nipy · DimitriPapadopoulos · Dec 25, 2024 · Dec 25, 2024 · Dec 25, 2024 · Dec 25, 2024
diff --git a/doc/sphinxext/autosummary_generate.py b/doc/sphinxext/autosummary_generate.py
@@ -153,8 +153,8 @@ def get_documented_in_lines(lines, module=None, filename=None):
         (if present) of the directive.
 
     """
-    title_underline_re = re.compile("^[-=*_^#]{3,}\s*$")
-    autodoc_re = re.compile(".. auto(function|method|attribute|class|exception|module)::\s*([A-Za-z0-9_.]+)\s*$")
+    title_underline_re = re.compile(r"^[-=*_^#]{3,}\s*$")
+    autodoc_re = re.compile(r".. auto(function|method|attribute|class|exception|module)::\s*([A-Za-z0-9_.]+)\s*$")
     autosummary_re = re.compile(r'^\.\.\s+autosummary::\s*')
     module_re = re.compile(r'^\.\.\s+(current)?module::\s*([a-zA-Z0-9_.]+)\s*$')
     autosummary_item_re = re.compile(r'^\s+([_a-zA-Z][a-zA-Z0-9_.]*)\s*.*?')

diff --git a/doc/users/plots/hrf_different.py b/doc/users/plots/hrf_different.py
@@ -14,8 +14,10 @@
 glover = hrf.glover(T)
 afni = hrf.afni(T)
 
-ta = [0,4,8,12,16]; tb = [2,6,10,14,18]
-ba = 1; bb = -2
+ta = [0,4,8,12,16]
+tb = [2,6,10,14,18]
+ba = 1
+bb = -2
 na = ba * sum(glover.subs(T, T - t) for t in ta)
 nb = bb * sum(afni.subs(T, T - t) for t in tb)
 

diff --git a/doc/users/plots/neuronal_block.py b/doc/users/plots/neuronal_block.py
@@ -12,8 +12,11 @@
 import pylab
 from sympy import Piecewise, Symbol, lambdify
 
-ta = [0,4,8,12,16]; tb = [2,6,10,14,18]
-ba = Symbol('ba'); bb = Symbol('bb'); t = Symbol('t')
+ta = [0,4,8,12,16]
+tb = [2,6,10,14,18]
+ba = Symbol('ba')
+bb = Symbol('bb')
+t = Symbol('t')
 fa = sum(Piecewise((0, (t<_t)), ((t-_t)/0.5, (t<_t+0.5)), (1, (t >= _t+0.5))) for _t in ta)*ba
 fb = sum(Piecewise((0, (t<_t)), ((t-_t)/0.5, (t<_t+0.5)), (1, (t >= _t+0.5))) for _t in tb)*bb
 N = fa+fb

diff --git a/examples/ds105/ds105_example.py b/examples/ds105/ds105_example.py
@@ -228,7 +228,8 @@ def run_model(subj, run):
 
     # We split the contrasts into F-tests and t-tests.
     # XXX helper function should do this
-    fcons = {}; tcons = {}
+    fcons = {}
+    tcons = {}
     for n, v in cons.items():
         v = np.squeeze(v)
         if v.ndim == 1:

diff --git a/examples/fiac/fiac_example.py b/examples/fiac/fiac_example.py
@@ -215,7 +215,8 @@ def run_model(subj, run):
 
     # We split the contrasts into F-tests and t-tests.
     # XXX helper function should do this
-    fcons = {}; tcons = {}
+    fcons = {}
+    tcons = {}
     for n, v in cons.items():
         v = np.squeeze(v)
         if v.ndim == 1:

diff --git a/examples/formula/multi_session_contrast.py b/examples/formula/multi_session_contrast.py
@@ -25,21 +25,21 @@
 # The events utility returns a formula in terms of 't' - general time
 c11 = c11.subs(t, t1) # Now make it in terms of time in run 1
 # Same for conditions 2 and 3
-c21 = utils.events([1, 3, 9], f=h1); c21 = c21.subs(t, t1)
-c31 = utils.events([2, 4, 8], f=h1); c31 = c31.subs(t, t1)
+c21 = utils.events([1, 3, 9], f=h1).subs(t, t1)
+c31 = utils.events([2, 4, 8], f=h1).subs(t, t1)
 # Add also a Fourier basis set for drift with frequencies 0.3, 0.5, 0.7
-d1 = utils.fourier_basis([0.3, 0.5, 0.7]); d1 = d1.subs(t, t1)
+d1 = utils.fourier_basis([0.3, 0.5, 0.7]).subs(t, t1)
 
