STY: Apply suggestions from code review

jond01 · effigies · web-flow · commit 092dc9b2375f · 2020-06-22T21:53:14.000+03:00
Co-authored-by: Chris Markiewicz &lt;effigies@gmail.com&gt;
diff --git a/nibabel/benchmarks/bench_arrayproxy_slicing.py b/nibabel/benchmarks/bench_arrayproxy_slicing.py
@@ -100,8 +100,7 @@ def fmt_sliceobj(sliceobj):
 
     with InTemporaryDirectory():
 
-        print(f'Generating test data... '
-              f'({int(round(np.prod(SHAPE) * 4 / 1048576.0))} MB)')
+        print(f'Generating test data... ({int(round(np.prod(SHAPE) * 4 / 1048576.0))} MB)')
 
         data = np.array(np.random.random(SHAPE), dtype=np.float32)
 
@@ -180,8 +179,7 @@ def testfunc():
         data[:, 2] = np.nan
     data[:, 3] = [r[5] - r[6] for r in results]
 
-    rowlbls = [(f'Type {r[0]}, keep_open {r[1]}, '
-                f'slice {fmt_sliceobj(r[2])}') for r in results]
+    rowlbls = [f'Type {r[0]}, keep_open {r[1]}, slice {fmt_sliceobj(r[2])}' for r in results]
     collbls = ['Time', 'Baseline time', 'Time ratio', 'Memory deviation']
 
     print(rst_table(data, rowlbls, collbls))
diff --git a/nibabel/benchmarks/bench_fileslice.py b/nibabel/benchmarks/bench_fileslice.py
@@ -20,8 +20,7 @@
 from ..tmpdirs import InTemporaryDirectory
 
 SHAPE = (64, 64, 32, 100)
-ROW_NAMES = [f'axis {i}, len {SHAPE[i]}'
-             for i in range(len(SHAPE))]
+ROW_NAMES = [f'axis {i}, len {dim}' for i, dim in enumerate(SHAPE)]
 COL_NAMES = ['mid int',
              'step 1',
              'half step 1',
diff --git a/nibabel/brikhead.py b/nibabel/brikhead.py
@@ -114,7 +114,7 @@ def _unpack_var(var):
     TEMPLATE_SPACE ORIG
     """
 
-    err_msg = (f'Please check HEAD file to ensure it is AFNI compliant. '
+    err_msg = ('Please check HEAD file to ensure it is AFNI compliant. '
                f'Offending attribute:\n{var}')
     atype, aname = TYPE_RE.findall(var), NAME_RE.findall(var)
     if len(atype) != 1:
@@ -127,7 +127,7 @@ def _unpack_var(var):
         try:
             attr = [atype(f) for f in attr.split()]
         except ValueError:
-            raise AFNIHeaderError(f'Failed to read variable from HEAD file '
+            raise AFNIHeaderError('Failed to read variable from HEAD file '
                                   f'due to improper type casting. {err_msg}')
     else:
         # AFNI string attributes will always start with open single quote and
diff --git a/nibabel/casting.py b/nibabel/casting.py
@@ -296,8 +296,7 @@ def type_info(np_type):
                    maxexp=16384,
                    width=width)
     else:  # don't recognize the type
-        raise FloatingError(f'We had not expected long double '
-                            f'type {np_type} with info {info}')
+        raise FloatingError(f'We had not expected long double type {np_type} with info {info}')
     return ret
 
 
diff --git a/nibabel/cifti2/cifti2.py b/nibabel/cifti2/cifti2.py
@@ -291,8 +291,7 @@ def _to_xml_element(self):
                 v = _float_01(getattr(self, c_))
             except ValueError:
                 raise Cifti2HeaderError(
-                    f'Label invalid {c_} needs to be a '
-                    f'float between 0 and 1. and it is {v}'
+                    f'Label invalid {c_} needs to be a float between 0 and 1. and it is {v}'
                 )
 
         lab = xml.Element('Label')
diff --git a/nibabel/cifti2/cifti2_axes.py b/nibabel/cifti2/cifti2_axes.py
@@ -538,7 +538,7 @@ def to_cifti_brain_structure_name(name):
             proposed_name = f'CIFTI_STRUCTURE_{structure.upper()}_{orientation.upper()}'
         if proposed_name not in cifti2.CIFTI_BRAIN_STRUCTURES:
             raise ValueError(f'{name} was interpreted as {proposed_name}, which is not '
-                             f'a valid CIFTI brain structure')
+                             'a valid CIFTI brain structure')
         return proposed_name
 
