MNT: Apply pyupgrade suggestions

Author: DimitriPapadopoulos

doc/tools/apigen.py

@@ -42,7 +42,7 @@ def __init__(self,
                  module_skip_patterns=None,
                  other_defines=True
                  ):
-        """ Initialize package for parsing
+        r""" Initialize package for parsing
 
         Parameters
         ----------
@@ -358,7 +358,7 @@ def _survives_exclude(self, matchstr, match_type):
         return True
 
     def discover_modules(self):
-        """ Return module sequence discovered from ``self.package_name``
+        r""" Return module sequence discovered from ``self.package_name``
 
 
         Parameters

nibabel/arraywriters.py

@@ -438,8 +438,8 @@ def _range_scale(self, in_min, in_max):
             # not lose precision because min/max are of fp type.
             out_min, out_max = np.array((out_min, out_max), dtype=big_float)
         else:  # (u)int
-            out_min, out_max = [int_to_float(v, big_float)
-                                for v in (out_min, out_max)]
+            out_min, out_max = (int_to_float(v, big_float)
+                                for v in (out_min, out_max))
         if self._out_dtype.kind == 'u':
             if in_min < 0 and in_max > 0:
                 raise WriterError('Cannot scale negative and positive '
@@ -562,15 +562,15 @@ def to_fileobj(self, fileobj, order='F', nan2zero=None):
 
     def _iu2iu(self):
         # (u)int to (u)int
-        mn, mx = [as_int(v) for v in self.finite_range()]
+        mn, mx = (as_int(v) for v in self.finite_range())
         # range may be greater than the largest integer for this type.
         # as_int needed to work round numpy 1.4.1 int casting bug
         out_dtype = self._out_dtype
         # Options in this method are scaling using intercept only.  These will
         # have to pass through ``self.scaler_dtype`` (because the intercept is
         # in this type).
-        o_min, o_max = [as_int(v)
-                        for v in shared_range(self.scaler_dtype, out_dtype)]
+        o_min, o_max = (as_int(v)
+                        for v in shared_range(self.scaler_dtype, out_dtype))
         type_range = o_max - o_min
         mn2mx = mx - mn
         if mn2mx <= type_range:  # might offset be enough?
@@ -619,8 +619,8 @@ def _range_scale(self, in_min, in_max):
             in_min, in_max = as_int(in_min), as_int(in_max)
             in_range = int_to_float(in_max - in_min, big_float)
             # Cast to float for later processing.
-            in_min, in_max = [int_to_float(v, big_float)
-                              for v in (in_min, in_max)]
+            in_min, in_max = (int_to_float(v, big_float)
+                              for v in (in_min, in_max))
         if out_dtype.kind == 'f':
             # Type range, these are also floats
             info = type_info(out_dtype)

nibabel/cifti2/cifti2.py

@@ -648,8 +648,8 @@ def __init__(self, name=None, voxel_indices_ijk=None, vertices=None):
         self.vertices = vertices if vertices is not None else []
         for val in self.vertices:
             if not isinstance(val, Cifti2Vertices):
-                raise ValueError(('Cifti2Parcel vertices must be instances of '
-                                  'Cifti2Vertices'))
+                raise ValueError('Cifti2Parcel vertices must be instances of '
+                                 'Cifti2Vertices')
 
     @property
     def voxel_indices_ijk(self):

nibabel/cifti2/tests/test_axes.py

@@ -93,10 +93,8 @@ def get_axes():
     yield get_parcels()
     yield get_scalar()
     yield get_label()
-    for elem in get_brain_models():
-        yield elem
-    for elem in get_series():
-        yield elem
+    yield from get_brain_models()
+    yield from get_series()
 
 
 def test_brain_models():

