STY: Old formatting to f-strings (PEP-498)

bin/nib-dicomfs

@@ -12,4 +12,4 @@
 from nibabel.cmdline.dicomfs import main
 
 if __name__ == '__main__':
-    main()
+    main()

doc/source/conf.py

@@ -92,7 +92,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2020, %(maintainer)s <%(author_email)s>' % metadata
+copyright = f"2006-2020, {metadata['maintainer']} <{metadata['author_email']}>"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -206,7 +206,8 @@
 #html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'index': ['localtoc.html', 'relations.html', 'sourcelink.html', 'indexsidebar.html', 'searchbox.html', 'reggie.html']}
+html_sidebars = {'index': ['localtoc.html', 'relations.html', 'sourcelink.html',
+                           'indexsidebar.html', 'searchbox.html', 'reggie.html']}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.

doc/source/devel/register_me.py

@@ -40,7 +40,7 @@ def main():
     dsource.set(name, version, OUR_PATH)
     dsource.write(file(ini_fname, 'wt'))
 
-    print('Registered package %s, %s to %s' % (name, version, ini_fname))
+    print(f'Registered package {name}, {version} to {ini_fname}')
 
 
 if __name__ == '__main__':

doc/tools/apigen.py

@@ -342,8 +342,7 @@ def _survives_exclude(self, matchstr, match_type):
         elif match_type == 'package':
             patterns = self.package_skip_patterns
         else:
-            raise ValueError('Cannot interpret match type "%s"'
-                             % match_type)
+            raise ValueError(f'Cannot interpret match type "{match_type}"')
         # Match to URI without package name
         L = len(self.package_name)
         if matchstr[:L] == self.package_name:
@@ -424,7 +423,7 @@ def write_modules_api(self, modules, outdir):
         written_modules = []
 
         for ulm, mods in module_by_ulm.items():
-            print("Generating docs for %s:" % ulm)
+            print(f"Generating docs for {ulm}:")
             document_head = []
             document_body = []
 
@@ -505,5 +504,5 @@ def write_index(self, outdir, froot='gen', relative_to=None):
         w("=" * len(title) + "\n\n")
         w('.. toctree::\n\n')
         for f in self.written_modules:
-            w('   %s\n' % os.path.join(relpath, f))
+            w(f'   {os.path.join(relpath, f)}\n')
         idx.close()

doc/tools/build_modref_templates.py

@@ -18,7 +18,7 @@
 
 
 def abort(error):
-    print('*WARNING* API documentation not generated: %s' % error)
+    print(f'*WARNING* API documentation not generated: {error}')
     exit(1)
 
 

nibabel/_version.py

@@ -87,20 +87,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
             if e.errno == errno.ENOENT:
                 continue
             if verbose:
-                print("unable to run %s" % dispcmd)
+                print(f"unable to run {dispcmd}")
                 print(e)
             return None, None
     else:
         if verbose:
-            print("unable to find command, tried %s" % (commands,))
+            print(f"unable to find command, tried {commands}")
         return None, None
     stdout = p.communicate()[0].strip()
     if sys.version_info[0] >= 3:
         stdout = stdout.decode()
     if p.returncode != 0:
         if verbose:
-            print("unable to run %s (error)" % dispcmd)
-            print("stdout was %s" % stdout)
+            print(f"unable to run {dispcmd} (error)")
+            print(f"stdout was {stdout}")
         return None, p.returncode
     return stdout, p.returncode
 
