Merge pull request #721 from rapidsai/branch-24.04

[RELEASE] cucim v24.04
rapidsai · Apr 10, 2024 · 9b9f699 · 9b9f699
2 parents 7d08ffc + e65c162
commit 9b9f699
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Showing 43 changed files with 181 additions and 130 deletions.
diff --git a/.github/ops-bot.yaml b/.github/ops-bot.yaml
@@ -7,3 +7,4 @@ label_checker: true
 release_drafter: true
 external_contributors: false
 recently_updated: true
+forward_merger: true
diff --git a/.github/workflows/build.yaml b/.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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/conda-upload-packages.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-publish.yaml@branch-24.04
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}

diff --git a/.github/workflows/pr.yaml b/.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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/pr-builder.yaml@branch-24.04
   checks:
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.04
   conda-cpp-build:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.04
     with:
       build_type: pull-request
   docs-build:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.04
     with:
       build_type: pull-request
       script: ci/test_wheel.sh
diff --git a/.github/workflows/test.yaml b/.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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.04
     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-24.02
+    uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.04
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -28,3 +28,8 @@ repos:
         args: ["--toml", "python/cucim/pyproject.toml"]
         additional_dependencies:
           - tomli
+  - repo: https://github.com/rapidsai/dependency-file-generator
+    rev: v1.8.0
+    hooks:
+        - id: rapids-dependency-file-generator
+          args: ["--clean"]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,29 @@
+# cuCIM 24.04.00 (10 Apr 2024)
+
+## 🐛 Bug Fixes
+
+- Require `click` as a wheel dependency ([#719](https://github.com/rapidsai/cucim/pull/719)) [@jakirkham](https://github.com/jakirkham)
+- Fix docs upload directory ([#714](https://github.com/rapidsai/cucim/pull/714)) [@raydouglass](https://github.com/raydouglass)
+- Fix `popd` indent in `run` ([#693](https://github.com/rapidsai/cucim/pull/693)) [@jakirkham](https://github.com/jakirkham)
+- Re-run `ci/release/update-version.sh 24.04.00` ([#690](https://github.com/rapidsai/cucim/pull/690)) [@jakirkham](https://github.com/jakirkham)
+
+## 🚀 New Features
+
+- Support CUDA 12.2 ([#672](https://github.com/rapidsai/cucim/pull/672)) [@jameslamb](https://github.com/jameslamb)
+
+## 🛠️ Improvements
+
+- Use `conda env create --yes` instead of `--force` ([#716](https://github.com/rapidsai/cucim/pull/716)) [@bdice](https://github.com/bdice)
+- Add upper bound to prevent usage of NumPy 2 ([#712](https://github.com/rapidsai/cucim/pull/712)) [@bdice](https://github.com/bdice)
+- Remove hard-coding of RAPIDS version ([#711](https://github.com/rapidsai/cucim/pull/711)) [@KyleFromNVIDIA](https://github.com/KyleFromNVIDIA)
+- Switch `pytest-xdist` algorithm to `worksteal` ([#708](https://github.com/rapidsai/cucim/pull/708)) [@bdice](https://github.com/bdice)
+- Simplify version update script ([#705](https://github.com/rapidsai/cucim/pull/705)) [@jakirkham](https://github.com/jakirkham)
+- Add support for Python 3.11, require NumPy 1.23+ ([#704](https://github.com/rapidsai/cucim/pull/704)) [@jameslamb](https://github.com/jameslamb)
+- target branch-24.04 for GitHub Actions workflows ([#702](https://github.com/rapidsai/cucim/pull/702)) [@jameslamb](https://github.com/jameslamb)
+- Refactor CUDA libraries in dependencies.yaml ([#699](https://github.com/rapidsai/cucim/pull/699)) [@bdice](https://github.com/bdice)
+- Update ops-bot.yaml ([#694](https://github.com/rapidsai/cucim/pull/694)) [@AyodeAwe](https://github.com/AyodeAwe)
+- add rapids-dependency-file-generator pre-commmit hook ([#682](https://github.com/rapidsai/cucim/pull/682)) [@jameslamb](https://github.com/jameslamb)
+
 # cuCIM 24.02.00 (12 Feb 2024)
 
 ## 🐛 Bug Fixes

diff --git a/README.md b/README.md
@@ -79,7 +79,7 @@ pip install cucim-cu11
 
 ### Notebooks
 
-Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-24.02/notebooks/Welcome.ipynb))
+Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.org/github/rapidsai/cucim/blob/main/notebooks/Welcome.ipynb))
 
 #### Downloading sample images
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-24.02.00
+24.04.00
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -3,16 +3,15 @@
 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):

diff --git a/benchmarks/skimage/cucim_restoration_bench.py b/benchmarks/skimage/cucim_restoration_bench.py
@@ -3,18 +3,17 @@
 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 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
@@ -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