Update cuCIM for consistency with scikit-image 0.26 (#1038)

.pre-commit-config.yaml

@@ -231,6 +231,7 @@ repos:
             ^python/cucim/src/cucim/skimage/restoration/tests/test_restoration[.]py$|
             ^python/cucim/src/cucim/skimage/restoration/uft[.]py$|
             ^python/cucim/src/cucim/skimage/segmentation/__init__[.]py$|
+            ^python/cucim/src/cucim/skimage/segmentation/__init__[.]pyi$|
             ^python/cucim/src/cucim/skimage/segmentation/_chan_vese[.]py$|
             ^python/cucim/src/cucim/skimage/segmentation/_clear_border[.]py$|
             ^python/cucim/src/cucim/skimage/segmentation/_join[.]py$|
@@ -509,6 +510,7 @@ repos:
             python/cucim/src/cucim/skimage/restoration/tests/test_restoration[.]py$|
             python/cucim/src/cucim/skimage/restoration/uft[.]py$|
             python/cucim/src/cucim/skimage/segmentation/__init__[.]py$|
+            python/cucim/src/cucim/skimage/segmentation/__init__[.]pyi$|
             python/cucim/src/cucim/skimage/segmentation/_chan_vese[.]py$|
             python/cucim/src/cucim/skimage/segmentation/_clear_border[.]py$|
             python/cucim/src/cucim/skimage/segmentation/_join[.]py$|

conda/environments/all_cuda-129_arch-aarch64.yaml

@@ -39,7 +39,7 @@ dependencies:
 - python>=3.11,<3.14
 - pywavelets>=1.6
 - recommonmark
-- scikit-image>=0.19.0,<0.26.0
+- scikit-image>=0.23.2,<0.27.0
 - scipy>=1.11.2
 - sphinx>=8.0.0,<8.2.0
 - sysroot_linux-aarch64==2.28

conda/environments/all_cuda-129_arch-x86_64.yaml

@@ -40,7 +40,7 @@ dependencies:
 - python>=3.11,<3.14
 - pywavelets>=1.6
 - recommonmark
-- scikit-image>=0.19.0,<0.26.0
+- scikit-image>=0.23.2,<0.27.0
 - scipy>=1.11.2
 - sphinx>=8.0.0,<8.2.0
 - sysroot_linux-64==2.28

conda/environments/all_cuda-131_arch-aarch64.yaml

@@ -39,7 +39,7 @@ dependencies:
 - python>=3.11,<3.14
 - pywavelets>=1.6
 - recommonmark
-- scikit-image>=0.19.0,<0.26.0
+- scikit-image>=0.23.2,<0.27.0
 - scipy>=1.11.2
 - sphinx>=8.0.0,<8.2.0
 - sysroot_linux-aarch64==2.28

conda/environments/all_cuda-131_arch-x86_64.yaml

@@ -40,7 +40,7 @@ dependencies:
 - python>=3.11,<3.14
 - pywavelets>=1.6
 - recommonmark
-- scikit-image>=0.19.0,<0.26.0
+- scikit-image>=0.23.2,<0.27.0
 - scipy>=1.11.2
 - sphinx>=8.0.0,<8.2.0
 - sysroot_linux-64==2.28

dependencies.yaml

@@ -237,7 +237,7 @@ dependencies:
           - click
           - lazy-loader>=0.4
           - numpy>=1.23.4,<3.0
-          - scikit-image>=0.19.0,<0.26.0
+          - scikit-image>=0.23.2,<0.27.0
           - scipy>=1.11.2
       - output_types: conda
         packages:

python/cucim/pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "lazy-loader>=0.4",
     "numpy>=1.23.4,<3.0",
     "nvidia-nvimgcodec-cu13>=0.7.0,<0.8.0",
-    "scikit-image>=0.19.0,<0.26.0",
+    "scikit-image>=0.23.2,<0.27.0",
     "scipy>=1.11.2",
 ] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 classifiers = [

python/cucim/src/cucim/skimage/_shared/compat.py

@@ -1,5 +1,5 @@
 # SPDX-FileCopyrightText: 2009-2022 the scikit-image team
-# SPDX-FileCopyrightText: Copyright (c) 2024-2025, NVIDIA CORPORATION. All rights reserved.
+# SPDX-FileCopyrightText: Copyright (c) 2024-2026, NVIDIA CORPORATION. All rights reserved.
 # SPDX-License-Identifier: Apache-2.0 AND BSD-3-Clause
 
 """Compatibility helpers for dependencies."""
@@ -28,6 +28,7 @@
 # check CuPy instead of SciPy
 CUPY_LT_14 = parse(cp.__version__) < parse("14.0.0a1")
 
+
 # Starting in SciPy v1.12, 'scipy.sparse.linalg.cg' keyword argument `tol` is
 # deprecated in favor of `rtol`. The corresponding change in cupyx.scipy.sparse
 # was made in v14.0

python/cucim/src/cucim/skimage/_shared/coord.py

@@ -1,5 +1,5 @@
 # SPDX-FileCopyrightText: 2009-2022 the scikit-image team
-# SPDX-FileCopyrightText: Copyright (c) 2021-2025, NVIDIA CORPORATION. All rights reserved.
+# SPDX-FileCopyrightText: Copyright (c) 2021-2026, NVIDIA CORPORATION. All rights reserved.
 # SPDX-License-Identifier: Apache-2.0 AND BSD-3-Clause
 
 import cupy as cp
@@ -22,7 +22,7 @@ def _ensure_spacing(coord, spacing, p_norm, max_out):
         A finite large p may cause a ValueError if overflow can occur.
         ``inf`` corresponds to the Chebyshev distance and 2 to the
         Euclidean distance.
-    max_out: int
+    max_out : int
         If not None, at most the first ``max_out`` candidates are
         returned.
 