 # Here's our formula for run 1 signal terms of time in run 1 (t1)
 f1 = Formula([c11,c21,c31]) + d1
 
 # run 2
 t2 = Term('t2') # Time within run 2
 # Conditions 1 through 3 in run 2
-c12 = utils.events([3.3, 7, 10], f=h2); c12 = c12.subs(t, t2)
-c22 = utils.events([1, 3.2, 9], f=h2); c22 = c22.subs(t, t2)
-c32 = utils.events([2, 4.2, 8], f=h2); c32 = c32.subs(t, t2)
-d2 = utils.fourier_basis([0.3, 0.5, 0.7]); d2 = d2.subs(t, t2)
+c12 = utils.events([3.3, 7, 10], f=h2).subs(t, t2)
+c22 = utils.events([1, 3.2, 9], f=h2).subs(t, t2)
+c32 = utils.events([2, 4.2, 8], f=h2).subs(t, t2)
+d2 = utils.fourier_basis([0.3, 0.5, 0.7]).subs(t, t2)
 
 # Formula for run 2 signal in terms of time in run 2 (t2)
 f2 = Formula([c12, c22, c32]) + d2

diff --git a/examples/labs/need_data/one_sample_t_test.py b/examples/labs/need_data/one_sample_t_test.py
@@ -82,6 +82,6 @@
          vmax=vmax,
          threshold=3.,
          black_bg=True)
-plt.savefig(path.join(write_dir, f'one_sample_z_map.png'))
+plt.savefig(path.join(write_dir, 'one_sample_z_map.png'))
 plt.show()
 print(f"Wrote all the results in directory {write_dir}")
diff --git a/lib/lapack_lite/remake/make_lite.py b/lib/lapack_lite/remake/make_lite.py
@@ -6,10 +6,6 @@
 import clapack_scrub
 import fortran
 
-try: set
-except NameError:
-    from sets import Set as set
-
 # Arguments to pass to f2c. You'll always want -A for ANSI C prototypes
 # Others of interest: -a to not make variables static by default
 #                     -C to check array subscripts

diff --git a/nipy/algorithms/clustering/tests/test_clustering.py b/nipy/algorithms/clustering/tests/test_clustering.py
@@ -15,7 +15,7 @@ class TestClustering(TestCase):
     def testkmeans1(self):
         X = nr.randn(10, 2)
         A = np.concatenate([np.ones((7, 2)),np.zeros((3, 2))])
-        X = X + 3 * A;
+        X = X + 3 * A
         L = np.array([0, 0, 0, 0, 0, 1, 1, 1, 1, 1])
         C, L, J = kmeans(X, 2, L)
         self.assertLess(np.mean(L[:7]), 0.5)

diff --git a/nipy/algorithms/diagnostics/tests/test_commands.py b/nipy/algorithms/diagnostics/tests/test_commands.py
@@ -94,7 +94,7 @@ def test_parse_fname_axes(in_tmp_path):
         assert slice_axis == 'j'
 
 
-class Args: pass
+class Args: ...
 
 
 def check_axes(axes, img_shape, time_axis, slice_axis):

diff --git a/nipy/algorithms/graph/tests/test_forest.py b/nipy/algorithms/graph/tests/test_forest.py
@@ -74,7 +74,7 @@ def test_all_distances():
     dg = f.all_distances(1)
     assert dg[3] == 3.
 
-def test_depth():
+def test_depth_from_leaves():
     """ test the depth_from_leaves() methods
     """
     f =  simple_forest()

diff --git a/nipy/algorithms/graph/tests/test_graph.py b/nipy/algorithms/graph/tests/test_graph.py
@@ -350,7 +350,7 @@ def test_voronoi():
     """
     a = np.array([0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6])
     b = np.array([1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 0, 0, 1])
-    d = np.array([1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2]);
+    d = np.array([1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2])
     edges = np.transpose(np.vstack((a, b)))
     G = WeightedGraph(7, edges,d)
     G.symmeterize()
@@ -364,7 +364,7 @@ def test_voronoi2():
     """
     a = np.array([0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6])
     b = np.array([1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 0, 0, 1])
-    d = np.array([1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2]);
+    d = np.array([1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2, 1, 2])
     edges = np.vstack((a, b)).T
     G = WeightedGraph(7, edges,d)
     G.symmeterize()
@@ -378,7 +378,7 @@ def test_voronoi3():
     """
     a = np.array([0, 1, 2, 5, 6])
     b = np.array([1, 2, 3, 6, 0])
-    d = np.array([1, 1, 1, 1, 1]);
+    d = np.array([1, 1, 1, 1, 1])
     edges = np.vstack((a, b)).T
     G = WeightedGraph(7, edges,d)
     G.symmeterize()

diff --git a/nipy/algorithms/registration/scripting.py b/nipy/algorithms/registration/scripting.py
@@ -24,7 +24,7 @@
 