     @property
@@ -650,7 +650,7 @@ def __add__(self, other):
         nvertices = dict(self.nvertices)
         for name, value in other.nvertices.items():
             if name in nvertices.keys() and nvertices[name] != value:
-                raise ValueError(f"Trying to concatenate two BrainModels with "
+                raise ValueError("Trying to concatenate two BrainModels with "
                                  f"inconsistent number of vertices for {name}")
             nvertices[name] = value
         return self.__class__(
@@ -804,7 +804,7 @@ def from_brain_models(cls, named_brain_models):
             for name, _, bm_part in bm.iter_structures():
                 if name in bm.nvertices.keys():
                     if name in nvertices.keys() and nvertices[name] != bm.nvertices[name]:
-                        raise ValueError(f"Got multiple conflicting number of "
+                        raise ValueError("Got multiple conflicting number of "
                                          f"vertices for surface structure {name}")
                     nvertices[name] = bm.nvertices[name]
                     vertices[name] = bm_part.vertex
@@ -967,7 +967,7 @@ def __add__(self, other):
         nvertices = dict(self.nvertices)
         for name, value in other.nvertices.items():
             if name in nvertices.keys() and nvertices[name] != value:
-                raise ValueError(f"Trying to concatenate two ParcelsAxis with "
+                raise ValueError("Trying to concatenate two ParcelsAxis with "
                                  f"inconsistent number of vertices for {name}")
             nvertices[name] = value
         return self.__class__(
diff --git a/nibabel/cmdline/ls.py b/nibabel/cmdline/ls.py
@@ -116,7 +116,7 @@ def proc_file(f, opts):
         else:
             row += ['']
     except Exception as e:
-        verbose(2, f"Failed to obtain qform or sform -- {str(e)}")
+        verbose(2, f"Failed to obtain qform or sform -- {e}")
         if isinstance(h, nib.AnalyzeHeader):
             row += ['']
         else:
@@ -136,7 +136,7 @@ def proc_file(f, opts):
                 # just # of elements
                 row += ["@l[%d]" % np.prod(d.shape)]
                 # stats
-                row += [len(d) and f'@l[{np.min(d):.2g}, {np.max(d):.2g}]' or '-']
+                row += [f'@l[{np.min(d):.2g}, {np.max(d):.2g}]' if len(d) else '-']
             if opts.counts:
                 items, inv = np.unique(d, return_inverse=True)
                 if len(items) > 1000 and not opts.all_counts:
@@ -146,7 +146,7 @@ def proc_file(f, opts):
                     counts = " ".join("%g:%d" % (i, f) for i, f in zip(items, freq))
                 row += ["@l" + counts]
         except IOError as e:
-            verbose(2, f"Failed to obtain stats/counts -- {str(e)}")
+            verbose(2, f"Failed to obtain stats/counts -- {e}")
             row += [_err()]
     return row
 
diff --git a/nibabel/cmdline/parrec2nii.py b/nibabel/cmdline/parrec2nii.py
@@ -136,7 +136,7 @@ def get_opt_parser():
 
 def verbose(msg, indent=0):
     if verbose.switch:
-        print(f"{' ' * indent}{msg}")
+        print(' ' * indent + msg)
 
 
 def error(msg, exit_code):
@@ -158,8 +158,7 @@ def proc_file(infile, opts):
     else:
         outfilename = basefilename + '.nii'
     if os.path.isfile(outfilename) and not opts.overwrite:
-        raise IOError(f'Output file "{outfilename}" exists, '
-                      f'use --overwrite to overwrite it')
+        raise IOError(f'Output file "{outfilename}" exists, use --overwrite to overwrite it')
 
