From 8aeb320d8b0c68785127b7f1140b341a383617b4 Mon Sep 17 00:00:00 2001
From: Benjamin A. Beasley <code@musicinmybrain.net>
Date: Sep 25 2023 17:04:00 +0000
Subject: Update to a current snapshot (5d53932)


---

diff --git a/.gitignore b/.gitignore
index 7048709..1c43c2d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
 /nipy-35a5f5205ba2aa54f1f0524564a6f1f8dafb237f.tar.gz
 /nipy-9512cd93b7215b4c750be3968a600c06f2bd22f6.tar.gz
 /nipy-7eede02471567487e454016c1e7cf637d3afac9e.tar.gz
+/nipy-5d539326c92f23a2fa782a70d5b4b5f70a0097d7.tar.gz
diff --git a/0001-Account-for-nibabel-5.0.0-removal-of-.py3k-shim-use-.patch b/0001-Account-for-nibabel-5.0.0-removal-of-.py3k-shim-use-.patch
index 7da6010..7211eb7 100644
--- a/0001-Account-for-nibabel-5.0.0-removal-of-.py3k-shim-use-.patch
+++ b/0001-Account-for-nibabel-5.0.0-removal-of-.py3k-shim-use-.patch
@@ -1,4 +1,4 @@
-From a8faab52ca5e59069ac871f63a8604d2ac26c433 Mon Sep 17 00:00:00 2001
+From 86bed318417caa13c4a95ffb027d7c98edd3067c Mon Sep 17 00:00:00 2001
 From: "Benjamin A. Beasley" <code@musicinmybrain.net>
 Date: Tue, 7 Feb 2023 17:49:20 -0500
 Subject: [PATCH] Account for nibabel 5.0.0 removal of .py3k shim - use
@@ -57,7 +57,7 @@ index c349e381..72c5a096 100644
      True
      """
 diff --git a/nipy/core/image/tests/test_image_spaces.py b/nipy/core/image/tests/test_image_spaces.py
-index 262b27f7..528bdf7f 100644
+index f48317d1..41bf724f 100644
 --- a/nipy/core/image/tests/test_image_spaces.py
 +++ b/nipy/core/image/tests/test_image_spaces.py
 @@ -34,7 +34,7 @@ def test_image_xyz_affine():
@@ -70,7 +70,7 @@ index 262b27f7..528bdf7f 100644
      assert_array_equal(xyz_affine(nimg), aff)
      # Any dimensions not spatial, AxesError
 @@ -77,7 +77,7 @@ def test_image_as_xyz_image():
-     assert_array_equal(img.get_data(), img_t0_r.get_data())
+     assert_array_equal(img.get_fdata(), img_t0_r.get_fdata())
      assert_equal(img.coordmap, img_t0_r.coordmap)
      # Test against nibabel image
 -    nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]))
@@ -79,10 +79,10 @@ index 262b27f7..528bdf7f 100644
      assert_true(nimg is nimg_r)
      # It's sometimes impossible to make an xyz affable image
 diff --git a/nipy/io/tests/test_image_io.py b/nipy/io/tests/test_image_io.py
-index 5c5d940f..b15fea54 100644
+index 695f9313..37aaaca3 100644
 --- a/nipy/io/tests/test_image_io.py
 +++ b/nipy/io/tests/test_image_io.py
-@@ -44,7 +44,7 @@ def test_badfile():
+@@ -45,7 +45,7 @@ def test_badfile():
      # nibabel prior 2.1.0 was throwing a ImageFileError for the not-recognized
      # file type.  >=2.1.0 give a FileNotFoundError.
      try:
@@ -92,7 +92,7 @@ index 5c5d940f..b15fea54 100644
          FileNotFoundError = IOError
      assert_raises((ImageFileError, FileNotFoundError), load_image, filename)
 diff --git a/nipy/labs/spatial_models/parcel_io.py b/nipy/labs/spatial_models/parcel_io.py
-index 89030f8d..934d9faa 100644
+index d50f50d2..4eed7931 100644
 --- a/nipy/labs/spatial_models/parcel_io.py
 +++ b/nipy/labs/spatial_models/parcel_io.py
 @@ -53,7 +53,7 @@ def mask_parcellation(mask_images, nb_parcel, threshold=0, output_image=None):
@@ -127,22 +127,22 @@ index c2c6ece2..d3b269dc 100644
      ddom = grid_domain_from_image(mim)
      ddom.make_feature_from_image(nim, 'noise')
 diff --git a/nipy/labs/spatial_models/tests/test_mroi.py b/nipy/labs/spatial_models/tests/test_mroi.py
-index 7f8c5420..0ceb7ad8 100644
+index 26b02da9..4c5cc35c 100644
 --- a/nipy/labs/spatial_models/tests/test_mroi.py
 +++ b/nipy/labs/spatial_models/tests/test_mroi.py
 @@ -205,8 +205,8 @@ def test_example():
      # Test example runs correctly
      eg_img = pjoin(dirname(__file__), 'some_blobs.nii')
      nim = load(eg_img)
--    mask_image = Nifti1Image((nim.get_data() ** 2 > 0).astype('u8'),
+-    mask_image = Nifti1Image((nim.get_fdata() ** 2 > 0).astype('u8'),
 -                             get_affine(nim))
-+    arr = nim.get_data() ** 2 > 0
++    arr = nim.get_fdata() ** 2 > 0
 +    mask_image = Nifti1Image(arr.astype('u1'), get_affine(nim))
      domain = grid_domain_from_image(mask_image)
-     data = nim.get_data()
+     data = nim.get_fdata()
      values = data[data != 0]
 diff --git a/nipy/labs/spatial_models/tests/test_parcel_io.py b/nipy/labs/spatial_models/tests/test_parcel_io.py
-index 62d03318..87e8f26b 100644
+index c158841f..4d880c59 100644
 --- a/nipy/labs/spatial_models/tests/test_parcel_io.py
 +++ b/nipy/labs/spatial_models/tests/test_parcel_io.py
 @@ -17,7 +17,7 @@ def test_mask_parcel():
@@ -152,7 +152,7 @@ index 62d03318..87e8f26b 100644
 -    mask_image = Nifti1Image(np.ones(shape), np.eye(4))
 +    mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
      wim = mask_parcellation(mask_image, n_parcels)
-     assert_equal(np.unique(wim.get_data()), np.arange(n_parcels))
+     assert_equal(np.unique(wim.get_fdata()), np.arange(n_parcels))
  
