From e7581a38ae36a14e2f154c062000c1b0c0a547bb Mon Sep 17 00:00:00 2001
From: James Lamb <jlamb@nvidia.com>
Date: Mon, 26 Feb 2024 17:18:57 -0600
Subject: [PATCH 1/5] Add support for Python 3.11.

---
 benchmarks/skimage/_image_bench.py                      | 1 -
 benchmarks/skimage/bench_convolve.py                    | 3 +--
 benchmarks/skimage/cucim_color_bench.py                 | 5 ++---
 benchmarks/skimage/cucim_exposure_bench.py              | 5 ++---
 benchmarks/skimage/cucim_feature_bench.py               | 7 +++----
 benchmarks/skimage/cucim_filters_bench.py               | 5 ++---
 benchmarks/skimage/cucim_measure_bench.py               | 5 ++---
 benchmarks/skimage/cucim_metrics_bench.py               | 5 ++---
 benchmarks/skimage/cucim_morphology_bench.py            | 5 ++---
 benchmarks/skimage/cucim_registration_bench.py          | 5 ++---
 benchmarks/skimage/cucim_restoration_bench.py           | 7 +++----
 benchmarks/skimage/cucim_segmentation_bench.py          | 3 +--
 benchmarks/skimage/cucim_transform_bench.py             | 5 ++---
 ci/wheel_smoke_test.py                                  | 4 +---
 dependencies.yaml                                       | 4 ++++
 examples/python/distance_transform_edt_demo.py          | 3 +--
 examples/python/gds_whole_slide/benchmark_round_trip.py | 5 ++---
 examples/python/gds_whole_slide/benchmark_zarr_write.py | 3 +--
 examples/python/gds_whole_slide/demo_implementation.py  | 3 +--
 examples/python/tiff_image/main.py                      | 3 +--
 experiments/Supporting_Aperio_SVS_Format/benchmark.py   | 3 +--
 experiments/Using_Cache/benchmark.py                    | 3 +--
 22 files changed, 37 insertions(+), 55 deletions(-)

diff --git a/benchmarks/skimage/_image_bench.py b/benchmarks/skimage/_image_bench.py
index 9d55c6be0..abb2ffbbb 100644
--- a/benchmarks/skimage/_image_bench.py
+++ b/benchmarks/skimage/_image_bench.py
@@ -12,7 +12,6 @@
 import pandas as pd
 import scipy.ndimage
 import skimage.data
-
 from cucim.time import repeat
 
 
diff --git a/benchmarks/skimage/bench_convolve.py b/benchmarks/skimage/bench_convolve.py
index f44714306..a43636931 100644
--- a/benchmarks/skimage/bench_convolve.py
+++ b/benchmarks/skimage/bench_convolve.py
@@ -3,8 +3,6 @@
 """
 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,
@@ -18,6 +16,7 @@
     uniform_filter,
     uniform_filter1d,
 )
+from cupyx.profiler import benchmark
 
 d = cp.cuda.Device()
 
diff --git a/benchmarks/skimage/cucim_color_bench.py b/benchmarks/skimage/cucim_color_bench.py
index b9886d2b8..8f394daef 100644
--- a/benchmarks/skimage/cucim_color_bench.py
+++ b/benchmarks/skimage/cucim_color_bench.py
@@ -2,6 +2,8 @@
 import os
 import pickle
 
+import cucim.skimage
+import cucim.skimage.color
 import cupy
 import cupy as cp
 import cupyx.scipy.ndimage
@@ -12,9 +14,6 @@
 import skimage.color
 from _image_bench import ImageBench
 
-import cucim.skimage
-import cucim.skimage.color
-
 func_name_choices = [
     "convert_colorspace",
     "rgb2hed",
diff --git a/benchmarks/skimage/cucim_exposure_bench.py b/benchmarks/skimage/cucim_exposure_bench.py
index 317c4efe6..558a2282f 100644
--- a/benchmarks/skimage/cucim_exposure_bench.py
+++ b/benchmarks/skimage/cucim_exposure_bench.py
@@ -2,6 +2,8 @@
 import os
 import pickle
 