@@ -125,8 +125,8 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
             root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print("Tried directories %s but none started with prefix %s" %
-              (str(rootdirs), parentdir_prefix))
+        print(f"Tried directories {str(rootdirs)} but "
+              f"none started with prefix {parentdir_prefix}")
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
@@ -201,9 +201,9 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # "stabilization", as well as "HEAD" and "master".
         tags = set([r for r in refs if re.search(r'\d', r)])
         if verbose:
-            print("discarding '%s', no digits" % ",".join(refs - tags))
+            print(f"discarding '{','.join(refs - tags)}', no digits")
     if verbose:
-        print("likely tags: %s" % ",".join(sorted(tags)))
+        print(f"likely tags: {','.join(sorted(tags))}")
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
@@ -214,7 +214,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
             if not re.match(r'\d', r):
                 continue
             if verbose:
-                print("picking %s" % r)
+                print(f"picking {r}")
             return {"version": r,
                     "full-revisionid": keywords["full"].strip(),
                     "dirty": False, "error": None,
@@ -243,14 +243,14 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
                           hide_stderr=True)
     if rc != 0:
         if verbose:
-            print("Directory %s not under git control" % root)
+            print(f"Directory {root} not under git control")
         raise NotThisMethod("'git rev-parse --git-dir' returned error")
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
     describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
                                           "--always", "--long",
-                                          "--match", "%s*" % tag_prefix],
+                                          "--match", f"{tag_prefix}*"],
                                    cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
@@ -283,18 +283,17 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
             # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = ("unable to parse git-describe output: '%s'"
-                               % describe_out)
+            pieces["error"] = f"unable to parse git-describe output: '{describe_out}'"
             return pieces
 
         # tag
         full_tag = mo.group(1)
         if not full_tag.startswith(tag_prefix):
             if verbose:
-                fmt = "tag '%s' doesn't start with prefix '%s'"
-                print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
-                               % (full_tag, tag_prefix))
+                txt = f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'"
+                print(txt)
+            pieces["error"] = (f"tag '{full_tag}' doesn't start with prefix "
+                               f"'{tag_prefix}'")
             return pieces
         pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
@@ -384,13 +383,13 @@ def render_pep440_post(pieces):
             if pieces["dirty"]:
                 rendered += ".dev0"
             rendered += plus_or_dot(pieces)
-            rendered += "g%s" % pieces["short"]
+            rendered += f"g{pieces['short']}"
     else:
         # exception #1
         rendered = "0.post%d" % pieces["distance"]
         if pieces["dirty"]:
             rendered += ".dev0"
-        rendered += "+g%s" % pieces["short"]
+        rendered += f"+g{pieces['short']}"
     return rendered
 
 
@@ -481,7 +480,7 @@ def render(pieces, style):
     elif style == "git-describe-long":
         rendered = render_git_describe_long(pieces)
     else:
-        raise ValueError("unknown style '%s'" % style)
+        raise ValueError(f"unknown style '{style}'")
 
     return {"version": rendered, "full-revisionid": pieces["long"],
             "dirty": pieces["dirty"], "error": None,

nibabel/analyze.py

@@ -394,11 +394,9 @@ def from_header(klass, header=None, check=True):
         try:
             obj.set_data_dtype(orig_code)
         except HeaderDataError:
-            raise HeaderDataError('Input header %s has datatype %s but '
-                                  'output header %s does not support it'
-                                  % (header.__class__,
-                                     header.get_value_label('datatype'),
-                                     klass))
+            raise HeaderDataError(f"Input header {header.__class__} has "
+                                  f"datatype {header.get_value_label('datatype')} "
+                                  f"but output header {klass} does not support it")
         obj.set_data_dtype(header.get_data_dtype())
         obj.set_data_shape(header.get_data_shape())
         obj.set_zooms(header.get_zooms())
@@ -571,16 +569,16 @@ def set_data_dtype(self, datatype):
                 dt = np.dtype(dt)
             except TypeError:
                 raise HeaderDataError(
-                    'data dtype "{0}" not recognized'.format(datatype))
+                    f'data dtype "{datatype}" not recognized')
             if dt not in self._data_type_codes:
                 raise HeaderDataError(
-                    'data dtype "{0}" not supported'.format(datatype))
+                    f'data dtype "{datatype}" not supported')
         code = self._data_type_codes[dt]
         dtype = self._data_type_codes.dtype[code]
         # test for void, being careful of user-defined types
         if dtype.type is np.void and not dtype.fields:
             raise HeaderDataError(
-                'data dtype "{0}" known but not supported'.format(datatype))
+                f'data dtype "{datatype}" known but not supported')
         self._structarr['datatype'] = code
         self._structarr['bitpix'] = dtype.itemsize * 8
 