 @@ -33,8 +33,8 @@ def test_mask_parcel_multi_subj():
      with InTemporaryDirectory():
@@ -231,5 +231,5 @@ index d3fd0fab..e98c47ce 100755
  from argparse import ArgumentParser, RawDescriptionHelpFormatter
  
 -- 
-2.39.1
+2.41.0
 
diff --git a/509.patch b/509.patch
deleted file mode 100644
index cbd9961..0000000
--- a/509.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-From b0de4e839a968520d569a021327df81e5c3841a9 Mon Sep 17 00:00:00 2001
-From: "Benjamin A. Beasley" <code@musicinmybrain.net>
-Date: Thu, 21 Sep 2023 09:34:56 -0400
-Subject: [PATCH] Stop using deprecated unittest.TestCase.assert_() alias
-
-This was removed in Python 3.12.
----
- nipy/algorithms/clustering/tests/test_clustering.py | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/nipy/algorithms/clustering/tests/test_clustering.py b/nipy/algorithms/clustering/tests/test_clustering.py
-index 361315701..d365748b8 100644
---- a/nipy/algorithms/clustering/tests/test_clustering.py
-+++ b/nipy/algorithms/clustering/tests/test_clustering.py
-@@ -17,7 +17,7 @@ def testkmeans1(self):
-         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.assert_(np.mean(L[:7]) < 0.5)
-+        self.assertLess(np.mean(L[:7]), 0.5)
- 
-     def testkmeans2(self):
-         X = nr.randn(10000, 2)
-@@ -26,7 +26,7 @@ def testkmeans2(self):
-         L = np.concatenate([np.ones(5000), np.zeros(5000)]).astype(np.int_)
-         C, L, J = kmeans(X, 2, L)
-         l = L[:7000].astype(np.float64)
--        self.assert_(np.mean(l) > 0.9)
-+        self.assertGreater(np.mean(l), 0.9)
- 
- 
- if __name__ == '__main__':
diff --git a/python-nipy.spec b/python-nipy.spec
index 0072d10..7f953c1 100644
--- a/python-nipy.spec
+++ b/python-nipy.spec
@@ -10,8 +10,8 @@
 # https://github.com/nipy/nipy/pull/503#issuecomment-1421508175
 %bcond_with doc_pdf
 
-%global commit 7eede02471567487e454016c1e7cf637d3afac9e
-%global snapdate 20230405
+%global commit 5d539326c92f23a2fa782a70d5b4b5f70a0097d7
+%global snapdate 20230921
 
 Name:           python-nipy
 Version:        0.5.0^%{snapdate}git%(c='%{commit}'; echo "${c:0:7}")
@@ -49,9 +49,6 @@ Patch:          https://github.com/nipy/nipy/pull/504/commits/a6de01c7484114aa52
 # Nipy using deprecated nibabel decorator
 # https://github.com/nipy/nipy/issues/505
 Patch:          https://github.com/nipy/nipy/pull/507/commits/9fbe55494c62727006f143dc66cf6423c0884a56.patch
-# Stop using deprecated unittest.TestCase.assert_() alias
-# https://github.com/nipy/nipy/pull/509
-Patch:          https://github.com/nipy/nipy/pull/509.patch
 
 BuildRequires:  gcc
 BuildRequires:  flexiblas-devel
diff --git a/sources b/sources
index 730d68c..5d041ef 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-SHA512 (nipy-7eede02471567487e454016c1e7cf637d3afac9e.tar.gz) = b9bc48965590d7ad3059cb9468e8add69a345c332bd7af80987ad960cd5ca3b4046d76af1d2ca2e7d29b9721ceb16337ef6c9d40de9ae372a5f299494c613f1e
+SHA512 (nipy-5d539326c92f23a2fa782a70d5b4b5f70a0097d7.tar.gz) = 3a84f92272d7219e9f1e20d98812c3d11434350e17559c47416c6a0fc276db55079b226e5b599379412133e64b8d15023d8e98fd5b9eb231ccc0881f0f2e51c0