Incorporate upstream changes from scikit-image 0.25

conda/environments/all_cuda-118_arch-x86_64.yaml

@@ -16,12 +16,12 @@ dependencies:
 - gcc_linux-64=11.*
 - imagecodecs>=2021.6.8
 - ipython
-- lazy_loader>=0.1
+- lazy-loader>=0.4
 - libcufile-dev=1.4.0.31
 - libcufile=1.4.0.31
 - libnvjpeg-dev=11.6.0.55
 - libnvjpeg=11.6.0.55
-- matplotlib-base
+- matplotlib-base>=3.7
 - nbsphinx
 - ninja
 - numpy>=1.23.4,<3.0a0
@@ -36,15 +36,15 @@ dependencies:
 - pytest-cov>=2.12.1
 - pytest-lazy-fixtures>=1.0.0
 - pytest-xdist
-- pytest>=6.2.4,<8.0.0a0
+- pytest>=7.0.0,<9.0.0a0
 - python>=3.10,<3.13
-- pywavelets>=1.0
+- pywavelets>=1.6
 - recommonmark
-- scikit-image>=0.19.0,<0.25.0a0
-- scipy>=1.6.0
+- scikit-image>=0.19.0,<0.26.0a0
+- scipy>=1.11.2
 - sphinx<6
 - sysroot_linux-64==2.17
-- tifffile>=2022.7.28
+- tifffile>=2022.8.12
 - yasm
 - pip:
   - opencv-python-headless>=4.6

conda/environments/all_cuda-125_arch-x86_64.yaml

@@ -17,11 +17,11 @@ dependencies:
 - gcc_linux-64=11.*
 - imagecodecs>=2021.6.8
 - ipython
-- lazy_loader>=0.1
+- lazy-loader>=0.4
 - libcufile-dev
 - libnvjpeg-dev
 - libnvjpeg-static
-- matplotlib-base
+- matplotlib-base>=3.7
 - nbsphinx
 - ninja
 - numpy>=1.23.4,<3.0a0
@@ -35,15 +35,15 @@ dependencies:
 - pytest-cov>=2.12.1
 - pytest-lazy-fixtures>=1.0.0
 - pytest-xdist
-- pytest>=6.2.4,<8.0.0a0
+- pytest>=7.0.0,<9.0.0a0
 - python>=3.10,<3.13
-- pywavelets>=1.0
+- pywavelets>=1.6
 - recommonmark
-- scikit-image>=0.19.0,<0.25.0a0
-- scipy>=1.6.0
+- scikit-image>=0.19.0,<0.26.0a0
+- scipy>=1.11.2
 - sphinx<6
 - sysroot_linux-64==2.17
-- tifffile>=2022.7.28
+- tifffile>=2022.8.12
 - yasm
 - pip:
   - opencv-python-headless>=4.6

dependencies.yaml

@@ -258,10 +258,10 @@ dependencies:
       - output_types: [conda, requirements, pyproject]
         packages:
           - click
-          - lazy_loader>=0.1
+          - lazy-loader>=0.4
           - numpy>=1.23.4,<3.0a0
-          - scikit-image>=0.19.0,<0.25.0a0
-          - scipy>=1.6.0
+          - scikit-image>=0.19.0,<0.26.0a0
+          - scipy>=1.11.2
       - output_types: conda
         packages:
           - cupy>=12.0.0
@@ -285,17 +285,17 @@ dependencies:
       - output_types: [conda, requirements, pyproject]
         packages:
           - psutil>=5.8.0
-          - pytest>=6.2.4,<8.0.0a0
+          - pytest>=7.0.0,<9.0.0a0
           - pytest-cov>=2.12.1
           - pytest-lazy-fixtures>=1.0.0
           - pytest-xdist
-          - tifffile>=2022.7.28
+          - tifffile>=2022.8.12
           - pooch>=1.6.0  # needed to download scikit-image sample data
-          - pywavelets>=1.0
+          - pywavelets>=1.6
       - output_types: [conda]
         packages:
           - imagecodecs>=2021.6.8
-          - matplotlib-base
+          - matplotlib-base>=3.7
           - openslide-python>=1.3.0
           - pip
           - pip:
@@ -305,9 +305,9 @@ dependencies:
           # skip packages on arm64 that don't provide a wheel
           - imagecodecs>=2021.6.8; platform_machine=='x86_64'
           - openslide-python>=1.3.0; platform_machine=='x86_64'
-          - matplotlib
+          - matplotlib>=3.7
           - opencv-python-headless>=4.6
       - output_types: [pyproject]
         packages:
           # Already added to requirements via docs. This is for tests.
-          - numpydoc>=1.5
+          - numpydoc>=1.7