     # load the PAR header and data
     scaling = 'dv' if opts.scaling == 'off' else opts.scaling
diff --git a/nibabel/cmdline/tck2trk.py b/nibabel/cmdline/tck2trk.py
@@ -41,9 +41,7 @@ def main():
         filename, _ = os.path.splitext(tractogram)
         output_filename = filename + '.trk'
         if os.path.isfile(output_filename) and not args.force:
-            msg = (f"Skipping existing file: '{output_filename}'. "
-                   f"Use -f to overwrite.")
-            print(msg)
+            print(f"Skipping existing file: '{output_filename}'. Use -f to overwrite.")
             continue
 
         # Build header using infos from the anatomical image.
diff --git a/nibabel/cmdline/trk2tck.py b/nibabel/cmdline/trk2tck.py
@@ -31,9 +31,7 @@ def main():
         filename, _ = os.path.splitext(tractogram)
         output_filename = filename + '.tck'
         if os.path.isfile(output_filename) and not args.force:
-            msg = (f"Skipping existing file: '{output_filename}'. "
-                   f"Use -f to overwrite.")
-            print(msg)
+            print(f"Skipping existing file: '{output_filename}'. Use -f to overwrite.")
             continue
 
         trk = nib.streamlines.load(tractogram)
diff --git a/nibabel/cmdline/utils.py b/nibabel/cmdline/utils.py
@@ -33,7 +33,7 @@ def verbose(thing, msg):
     """
     # TODO: consider using nibabel's logger
     if thing <= int(verbose_level):
-        print(f"{' ' * thing}{msg}")
+        print(' ' * thing + msg)
 
 
 def table2string(table, out=None):
diff --git a/nibabel/data.py b/nibabel/data.py
@@ -293,7 +293,7 @@ def make_datasource(pkg_def, **kwargs):
         pth = [pjoin(this_data_path, *names)
                for this_data_path in data_path]
         pkg_hint = pkg_def.get('install hint', DEFAULT_INSTALL_HINT)
-        msg = (f'{e}; Is it possible you have not installed a data package?')
+        msg = f'{e}; Is it possible you have not installed a data package?'
         if 'name' in pkg_def:
             msg += f"\n\nYou may need the package \"{pkg_def['name']}\""
         if pkg_hint is not None:
@@ -356,6 +356,5 @@ def datasource_or_bomber(pkg_def, **options):
         pkg_name = pkg_def['name']
     else:
         pkg_name = 'data at ' + unix_relpath
-    msg = (f"{pkg_name} is version {ds.version} but we need "
-           f"version >= {version}\n\n{pkg_hint}")
+    msg = f"{pkg_name} is version {ds.version} but we need version >= {version}\n\n{pkg_hint}"
     return Bomber(sys_relpath, DataError(msg))
diff --git a/nibabel/dft.py b/nibabel/dft.py
@@ -395,7 +395,7 @@ def _update_file(c, path, fname, studies, series, storage_instances):
     except AttributeError:
         study_comments = ''
     try:
-        logger.debug(f'        storage instance {str(do.SOPInstanceUID)}')
+        logger.debug(f'        storage instance {do.SOPInstanceUID}')
         if str(do.StudyInstanceUID) not in studies:
             query = """INSERT INTO study (uid,
                                           date,
@@ -444,7 +444,7 @@ def _update_file(c, path, fname, studies, series, storage_instances):
             c.execute(query, params)
             storage_instances.append(str(do.SOPInstanceUID))
     except AttributeError as data:
-        logger.debug(f'        {str(data)}')
+        logger.debug(f'        {data}')
         return None
     return str(do.SOPInstanceUID)
 
diff --git a/nibabel/ecat.py b/nibabel/ecat.py
@@ -425,8 +425,8 @@ def get_frame_order(mlist):
     valid_order = np.argsort(ids)
     if not all(valid_order == sorted(valid_order)):
         # raise UserWarning if Frames stored out of order
-        warnings.warn_explicit(f'Frames stored out of order;true order = {valid_order}\n'
-                               f'frames will be accessed in order STORED, NOT true order',
+        warnings.warn_explicit(f'Frames stored out of order; true order = {valid_order}\n'
+                               'frames will be accessed in order STORED, NOT true order',
                                UserWarning, 'ecat', 0)
     id_dict = {}
     for i in range(n_valid):
diff --git a/nibabel/filebasedimages.py b/nibabel/filebasedimages.py
@@ -34,7 +34,7 @@ def from_header(klass, header=None):
         # different field names
         if type(header) == klass:
             return header.copy()
-        raise NotImplementedError(f"Header class requires a conversion "
+        raise NotImplementedError("Header class requires a conversion "
                                   f"from {klass} to {type(header)}")
 
