Merge pull request #1153 from DimitriPapadopoulos/linter

MNT: Apply refurb suggestions

Author: effigies

nibabel/cifti2/tests/test_cifti2.py

@@ -326,8 +326,7 @@ def test_matrixindicesmap():
     parcel = ci.Cifti2Parcel()
 
     assert mim.volume is None
-    mim.append(volume)
-    mim.append(parcel)
+    mim.extend((volume, parcel))
 
 
     assert mim.volume == volume

nibabel/cifti2/tests/test_new_cifti2.py

@@ -232,8 +232,7 @@ def test_dtseries():
     series_map = create_series_map((0, ))
     geometry_map = create_geometry_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(series_map)
-    matrix.append(geometry_map)
+    matrix.extend((series_map, geometry_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(13, 10)
     img = ci.Cifti2Image(data, hdr)
@@ -254,8 +253,7 @@ def test_dscalar():
     scalar_map = create_scalar_map((0, ))
     geometry_map = create_geometry_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(scalar_map)
-    matrix.append(geometry_map)
+    matrix.extend((scalar_map, geometry_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 10)
     img = ci.Cifti2Image(data, hdr)
@@ -276,8 +274,7 @@ def test_dlabel():
     label_map = create_label_map((0, ))
     geometry_map = create_geometry_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(label_map)
-    matrix.append(geometry_map)
+    matrix.extend((label_map, geometry_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 10)
     img = ci.Cifti2Image(data, hdr)
@@ -318,8 +315,7 @@ def test_ptseries():
     series_map = create_series_map((0, ))
     parcel_map = create_parcel_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(series_map)
-    matrix.append(parcel_map)
+    matrix.extend((series_map, parcel_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(13, 4)
     img = ci.Cifti2Image(data, hdr)
@@ -340,8 +336,7 @@ def test_pscalar():
     scalar_map = create_scalar_map((0, ))
     parcel_map = create_parcel_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(scalar_map)
-    matrix.append(parcel_map)
+    matrix.extend((scalar_map, parcel_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 4)
     img = ci.Cifti2Image(data, hdr)
@@ -362,8 +357,7 @@ def test_pdconn():
     geometry_map = create_geometry_map((0, ))
     parcel_map = create_parcel_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(geometry_map)
-    matrix.append(parcel_map)
+    matrix.extend((geometry_map, parcel_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(10, 4)
     img = ci.Cifti2Image(data, hdr)
@@ -384,8 +378,7 @@ def test_dpconn():
     parcel_map = create_parcel_map((0, ))
     geometry_map = create_geometry_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(parcel_map)
-    matrix.append(geometry_map)
+    matrix.extend((parcel_map, geometry_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(4, 10)
     img = ci.Cifti2Image(data, hdr)
@@ -406,8 +399,7 @@ def test_plabel():
     label_map = create_label_map((0, ))
     parcel_map = create_parcel_map((1, ))
     matrix = ci.Cifti2Matrix()
-    matrix.append(label_map)
-    matrix.append(parcel_map)
+    matrix.extend((label_map, parcel_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(2, 4)
     img = ci.Cifti2Image(data, hdr)
@@ -448,8 +440,7 @@ def test_pconnseries():
     series_map = create_series_map((2, ))
 
     matrix = ci.Cifti2Matrix()
-    matrix.append(parcel_map)
-    matrix.append(series_map)
+    matrix.extend((parcel_map, series_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(4, 4, 13)
     img = ci.Cifti2Image(data, hdr)
@@ -473,8 +464,7 @@ def test_pconnscalar():
     scalar_map = create_scalar_map((2, ))
 
     matrix = ci.Cifti2Matrix()
-    matrix.append(parcel_map)
-    matrix.append(scalar_map)
+    matrix.extend((parcel_map, scalar_map))
     hdr = ci.Cifti2Header(matrix)
     data = np.random.randn(4, 4, 2)
     img = ci.Cifti2Image(data, hdr)
@@ -499,8 +489,7 @@ def test_wrong_shape():
     brain_model_map = create_geometry_map((1, ))
 
     matrix = ci.Cifti2Matrix()
-    matrix.append(scalar_map)
-    matrix.append(brain_model_map)
+    matrix.extend((scalar_map, brain_model_map))
     hdr = ci.Cifti2Header(matrix)
 