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -50,7 +50,7 @@ def test_read_nifti2():
     # Error trying to read a CIFTI-2 image from a NIfTI2-only image.
     filemap = ci.Cifti2Image.make_file_map()
     for k in filemap:
-        filemap[k].fileobj = io.open(NIFTI2_DATA)
+        filemap[k].fileobj = open(NIFTI2_DATA)
     with pytest.raises(ValueError):
         ci.Cifti2Image.from_file_map(filemap)
 

nibabel/cmdline/diff.py

@@ -234,7 +234,7 @@ def get_data_diff(files, max_abs=0, max_rel=0, dtype=np.float64):
                         # Since we operated on sub-selected values already, we need
                         # to plug them back in
                         candidates[
-                            tuple((indexes[sub_thr] for indexes in np.where(candidates)))
+                            tuple(indexes[sub_thr] for indexes in np.where(candidates))
                         ] = False
                     max_rel_diff = np.max(rel_diff)
                 else:

nibabel/cmdline/ls.py

@@ -145,7 +145,7 @@ def proc_file(f, opts):
                     freq = np.bincount(inv)
                     counts = " ".join("%g:%d" % (i, f) for i, f in zip(items, freq))
                 row += ["@l" + counts]
-        except IOError as e:
+        except OSError as e:
             verbose(2, f"Failed to obtain stats/counts -- {e}")
             row += [_err()]
     return row

nibabel/cmdline/parrec2nii.py

@@ -158,7 +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, use --overwrite to overwrite it')
+        raise OSError(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

nibabel/cmdline/roi.py

@@ -21,7 +21,7 @@ def lossless_slice(img, slicers):
 def parse_slice(crop, allow_step=True):
     if crop is None:
         return slice(None)
-    start, stop, *extra = [int(val) if val else None for val in crop.split(":")]
+    start, stop, *extra = (int(val) if val else None for val in crop.split(":"))
     if len(extra) > 1:
         raise ValueError(f"Cannot parse specification: {crop}")
     if not allow_step and extra and extra[0] not in (1, None):

nibabel/ecat.py

@@ -471,7 +471,7 @@ def get_series_framenumbers(mlist):
         try:
             frame_dict[frame_stored] = trueframenumbers[true_order] + 1
         except IndexError:
-            raise IOError('Error in header or mlist order unknown')
+            raise OSError('Error in header or mlist order unknown')
     return frame_dict
 
 

nibabel/filebasedimages.py

@@ -430,7 +430,7 @@ def _sniff_meta_for(klass, filename, sniff_nbytes, sniff=None):
         try:
             with ImageOpener(meta_fname, 'rb') as fobj:
                 binaryblock = fobj.read(sniff_nbytes)
-        except (IOError, EOFError):
+        except (OSError, EOFError):
             return None
         return (binaryblock, meta_fname)
 
@@ -564,7 +564,7 @@ def from_stream(klass, io_obj: io.IOBase):
         return klass.from_file_map(klass._filemap_from_iobase(io_obj))
 
     def to_stream(self, io_obj: io.IOBase, **kwargs):
-        """Save image to writable IO stream
+        r"""Save image to writable IO stream
 
         Parameters
         ----------

nibabel/freesurfer/io.py

@@ -68,7 +68,7 @@ def _read_volume_info(fobj):
                 'zras', 'cras']:
         pair = fobj.readline().decode('utf-8').split('=')
         if pair[0].strip() != key or len(pair) != 2:
-            raise IOError('Error parsing volume info.')
+            raise OSError('Error parsing volume info.')
         if key in ('valid', 'filename'):
             volume_info[key] = pair[1].strip()
         elif key == 'volume':

nibabel/gifti/gifti.py

@@ -154,7 +154,7 @@ class GiftiNVPairs:
         'GiftiNVPairs objects are deprecated. Use the GiftiMetaData object '
         'as a dict, instead.',
         '4.0', '6.0')
-    def __init__(self, name=u'', value=u''):
+    def __init__(self, name='', value=''):
         self._name = name
         self._value = value
         self._container = None
@@ -480,7 +480,7 @@ def __init__(self,
                  coordsys=None,
                  ordering="C",
                  meta=None,
-                 ext_fname=u'',
+                 ext_fname='',
                  ext_offset=0):
         """
         Returns a shell object that cannot be saved.
@@ -702,7 +702,7 @@ class GiftiImage(xml.XmlSerializable, SerializableImage):
     parser = None
 
     def __init__(self, header=None, extra=None, file_map=None, meta=None,
-                 labeltable=None, darrays=None, version=u"1.0"):
+                 labeltable=None, darrays=None, version="1.0"):
         super(GiftiImage, self).__init__(header=header, extra=extra,
                                          file_map=file_map)
         if darrays is None:

