Drop Python 3.9 support

.pre-commit-config.yaml

@@ -16,11 +16,11 @@ repos:
       - id: black
         args: ["--config", "python/cucim/pyproject.toml"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.6.1
     hooks:
       - id: ruff
         types_or: [python, pyi]
-        args: [--fix, --exit-non-zero-on-fix]
+        args: [--fix, --exit-non-zero-on-fix, --config, "python/cucim/pyproject.toml"]
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:

benchmarks/skimage/_image_bench.py

@@ -12,6 +12,7 @@
 import pandas as pd
 import scipy.ndimage
 import skimage.data
+
 from cucim.time import repeat
 
 
@@ -23,7 +24,7 @@ def product_dict(**kwargs):
         yield dict(zip(keys, instance))
 
 
-class ImageBench(object):
+class ImageBench:
     def __init__(
         self,
         function_name,

benchmarks/skimage/bench_convolve.py

@@ -3,6 +3,8 @@
 """
 import cupy as cp
 import cupyx.scipy.ndimage as ndi
+from cupyx.profiler import benchmark
+
 from cucim.skimage._vendored.ndimage import (  # noqa: F401
     convolve1d,
     correlate1d,
@@ -16,7 +18,6 @@
     uniform_filter,
     uniform_filter1d,
 )
-from cupyx.profiler import benchmark
 
 d = cp.cuda.Device()
 

benchmarks/skimage/cucim_color_bench.py

@@ -2,8 +2,6 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.color
 import cupy
 import cupy as cp
 import cupyx.scipy.ndimage
@@ -14,6 +12,9 @@
 import skimage.color
 from _image_bench import ImageBench
 
+import cucim.skimage
+import cucim.skimage.color
+
 func_name_choices = [
     "convert_colorspace",
     "rgb2hed",
@@ -223,7 +224,7 @@ def main(args):
     try:
         import tabular  # noqa: F401
 
-        with open(fbase + ".md", "wt") as f:
+        with open(fbase + ".md", "w") as f:
             f.write(all_results.to_markdown())
     except ImportError:
         pass

benchmarks/skimage/cucim_exposure_bench.py

@@ -2,8 +2,6 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.exposure
 import cupy
 import cupy as cp
 import numpy as np
@@ -12,6 +10,9 @@
 import skimage.exposure
 from _image_bench import ImageBench
 
+import cucim.skimage
+import cucim.skimage.exposure
+
 
 class ExposureBench(ImageBench):
     def set_args(self, dtype):
@@ -129,7 +130,7 @@ def main(args):
     fbase = os.path.splitext(pfile)[0]
     all_results.to_csv(fbase + ".csv")
     all_results.to_pickle(pfile)
-    with open(fbase + ".md", "wt") as f:
+    with open(fbase + ".md", "w") as f:
         f.write(all_results.to_markdown())
 
 

benchmarks/skimage/cucim_feature_bench.py

@@ -3,17 +3,18 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.feature
 import cupy as cp
 import numpy as np
 import pandas as pd
 import skimage
 import skimage.feature
 from _image_bench import ImageBench
-from cucim.skimage import exposure
 from skimage import data, draw
 
+import cucim.skimage
+import cucim.skimage.feature
+from cucim.skimage import exposure
+
 
 class BlobDetectionBench(ImageBench):
     def set_args(self, dtype):
@@ -218,7 +219,7 @@ def main(args):
     fbase = os.path.splitext(pfile)[0]
     all_results.to_csv(fbase + ".csv")
     all_results.to_pickle(pfile)
-    with open(fbase + ".md", "wt") as f:
+    with open(fbase + ".md", "w") as f:
         f.write(all_results.to_markdown())
 
 

benchmarks/skimage/cucim_filters_bench.py

@@ -2,14 +2,15 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.filters
 import numpy as np
 import pandas as pd
 import skimage
 import skimage.filters
 from _image_bench import ImageBench
 
