Merge pull request #788 from rapidsai/branch-24.10

[RELEASE] cucim v24.10

.github/workflows/build.yaml

@@ -28,7 +28,7 @@ concurrency:
 jobs:
   cpp-build:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
@@ -38,7 +38,7 @@ jobs:
     if: github.ref_type == 'branch'
     needs: [python-build]
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.10
     with:
       arch: "amd64"
       branch: ${{ inputs.branch }}
@@ -51,7 +51,7 @@ jobs:
   python-build:
     needs: [cpp-build]
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
@@ -60,15 +60,15 @@ jobs:
   upload-conda:
     needs: [cpp-build, python-build]
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-upload-packages.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/conda-upload-packages.yaml@branch-24.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
       date: ${{ inputs.date }}
       sha: ${{ inputs.sha }}
   wheel-build:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
@@ -78,7 +78,7 @@ jobs:
   wheel-publish:
     needs: wheel-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-publish.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-publish.yaml@branch-24.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}

.github/workflows/pr.yaml

@@ -20,32 +20,32 @@ jobs:
       - wheel-build
       - wheel-tests
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/pr-builder.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/pr-builder.yaml@branch-24.10
   checks:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.10
   conda-cpp-build:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.10
     with:
       build_type: pull-request
   conda-python-build:
     needs: conda-cpp-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.10
     with:
       build_type: pull-request
   conda-python-tests:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.10
     with:
       build_type: pull-request
   docs-build:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.10
     with:
       build_type: pull-request
       node_type: "gpu-v100-latest-1"
@@ -55,14 +55,14 @@ jobs:
   wheel-build:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.10
     with:
       build_type: pull-request
       script: ci/build_wheel.sh
   wheel-tests:
     needs: wheel-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.10
     with:
       build_type: pull-request
       script: ci/test_wheel.sh

.github/workflows/test.yaml

@@ -16,15 +16,15 @@ on:
 jobs:
   conda-python-tests:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.10
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}
       date: ${{ inputs.date }}
       sha: ${{ inputs.sha }}
   wheel-tests:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.08
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.10
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}

.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:
@@ -29,7 +29,7 @@ repos:
         additional_dependencies:
           - tomli
   - repo: https://github.com/rapidsai/pre-commit-hooks
-    rev: v0.2.0
+    rev: v0.4.0
     hooks:
       - id: verify-alpha-spec
         args: ["--fix", "--mode=release"]

3rdparty/LICENSE.pytest-lazy-fixture → 3rdparty/LICENSE.pytest-lazy-fixtures

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+MIT License
 
-Copyright (c) 2016 Marsel Zaripov
+Copyright (c) 2023 Anton Petrov
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -9,13 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 copies of the Software, and to permit persons to whom the Software is
 furnished to do so, subject to the following conditions:
 
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

CHANGELOG.md

@@ -1,11 +1,36 @@
+# cucim 24.10.00 (9 Oct 2024)
+
+## 🐛 Bug Fixes
+
+- Use cupy to measure memory leak ([#777](https://github.com/rapidsai/cucim/pull/777)) [@bdice](https://github.com/bdice)
+- Fix wheel tests for Rocky Linux 8. ([#774](https://github.com/rapidsai/cucim/pull/774)) [@bdice](https://github.com/bdice)
+- Disable custom 2D separable filtering kernels on windows ([#770](https://github.com/rapidsai/cucim/pull/770)) [@grlee77](https://github.com/grlee77)
+- chan_vese: pass all constants to `_fused_variance_kernel2` as device scalars ([#764](https://github.com/rapidsai/cucim/pull/764)) [@grlee77](https://github.com/grlee77)
+- Fix "compatibility" spelling in CHANGELOG ([#759](https://github.com/rapidsai/cucim/pull/759)) [@jakirkham](https://github.com/jakirkham)
+- Fix error in dependencies.yaml causing incomplete pyproject.toml generation ([#757](https://github.com/rapidsai/cucim/pull/757)) [@grlee77](https://github.com/grlee77)
+
+## 🛠️ Improvements
+
+- Do not depends on unused libraries for libtiff ([#785](https://github.com/rapidsai/cucim/pull/785)) [@gigony](https://github.com/gigony)
+- Fix a couple of performance issues in `peak_local_max` (improve performance of blob detectors and `corner_peaks`) ([#782](https://github.com/rapidsai/cucim/pull/782)) [@grlee77](https://github.com/grlee77)
+- update vendored CUDA includes to match CuPy >= 13.3 ([#781](https://github.com/rapidsai/cucim/pull/781)) [@grlee77](https://github.com/grlee77)
+- Use CI workflow branch 'branch-24.10' again ([#780](https://github.com/rapidsai/cucim/pull/780)) [@jameslamb](https://github.com/jameslamb)
+- Add support for Python 3.12 ([#773](https://github.com/rapidsai/cucim/pull/773)) [@jameslamb](https://github.com/jameslamb)
+- Update rapidsai/pre-commit-hooks ([#772](https://github.com/rapidsai/cucim/pull/772)) [@KyleFromNVIDIA](https://github.com/KyleFromNVIDIA)
+- bump scikit-image upper bound (allow 0.24.x) ([#769](https://github.com/rapidsai/cucim/pull/769)) [@grlee77](https://github.com/grlee77)
+- Drop Python 3.9 support ([#766](https://github.com/rapidsai/cucim/pull/766)) [@jameslamb](https://github.com/jameslamb)
+- Remove NumPy <2 pin ([#762](https://github.com/rapidsai/cucim/pull/762)) [@seberg](https://github.com/seberg)
+- Update pre-commit hooks ([#760](https://github.com/rapidsai/cucim/pull/760)) [@KyleFromNVIDIA](https://github.com/KyleFromNVIDIA)
+- Switch to pytest-lazy-fixtures ([#756](https://github.com/rapidsai/cucim/pull/756)) [@gigony](https://github.com/gigony)
+
 # cucim 24.08.00 (7 Aug 2024)
 