@@ -632,8 +630,7 @@ def set_data_shape(self, shape):
             values_fit = np.all(dims[1:ndims + 1] == shape)
         # Error if we did not succeed setting dimensions
         if not values_fit:
-            raise HeaderDataError('shape %s does not fit in dim datatype' %
-                                  (shape,))
+            raise HeaderDataError(f'shape {shape} does not fit in dim datatype')
         self._structarr['pixdim'][ndims + 1:] = 1.0
 
     def get_base_affine(self):

nibabel/arrayproxy.py

@@ -255,8 +255,8 @@ def _should_keep_file_open(self, file_like, keep_file_open):
         if keep_file_open is None:
             keep_file_open = KEEP_FILE_OPEN_DEFAULT
             if keep_file_open not in (True, False):
-                raise ValueError("nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT must be boolean. "
-                                 "Found: {}".format(keep_file_open))
+                raise ValueError(f"nibabel.arrayproxy.KEEP_FILE_OPEN_DEFAULT "
+                                 f"must be boolean. Found: {keep_file_open}")
         elif keep_file_open not in (True, False):
             raise ValueError('keep_file_open must be one of {None, True, False}')
 
@@ -412,8 +412,8 @@ def reshape(self, shape):
             shape = tuple(unknown_size if e == -1 else e for e in shape)
 
         if np.prod(shape) != size:
-            raise ValueError("cannot reshape array of size {:d} into shape "
-                             "{!s}".format(size, shape))
+            raise ValueError(f"cannot reshape array of size {size:d} "
+                             f"into shape {shape!s}")
         return self.__class__(file_like=self.file_like,
                               spec=(shape, self._dtype, self._offset,
                                     self._slope, self._inter),

nibabel/batteryrunners.py

@@ -291,8 +291,7 @@ def write_raise(self, stream, error_level=40, log_level=30):
            write the report to `stream`, otherwise we write nothing.
         """
         if self.problem_level >= log_level:
-            stream.write('Level %s: %s\n' %
-                         (self.problem_level, self.message))
+            stream.write(f'Level {self.problem_level}: {self.message}\n')
         if self.problem_level and self.problem_level >= error_level:
             if self.error:
                 raise self.error(self.problem_msg)

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -96,12 +96,12 @@ def fmt_sliceobj(sliceobj):
                 slcstr.append(s)
             else:
                 slcstr.append(str(int(s * SHAPE[i])))
-        return '[{}]'.format(', '.join(slcstr))
+        return f"[{', '.join(slcstr)}]"
 
     with InTemporaryDirectory():
 
-        print('Generating test data... ({} MB)'.format(
-            int(round(np.prod(SHAPE) * 4 / 1048576.))))
+        print(f'Generating test data... '
+              f'({int(round(np.prod(SHAPE) * 4 / 1048576.0))} MB)')
 
         data = np.array(np.random.random(SHAPE), dtype=np.float32)
 
@@ -133,8 +133,7 @@ def fmt_sliceobj(sliceobj):
             have_igzip, keep_open, sliceobj = test
             seed = seeds[SLICEOBJS.index(sliceobj)]
 
-            print('Running test {} of {} ({})...'.format(
-                ti + 1, len(tests), label))
+            print(f'Running test {ti + 1} of {len(tests)} ({label})...')
 
             # load uncompressed and compressed versions of the image
             img = nib.load(testfile, keep_file_open=keep_open)
@@ -181,8 +180,8 @@ def testfunc():
         data[:, 2] = np.nan
     data[:, 3] = [r[5] - r[6] for r in results]
 
-    rowlbls = ['Type {}, keep_open {}, slice {}'.format(
-        r[0], r[1], fmt_sliceobj(r[2])) for r in results]
+    rowlbls = [(f'Type {r[0]}, keep_open {r[1]}, '
+                f'slice {fmt_sliceobj(r[2])}') for r in results]
     collbls = ['Time', 'Baseline time', 'Time ratio', 'Memory deviation']
 
     print(rst_table(data, rowlbls, collbls))