+import cucim.skimage
+import cucim.skimage.exposure
 import cupy
 import cupy as cp
 import numpy as np
@@ -10,9 +12,6 @@
 import skimage.exposure
 from _image_bench import ImageBench
 
-import cucim.skimage
-import cucim.skimage.exposure
-
 
 class ExposureBench(ImageBench):
     def set_args(self, dtype):
diff --git a/benchmarks/skimage/cucim_feature_bench.py b/benchmarks/skimage/cucim_feature_bench.py
index b390f02e6..4142d7965 100644
--- a/benchmarks/skimage/cucim_feature_bench.py
+++ b/benchmarks/skimage/cucim_feature_bench.py
@@ -3,17 +3,16 @@
 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 skimage import data, draw
-
-import cucim.skimage
-import cucim.skimage.feature
 from cucim.skimage import exposure
+from skimage import data, draw
 
 
 class BlobDetectionBench(ImageBench):
diff --git a/benchmarks/skimage/cucim_filters_bench.py b/benchmarks/skimage/cucim_filters_bench.py
index 9dcbf2867..09a47e346 100644
--- a/benchmarks/skimage/cucim_filters_bench.py
+++ b/benchmarks/skimage/cucim_filters_bench.py
@@ -2,15 +2,14 @@
 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"
diff --git a/benchmarks/skimage/cucim_measure_bench.py b/benchmarks/skimage/cucim_measure_bench.py
index 15ec470ce..e7e7b40df 100644
--- a/benchmarks/skimage/cucim_measure_bench.py
+++ b/benchmarks/skimage/cucim_measure_bench.py
@@ -3,6 +3,8 @@
 import os
 import pickle
 
+import cucim.skimage
+import cucim.skimage.measure
 import cupy as cp
 import numpy as np
 import pandas as pd
@@ -11,9 +13,6 @@
 from _image_bench import ImageBench
 from cucim_metrics_bench import MetricsBench
 
-import cucim.skimage
-import cucim.skimage.measure
-
 
 class LabelBench(ImageBench):
     def __init__(
diff --git a/benchmarks/skimage/cucim_metrics_bench.py b/benchmarks/skimage/cucim_metrics_bench.py
index 8ac43a086..585dd7be8 100644
--- a/benchmarks/skimage/cucim_metrics_bench.py
+++ b/benchmarks/skimage/cucim_metrics_bench.py
@@ -2,15 +2,14 @@
 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
 
 
diff --git a/benchmarks/skimage/cucim_morphology_bench.py b/benchmarks/skimage/cucim_morphology_bench.py
index 47658e502..aeab0e142 100644
--- a/benchmarks/skimage/cucim_morphology_bench.py
+++ b/benchmarks/skimage/cucim_morphology_bench.py
@@ -6,6 +6,8 @@
 import os
 import pickle
 
+import cucim.skimage
+import cucim.skimage.morphology
 import cupy as cp
 import numpy as np
 import pandas as pd
@@ -15,9 +17,6 @@
 import skimage.morphology
 from _image_bench import ImageBench
 
-import cucim.skimage
-import cucim.skimage.morphology
-
 
 class BinaryMorphologyBench(ImageBench):
     def __init__(
diff --git a/benchmarks/skimage/cucim_registration_bench.py b/benchmarks/skimage/cucim_registration_bench.py
index 86070ecb5..be5b94594 100644
--- a/benchmarks/skimage/cucim_registration_bench.py
+++ b/benchmarks/skimage/cucim_registration_bench.py
@@ -3,6 +3,8 @@
 import os
 import pickle
 
+import cucim.skimage
+import cucim.skimage.registration
 import cupy as cp
 import numpy as np
 import pandas as pd
@@ -10,9 +12,6 @@
 import skimage.registration
 from _image_bench import ImageBench
 
