Merge pull request #735 from rapidsai/branch-24.06

[RELEASE] cucim v24.06

.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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/conda-upload-packages.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/wheels-publish.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/pr-builder.yaml@branch-24.06
  checks:
  secrets: inherit
- uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/checks.yaml@branch-24.06
  conda-cpp-build:
  needs: checks
  secrets: inherit
- uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/conda-cpp-build.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/conda-python-build.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.06
  with:
  build_type: pull-request
  docs-build:
  needs: conda-python-build
  secrets: inherit
- uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/custom-job.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/wheels-build.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/conda-python-tests.yaml@branch-24.06
  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-24.04
+ uses: rapidsai/shared-workflows/.github/workflows/wheels-test.yaml@branch-24.06
  with:
  build_type: nightly
  branch: ${{ inputs.branch }}

CHANGELOG.md

@@ -1,3 +1,44 @@
+# cucim 24.06.00 (5 Jun 2024)
+
+## 🚨 Breaking Changes
+
+- The `output` argument of `cucim.skimage.filters.gaussian` has been renamed to `out`. The old name is deprecated and will be removed in release 25.02 (#727)
+- Renamed `get_xyz_coords` function is now removed (use `skimage.color.xyz_tristimulus_values` instead) (#724)
+- Removed deprecated `return_error` kwarg from `phase_cross_correlation` (the error is now always returned) (#724)
+- Removed deprecated `random_state` kwarg from `medial_axis` (it was renamed to `rng` previously) (#724)
+
+## 🐛 Bug Fixes
+
+- Use SciPy's KDTree instead of deprecated cKDTree ([#733](https://github.com/rapidsai/cucim/pull/733)) [@grlee77](https://github.com/grlee77)
+- Binary and grayscale morphology functions have bug fixes in the case of even-sized/non-symmetric footprints (for details see upstream MR: https://github.com/scikit-image/scikit-image/pull/6695) (#728)
+
+## 🚀 New Features
+
+- `cucim.skimage.measure.regionprops` (and `regionprops_table`) support one new region property: `intensity_std` (#727)
+- `cucim.skimage.segmentation.expand_labels` now supports a `spacing` keyword argument to take a pixel's physical dimensions into account (#727)
+- binary morphology functions have a new `mode` argument that controls how values outside the image boundaries are interpreted (#728)
+- grayscale morphology functions have new `mode` and `cval` arguments that control how boundaries are extended (#728)
+
+## 🛠️ Improvements
+
+- Enable FutureWarnings/DeprecationWarnings as errors ([#734](https://github.com/rapidsai/cucim/pull/734)) [@mroeschke](https://github.com/mroeschke)
+- Migrate to `{{ stdlib("c") }}` ([#731](https://github.com/rapidsai/cucim/pull/731)) [@hcho3](https://github.com/hcho3)
+- Implement upstream changes from scikit-image 0.23 (part 2 of 2: morphology) ([#728](https://github.com/rapidsai/cucim/pull/728)) [@grlee77](https://github.com/grlee77)
+- Implement upstream changes from scikit-image 0.23 (part 1 of 2) ([#727](https://github.com/rapidsai/cucim/pull/727)) [@grlee77](https://github.com/grlee77)
+- Update the test criteria for test_read_random_region_cpu_memleak ([#726](https://github.com/rapidsai/cucim/pull/726)) [@gigony](https://github.com/gigony)
+- Remove code needed to support Python < 3.9 and apply ruff's pyupgrade rules ([#725](https://github.com/rapidsai/cucim/pull/725)) [@grlee77](https://github.com/grlee77)
+- removal of deprecated functions/kwargs scheduled for release 24.06 ([#724](https://github.com/rapidsai/cucim/pull/724)) [@grlee77](https://github.com/grlee77)
+- Enable all tests for `arm` jobs ([#717](https://github.com/rapidsai/cucim/pull/717)) [@galipremsagar](https://github.com/galipremsagar)
+- prevent path conflict ([#713](https://github.com/rapidsai/cucim/pull/713)) [@AyodeAwe](https://github.com/AyodeAwe)
+- Updated cuCIM APIs for consistency with scikit-image 0.23.2 (#727 and #728)
+- Additional modules use `__init__.pyi` instead of just `__init__.py` (#727)
+- Some grayscale tests now compare directly to `skimage` CPU outputs instead fetching previously saved values (#728)
+- Refactored some test cases to better use `pytest.mark.parametrize` (#728)
+- Bumped version pinning for scikit-image to allow 0.23.x to be installed (#728)
+
+## 📖 Documentation
+- Various fixes to documentation strings (consistent shape notation, etc.) (#727)
+
 # cuCIM 24.04.00 (10 Apr 2024)
 
 ## 🐛 Bug Fixes

VERSION

@@ -1 +1 @@
-24.04.00
+24.06.00

benchmarks/skimage/cucim_morphology_bench.py

@@ -151,7 +151,7 @@ def main(args):
  # _skeletonize.py
  (
  "medial_axis",
- dict(random_state=123),
+ dict(rng=123),
  dict(return_distance=[False, True]),
  False,
  False,

ci/build_cpp.sh

@@ -17,6 +17,8 @@ version=$(rapids-generate-version)
 
 rapids-logger "Begin cpp build"
 