python/cucim/pyproject.toml

@@ -26,10 +26,10 @@ requires-python = ">=3.10"
 dependencies = [
     "click",
     "cupy-cuda11x>=12.0.0",
-    "lazy_loader>=0.1",
+    "lazy-loader>=0.4",
     "numpy>=1.23.4,<3.0a0",
-    "scikit-image>=0.19.0,<0.25.0a0",
-    "scipy>=1.6.0",
+    "scikit-image>=0.19.0,<0.26.0a0",
+    "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 = [
     "Development Status :: 4 - Beta",
@@ -58,18 +58,18 @@ Tracker = "https://github.com/rapidsai/cucim/issues"
 [project.optional-dependencies]
 test = [
     "imagecodecs>=2021.6.8; platform_machine=='x86_64'",
-    "matplotlib",
-    "numpydoc>=1.5",
+    "matplotlib>=3.7",
+    "numpydoc>=1.7",
     "opencv-python-headless>=4.6",
     "openslide-python>=1.3.0; platform_machine=='x86_64'",
     "pooch>=1.6.0",
     "psutil>=5.8.0",
     "pytest-cov>=2.12.1",
     "pytest-lazy-fixtures>=1.0.0",
     "pytest-xdist",
-    "pytest>=6.2.4,<8.0.0a0",
-    "pywavelets>=1.0",
-    "tifffile>=2022.7.28",
+    "pytest>=7.0.0,<9.0.0a0",
+    "pywavelets>=1.6",
+    "tifffile>=2022.8.12",
 ] # This list was generated by `rapids-dependency-file-generator`. To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
 developer = [
     "black",

python/cucim/src/cucim/__init__.py

@@ -59,9 +59,9 @@
 except ImportError:
     pass
 
-import lazy_loader as lazy
+import lazy_loader as _lazy
 
-__getattr__, __lazy_dir__, _ = lazy.attach_stub(__name__, __file__)
+__getattr__, __lazy_dir__, _ = _lazy.attach_stub(__name__, __file__)
 
 
 def __dir__():

python/cucim/src/cucim/skimage/__init__.py

@@ -17,21 +17,24 @@
 exposure
     Image intensity adjustment, e.g., histogram equalization, etc.
 feature
-    Feature detection and extraction, e.g., texture analysis corners, etc.
+    Feature detection and extraction, e.g., texture analysis, corners, etc.
 filters
     Sharpening, edge finding, rank filters, thresholding, etc.
 measure
-    Measurement of image properties, e.g., region properties and contours.
+    Measurement of image properties, e.g., region properties, moments.
 metrics
-    Metrics corresponding to images, e.g. distance metrics, similarity, etc.
+    Metrics corresponding to images, e.g., distance metrics, similarity, etc.
 morphology
-    Morphological operations, e.g., opening or skeletonization.
+    Morphological algorithms, e.g., closing, opening, skeletonization.
+registration
+    Image registration algorithms, e.g., optical flow or phase cross
+    correlation.
 restoration
     Restoration algorithms, e.g., deconvolution algorithms, denoising, etc.
 segmentation
-    Partitioning an image into multiple regions.
+    Algorithms to partition images into meaningful regions or boundaries.
 transform
-    Geometric and other transforms, e.g., rotation or the Radon transform.
+    Geometric and other transformations, e.g., rotations, warp.
 util
     Generic utilities.
 
@@ -60,13 +63,32 @@
 
 """
 
-import lazy_loader as lazy
+import lazy_loader as _lazy
 
-__getattr__, __lazy_dir__, _ = lazy.attach_stub(__name__, __file__)
+__getattr__, __lazy_dir__, _ = _lazy.attach_stub(__name__, __file__)
+
+# Don't use the `__all__` and `__dir__` returned by `attach_stub` since that
+# one would expose utility functions we don't want to advertise in our
+# top-level module anymore.
+__all__ = [
+    "color",
+    "data",
+    "exposure",
+    "feature",
+    "filters",
+    "measure",
+    "metrics",
+    "morphology",
+    "registration",
+    "restoration",
+    "segmentation",
+    "transform",
+    "util",
+]
 
 
 def __dir__():
-    return __lazy_dir__()
+    return __all__.copy()
 
 
 # Legacy imports into the root namespace; not advertised in __all__

python/cucim/src/cucim/skimage/__init__.pyi

@@ -1,5 +1,3 @@
-import lazy_loader as lazy  # noqa: F401
-
 submodules = [
     "color",
     "data",

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

@@ -10,21 +10,12 @@
 
 import cucim.skimage._vendored.ndimage as ndi
 
-from .._shared.utils import (
-    DEPRECATED,
-    _supported_float_type,
-    convert_to_float,
-    deprecate_parameter,
-)
+from .._shared.utils import _supported_float_type, convert_to_float
 
 
-@deprecate_parameter(
-    "output", new_name="out", start_version="24.06", stop_version="25.02"
-)
 def gaussian(
     image,
     sigma=1,
-    output=DEPRECATED,
     mode="nearest",
     cval=0,
     preserve_range=False,

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

@@ -50,7 +50,7 @@ def assert_stacklevel(warnings, *, offset=-1):
     When cucim.skimage raises warnings, the stacklevel should ideally be set
     so that the origin of the warnings will point to the public function
     that was called by the user and not necessarily the very place where the
-    warnings were emitted (which may be inside of some internal function).
+    warnings were emitted (which may be inside some internal function).
     This utility function helps with checking that
     the stacklevel was set correctly on warnings captured by `pytest.warns`.
 
