Merge pull request #1124 from effigies/sty/normalize

STY: Normalize to blue and isort

.git-blame-ignore-revs

@@ -0,0 +1,12 @@
+# Thu Dec 29 22:53:17 2022 -0500 - effigies@gmail.com - STY: Reduce array().astype() and similar constructs
+bf298113da99079c9c7b5e1690e41879828cd472
+# Thu Dec 29 22:32:46 2022 -0500 - effigies@gmail.com - STY: pyupgrade --py37-plus
+4481a4c2640bd4be6e9c468e550d01aae448ab99
+# Fri Dec 30 11:01:19 2022 -0500 - effigies@gmail.com - STY: Run vanilla blue
+6b0ddd23b1da1df7ca9ae275673f82bfa20a754c
+# Thu Dec 29 21:46:13 2022 -0500 - markiewicz@stanford.edu - STY: Manual, blue-compatible touchups
+263fca9bf6d4ca314a5a322b4824d6f53d0589df
+# Thu Dec 29 21:32:00 2022 -0500 - effigies@gmail.com - STY: isort
+0ab2856cac4d4baae7ab3e2f6d58421db55d807f
+# Thu Dec 29 21:30:29 2022 -0500 - effigies@gmail.com - STY: blue
+1a8dd302ff85b1136c81d492509b80e7748339f0

Makefile

@@ -78,6 +78,9 @@ distclean: clean
 $(WWW_DIR):
 	if [ ! -d $(WWW_DIR) ]; then mkdir -p $(WWW_DIR); fi
 
+.git-blame-ignore-revs:
+	git log --grep "\[git-blame-ignore-rev\]" --pretty=format:"# %ad - %ae - %s%n%H" \
+		> .git-blame-ignore-revs
 
 #
 # Tests
@@ -288,4 +291,4 @@ rm-orig:
 	# Remove .orig temporary diff files generated by git
 	find . -name "*.orig" -print | grep -v "fsaverage" | xargs rm
 
-.PHONY: orig-src pylint all build
+.PHONY: orig-src pylint all build .git-blame-ignore-revs

nibabel/__init__.py

@@ -9,8 +9,9 @@
 
 import os
 
-from .pkg_info import __version__
 from .info import long_description as __doc__
+from .pkg_info import __version__
+
 __doc__ += """
 Quickstart
 ==========
@@ -38,32 +39,39 @@
 
 # module imports
 from . import analyze as ana
-from . import spm99analyze as spm99
-from . import spm2analyze as spm2
+from . import ecat, mriutils
 from . import nifti1 as ni1
-from . import ecat
+from . import spm2analyze as spm2
+from . import spm99analyze as spm99
+from . import streamlines, viewers
+
+# isort: split
+
 # object imports
-from .fileholders import FileHolder, FileHolderError
-from .loadsave import load, save
-from .arrayproxy import is_proxy
 from .analyze import AnalyzeHeader, AnalyzeImage
-from .spm99analyze import Spm99AnalyzeHeader, Spm99AnalyzeImage
-from .spm2analyze import Spm2AnalyzeHeader, Spm2AnalyzeImage
-from .nifti1 import Nifti1Header, Nifti1Image, Nifti1Pair
-from .nifti2 import Nifti2Header, Nifti2Image, Nifti2Pair
-from .minc1 import Minc1Image
-from .minc2 import Minc2Image
+from .arrayproxy import is_proxy
 from .cifti2 import Cifti2Header, Cifti2Image
-from .gifti import GiftiImage
+from .fileholders import FileHolder, FileHolderError
 from .freesurfer import MGHImage
-from .funcs import (squeeze_image, concat_images, four_to_three,
-                    as_closest_canonical)
-from .orientations import (io_orientation, flip_axis, OrientationError,
-                           apply_orientation, aff2axcodes)
+from .funcs import as_closest_canonical, concat_images, four_to_three, squeeze_image
+from .gifti import GiftiImage
 from .imageclasses import all_image_classes
-from . import mriutils
-from . import streamlines
-from . import viewers
+from .loadsave import load, save
+from .minc1 import Minc1Image
+from .minc2 import Minc2Image
+from .nifti1 import Nifti1Header, Nifti1Image, Nifti1Pair
+from .nifti2 import Nifti2Header, Nifti2Image, Nifti2Pair
+from .orientations import (
+    OrientationError,
+    aff2axcodes,
+    apply_orientation,
+    flip_axis,
+    io_orientation,
+)
+from .spm2analyze import Spm2AnalyzeHeader, Spm2AnalyzeImage
+from .spm99analyze import Spm99AnalyzeHeader, Spm99AnalyzeImage
+
+# isort: split
 
 from .pkg_info import get_pkg_info as _get_pkg_info
 
@@ -72,9 +80,15 @@ def get_info():
     return _get_pkg_info(os.path.dirname(__file__))
 
 
-def test(label=None, verbose=1, extra_argv=None,
-         doctests=False, coverage=False, raise_warnings=None,
-         timer=False):
+def test(
+    label=None,
+    verbose=1,
+    extra_argv=None,
+    doctests=False,
+    coverage=False,
+    raise_warnings=None,
+    timer=False,
+):
     """
     Run tests for nibabel using pytest
 