nibabel/benchmarks/bench_fileslice.py

@@ -20,7 +20,7 @@
 from ..tmpdirs import InTemporaryDirectory
 
 SHAPE = (64, 64, 32, 100)
-ROW_NAMES = ['axis {0}, len {1}'.format(i, SHAPE[i])
+ROW_NAMES = [f'axis {i}, len {SHAPE[i]}'
              for i in range(len(SHAPE))]
 COL_NAMES = ['mid int',
              'step 1',
@@ -79,7 +79,7 @@ def my_table(title, times, base):
         print()
         print(rst_table(times, ROW_NAMES, COL_NAMES, title,
                         val_fmt='{0[0]:3.2f} ({0[1]:3.2f})'))
-        print('Base time: {0:3.2f}'.format(base))
+        print(f'Base time: {base:3.2f}')
     if bytes:
         fobj = BytesIO()
         times, base = run_slices(fobj, repeat)

nibabel/benchmarks/bench_streamlines.py

@@ -44,16 +44,14 @@ def bench_load_trk():
         streamlines_old = [d[0] - 0.5
                            for d in tv.read(trk_file, points_space="rasmm")[0]]
         mtime_old = measure('tv.read(trk_file, points_space="rasmm")', repeat)
-        print("Old: Loaded {:,} streamlines in {:6.2f}".format(NB_STREAMLINES,
-                                                               mtime_old))
+        print(f"Old: Loaded {NB_STREAMLINES:,} streamlines in {mtime_old:6.2f}")
 
         trk = nib.streamlines.load(trk_file, lazy_load=False)
         streamlines_new = trk.streamlines
         mtime_new = measure('nib.streamlines.load(trk_file, lazy_load=False)',
                             repeat)
-        print("\nNew: Loaded {:,} streamlines in {:6.2}".format(NB_STREAMLINES,
-                                                                mtime_new))
-        print("Speedup of {:.2f}".format(mtime_old / mtime_new))
+        print(f"\nNew: Loaded {NB_STREAMLINES:,} streamlines in {mtime_new:6.2}")
+        print(f"Speedup of {mtime_old / mtime_new:.2f}")
         for s1, s2 in zip(streamlines_new, streamlines_old):
             assert_array_equal(s1, s2)
 
@@ -81,7 +79,7 @@ def bench_load_trk():
                             repeat)
         msg = "New: Loaded {:,} streamlines with scalars in {:6.2f}"
         print(msg.format(NB_STREAMLINES, mtime_new))
-        print("Speedup of {:2f}".format(mtime_old / mtime_new))
+        print(f"Speedup of {mtime_old / mtime_new:2f}")
         for s1, s2 in zip(scalars_new, scalars_old):
             assert_array_equal(s1, s2)
 

nibabel/benchmarks/butils.py

@@ -7,8 +7,6 @@
 def print_git_title(title):
     """ Prints title string with git hash if possible, and underline
     """
-    title = '{0} for git revision {1}'.format(
-        title,
-        get_info()['commit_hash'])
+    title = f"{title} for git revision {get_info()['commit_hash']}"
     print(title)
     print('-' * len(title))

nibabel/brikhead.py

@@ -114,23 +114,21 @@ def _unpack_var(var):
     TEMPLATE_SPACE ORIG
     """
 
-    err_msg = ('Please check HEAD file to ensure it is AFNI compliant. '
-               'Offending attribute:\n%s' % var)
+    err_msg = (f'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:
-        raise AFNIHeaderError('Invalid attribute type entry in HEAD file. '
-                              '%s' % err_msg)
+        raise AFNIHeaderError(f'Invalid attribute type entry in HEAD file. {err_msg}')
     if len(aname) != 1:
-        raise AFNIHeaderError('Invalid attribute name entry in HEAD file. '
-                              '%s' % err_msg)
+        raise AFNIHeaderError(f'Invalid attribute name entry in HEAD file. {err_msg}')
     atype = _attr_dic.get(atype[0], str)
     attr = ' '.join(var.strip().splitlines()[3:])
     if atype is not str:
         try:
             attr = [atype(f) for f in attr.split()]
         except ValueError:
-            raise AFNIHeaderError('Failed to read variable from HEAD file due '
-                                  'to improper type casting. %s' % err_msg)
+            raise AFNIHeaderError(f'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
         # end with a tilde (NUL). These attributes CANNOT contain tildes (so