     # correct shape is (2, 10)

nibabel/cmdline/dicomfs.py

@@ -48,7 +48,6 @@ def __init__(self, fno):
         self.fno = fno
         self.keep_cache = False
         self.direct_io = False
-        return
 
     def __str__(self):
         return 'FileHandle(%d)' % self.fno
@@ -64,7 +63,6 @@ def __init__(self, *args, **kwargs):
         self.dicom_path = kwargs.pop('dicom_path', None)
         fuse.Fuse.__init__(self, *args, **kwargs)
         self.fhs = {}
-        return
 
     def get_paths(self):
         paths = {}
@@ -119,8 +117,7 @@ def readdir(self, path, fh):
             return -errno.ENOENT
         logger.debug(f'matched {matched_path}')
         fnames = [k.encode('ascii', 'replace') for k in matched_path.keys()]
-        fnames.append('.')
-        fnames.append('..')
+        fnames.extend(('.', '..'))
         return [fuse.Direntry(f) for f in fnames]
 
     def getattr(self, path):
@@ -190,7 +187,6 @@ def release(self, path, flags, fh):
         logger.debug(path)
         logger.debug(fh)
         del self.fhs[fh.fno]
-        return
 
 
 def get_opt_parser():

nibabel/cmdline/utils.py

@@ -32,7 +32,7 @@ def verbose(thing, msg):
     """Print `s` if `thing` is less than the `verbose_level`
     """
     # TODO: consider using nibabel's logger
-    if thing <= int(verbose_level):
+    if thing <= verbose_level:
         print(' ' * thing + msg)
 
 

nibabel/deprecator.py

@@ -161,8 +161,8 @@ def __call__(self, message, since='', until='',
         deprecator : func
             Function returning a decorator.
         """
-        warn_class = warn_class if warn_class else self.warn_class
-        error_class = error_class if error_class else self.error_class
+        warn_class = warn_class or self.warn_class
+        error_class = error_class or self.error_class
         messages = [message]
         if (since, until) != ('', ''):
             messages.append('')

nibabel/dft.py

@@ -51,7 +51,6 @@ def __init__(self, series, i, si):
         self.series = series
         self.i = i
         self.si = si
-        return
 
     def __str__(self):
         fmt = 'expecting instance number %d, got %d'
@@ -70,7 +69,6 @@ def __init__(self, d):
         self.patient_birth_date = d['patient_birth_date']
         self.patient_sex = d['patient_sex']
         self.series = None
-        return
 
     def __getattribute__(self, name):
         val = object.__getattribute__(self, name)
@@ -103,7 +101,6 @@ def __init__(self, d):
         self.bits_allocated = d['bits_allocated']
         self.bits_stored = d['bits_stored']
         self.storage_instances = None
-        return
 
     def __getattribute__(self, name):
         val = object.__getattribute__(self, name)
@@ -226,7 +223,6 @@ def __init__(self, d):
         self.instance_number = d['instance_number']
         self.series = d['series']
         self.files = None
-        return
 
     def __getattribute__(self, name):
         val = object.__getattribute__(self, name)
@@ -256,7 +252,6 @@ def __exit__(self, type, value, traceback):
         if type is None:
             self.c.close()
         DB.rollback()
-        return
 
 
 class _db_change:
@@ -272,7 +267,6 @@ def __exit__(self, type, value, traceback):
             DB.commit()
         else:
             DB.rollback()
-        return
 
 
 def _get_subdirs(base_dir, files_dict=None, followlinks=False):
@@ -316,7 +310,6 @@ def update_cache(base_dir, followlinks=False):
             else:
                 query = "INSERT INTO directory (path, mtime) VALUES (?, ?)"
                 c.execute(query, (dir, mtimes[dir]))
-    return
 