 timefuncs = st.timefuncs.SLICETIME_FUNCTIONS
 
-__all__ = ["space_time_realign", "aff2euler"]
+__all__ = ["aff2euler", "space_time_realign"]
 
 
 def aff2euler(affine):

diff --git a/nipy/algorithms/statistics/models/tests/test_model.py b/nipy/algorithms/statistics/models/tests/test_model.py
@@ -82,19 +82,19 @@ def test_t_output():
     assert_array_almost_equal(res.effect, exp_effect)
     assert_array_almost_equal(res.sd, exp_sd)
     res = RESULTS.Tcontrast([1,0], store=('effect',))
-    assert res.t == None
+    assert res.t is None
     assert_array_almost_equal(res.effect, exp_effect)
-    assert res.sd == None
+    assert res.sd is None
     res = RESULTS.Tcontrast([1,0], store=('t',))
     assert_array_almost_equal(res.t, exp_t)
-    assert res.effect == None
-    assert res.sd == None
+    assert res.effect is None
+    assert res.sd is None
     res = RESULTS.Tcontrast([1,0], store=('sd',))
-    assert res.t == None
-    assert res.effect == None
+    assert res.t is None
+    assert res.effect is None
     assert_array_almost_equal(res.sd, exp_sd)
     res = RESULTS.Tcontrast([1,0], store=('effect', 'sd'))
-    assert res.t == None
+    assert res.t is None
     assert_array_almost_equal(res.effect, exp_effect)
     assert_array_almost_equal(res.sd, exp_sd)
 

diff --git a/nipy/algorithms/statistics/rft.py b/nipy/algorithms/statistics/rft.py
@@ -199,7 +199,8 @@ def __setattr__(self, key, val):
                 self.__dict__[key] = val
             else:
                 raise ValueError('expecting positive float or inf')
-        else: np.poly1d.__setattr__(self, key, val)
+        else:
+            np.poly1d.__setattr__(self, key, val)
 
     def compatible(self, other):
         """ Check compatibility of degrees of freedom
@@ -220,7 +221,7 @@ def compatible(self, other):
         False
         >>>
         """
-        if self.m != other.m:
+        if self.m != other.m:  # noqa: SIM103
             #raise ValueError, 'quasi polynomials are not compatible, m disagrees'
             return False
         return True

diff --git a/nipy/algorithms/statistics/tests/test_intrinsic_volumes.py b/nipy/algorithms/statistics/tests/test_intrinsic_volumes.py
@@ -43,7 +43,8 @@ def randombox(shape):
     for j in range(len(shape)):
         edges[j].sort()
         if edges[j][0] == edges[j][1]:
-            edges[j][0] = 0; edges[j][1] = shape[j]/2+1
+            edges[j][0] = 0
+            edges[j][1] = shape[j]/2+1
     return edges, box(shape, edges)
 
 

diff --git a/nipy/algorithms/statistics/utils.py b/nipy/algorithms/statistics/utils.py
@@ -196,20 +196,22 @@
                    (0, 7, 5, 1),
                    (0, 7, 4, 6),
                    (0, 3, 1, 7)]
-        vertices = []
-        for k in range(2):
-            for j in range(2):
-                for i in range(2):
-                    vertices.append((center[0]+i)*strides[0] +
-                                    (center[1]+j)*strides[1] +
-                                    (center[2]+k)*strides[2])
+        vertices = [
+            (center[0]+i)*strides[0] +
+            (center[1]+j)*strides[1] +
+            (center[2]+k)*strides[2]
+            for k in range(2)
+            for j in range(2)
+            for i in range(2)
+        ]
     elif d == 2:
         maximal = [(0,1,3), (0,2,3)]
-        vertices = []
-        for j in range(2):
-            for i in range(2):
-                    vertices.append((center[0]+i)*strides[0] +
-                                    (center[1]+j)*strides[1])
+        vertices = [
+            (center[0]+i)*strides[0] +
+            (center[1]+j)*strides[1]
+            for j in range(2)
+            for i in range(2)
+        ]
     elif d == 1:
         maximal = [(0,1)]
         vertices = [center[0],center[0]+strides[0]]
@@ -384,13 +386,17 @@
     ec = 0
 
     for t in decompose3d(shape, dim=4):
-        ec -= 1; ts += 1
+        ec -= 1
+        ts += 1
     for f in decompose3d(shape, dim=3):
-        ec += 1; fs += 1
+        ec += 1
+        fs += 1
     for e in decompose3d(shape, dim=2):
-        ec -= 1; es += 1
+        ec -= 1
+        es += 1
     for v in decompose3d(shape, dim=1):
-        ec += 1; vs += 1
+        ec += 1
+        vs += 1
     return ts, fs, es, vs, ec
 