 ## 🛠️ Improvements
 
 - Drop NumPy build dependency ([#751](https://github.com/rapidsai/cucim/pull/751)) [@jakirkham](https://github.com/jakirkham)
 - Use workflow branch 24.08 again ([#749](https://github.com/rapidsai/cucim/pull/749)) [@KyleFromNVIDIA](https://github.com/KyleFromNVIDIA)
 - Build and test with CUDA 12.5.1 ([#747](https://github.com/rapidsai/cucim/pull/747)) [@KyleFromNVIDIA](https://github.com/KyleFromNVIDIA)
-- Minor fixes for NumPy 2.0 compatiblity ([#746](https://github.com/rapidsai/cucim/pull/746)) [@grlee77](https://github.com/grlee77)
+- Minor fixes for NumPy 2.0 compatibility ([#746](https://github.com/rapidsai/cucim/pull/746)) [@grlee77](https://github.com/grlee77)
 - skip CMake 3.30.0, require CMake >=3.26.4 ([#745](https://github.com/rapidsai/cucim/pull/745)) [@jameslamb](https://github.com/jameslamb)
 - Use verify-alpha-spec hook ([#744](https://github.com/rapidsai/cucim/pull/744)) [@KyleFromNVIDIA](https://github.com/KyleFromNVIDIA)
 - remove .gitattributes ([#740](https://github.com/rapidsai/cucim/pull/740)) [@jameslamb](https://github.com/jameslamb)

CONTRIBUTING.md

@@ -123,7 +123,7 @@ cd $CUCIM_HOME
 
 Conda can be used to setup an environment which includes all of the necessary dependencies (as shown in `./conda/environments/all_cuda-118_arch-x86_64.yaml`) for building cuCIM.
 
-Otherwise, you may need to install dependencies (such as zlib, xz, yasm) through your OS's package manager (`apt`, `yum`, and so on).
+Otherwise, you may need to install dependencies (such as yasm) through your OS's package manager (`apt`, `yum`, and so on).
 
 
 ### Creating the Conda Development Environment `cucim`

LICENSE-3rdparty.md

@@ -243,10 +243,11 @@ libcuckoo
 - Copyright: Carnegie Mellon University and Intel Corporation
 - Usage: Using concurrent hash table implementation for cache mechanism.
 
-pytest-lazy-fixture
+pytest-lazy-fixtures
 - License: MIT License
-  - https://github.com/TvoroG/pytest-lazy-fixture/blob/master/LICENSE
-- Copyright: Marsel Zaripov
+- https://github.com/dev-petrov/pytest-lazy-fixtures
+  - https://github.com/dev-petrov/pytest-lazy-fixtures/blob/master/LICENSE
+- Copyright: Anton Petrov
 - Usage: Using lazy fixture feature in PyTest.
 
 psutil

VERSION

@@ -1 +1 @@
-24.08.00
+24.10.00

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())