+import cucim.skimage
+import cucim.skimage.filters
+
 
 def main(args):
     pfile = "cucim_filters_results.pickle"
@@ -189,7 +190,7 @@ def main(args):
     fbase = os.path.splitext(pfile)[0]
     all_results.to_csv(fbase + ".csv")
     all_results.to_pickle(pfile)
-    with open(fbase + ".md", "wt") as f:
+    with open(fbase + ".md", "w") as f:
         f.write(all_results.to_markdown())
 
 

benchmarks/skimage/cucim_measure_bench.py

@@ -3,8 +3,6 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.measure
 import cupy as cp
 import numpy as np
 import pandas as pd
@@ -13,6 +11,9 @@
 from _image_bench import ImageBench
 from cucim_metrics_bench import MetricsBench
 
+import cucim.skimage
+import cucim.skimage.measure
+
 
 class LabelBench(ImageBench):
     def __init__(
@@ -328,7 +329,7 @@ def main(args):
     fbase = os.path.splitext(pfile)[0]
     all_results.to_csv(fbase + ".csv")
     all_results.to_pickle(pfile)
-    with open(fbase + ".md", "wt") as f:
+    with open(fbase + ".md", "w") as f:
         f.write(all_results.to_markdown())
 
 

benchmarks/skimage/cucim_metrics_bench.py

@@ -2,14 +2,15 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.metrics
 import cupy as cp
 import numpy as np
 import pandas as pd
 import skimage
 import skimage.metrics
 from _image_bench import ImageBench
+
+import cucim.skimage
+import cucim.skimage.metrics
 from cucim.skimage import data, measure
 
 
@@ -176,7 +177,7 @@ def main(args):
     fbase = os.path.splitext(pfile)[0]
     all_results.to_csv(fbase + ".csv")
     all_results.to_pickle(pfile)
-    with open(fbase + ".md", "wt") as f:
+    with open(fbase + ".md", "w") as f:
         f.write(all_results.to_markdown())
 
 

benchmarks/skimage/cucim_morphology_bench.py

@@ -6,8 +6,6 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.morphology
 import cupy as cp
 import numpy as np
 import pandas as pd
@@ -17,6 +15,9 @@
 import skimage.morphology
 from _image_bench import ImageBench
 
+import cucim.skimage
+import cucim.skimage.morphology
+
 
 class BinaryMorphologyBench(ImageBench):
     def __init__(
@@ -281,7 +282,7 @@ def main(args):
     try:
         import tabular  # noqa: F401
 
-        with open(fbase + ".md", "wt") as f:
+        with open(fbase + ".md", "w") as f:
             f.write(all_results.to_markdown())
     except ImportError:
         pass

benchmarks/skimage/cucim_registration_bench.py

@@ -3,15 +3,16 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.registration
 import cupy as cp
 import numpy as np
 import pandas as pd
 import skimage
 import skimage.registration
 from _image_bench import ImageBench
 
+import cucim.skimage
+import cucim.skimage.registration
+
 
 class RegistrationBench(ImageBench):
     def set_args(self, dtype):
@@ -145,7 +146,7 @@ def main(args):
     try:
         import tabular  # noqa: F401
 
-        with open(fbase + ".md", "wt") as f:
+        with open(fbase + ".md", "w") as f:
             f.write(all_results.to_markdown())
     except ImportError:
         pass

benchmarks/skimage/cucim_restoration_bench.py

@@ -3,18 +3,19 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.restoration
 import cupy as cp
 import cupyx.scipy.ndimage as ndi
 import numpy as np
 import pandas as pd
 import skimage
 import skimage.restoration
 from _image_bench import ImageBench
-from cucim.skimage.restoration import denoise_tv_chambolle as tv_gpu
 from skimage.restoration import denoise_tv_chambolle as tv_cpu
 
