def _applytfms(args):
 
     in_file, in_xform, ifargs, index, newpath = args
     out_file = fname_presuffix(
-        in_file, suffix='_xform-%05d' % index, newpath=newpath, use_ext=True
+        in_file, suffix=f'_xform-{index:05d}', newpath=newpath, use_ext=True
     )
 
     copy_dtype = ifargs.pop('copy_dtype', False)
@@ -244,19 +244,19 @@ def _arrange_xfms(transforms, num_files, tmp_folder):
 
         if nxforms != num_files:
             raise RuntimeError(
-                'Number of transforms (%d) found in the ITK file does not match'
-                ' the number of input image files (%d).' % (nxforms, num_files)
+                f'Number of transforms ({nxforms}) found in the ITK file does not'
+                f' match the number of input image files ({num_files}).'
             )
 
         # At this point splitting transforms will be necessary, generate a base name
         out_base = fname_presuffix(
-            tf_file, suffix='_pos-%03d_xfm-{:05d}' % i, newpath=tmp_folder.name
+            tf_file, suffix=f'_pos-{i:03d}_xfm-{{:05d}}', newpath=tmp_folder.name
         ).format
         # Split combined ITK transforms file
         split_xfms = []
         for xform_i in range(nxforms):
             # Find start token to extract
-            startidx = tfdata.index('#Transform %d' % xform_i)
+            startidx = tfdata.index(f'#Transform {xform_i}')
             next_xform = base_xform + tfdata[startidx + 1 : startidx + 4] + ['']
             xfm_file = out_base(xform_i)
             with open(xfm_file, 'w') as out_xfm:

niworkflows/interfaces/norm.py

@@ -222,7 +222,7 @@ def _run_interface(self, runtime):
             if interface_result.runtime.returncode != 0:
                 NIWORKFLOWS_LOG.warning('Retry #%d failed.', self.retry)
                 # Save outputs (if available)
-                term_out = _write_outputs(interface_result.runtime, '.nipype-%04d' % self.retry)
+                term_out = _write_outputs(interface_result.runtime, f'.nipype-{self.retry:04d}')
                 if term_out:
                     NIWORKFLOWS_LOG.warning('Log of failed retry saved (%s).', ', '.join(term_out))
             else:
@@ -235,9 +235,7 @@ def _run_interface(self, runtime):
             self.retry += 1
 
         # If all tries fail, raise an error.
-        raise RuntimeError(
-            'Robust spatial normalization failed after %d retries.' % (self.retry - 1)
-        )
+        raise RuntimeError(f'Robust spatial normalization failed after {self.retry - 1} retries.')
 
     def _get_ants_args(self):
         args = {

niworkflows/interfaces/tests/test_images.py

@@ -60,13 +60,13 @@ def test_signal_extraction_equivalence(tmp_path, nvols, nmasks, ext, factor):
     se1 = nl.SignalExtraction(
         in_file=img_fname,
         label_files=masks_fname,
-        class_labels=['a%d' % i for i in range(nmasks)],
+        class_labels=[f'a{i}' for i in range(nmasks)],
         out_file=nlsignals,
     )
     se2 = im.SignalExtraction(
         in_file=img_fname,
         label_files=masks_fname,
-        class_labels=['a%d' % i for i in range(nmasks)],
+        class_labels=[f'a{i}' for i in range(nmasks)],
         out_file=imsignals,
     )
 

niworkflows/interfaces/tests/test_itk.py

@@ -52,7 +52,7 @@ def test_applytfms(tmpdir, ext, copy_dtype, in_dtype):
     args = (in_file, in_xform, ifargs, 0, str(tmpdir))
     out_file, cmdline = _applytfms(args)
 
-    assert out_file == str(tmpdir / ('src_xform-%05d%s' % (0, ext)))
+    assert out_file == str(tmpdir / (f'src_xform-00000{ext}'))
 
     out_nii = nb.load(out_file)
     assert np.allclose(nii.affine, out_nii.affine)

niworkflows/reports/core.py

@@ -537,7 +537,7 @@ def generate_reports(
 
         logger = logging.getLogger('cli')
         error_list = ', '.join(
-            '%s (%d)' % (subid, err) for subid, err in zip(subject_list, report_errors) if err
+            f'{subid} ({err})' for subid, err in zip(subject_list, report_errors) if err
         )
         logger.error(
             'Preprocessing did not finish successfully. Errors occurred while processing '

niworkflows/tests/test_segmentation.py

@@ -129,7 +129,7 @@ def test_ROIsPlot2(tmp_path):
     for i in range(1, 5):
         seg = np.zeros_like(newdata, dtype='uint8')
         seg[(newdata > 0) & (newdata <= i)] = 1
-        out_file = str(tmp_path / ('segments%02d.nii.gz' % i))
+        out_file = str(tmp_path / f'segments{i:02d}.nii.gz')
         nb.Nifti1Image(seg, im.affine, hdr).to_filename(out_file)
         out_files.append(out_file)
     roi_rpt = ROIsPlot(

niworkflows/tests/test_utils.py

@@ -89,6 +89,6 @@ def test_compression(tmp_path):
     size = int(os.stat(uncompressed).st_size)
     size_compress = int(os.stat(compressed).st_size)
     assert size >= size_compress, (
-        'The uncompressed report is smaller (%d)'
-        'than the compressed report (%d)' % (size, size_compress)
+        f'The uncompressed report is smaller ({size})'
+        f'than the compressed report ({size_compress})'
     )