-import cucim.skimage
-import cucim.skimage.registration
-
 
 class RegistrationBench(ImageBench):
     def set_args(self, dtype):
diff --git a/benchmarks/skimage/cucim_restoration_bench.py b/benchmarks/skimage/cucim_restoration_bench.py
index 064b9a068..c876cae12 100644
--- a/benchmarks/skimage/cucim_restoration_bench.py
+++ b/benchmarks/skimage/cucim_restoration_bench.py
@@ -3,6 +3,8 @@
 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
@@ -10,11 +12,8 @@
 import skimage
 import skimage.restoration
 from _image_bench import ImageBench
-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
+from skimage.restoration import denoise_tv_chambolle as tv_cpu
 
 
 class DenoiseBench(ImageBench):
diff --git a/benchmarks/skimage/cucim_segmentation_bench.py b/benchmarks/skimage/cucim_segmentation_bench.py
index fcba7073c..77bbae630 100644
--- a/benchmarks/skimage/cucim_segmentation_bench.py
+++ b/benchmarks/skimage/cucim_segmentation_bench.py
@@ -3,14 +3,13 @@
 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
 
 
diff --git a/benchmarks/skimage/cucim_transform_bench.py b/benchmarks/skimage/cucim_transform_bench.py
index 3d64d60d3..6cc007af9 100644
--- a/benchmarks/skimage/cucim_transform_bench.py
+++ b/benchmarks/skimage/cucim_transform_bench.py
@@ -2,15 +2,14 @@
 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"
diff --git a/ci/wheel_smoke_test.py b/ci/wheel_smoke_test.py
index e86a8888e..5311c6a96 100644
--- a/ci/wheel_smoke_test.py
+++ b/ci/wheel_smoke_test.py
@@ -1,8 +1,6 @@
-import cupy as cp
-
 import cucim
 import cucim.skimage
-
+import cupy as cp
 
 if __name__ == "__main__":
     # verify that all top-level modules are available
diff --git a/dependencies.yaml b/dependencies.yaml
index 2c9159c50..fa72cb440 100644
--- a/dependencies.yaml
+++ b/dependencies.yaml
@@ -233,6 +233,10 @@ dependencies:
               py: "3.10"
             packages:
               - python=3.10
+          - matrix:
+              py: "3.11"
+            packages:
+              - python=3.11
           - matrix:
             packages:
               - python>=3.8,<3.11
diff --git a/examples/python/distance_transform_edt_demo.py b/examples/python/distance_transform_edt_demo.py
index 405cd0f23..d9813b2f4 100644
--- a/examples/python/distance_transform_edt_demo.py
+++ b/examples/python/distance_transform_edt_demo.py
@@ -10,11 +10,10 @@
     print("This demo requires the matplotlib and colorcet packages.")
     raise (e)
 
-from skimage import data
-
 from cucim.core.operations.morphology import distance_transform_edt
 from cucim.skimage.color import label2rgb
 from cucim.skimage.segmentation import relabel_sequential
+from skimage import data
 
 
 def coords_to_labels(coords):
diff --git a/examples/python/gds_whole_slide/benchmark_round_trip.py b/examples/python/gds_whole_slide/benchmark_round_trip.py
index 21f4ec278..2335e73a0 100644
--- a/examples/python/gds_whole_slide/benchmark_round_trip.py
+++ b/examples/python/gds_whole_slide/benchmark_round_trip.py
@@ -1,16 +1,15 @@
 import os
 from time import time
 
+import cucim.skimage.filters
 import cupy as cp
 import kvikio
 import kvikio.defaults
 import numpy as np
+from cucim.core.operations.color import image_to_absorbance
 from cupyx.profiler import benchmark
 from demo_implementation import cupy_to_zarr, read_tiled
 
-import cucim.skimage.filters
-from cucim.core.operations.color import image_to_absorbance
-
 data_dir = os.environ.get("WHOLE_SLIDE_DATA_DIR", os.path.dirname("__file__"))
 fname = os.path.join(data_dir, "resize.tiff")
 if not os.path.exists(fname):
diff --git a/examples/python/gds_whole_slide/benchmark_zarr_write.py b/examples/python/gds_whole_slide/benchmark_zarr_write.py
index 13376f410..f1f4a021b 100644
--- a/examples/python/gds_whole_slide/benchmark_zarr_write.py
+++ b/examples/python/gds_whole_slide/benchmark_zarr_write.py
@@ -4,12 +4,11 @@
 import cupy as cp
 import kvikio.defaults
 import numpy as np
+from cucim.core.operations.color import image_to_absorbance
 from cupyx.profiler import benchmark
 from demo_implementation import cupy_to_zarr, get_n_tiles, read_tiled
 from tifffile import TiffFile
 