     @classmethod
diff --git a/nibabel/freesurfer/io.py b/nibabel/freesurfer/io.py
@@ -619,6 +619,6 @@ def _serialize_volume_info(volume_info):
             strings.append(f'{key} = {val[0]} {val[1]} {val[2]}\n'.encode('utf-8'))
         else:
             val = volume_info[key]
-            strings.append(f'{key.ljust(6)} = {val[0]:0.10g} {val[1]:0.10g} '
-                           f'{val[2]:0.10g}\n'.encode('utf-8'))
+            strings.append(
+                f'{key:6s} = {val[0]:.10g} {val[1]:.10g} {val[2]:.10g}\n'.encode('utf-8'))
     return b''.join(strings)
diff --git a/nibabel/freesurfer/mghformat.py b/nibabel/freesurfer/mghformat.py
@@ -278,12 +278,12 @@ def set_zooms(self, zooms):
         if len(zooms) > ndims:
             raise HeaderDataError('Expecting %d zoom values' % ndims)
         if np.any(zooms[:3] <= 0):
-            raise HeaderDataError(f'Spatial (first three) zooms must be '
-                                  f'positive; got {tuple(zooms[:3])!r}')
+            raise HeaderDataError('Spatial (first three) zooms must be positive; got '
+                                  f'{tuple(zooms[:3])}')
         hdr['delta'] = zooms[:3]
         if len(zooms) == 4:
             if zooms[3] < 0:
-                raise HeaderDataError(f'TR must be non-negative; got {zooms[3]!r}')
+                raise HeaderDataError(f'TR must be non-negative; got {zooms[3]}')
             hdr['tr'] = zooms[3]
 
     def get_data_shape(self):
diff --git a/nibabel/freesurfer/tests/test_io.py b/nibabel/freesurfer/tests/test_io.py
@@ -49,12 +49,12 @@ def _hash_file_content(fname):
 @freesurfer_test
 def test_geometry():
     """Test IO of .surf"""
-    surf_path = pjoin(data_path, "surf", f"{'lh'}.{'inflated'}")
+    surf_path = pjoin(data_path, "surf", "lh.inflated")
     coords, faces = read_geometry(surf_path)
     assert 0 == faces.min()
     assert coords.shape[0] == faces.max() + 1
 
-    surf_path = pjoin(data_path, "surf", f"{'lh'}.{'sphere'}")
+    surf_path = pjoin(data_path, "surf", "lh.sphere")
     coords, faces, volume_info, create_stamp = read_geometry(
         surf_path, read_metadata=True, read_stamp=True)
 
@@ -132,7 +132,7 @@ def test_quad_geometry():
 @freesurfer_test
 def test_morph_data():
     """Test IO of morphometry data file (eg. curvature)."""
-    curv_path = pjoin(data_path, "surf", f"{'lh'}.{'curv'}")
+    curv_path = pjoin(data_path, "surf", "lh.curv")
     curv = read_morph_data(curv_path)
     assert -1.0 < curv.min() < 0
     assert 0 < curv.max() < 1.0
@@ -170,7 +170,7 @@ def test_annot():
     """Test IO of .annot against freesurfer example data."""
     annots = ['aparc', 'aparc.a2005s']
     for a in annots:
-        annot_path = pjoin(data_path, "label", f"{'lh'}.{a}.annot")
+        annot_path = pjoin(data_path, "label", f"lh.{a}.annot")
         hash_ = _hash_file_content(annot_path)
 
         labels, ctab, names = read_annot(annot_path)
diff --git a/nibabel/funcs.py b/nibabel/funcs.py
@@ -139,8 +139,7 @@ def concat_images(images, check_affines=True, axis=None):
             raise ValueError(f'shape {img.shape} for image {i} not compatible with '
                              f'first image shape {shape0} with axis == {axis}')
         if check_affines and not np.all(img.affine == affine):
-            raise ValueError(f'Affine for image {i} does not match affine for '
-                             f'first image')
+            raise ValueError(f'Affine for image {i} does not match affine for first image')
         # Do not fill cache in image if it is empty
         out_data[i] = np.asanyarray(img.dataobj)
 