nibabel/nicom/dicomreaders.py

@@ -83,7 +83,7 @@ def read_mosaic_dir(dicom_path,
     gradients = []
     arrays = []
     if len(filenames) == 0:
-        raise IOError(f'Found no files with "{full_globber}"')
+        raise OSError(f'Found no files with "{full_globber}"')
     for fname in filenames:
         dcm_w = wrapper_from_file(fname, **dicom_kwargs)
         # Because the routine sorts by filename, it only makes sense to use

nibabel/nicom/tests/test_dicomreaders.py

@@ -30,7 +30,7 @@ def test_read_dwis():
     assert_array_almost_equal(aff, EXPECTED_AFFINE)
     assert_array_almost_equal(bs, (0, EXPECTED_PARAMS[0]))
     assert_array_almost_equal(gs, (np.zeros((3,)), EXPECTED_PARAMS[1]))
-    with pytest.raises(IOError):
+    with pytest.raises(OSError):
         didr.read_mosaic_dwi_dir('improbable')
 
 

nibabel/nifti1.py

@@ -2269,7 +2269,7 @@ def load(filename):
     ------
     ImageFileError
         if `filename` doesn't look like NIfTI1;
-    IOError
+    OSError
         if `filename` does not exist.
     """
     try:

nibabel/nifti2.py

@@ -265,7 +265,7 @@ def load(filename):
     ------
     ImageFileError
         if `filename` doesn't look like nifti2;
-    IOError
+    OSError
         if `filename` does not exist.
     """
     try:

nibabel/spm99analyze.py

@@ -278,7 +278,7 @@ def from_file_map(klass, file_map, *, mmap=True, keep_file_open=None):
             file_map, mmap=mmap, keep_file_open=keep_file_open)
         try:
             matf = file_map['mat'].get_prepare_fileobj()
-        except IOError:
+        except OSError:
             return ret
         # Allow for possibility of empty file -> no update to affine
         with matf:

nibabel/streamlines/__init__.py

@@ -53,7 +53,7 @@ def detect_format(fileobj):
         try:
             if format.is_correct_format(fileobj):
                 return format
-        except IOError:
+        except OSError:
             pass
 
     if isinstance(fileobj, str):

nibabel/streamlines/tests/test_array_sequence.py

@@ -101,7 +101,7 @@ def test_deprecated_data_attribute(self):
             seq.data
 
     def test_creating_arraysequence_from_generator(self):
-        gen_1, gen_2 = itertools.tee((e for e in SEQ_DATA['data']))
+        gen_1, gen_2 = itertools.tee(e for e in SEQ_DATA['data'])
         seq = ArraySequence(gen_1)
         seq_with_buffer = ArraySequence(gen_2, buffer_size=256)
 
@@ -201,7 +201,7 @@ def test_arraysequence_extend(self):
 
         # Extend with a generator.
         seq = SEQ_DATA['seq'].copy()  # Copy because of in-place modification.
-        seq.extend((d for d in new_data))
+        seq.extend(d for d in new_data)
         check_arr_seq(seq, SEQ_DATA['data'] + new_data)
 
         # Extend with another `ArraySequence` object.

nibabel/streamlines/trk.py

@@ -504,8 +504,8 @@ def save(self, fileobj):
             header['scalar_name'][:] = scalar_name
 
             for t in tractogram:
-                if any((len(d) != len(t.streamline)
-                        for d in t.data_for_points.values())):
+                if any(len(d) != len(t.streamline)
+                       for d in t.data_for_points.values()):
                     raise DataError("Missing scalars for some points!")
 
                 points = np.asarray(t.streamline)

nibabel/tests/test_arrayproxy.py

@@ -440,7 +440,7 @@ def _count_ImageOpeners(proxy, data, voxels):
     CountingImageOpener.num_openers = 0
     # expected data is defined in the test_keep_file_open_* tests
     for i in range(voxels.shape[0]):
-        x, y, z = [int(c) for c in voxels[i, :]]
+        x, y, z = (int(c) for c in voxels[i, :])
         assert proxy[x, y, z] == x * 100 + y * 10 + z
     return CountingImageOpener.num_openers
 

nibabel/tests/test_casting.py

@@ -45,7 +45,7 @@ def test_shared_range():
             if thresh_overflow:
                 assert np.all((bit_bigger == casted_mx) | (bit_bigger == imax))
             else:
-                assert np.all((bit_bigger <= casted_mx))
+                assert np.all(bit_bigger <= casted_mx)
             if it in np.sctypes['uint']:
                 assert mn == 0
                 continue
@@ -71,7 +71,7 @@ def test_shared_range():
             if thresh_overflow:
                 assert np.all((bit_smaller == casted_mn) | (bit_smaller == imin))
             else:
-                assert np.all((bit_smaller >= casted_mn))
+                assert np.all(bit_smaller >= casted_mn)
 
