From 02a345973c2124429fcb916d51b2120ccfcc75ad Mon Sep 17 00:00:00 2001
From: Ghislain Vaillant <ghislain.vaillant@inria.fr>
Date: Mon, 3 Nov 2025 00:08:02 +0100
Subject: neuroscience: python-nitransforms: Update to 25.1.0.

* guix-science/packages/neuroscience.scm (python-nitransforms): Update to 25.1.0.
  [source]: Switch to git.
  [arguments]: Enable check.
---
 guix-science/packages/neuroscience.scm | 62 ++++++++++++++++++++++++++++------
 1 file changed, 51 insertions(+), 11 deletions(-)

diff --git a/guix-science/packages/neuroscience.scm b/guix-science/packages/neuroscience.scm
index 6dad6a0..69ca360 100644
--- a/guix-science/packages/neuroscience.scm
+++ b/guix-science/packages/neuroscience.scm
@@ -1517,22 +1517,62 @@ and semantically clear code.")
 (define-public python-nitransforms
   (package
     (name "python-nitransforms")
-    (version "24.1.4") ;NOTE: Version 25 requires numpy>=2.1.
+    (version "25.1.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "nitransforms" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/nipy/nitransforms")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0il1m5faf5k1s92wk6kwnfck07fw7j7i2418rcr6s60byjca98hd"))))
+        (base32 "1aiffnp9bvxqav6rkdhw49nph416shzbciha3chbag03f9w2pw02"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:tests? #f)) ;Requires external data.
-    (propagated-inputs (list python-h5py
-                             python-lxml
-                             python-nibabel
-                             python-numpy
-                             python-scipy))
+      #:test-flags
+      #~(list
+         ;; No traceback.
+         "--ignore=nitransforms/linear.py"
+         "--ignore=nitransforms/nonlinear.py"
+         ;; Requires external data.
+         "--ignore=nitransforms/tests/test_base.py"
+         "--ignore=nitransforms/tests/test_io.py"
+         "--ignore=nitransforms/tests/test_io_itk.py"
+         "--ignore=nitransforms/tests/test_resampling.py"
+         "--ignore=nitransforms/tests/test_surface.py"
+         "--deselect=nitransforms/tests/test_cli.py::test_apply_linear"
+         "--deselect=nitransforms/tests/test_cli.py::test_apply_nl"
+         "--deselect=nitransforms/tests/test_conversions.py::test_fsl2lta_conversions"
+         "--deselect=nitransforms/tests/test_conversions.py::test_itk2lta_conversions"
+         "--deselect=nitransforms/tests/test_conversions.py::test_lta2fsl_conversions"
+         "--deselect=nitransforms/tests/test_linear.py::test_loadsave"
+         "--deselect=nitransforms/tests/test_linear.py::test_linear_save"
+         "--deselect=nitransforms/tests/test_linear.py::test_mulmat_operator"
+         "--deselect=nitransforms/tests/test_nonlinear.py::test_densefield_map"
+         "--deselect=nitransforms/tests/test_nonlinear.py::test_displacements_to_filename"
+         "--deselect=nitransforms/tests/test_nonlinear.py::test_bspline_map_gridpoints"
+         "--deselect=nitransforms/tests/test_nonlinear.py::test_bsplines_references")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-pyproject
+            (lambda _
+              (substitute* "pyproject.toml"
+                ;; Relax minimum version for numpy.
+                (("\"numpy.*>=.*\",")
+                 "\"numpy\",")
+                ;; Do not stop after first test failure.
+                (("-svx")
+                 "-sv"))))
+          (add-before 'build 'set-version
+            (lambda _
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+                      #$version)))
+          (add-before 'check 'set-home
+            (lambda _
+              (setenv "HOME" "/tmp"))))))
+    (propagated-inputs (list python-h5py python-lxml python-nibabel
+                             python-numpy python-scipy))
     (native-inputs (list python-pytest
                          python-pytest-cov
                          python-pytest-env
@@ -1540,7 +1580,7 @@ and semantically clear code.")
                          python-setuptools
                          python-setuptools-scm))
     (home-page "https://nitransforms.readthedocs.io")
-    (synopsis "Neuroimaging spatial transforms in Python.")
+    (synopsis "Neuroimaging spatial transforms in Python")
     (description
      "@code{niworkflows} is capable of converting between formats and resampling
 images to apply transforms generated by the most popular neuroimaging packages
-- 
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