python/cucim/src/cucim/skimage/_shared/tests/test_utils.py

@@ -1,7 +1,7 @@
 # SPDX-FileCopyrightText: 2009-2022 the scikit-image team
-# SPDX-FileCopyrightText: Copyright (c) 2021-2025, NVIDIA CORPORATION. All rights reserved.
+# SPDX-FileCopyrightText: Copyright (c) 2021-2026, NVIDIA CORPORATION. All rights reserved.
 # SPDX-License-Identifier: Apache-2.0 AND BSD-3-Clause
-
+import re
 import sys
 import warnings
 
@@ -12,11 +12,14 @@
 from cucim.skimage._shared import testing
 from cucim.skimage._shared.utils import (
     DEPRECATED,
+    FailedEstimation,
+    FailedEstimationAccessError,
     _supported_float_type,
     _validate_interpolation_order,
     change_default_value,
     channel_as_last_axis,
     check_nD,
+    deprecate_func,
     deprecate_parameter,
 )
 
@@ -34,7 +37,9 @@
 
 
 def test_change_default_value():
-    @change_default_value("arg1", new_value=-1, changed_version="0.12")
+    @change_default_value(
+        "arg1", new_value=-1, changed_version="0.12", stacklevel=2
+    )
     def foo(arg0, arg1=0, arg2=1):
         """Expected docstring"""
         return arg0, arg1, arg2
@@ -44,6 +49,7 @@ def foo(arg0, arg1=0, arg2=1):
         new_value=-1,
         changed_version="0.12",
         warning_msg="Custom warning message",
+        stacklevel=2,
     )
     def bar(arg0, arg1=0, arg2=1):
         """Expected docstring"""
@@ -202,6 +208,29 @@ def test_decorated_channel_axis_shape(channel_axis):
         assert size == x.shape[channel_axis]
 
 
+@deprecate_func(
+    deprecated_version="x", removed_version="y", hint="You are on your own."
+)
+def _deprecated_func():
+    """Dummy function used in `test_deprecate_func`.
+
+    The decorated function must be outside the test function, otherwise it
+    seems that the warning does not point at the calling location.
+    """
+
+
+def test_deprecate_func():
+    with pytest.warns(FutureWarning) as record:
+        _deprecated_func()
+        testing.assert_stacklevel(record)
+
+    assert len(record) == 1
+    assert record[0].message.args[0] == (
+        "`_deprecated_func` is deprecated since version x and will be removed in "
+        "version y. You are on your own."
+    )
+
+
 @deprecate_parameter("old1", start_version="0.10", stop_version="0.12")
 @deprecate_parameter("old0", start_version="0.10", stop_version="0.12")
 def _func_deprecated_params(arg0, old0=DEPRECATED, old1=DEPRECATED, arg1=None):
@@ -478,15 +507,15 @@ def test_wrong_call_signature(self):
                 _func_deprecated_params(1, 2, old0=2)
 
     def test_wrong_param_name(self):
-        with pytest.raises(ValueError, match="'old' is not in list"):
+        with pytest.raises(ValueError, match="'old' not in parameters"):
 
             @deprecate_parameter(
                 "old", start_version="0.10", stop_version="0.12"
             )
             def foo(arg0):
                 pass
 
-        with pytest.raises(ValueError, match="'new' is not in list"):
+        with pytest.raises(ValueError, match="'new' not in parameters"):
 
             @deprecate_parameter(
                 "old", new_name="new", start_version="0.10", stop_version="0.12"
@@ -509,7 +538,8 @@ def test_stacklevel(self):
         def foo(arg0, old=DEPRECATED):
             pass
 
-        with pytest.raises(RuntimeError, match="Set stacklevel manually"):
+        regex = "Cannot determine stacklevel.*Set the stacklevel manually"
+        with pytest.raises(ValueError, match=regex):
             foo(0, 1)
 
         @deprecate_parameter(
@@ -526,3 +556,24 @@ def bar(arg0, old=DEPRECATED):
         ) as records:
             bar(0, 1)
             testing.assert_stacklevel(records)
+
+
+def test_failed_estimation():
+    msg = "Something went wrong with estimation"
+    fe = FailedEstimation(msg)
+    assert fe.message == msg
+    assert str(fe) == msg
+    assert repr(fe).startswith("FailedEstimation(")
+    assert bool(fe) is False
+
+    regex = re.compile(
+        "FailedEstimation is not callable.*Hint", flags=re.DOTALL
+    )
+    with pytest.raises(FailedEstimationAccessError, match=regex):
+        fe(np.ones((10, 2)))
+
+    regex = re.compile(
+        "FailedEstimation has no attribute 'params'.*Hint", flags=re.DOTALL
+    )
+    with pytest.raises(FailedEstimationAccessError, match=regex):
+        fe.params