 
 def test_shared_range_inputs():

nibabel/tests/test_ecat.py

@@ -144,7 +144,7 @@ def test_mlist_errors(self):
         neworder = [frames_order[x][0] for x in sorted(frames_order)]
         assert neworder == [1, 2, 3, 4, 5]
         with suppress_warnings():
-            with pytest.raises(IOError):
+            with pytest.raises(OSError):
                 get_series_framenumbers(mlist)
 
 

nibabel/tests/test_funcs.py

@@ -43,8 +43,8 @@ def test_concat():
 
     affine = np.eye(4)
     for dim in range(2, 6):
-        all_shapes_ND = tuple((shape[:dim] for shape in all_shapes_5D))
-        all_shapes_N1D_unary = tuple((shape + (1,) for shape in all_shapes_ND))
+        all_shapes_ND = tuple(shape[:dim] for shape in all_shapes_5D)
+        all_shapes_N1D_unary = tuple(shape + (1,) for shape in all_shapes_ND)
         all_shapes = all_shapes_ND + all_shapes_N1D_unary
 
         # Loop over all possible combinations of images, in first and

nibabel/tests/test_loadsave.py

@@ -139,7 +139,7 @@ def test_read_img_data_nifti():
             img.file_map = img.filespec_to_file_map(froot)
             # Trying to read from this filemap will generate an error because
             # we are going to read from files that do not exist
-            with pytest.deprecated_call(), pytest.raises(IOError):
+            with pytest.deprecated_call(), pytest.raises(OSError):
                 read_img_data(img)
             img.to_file_map()
             # Load - now the scaling and offset correctly applied

nibabel/tests/test_volumeutils.py

@@ -165,16 +165,14 @@ def test_array_from_file():
     arr = array_from_file((0,), np.dtype('f8'), BytesIO())
     assert len(arr) == 0
     # Check error from small file
-    with pytest.raises(IOError):
+    with pytest.raises(OSError):
         array_from_file(shape, dtype, BytesIO())
     # check on real file
     fd, fname = tempfile.mkstemp()
     with InTemporaryDirectory():
         open(fname, 'wb').write(b'1')
         in_buf = open(fname, 'rb')
-        # For windows this will raise a WindowsError from mmap, Unices
-        # appear to raise an IOError
-        with pytest.raises(Exception):
+        with pytest.raises(OSError):
             array_from_file(shape, dtype, in_buf)
         del in_buf
 
@@ -983,7 +981,7 @@ def test_seek_tell():
                 assert fobj.tell() == 10
                 seek_tell(fobj, 10)
                 assert fobj.tell() == 10
-                with pytest.raises(IOError):
+                with pytest.raises(OSError):
                     seek_tell(fobj, 5)
             # Make sure read seeks don't affect file
             with ImageOpener(in_file, 'rb') as fobj:
@@ -1003,10 +1001,10 @@ def test_seek_tell_logic():
     class BabyBio(BytesIO):
 
         def seek(self, *args):
-            raise IOError()
+            raise OSError()
     bio = BabyBio()
     # Fresh fileobj, position 0, can't seek - error
-    with pytest.raises(IOError):
+    with pytest.raises(OSError):
         bio.seek(10)
     # Put fileobj in correct position by writing
     ZEROB = b'\x00'
@@ -1015,7 +1013,7 @@ def seek(self, *args):
     assert bio.tell() == 10
     assert bio.getvalue() == ZEROB * 10
     # Try write zeros to get to new position
-    with pytest.raises(IOError):
+    with pytest.raises(OSError):
         bio.seek(20)
     seek_tell(bio, 20, write0=True)
     assert bio.getvalue() == ZEROB * 20
@@ -1206,7 +1204,7 @@ def read(self, n_bytes):
             return b''
     try:
         array_from_file(shape, np.int8, NoStringIO())
-    except IOError as err:
+    except OSError as err:
         message = str(err)
     assert message == ("Expected 11390625000000000000 bytes, got 0 "
                        "bytes from object\n - could the file be damaged?")