 
 def get_studies(base_dir=None, followlinks=False):
@@ -382,7 +375,6 @@ def _update_dir(c, dir, files, studies, series, storage_instances):
                               SET mtime = ?, storage_instance = ?
                             WHERE directory = ? AND name = ?"""
                 c.execute(query, (mtime, si_uid, dir, fname))
-    return
 
 
 def _update_file(c, path, fname, studies, series, storage_instances):
@@ -457,7 +449,6 @@ def clear_cache():
         c.execute("DELETE FROM storage_instance")
         c.execute("DELETE FROM series")
         c.execute("DELETE FROM study")
-    return
 
 
 CREATE_QUERIES = (

nibabel/nicom/dicomwrappers.py

@@ -737,7 +737,7 @@ def series_signature(self):
         ice = csar.get_ice_dims(self.csa_header)
         if ice is not None:
             ice = ice[:6] + ice[8:9]
-        signature['ICE_Dims'] = (ice, lambda x, y: x == y)
+        signature['ICE_Dims'] = (ice, operator.eq)
         return signature
 
     @one_time

nibabel/streamlines/__init__.py

@@ -129,7 +129,7 @@ def save(tractogram, filename, **kwargs):
                    " 'TractogramFile' object.")
             warnings.warn(msg, ExtensionWarning)
 
-        if len(kwargs) > 0:
+        if kwargs:
             msg = ("A 'TractogramFile' object was provided, no need for"
                    " keyword arguments.")
             raise ValueError(msg)

nibabel/streamlines/tck.py

@@ -249,12 +249,13 @@ def _write_header(fileobj, header):
                    Field.VOXEL_TO_RASMM,  # Streamlines are always in RAS+ mm.
                    "count", "datatype", "file"]  # Fields being replaced.
 
-        lines = []
-        lines.append(f"count: {header[Field.NB_STREAMLINES]:010}")
-        lines.append("datatype: Float32LE")  # Always Float32LE.
-        lines.extend([f"{k}: {v}"
-                      for k, v in header.items()
-                      if k not in exclude and not k.startswith("_")])
+        lines = [
+            f"count: {header[Field.NB_STREAMLINES]:010}",
+            "datatype: Float32LE",  # Always Float32LE.
+        ]
+        lines.extend(f"{k}: {v}"
+                     for k, v in header.items()
+                     if k not in exclude and not k.startswith("_"))
         out = "\n".join(lines)
 
         # Check the header is well formatted.

nibabel/tests/data/gen_standard.py

@@ -35,19 +35,17 @@ def _gen_straight_streamline(start, end, steps=3):
         return np.array(coords).T
 
     # Generate a 3D 'X' template fitting inside the voxel centered at (0,0,0).
-    X = []
-    X.append(_gen_straight_streamline((-0.5, -0.5, -0.5), (0.5, 0.5, 0.5)))
-    X.append(_gen_straight_streamline((-0.5, 0.5, -0.5), (0.5, -0.5, 0.5)))
-    X.append(_gen_straight_streamline((-0.5, 0.5, 0.5), (0.5, -0.5, -0.5)))
-    X.append(_gen_straight_streamline((-0.5, -0.5, 0.5), (0.5, 0.5, -0.5)))
+    X = [
+        _gen_straight_streamline((-0.5, -0.5, -0.5), (0.5, 0.5, 0.5)),
+        _gen_straight_streamline((-0.5, 0.5, -0.5), (0.5, -0.5, 0.5)),
+        _gen_straight_streamline((-0.5, 0.5, 0.5), (0.5, -0.5, -0.5)),
+        _gen_straight_streamline((-0.5, -0.5, 0.5), (0.5, 0.5, -0.5)),
+    ]
 
     # Get the coordinates of voxels 'on' in the mask.
     coords = np.array(zip(*np.where(mask)))
 
-    streamlines = []
-    for c in coords:
-        for line in X:
-            streamlines.append((line + c) * voxel_size)
+    streamlines = [(line + c) * voxel_size for c in coords for line in X]
 
     return streamlines