 # Tell testing framework not to run this as a test
@@ -405,11 +411,14 @@
     ec = 0
 
     for f in decompose2d(shape, dim=3):
-        ec += 1; fs += 1
+        ec += 1
+        fs += 1
     for e in decompose2d(shape, dim=2):
-        ec -= 1; es += 1
+        ec -= 1
+        es += 1
     for v in decompose2d(shape, dim=1):
-        ec += 1; vs += 1
+        ec += 1
+        vs += 1
     return fs, es, vs, ec
 
 # Tell testing framework not to run this as a test

diff --git a/nipy/algorithms/utils/tests/test_fast_distance.py b/nipy/algorithms/utils/tests/test_fast_distance.py
@@ -18,7 +18,7 @@ def test_euclidean_1():
     ED = ed(X, Y)
     ref = np.zeros((nx, ny))
     for i in range(nx):
-    	ref[i] = np.sqrt(np.sum((Y - X[i])**2, 1))
+        ref[i] = np.sqrt(np.sum((Y - X[i])**2, 1))
 
     assert_almost_equal(ED, ref)
 
@@ -31,6 +31,6 @@ def test_euclidean_2():
     ED = ed(X)
     ref = np.zeros((nx, nx))
     for i in range(nx):
-    	ref[i] = np.sqrt(np.sum((X - X[i])**2, 1))
+        ref[i] = np.sqrt(np.sum((X - X[i])**2, 1))
 
     assert_almost_equal(ED, ref)
diff --git a/nipy/algorithms/utils/tests/test_matrices.py b/nipy/algorithms/utils/tests/test_matrices.py
@@ -12,7 +12,9 @@
 def test_matrix_rank():
     # Full rank matrix
     assert 4 == matrix_rank(np.eye(4))
-    I=np.eye(4); I[-1,-1] = 0. # rank deficient matrix
+    # rank deficient matrix
+    I=np.eye(4)
+    I[-1,-1] = 0.
     assert matrix_rank(I) == 3
     # All zeros - zero rank
     assert matrix_rank(np.zeros((4,4))) == 0

diff --git a/nipy/core/image/tests/test_image.py b/nipy/core/image/tests/test_image.py
@@ -210,7 +210,7 @@ def test_from_image():
     assert_array_equal(img.get_fdata(), img2.get_fdata())
     assert img.coordmap == img2.coordmap
     assert img.metadata == img2.metadata
-    assert not img.metadata is img2.metadata
+    assert img.metadata is not img2.metadata
     # optional inputs - data
     arr2 = arr + 10
     new = Image.from_image(img, arr2)

diff --git a/nipy/core/image/tests/test_image_spaces.py b/nipy/core/image/tests/test_image_spaces.py
@@ -70,13 +70,13 @@ def test_image_as_xyz_image():
         for tmap in (img_ro_out, img_ro_in, img_ro_both):
             assert not is_xyz_affable(tmap)
             img_r = as_xyz_image(tmap)
-            assert not tmap is img_r
+            assert tmap is not img_r
             assert img == img_r
             assert_array_equal(img.get_fdata(), img_r.get_fdata())
     img_t0 = rollimg(img, 't')
     assert not is_xyz_affable(img_t0)
     img_t0_r = as_xyz_image(img_t0)
-    assert not img_t0 is img_t0_r
+    assert img_t0 is not img_t0_r
     assert_array_equal(img.get_fdata(), img_t0_r.get_fdata())
     assert img.coordmap == img_t0_r.coordmap
     # Test against nibabel image

diff --git a/nipy/core/reference/__init__.py b/nipy/core/reference/__init__.py
@@ -42,5 +42,8 @@
 
 from . import coordinate_map, coordinate_system, slices
 
-__all__ = ["coordinate_system", "coordinate_map",
-           "slices"]
+__all__ = [
+           "coordinate_map",
+           "coordinate_system",
+           "slices",
+]
diff --git a/nipy/core/reference/tests/test_array_coords.py b/nipy/core/reference/tests/test_array_coords.py
@@ -25,8 +25,12 @@ def test_array_coord_map():
     # lost dimension, with all zeros, except for the translation in the
     # now-removed dimension, encoding the position of that particular
     # slice
-    xz = 1.1; yz = 2.3; zz = 3.5
-    xt = 10.0; yt = 11; zt = 12
+    xz = 1.1
+    yz = 2.3
+    zz = 3.5
+    xt = 10.0
+    yt = 11
+    zt = 12
     aff = np.diag([xz, yz, zz, 1])
     aff[:3,3] = [xt, yt, zt]
     shape = (2,3,4)