@@ -107,29 +121,30 @@ def test(label=None, verbose=1, extra_argv=None,
         Returns the result of running the tests as a ``pytest.ExitCode`` enum
     """
     import pytest
+
     args = []
 
     if label is not None:
-        raise NotImplementedError("Labels cannot be set at present")
+        raise NotImplementedError('Labels cannot be set at present')
 
     verbose = int(verbose)
     if verbose > 0:
-        args.append("-" + "v" * verbose)
+        args.append('-' + 'v' * verbose)
     elif verbose < 0:
-        args.append("-" + "q" * -verbose)
+        args.append('-' + 'q' * -verbose)
 
     if extra_argv:
         args.extend(extra_argv)
     if doctests:
-        args.append("--doctest-modules")
+        args.append('--doctest-modules')
     if coverage:
-        args.extend(["--cov", "nibabel"])
+        args.extend(['--cov', 'nibabel'])
     if raise_warnings is not None:
-        raise NotImplementedError("Warning filters are not implemented")
+        raise NotImplementedError('Warning filters are not implemented')
     if timer:
-        raise NotImplementedError("Timing is not implemented")
+        raise NotImplementedError('Timing is not implemented')
 
-    args.extend(["--pyargs", "nibabel"])
+    args.extend(['--pyargs', 'nibabel'])
 
     return pytest.main(args=args)
 
@@ -157,9 +172,10 @@ def bench(label=None, verbose=1, extra_argv=None):
         Returns the result of running the tests as a ``pytest.ExitCode`` enum
     """
     from pkg_resources import resource_filename
-    config = resource_filename("nibabel", "benchmarks/pytest.benchmark.ini")
+
+    config = resource_filename('nibabel', 'benchmarks/pytest.benchmark.ini')
     args = []
     if extra_argv is not None:
         args.extend(extra_argv)
-    args.extend(["-c", config])
+    args.extend(['-c', config])
     return test(label, verbose, extra_argv=args)

nibabel/affines.py

@@ -1,21 +1,22 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-""" Utility routines for working with points and affine transforms
+"""Utility routines for working with points and affine transforms
 """
-import numpy as np
-
 from functools import reduce
 
+import numpy as np
+
 
 class AffineError(ValueError):
-    """ Errors in calculating or using affines """
+    """Errors in calculating or using affines"""
+
     # Inherits from ValueError to keep compatibility with ValueError previously
     # raised in append_diag
     pass
 
 
 def apply_affine(aff, pts, inplace=False):
-    """ Apply affine matrix `aff` to points `pts`
+    """Apply affine matrix `aff` to points `pts`
 
     Returns result of application of `aff` to the *right* of `pts`.  The
     coordinate dimension of `pts` should be the last.
@@ -142,7 +143,7 @@ def to_matvec(transform):
 
 
 def from_matvec(matrix, vector=None):
-    """ Combine a matrix and vector into an homogeneous affine
+    """Combine a matrix and vector into an homogeneous affine
 
     Combine a rotation / scaling / shearing matrix and translation vector into
     a transform in homogeneous coordinates.
@@ -185,14 +186,14 @@ def from_matvec(matrix, vector=None):
     nin, nout = matrix.shape
     t = np.zeros((nin + 1, nout + 1), matrix.dtype)
     t[0:nin, 0:nout] = matrix
-    t[nin, nout] = 1.
+    t[nin, nout] = 1.0
     if vector is not None:
         t[0:nin, nout] = vector
     return t
 
 
 def append_diag(aff, steps, starts=()):
-    """ Add diagonal elements `steps` and translations `starts` to affine
+    """Add diagonal elements `steps` and translations `starts` to affine
 
     Typical use is in expanding 4x4 affines to larger dimensions.  Nipy is the
     main consumer because it uses NxM affines, whereas we generally only use
@@ -236,8 +237,7 @@ def append_diag(aff, steps, starts=()):
         raise AffineError('Steps should have same length as starts')
     old_n_out, old_n_in = aff.shape[0] - 1, aff.shape[1] - 1
     # make new affine
-    aff_plus = np.zeros((old_n_out + n_steps + 1,
-                         old_n_in + n_steps + 1), dtype=aff.dtype)
+    aff_plus = np.zeros((old_n_out + n_steps + 1, old_n_in + n_steps + 1), dtype=aff.dtype)
     # Get stuff from old affine
     aff_plus[:old_n_out, :old_n_in] = aff[:old_n_out, :old_n_in]
     aff_plus[:old_n_out, -1] = aff[:old_n_out, -1]
@@ -250,7 +250,7 @@ def append_diag(aff, steps, starts=()):
 
 
 def dot_reduce(*args):
-    r""" Apply numpy dot product function from right to left on arrays
+    r"""Apply numpy dot product function from right to left on arrays
 
     For passed arrays :math:`A, B, C, ... Z` returns :math:`A \dot B \dot C ...
     \dot Z` where "." is the numpy array dot product.
@@ -270,7 +270,7 @@ def dot_reduce(*args):
 
 
 def voxel_sizes(affine):
-    r""" Return voxel size for each input axis given `affine`
+    r"""Return voxel size for each input axis given `affine`
 
     The `affine` is the mapping between array (voxel) coordinates and mm
     (world) coordinates.
@@ -308,7 +308,7 @@ def voxel_sizes(affine):
         but in general has length (N-1) where input `affine` is shape (M, N).
     """
     top_left = affine[:-1, :-1]
-    return np.sqrt(np.sum(top_left ** 2, axis=0))
+    return np.sqrt(np.sum(top_left**2, axis=0))
 
 
 def obliquity(affine):
@@ -340,7 +340,7 @@ def obliquity(affine):
 
 
 def rescale_affine(affine, shape, zooms, new_shape=None):
-    """ Return a new affine matrix with updated voxel sizes (zooms)
+    """Return a new affine matrix with updated voxel sizes (zooms)
 
     This function preserves the rotations and shears of the original
     affine, as well as the RAS location of the central voxel of the