@@ -84,10 +84,19 @@ def assert_stacklevel(warnings, *, offset=-1):
     ...         )
     ...     assert_stacklevel(record, offset=-3)
     """
+    __tracebackhide__ = True  # Hide traceback for py.test
+
     frame = inspect.stack()[1].frame  # 0 is current frame, 1 is outer frame
     line_number = frame.f_lineno + offset
     filename = frame.f_code.co_filename
     expected = f"{filename}:{line_number}"
     for warning in warnings:
         actual = f"{warning.filename}:{warning.lineno}"
         assert actual == expected, f"{actual} != {expected}"
+        msg = (
+            "Warning with wrong stacklevel:\n"
+            f"  Expected: {expected}\n"
+            f"  Actual: {actual}\n"
+            f"  {warning.category.__name__}: {warning.message}"
+        )
+        assert actual == expected, msg

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

@@ -319,31 +319,21 @@ def test_warning_removed_param(self):
             r".*_func_deprecated_params`."
         )
         with pytest.warns(FutureWarning, match=match):
-            assert _func_deprecated_params(1, 2) == (
-                1,
-                DEPRECATED,
-                DEPRECATED,
-                None,
-            )
+            assert _func_deprecated_params(1, 2) == (1, 2, DEPRECATED, None)
         with pytest.warns(FutureWarning, match=match):
-            assert _func_deprecated_params(1, 2, 3) == (
-                1,
-                DEPRECATED,
-                DEPRECATED,
-                None,
-            )
+            assert _func_deprecated_params(1, 2, 3) == (1, 2, 3, None)
         with pytest.warns(FutureWarning, match=match):
             assert _func_deprecated_params(1, old0=2) == (
                 1,
-                DEPRECATED,
+                2,
                 DEPRECATED,
                 None,
             )
         with pytest.warns(FutureWarning, match=match):
             assert _func_deprecated_params(1, old1=2) == (
                 1,
                 DEPRECATED,
-                DEPRECATED,
+                2,
                 None,
             )
 

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

@@ -294,14 +294,19 @@ def fixed_func(*args, **kwargs):
             # Extract value of deprecated parameter
             if len(args) > deprecated_idx:
                 deprecated_value = args[deprecated_idx]
-                args = (
-                    args[:deprecated_idx]
-                    + (DEPRECATED,)
-                    + args[deprecated_idx + 1 :]
-                )
+                # Overwrite old with DEPRECATED if replacement exists
+                if self.new_name is not None:
+                    args = (
+                        args[:deprecated_idx]
+                        + (DEPRECATED,)
+                        + args[deprecated_idx + 1 :]
+                    )
             if self.deprecated_name in kwargs.keys():
                 deprecated_value = kwargs[self.deprecated_name]
-                kwargs[self.deprecated_name] = DEPRECATED
+                # Overwrite old with DEPRECATED if replacement exists
+                if self.new_name is not None:
+                    kwargs[self.deprecated_name] = DEPRECATED
+
             # Extract value of new parameter (if present)
             if new_idx is not False and len(args) > new_idx:
                 new_value = args[new_idx]

python/cucim/src/cucim/skimage/color/__init__.py

@@ -1,3 +1,5 @@
+"""Color space conversion."""
+
 from .colorconv import (
     ahx_from_rgb,
     bex_from_rgb,

python/cucim/src/cucim/skimage/data/__init__.py

@@ -1,3 +1,3 @@
-import lazy_loader as lazy
+import lazy_loader as _lazy
 
-__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
+__getattr__, __dir__, __all__ = _lazy.attach_stub(__name__, __file__)

python/cucim/src/cucim/skimage/exposure/__init__.py

@@ -1,3 +1,5 @@
-import lazy_loader as lazy
+"""Image intensity adjustment, e.g., histogram equalization, etc."""
 
-__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
+import lazy_loader as _lazy
+
+__getattr__, __dir__, __all__ = _lazy.attach_stub(__name__, __file__)

python/cucim/src/cucim/skimage/feature/__init__.py

@@ -1,3 +1,5 @@
-import lazy_loader as lazy
+"""Feature detection and extraction, e.g., blobs, corners, etc."""
 
-__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
+import lazy_loader as _lazy
+
+__getattr__, __dir__, __all__ = _lazy.attach_stub(__name__, __file__)

python/cucim/src/cucim/skimage/filters/__init__.py

@@ -1,3 +1,5 @@
-import lazy_loader as lazy
+"""Sharpening, edge finding, thresholding, etc."""
 
-__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)
+import lazy_loader as _lazy
+
+__getattr__, __dir__, __all__ = _lazy.attach_stub(__name__, __file__)