+import cucim.skimage
+import cucim.skimage.restoration
+from cucim.skimage.restoration import denoise_tv_chambolle as tv_gpu
+
 
 class DenoiseBench(ImageBench):
     def set_args(self, dtype):
@@ -180,7 +181,7 @@ def main(args):
     try:
         import tabular  # noqa: F401
 
-        with open(fbase + ".md", "wt") as f:
+        with open(fbase + ".md", "w") as f:
             f.write(all_results.to_markdown())
     except ImportError:
         pass

benchmarks/skimage/cucim_segmentation_bench.py

@@ -3,13 +3,14 @@
 import os
 import pickle
 
-import cucim.skimage
 import cupy as cp
 import numpy as np
 import pandas as pd
 import skimage
 import skimage.segmentation
 from _image_bench import ImageBench
+
+import cucim.skimage
 from cucim.skimage import data, measure
 
 
@@ -296,7 +297,7 @@ def main(args):
     try:
         import tabular  # noqa: F401
 
-        with open(fbase + ".md", "wt") as f:
+        with open(fbase + ".md", "w") as f:
             f.write(all_results.to_markdown())
     except ImportError:
         pass

benchmarks/skimage/cucim_transform_bench.py

@@ -2,14 +2,15 @@
 import os
 import pickle
 
-import cucim.skimage
-import cucim.skimage.transform
 import numpy as np
 import pandas as pd
 import skimage
 import skimage.transform
 from _image_bench import ImageBench
 
+import cucim.skimage
+import cucim.skimage.transform
+
 
 def main(args):
     pfile = "cucim_transform_results.pickle"
@@ -164,7 +165,7 @@ def main(args):
     try:
         import tabular  # noqa: F401
 
-        with open(fbase + ".md", "wt") as f:
+        with open(fbase + ".md", "w") as f:
             f.write(all_results.to_markdown())
     except ImportError:
         pass

benchmarks/skimage/cupyx_scipy_ndimage_filter_bench.py

@@ -129,5 +129,5 @@ def set_args(self, dtype):
 fbase = os.path.splitext(pfile)[0]
 all_results.to_csv(fbase + ".csv")
 all_results.to_pickle(pfile)
-with open(fbase + ".md", "wt") as f:
+with open(fbase + ".md", "w") as f:
     f.write(all_results.to_markdown())

benchmarks/skimage/cupyx_scipy_ndimage_fourier_bench.py

@@ -50,5 +50,5 @@ def set_args(self, dtype):
 fbase = os.path.splitext(pfile)[0]
 all_results.to_csv(fbase + ".csv")
 all_results.to_pickle(pfile)
-with open(fbase + ".md", "wt") as f:
+with open(fbase + ".md", "w") as f:
     f.write(all_results.to_markdown())

benchmarks/skimage/cupyx_scipy_ndimage_interp_bench.py

@@ -153,5 +153,5 @@ def set_args(self, dtype):
 fbase = os.path.splitext(pfile)[0]
 all_results.to_csv(fbase + ".csv")
 all_results.to_pickle(pfile)
-with open(fbase + ".md", "wt") as f:
+with open(fbase + ".md", "w") as f:
     f.write(all_results.to_markdown())

benchmarks/skimage/cupyx_scipy_ndimage_measurements_bench.py

@@ -185,5 +185,5 @@ def set_args(self, dtype):
 fbase = os.path.splitext(pfile)[0]
 all_results.to_csv(fbase + ".csv")
 all_results.to_pickle(pfile)
-with open(fbase + ".md", "wt") as f:
+with open(fbase + ".md", "w") as f:
     f.write(all_results.to_markdown())

benchmarks/skimage/cupyx_scipy_ndimage_morphology_bench.py

@@ -152,5 +152,5 @@ def set_args(self, dtype):
 fbase = os.path.splitext(pfile)[0]
 all_results.to_csv(fbase + ".csv")
 all_results.to_pickle(pfile)
-with open(fbase + ".md", "wt") as f:
+with open(fbase + ".md", "w") as f:
     f.write(all_results.to_markdown())