diff --git a/nibabel/gifti/gifti.py b/nibabel/gifti/gifti.py
@@ -486,7 +486,7 @@ def to_xml_open(self):
 \tExternalFileOffset="%d">\n"""
         di = ""
         for i, n in enumerate(self.dims):
-            di = di + f'\tDim{str(i)}="{str(n)}\"\n'
+            di = di + f'\tDim{i}="{n}"\n'
         return out % (intent_codes.niistring[self.intent],
                       data_type_codes.niistring[self.datatype],
                       array_index_order_codes.label[self.ind_ord],
diff --git a/nibabel/gifti/parse_gifti_fast.py b/nibabel/gifti/parse_gifti_fast.py
@@ -177,7 +177,7 @@ def StartElementHandler(self, name, attrs):
                     attrs["ArrayIndexingOrder"]]
             num_dim = int(attrs.get("Dimensionality", 0))
             for i in range(num_dim):
-                di = f"Dim{str(i)}"
+                di = f"Dim{i}"
                 if di in attrs:
                     self.da.dims.append(int(attrs[di]))
             # dimensionality has to correspond to the number of DimX given
diff --git a/nibabel/gifti/tests/test_parse_gifti_fast.py b/nibabel/gifti/tests/test_parse_gifti_fast.py
@@ -106,7 +106,7 @@ def assert_default_types(loaded):
             continue
         loadedtype = type(getattr(loaded, attr))
         assert loadedtype == defaulttype, (
-            f"Type mismatch for attribute: {attr} ({loadedtype!s} != {defaulttype!s})")
+            f"Type mismatch for attribute: {attr} ({loadedtype} != {defaulttype})")
 
 
 def test_default_types():
diff --git a/nibabel/keywordonly.py b/nibabel/keywordonly.py
@@ -19,8 +19,7 @@ def decorator(func):
         def wrapper(*args, **kwargs):
             if len(args) > n:
                 raise TypeError(
-                    f"{func.__name__} takes at most {n} positional "
-                    f"argument{'s' if n > 1 else ''}")
+                    f"{func.__name__} takes at most {n} positional argument{'s' if n > 1 else ''}")
             return func(*args, **kwargs)
         return wrapper
     return decorator
diff --git a/nibabel/nicom/dicomreaders.py b/nibabel/nicom/dicomreaders.py
@@ -97,8 +97,8 @@ def read_mosaic_dir(dicom_path,
             if check_is_dwi:
                 raise DicomReadError(
                     f'Could not find diffusion information reading file "{fname}";  '
-                    f'is it possible this is not a _raw_ diffusion directory? '
-                    f'Could it be a processed dataset like ADC etc?')
+                    'is it possible this is not a _raw_ diffusion directory? '
+                    'Could it be a processed dataset like ADC etc?')
             b = np.nan
             g = np.ones((3,)) + np.nan
         else:
diff --git a/nibabel/nifti1.py b/nibabel/nifti1.py
diff --git a/nibabel/openers.py b/nibabel/openers.py
diff --git a/nibabel/optpkg.py b/nibabel/optpkg.py
diff --git a/nibabel/orientations.py b/nibabel/orientations.py
diff --git a/nibabel/parrec.py b/nibabel/parrec.py
diff --git a/nibabel/spatialimages.py b/nibabel/spatialimages.py
diff --git a/tools/make_tarball.py b/tools/make_tarball.py

Original file line number	Diff line number	Diff line change
`@@ -291,8 +291,7 @@ def _to_xml_element(self):`
`291`	`291`	`v = _float_01(getattr(self, c_))`
`292`	`292`	`except ValueError:`
`293`	`293`	`raise Cifti2HeaderError(`
`294`		`- f'Label invalid {c_} needs to be a '`
`295`		`- f'float between 0 and 1. and it is {v}'`
	`294`	`+ f'Label invalid {c_} needs to be a float between 0 and 1. and it is {v}'`
`296`	`295`	`)`
`297`	`296`
`298`	`297`	`lab = xml.Element('Label')`