Fix deprecated argument in 'scipy.sparse.linalg.cg'

.github/workflows/pythonapp.yml

@@ -130,10 +130,10 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - name: Set up Python 3.8
+    - name: Set up Python 3.9
       uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.9'
     - name: cache weekly timestamp
       id: pip-cache
       run: |

docs/requirements.txt

@@ -6,7 +6,7 @@ itk>=5.2
 nibabel
 parameterized
 scikit-image>=0.19.0
-scipy>=1.7.1
+scipy>=1.12.0; python_version >= '3.9'
 tensorboard
 commonmark==0.9.1
 recommonmark==0.6.0

monai/data/ultrasound_confidence_map.py

@@ -19,10 +19,10 @@
 __all__ = ["UltrasoundConfidenceMap"]
 
 cv2, _ = optional_import("cv2")
-csc_matrix, _ = optional_import("scipy.sparse", "1.7.1", min_version, "csc_matrix")
-spsolve, _ = optional_import("scipy.sparse.linalg", "1.7.1", min_version, "spsolve")
-cg, _ = optional_import("scipy.sparse.linalg", "1.7.1", min_version, "cg")
-hilbert, _ = optional_import("scipy.signal", "1.7.1", min_version, "hilbert")
+csc_matrix, _ = optional_import("scipy.sparse", "1.12.0", min_version, "csc_matrix")
+spsolve, _ = optional_import("scipy.sparse.linalg", "1.12.0", min_version, "spsolve")
+cg, _ = optional_import("scipy.sparse.linalg", "1.12.0", min_version, "cg")
+hilbert, _ = optional_import("scipy.signal", "1.12.0", min_version, "hilbert")
 ruge_stuben_solver, _ = optional_import("pyamg", "5.0.0", min_version, "ruge_stuben_solver")
 
 
@@ -285,7 +285,7 @@ def _solve_linear_system(self, lap, rhs):
             lap_sparse = lap.tocsr()
             ml = ruge_stuben_solver(lap_sparse, coarse_solver="pinv")
             m = ml.aspreconditioner(cycle="V")
-            x, _ = cg(lap, rhs, tol=self.cg_tol, maxiter=self.cg_maxiter, M=m)
+            x, _ = cg(lap, rhs, rtol=self.cg_tol, maxiter=self.cg_maxiter, M=m)
         else:
             x = spsolve(lap, rhs)
 

requirements-dev.txt

@@ -2,7 +2,7 @@
 -r requirements-min.txt
 pytorch-ignite==0.4.11
 gdown>=4.7.3
-scipy>=1.7.1
+scipy>=1.12.0; python_version >= '3.9'
 itk>=5.2
 nibabel
 pillow!=8.3.0  # https://github.com/python-pillow/Pillow/issues/5571

setup.cfg

@@ -49,7 +49,7 @@ all =
     nibabel
     ninja
     scikit-image>=0.14.2
-    scipy>=1.7.1
+    scipy>=1.12.0; python_version >= '3.9'
     pillow
     tensorboard
     gdown>=4.7.3
@@ -92,7 +92,7 @@ ninja =
 skimage =
     scikit-image>=0.14.2
 scipy =
-    scipy>=1.7.1
+    scipy>=1.12.0; python_version >= '3.9'
 pillow =
     pillow!=8.3.0
 tensorboard =

tests/test_ultrasound_confidence_map_transform.py

@@ -21,6 +21,9 @@
 
 from monai.transforms import UltrasoundConfidenceMapTransform
 from tests.utils import assert_allclose
+from monai.utils import optional_import
+
+_, has_scipy = optional_import("scipy")
 
 TEST_INPUT = np.array(
     [
@@ -482,6 +485,7 @@
 )
 
 
+@unittest.skipUnless(has_scipy, "Requires scipy")
 class TestUltrasoundConfidenceMapTransform(unittest.TestCase):
 
     def setUp(self):