FIX: Cleanups suggested by ruff (#18)

* FIX: Undefined variable should be unused ge_cas

* STY: Remove unused imports

* MNT: Configure ruff to ignore things that are okay

* RF: Clean up coef_file_parse()

* Use context manager to ensure file is closed promptly
* Skip unnecessary regex compilation
* Give line fields variable a meaningful name

* FIX: Provide a more informative error for get_ge_coef

* STY: Keep imports at top of files

* RF: Remove indirect import of math.factorial

* FIX: Revert "valid line" condition, but keep the shorter name

gradunwarp/core/coeffs.py

@@ -9,7 +9,6 @@
 import numpy as np
 import logging
 import re
-from . import globals
 from .globals import siemens_cas, ge_cas
 
 
@@ -44,19 +43,15 @@ def coef_file_parse(cfile, txt_var_map):
 
     modifies txt_var_map in place
     '''
-    # parse .coef file. Strip unneeded characters. a valid line in that file is
-    # broken into validline_list
-    coef_re = re.compile(r'^[^\#]')  # regex for first character not a '#'
-    coef_file = open(cfile, 'r')
-    for line in coef_file.readlines():
-        if coef_re.match(line):
-            validline_list = line.lstrip(' \t').rstrip(';\n').split()
-            if validline_list:
-                log.info('Parsed : %s' % validline_list)
-                l = validline_list
-                x = int(l[1])
-                y = int(l[2])
-                txt_var_map[l[0]][x, y] = float(l[3])
+    with open(cfile) as coef_file:
+        for line in coef_file:
+            if re.match(r'^[^#]', line):
+                fields = line.lstrip(' \t').rstrip(';\n').split()
+                if fields:
+                    log.info('Parsed : %s' % fields)
+                    x = int(fields[1])
+                    y = int(fields[2])
+                    txt_var_map[fields[0]][x, y] = float(fields[3])
 
 
 def get_siemens_coef(cfile):
@@ -96,7 +91,15 @@ def get_siemens_coef(cfile):
 def get_ge_coef(cfile):
     ''' Parse the GE .coef file.
     '''
-    txt_var_map = create_txt_var_map(coef_array_sz)
+    # R0_m has never been defined in gradunwarp for this function
+    # This function would raise a NameError if it were ever called, so
+    # let's provide a meaningful runtime error.
+    raise RuntimeError(
+        "R0_m has never been defined in gradunwarp for this function. "
+        "If you know how to determine it, please contact the developers."
+    )
+
+    txt_var_map = create_txt_var_map(ge_cas)
 
     coef_file_parse(cfile, txt_var_map)
 
@@ -107,7 +110,8 @@ def get_ge_coef(cfile):
         txt_var_map['beta_y'],
         txt_var_map['beta_x'],
         txt_var_map['beta_z'],
-        R0_m)
+        R0_m)  # noqa: F821
+
 
 def grad_file_parse(gfile, txt_var_map):
     xmax = 0

gradunwarp/core/gradient_unwarp.py

@@ -21,7 +21,7 @@ def argument_parse_gradunwarp():
     try:
         p = arg.ArgumentParser(usage=globals.usage)
         p.add_argument('--version', '-v', action='version', version=globals.VERSION)
-    except:
+    except TypeError:
         #maintain compatibility with pre py2.7 argparse (deprecated in py2.7 but fails in py3)
         p = arg.ArgumentParser(version=globals.VERSION, usage=globals.usage)
 

gradunwarp/core/tests/test_gradient_unwarp.py

@@ -1,5 +1,4 @@
 import os
-import tempfile
 
 import numpy as np
 import nibabel as nb
@@ -13,7 +12,7 @@ class Arguments:
 
 
 def test_trivial_unwarp():
-    with InTemporaryDirectory() as tmpdir:
+    with InTemporaryDirectory():
         # Siemens Allegra coefficient arrays are 15x15, keeping things small and fast
         coef_file = "allegra.coef"
         open(coef_file, 'wb').close()  # touch

gradunwarp/core/tests/test_regression.py

@@ -1,11 +1,13 @@
 import os
-DATA_DIR = os.path.join(os.path.dirname(__file__), 'data')
 
 import numpy as np
-from numpy.testing import assert_array_almost_equal, assert_allclose
+from numpy.testing import assert_array_almost_equal
+
+from gradunwarp.core.unwarp_resample import cart2sph, siemens_B
+from gradunwarp.core import coeffs
+
+DATA_DIR = os.path.join(os.path.dirname(__file__), 'data')
 
-from gradunwarp.core import coeffs, utils
-from gradunwarp.core.unwarp_resample import siemens_B, cart2sph
 
 def test_siemens_B():
     gradfile = os.path.join(DATA_DIR, 'gradunwarp_coeffs.grad')

gradunwarp/core/unwarp_resample.py

@@ -7,18 +7,14 @@
 from __future__ import absolute_import, print_function
 import numpy as np
 import sys
-import pdb
-import gc
 import math
 import logging
 from scipy import ndimage
 from . import utils
 from .utils import CoordsVector as CV
-from .utils import factorial
 from . import globals
 from .globals import siemens_max_det
 import nibabel as nib
-import subprocess
 import scipy.special
 
 #np.seterr(all='raise')
@@ -385,8 +381,8 @@ def siemens_B(alpha, beta, r, cosine_theta, theta, phi, R0):
             # this is Siemens normalization
             if m > 0:
                 normfact = math.pow(-1, m) * \
-                math.sqrt(float((2 * n + 1) * factorial(n - m)) \
-                          / float(2 * factorial(n + m)))
+                math.sqrt(float((2 * n + 1) * math.factorial(n - m)) \
+                          / float(2 * math.factorial(n + m)))
                 _p *= normfact
             b += f * _p * f2
     return b

gradunwarp/core/utils.py

@@ -4,12 +4,11 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-from __future__ import print_function
-import numpy as np
 from collections import namedtuple
-import math
-from math import sqrt, cos, pi
 
+import numpy as np
+import nibabel as nib
+from nibabel.affines import apply_affine
 
 # This is a container class that has 3 np.arrays which contain
 # the x, y and z coordinates respectively. For example, the output
@@ -18,19 +17,10 @@
 # cv = CoordsVector(x=x, y=y, z=z)
 CoordsVector = namedtuple('CoordsVector', 'x, y, z')
 
-from nibabel.affines import apply_affine
-
 def transform_coordinates(A, M):
     transformed = apply_affine(M, np.stack(A).T).T
     return CoordsVector(*transformed)
 
 def get_vol_affine(infile):
-    try:
-        import nibabel as nib
-    except ImportError:
-        raise ImportError('gradunwarp needs nibabel for I/O of mgz/nifti files.'
-                          ' Please install')
     nibimage = nib.load(infile)
     return np.asanyarray(nibimage.dataobj), nibimage.affine
-
-factorial = math.factorial

pyproject.toml

@@ -36,3 +36,6 @@ push = false
 [tool.cibuildwheel]
 # Do not bother building pypy wheels
 skip = "pp*"
+
+[tool.ruff.extend-per-file-ignores]
+"*/__init__.py" = ["F401"]