-from cucim.core.operations.color import image_to_absorbance
-
 data_dir = os.environ.get("WHOLE_SLIDE_DATA_DIR", os.path.dirname("__file__"))
 fname = os.path.join(data_dir, "resize.tiff")
 if not os.path.exists(fname):
diff --git a/examples/python/gds_whole_slide/demo_implementation.py b/examples/python/gds_whole_slide/demo_implementation.py
index 7d02c8407..89cb69342 100644
--- a/examples/python/gds_whole_slide/demo_implementation.py
+++ b/examples/python/gds_whole_slide/demo_implementation.py
@@ -8,14 +8,13 @@
 import numpy as np
 import openslide
 import tifffile
+from cucim.clara import filesystem
 from kvikio.cufile import IOFuture
 from kvikio.zarr import GDSStore
 from tifffile import TiffFile
 from zarr import DirectoryStore
 from zarr.creation import init_array
 
-from cucim.clara import filesystem
-
 """
 Developed with Dask 2022.05.2
 zarr >= 2.13.2
diff --git a/examples/python/tiff_image/main.py b/examples/python/tiff_image/main.py
index c36149a9e..42adf36e0 100644
--- a/examples/python/tiff_image/main.py
+++ b/examples/python/tiff_image/main.py
@@ -16,9 +16,8 @@
 import json
 
 import numpy as np
-from PIL import Image
-
 from cucim import CuImage
+from PIL import Image
 
 img = CuImage("image.tif")
 
diff --git a/experiments/Supporting_Aperio_SVS_Format/benchmark.py b/experiments/Supporting_Aperio_SVS_Format/benchmark.py
index 17085a8e9..db5deac70 100644
--- a/experiments/Supporting_Aperio_SVS_Format/benchmark.py
+++ b/experiments/Supporting_Aperio_SVS_Format/benchmark.py
@@ -19,10 +19,9 @@
 from itertools import repeat
 from time import perf_counter
 
-from openslide import OpenSlide
-
 from cucim import CuImage
 from cucim.clara.filesystem import discard_page_cache  # noqa: F401
+from openslide import OpenSlide
 
 
 class Timer(ContextDecorator):
diff --git a/experiments/Using_Cache/benchmark.py b/experiments/Using_Cache/benchmark.py
index d9667a44b..b1f69c5dc 100644
--- a/experiments/Using_Cache/benchmark.py
+++ b/experiments/Using_Cache/benchmark.py
@@ -21,11 +21,10 @@
 
 import numpy as np
 import rasterio
+from cucim import CuImage
 from openslide import OpenSlide
 from rasterio.windows import Window
 
-from cucim import CuImage
-
 
 class Timer(ContextDecorator):
     def __init__(self, message):

From 03f4bc69988e9d76359118d3d0eff80108659ec3 Mon Sep 17 00:00:00 2001
From: Kyle Edwards <kyedwards@nvidia.com>
Date: Tue, 27 Feb 2024 14:36:51 -0500
Subject: [PATCH 2/5] Update dependencies.yaml

---
 dependencies.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dependencies.yaml b/dependencies.yaml
index fa72cb440..21ce5f503 100644
--- a/dependencies.yaml
+++ b/dependencies.yaml
@@ -239,7 +239,7 @@ dependencies:
               - python=3.11
           - matrix:
             packages:
-              - python>=3.8,<3.11
+              - python>=3.8,<3.12
   run:
     common:
       - output_types: [conda, requirements, pyproject]

From 42289f72aa4f8cf7902d5830366895e3236d5156 Mon Sep 17 00:00:00 2001
From: Kyle Edwards <kyedwards@nvidia.com>
Date: Tue, 27 Feb 2024 14:41:35 -0500
Subject: [PATCH 3/5] Update conda environments

---
 conda/environments/all_cuda-118_arch-x86_64.yaml | 2 +-
 conda/environments/all_cuda-122_arch-x86_64.yaml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml
index 31c5e6077..de6a215c8 100644
--- a/conda/environments/all_cuda-118_arch-x86_64.yaml
+++ b/conda/environments/all_cuda-118_arch-x86_64.yaml
@@ -40,7 +40,7 @@ dependencies:
 - pytest-lazy-fixture>=0.6.3
 - pytest-xdist
 - pytest>=6.2.4,<8.0.0a0
-- python>=3.8,<3.11
+- python>=3.8,<3.12
 - pywavelets>=1.0
 - recommonmark
 - scikit-image>=0.19.0,<0.23.0a0
diff --git a/conda/environments/all_cuda-122_arch-x86_64.yaml b/conda/environments/all_cuda-122_arch-x86_64.yaml
index fb6453a6c..bfdec601c 100644
--- a/conda/environments/all_cuda-122_arch-x86_64.yaml
+++ b/conda/environments/all_cuda-122_arch-x86_64.yaml
@@ -39,7 +39,7 @@ dependencies:
 - pytest-lazy-fixture>=0.6.3
 - pytest-xdist
 - pytest>=6.2.4,<8.0.0a0
-- python>=3.8,<3.11
+- python>=3.8,<3.12
 - pywavelets>=1.0
 - recommonmark
 - scikit-image>=0.19.0,<0.23.0a0

From 5f87ea4741df2eb5720f3753f83fabefa57273c0 Mon Sep 17 00:00:00 2001
From: Kyle Edwards <kyedwards@nvidia.com>
Date: Tue, 27 Feb 2024 16:21:51 -0500
Subject: [PATCH 4/5] Bump numpy to 1.23

---
 conda/recipes/cucim/meta.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conda/recipes/cucim/meta.yaml b/conda/recipes/cucim/meta.yaml
index 04a94830a..61d85d080 100644
--- a/conda/recipes/cucim/meta.yaml
+++ b/conda/recipes/cucim/meta.yaml
@@ -63,7 +63,7 @@ requirements:
     {% endif %}
     - cupy >=12.0.0
     - libcucim ={{ version }}
-    - numpy 1.21
+    - numpy 1.23
     - python
     - scikit-image >=0.19.0,<0.23.0a0
     - scipy

From 5d2a6c1125a4238132c6d468ab3acf295867adc7 Mon Sep 17 00:00:00 2001
From: Kyle Edwards <kyedwards@nvidia.com>
Date: Tue, 27 Feb 2024 16:38:42 -0500
Subject: [PATCH 5/5] Require numpy 1.23.4

---
 conda/environments/all_cuda-118_arch-x86_64.yaml | 2 +-
 conda/environments/all_cuda-122_arch-x86_64.yaml | 2 +-
 dependencies.yaml                                | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml
index de6a215c8..da6d2d6ae 100644
--- a/conda/environments/all_cuda-118_arch-x86_64.yaml
+++ b/conda/environments/all_cuda-118_arch-x86_64.yaml
@@ -27,7 +27,7 @@ dependencies:
 - matplotlib-base
 - nbsphinx
 - ninja
-- numpy>=1.21.3
+- numpy>=1.23.4
 - numpydoc>=1.5
 - nvcc_linux-64=11.8
 - openslide-python>=1.3.0
diff --git a/conda/environments/all_cuda-122_arch-x86_64.yaml b/conda/environments/all_cuda-122_arch-x86_64.yaml
index bfdec601c..22532cbc3 100644
--- a/conda/environments/all_cuda-122_arch-x86_64.yaml
+++ b/conda/environments/all_cuda-122_arch-x86_64.yaml
@@ -27,7 +27,7 @@ dependencies:
 - matplotlib-base
 - nbsphinx
 - ninja
-- numpy>=1.21.3
+- numpy>=1.23.4
 - numpydoc>=1.5
 - openslide-python>=1.3.0
 - pip
diff --git a/dependencies.yaml b/dependencies.yaml
index 21ce5f503..1f8283432 100644
--- a/dependencies.yaml
+++ b/dependencies.yaml
@@ -250,7 +250,7 @@ dependencies:
       - output_types: conda
         packages:
           - cupy>=12.0.0
-          - numpy>=1.21.3
+          - numpy>=1.23.4
           # All dependencies below this point are specific to `cucim.clara` and
           # are not needed for either `cucim.core` or `cucim.skimage`. I did
           # not include these under a "pyproject" output so that it is still