+conda config --set path_conflict prevent
+
 RAPIDS_PACKAGE_VERSION=${version} rapids-conda-retry mambabuild conda/recipes/libcucim
 
 rapids-upload-conda-to-s3 cpp

ci/build_python.sh

@@ -25,6 +25,7 @@ echo "${version}" > VERSION
 sed -i "/^__git_commit__/ s/= .*/= \"${commit}\"/g" "${package_src_dir}/_version.py"
 
 rapids-logger "Begin py build"
+conda config --set path_conflict prevent
 
 CPP_CHANNEL=$(rapids-download-conda-from-s3 cpp)
 

ci/test_wheel.sh

@@ -11,27 +11,21 @@ python -m pip install $(echo ./dist/cucim*.whl)[test]
 
 CUDA_MAJOR_VERSION=${RAPIDS_CUDA_VERSION:0:2}
 
-# Run smoke tests for aarch64 pull requests
-if [[ "$(arch)" == "aarch64" && ${RAPIDS_BUILD_TYPE} == "pull-request" ]]; then
- python ./ci/wheel_smoke_test.py
-else
-
- DEBIAN_FRONTEND=noninteractive apt update
- DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends libopenslide0
+DEBIAN_FRONTEND=noninteractive apt update
+DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends libopenslide0
 
- if [[ ${CUDA_MAJOR_VERSION} == "11" ]]; then
- # Omit I/O-related tests in ./python/cucim/tests due to known CUDA bug
- # with dynamic loading of libcufile.
- python -m pytest \
- --junitxml="${RAPIDS_TESTS_DIR}/junit-cucim.xml" \
- --numprocesses=8 \
- --dist=worksteal \
- ./python/cucim/src/
- else
- python -m pytest \
- --junitxml="${RAPIDS_TESTS_DIR}/junit-cucim.xml" \
- --numprocesses=8 \
- --dist=worksteal \
- ./python/cucim
- fi
+if [[ ${CUDA_MAJOR_VERSION} == "11" ]]; then
+ # Omit I/O-related tests in ./python/cucim/tests due to known CUDA bug
+ # with dynamic loading of libcufile.
+ python -m pytest \
+ --junitxml="${RAPIDS_TESTS_DIR}/junit-cucim.xml" \
+ --numprocesses=8 \
+ --dist=worksteal \
+ ./python/cucim/src/
+else
+ python -m pytest \
+ --junitxml="${RAPIDS_TESTS_DIR}/junit-cucim.xml" \
+ --numprocesses=8 \
+ --dist=worksteal \
+ ./python/cucim
 fi

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

@@ -43,8 +43,8 @@ dependencies:
 - python>=3.8,<3.12
 - pywavelets>=1.0
 - recommonmark
-- scikit-image>=0.19.0,<0.23.0a0
-- scipy
+- scikit-image>=0.19.0,<0.24.0a0
+- scipy>=1.6.0
 - sphinx<6
 - sysroot_linux-64==2.17
 - tifffile>=2022.7.28

conda/environments/all_cuda-122_arch-x86_64.yaml

@@ -42,8 +42,8 @@ dependencies:
 - python>=3.8,<3.12
 - pywavelets>=1.0
 - recommonmark
-- scikit-image>=0.19.0,<0.23.0a0
-- scipy
+- scikit-image>=0.19.0,<0.24.0a0
+- scipy>=1.6.0
 - sphinx<6
 - sysroot_linux-64==2.17
 - tifffile>=2022.7.28

conda/recipes/cucim/conda_build_config.yaml

@@ -10,5 +10,8 @@ cuda_compiler:
 cuda11_compiler:
  - nvcc
 
-sysroot_version:
+c_stdlib:
+ - sysroot
+
+c_stdlib_version:
  - "2.17"

conda/recipes/cucim/meta.yaml

@@ -54,7 +54,7 @@ requirements:
  - cmake >=3.23.1,!=3.25.0
  - make
  - ninja
- - sysroot_{{ target_platform }} {{ sysroot_version }}
+ - {{ stdlib("c") }}
  host:
  - click
  - cuda-version ={{ cuda_version }}
@@ -66,7 +66,7 @@ requirements:
  - numpy 1.23
  - python
  - scikit-image >=0.19.0,<0.23.0a0
- - scipy
+ - scipy >=1.6
  run:
  - {{ pin_compatible('cuda-version', max_pin='x', min_pin='x') }}
  {% if cuda_major != "11" %}
@@ -79,7 +79,7 @@ requirements:
  - libcucim ={{ version }}
  - python
  - scikit-image >=0.19.0,<0.23.0a0
- - scipy
+ - scipy >=1.6
  run_constrained:
  - openslide-python >=1.3.0
 

conda/recipes/libcucim/conda_build_config.yaml

@@ -10,7 +10,10 @@ cuda_compiler:
 cuda11_compiler:
  - nvcc
 
-sysroot_version:
+c_stdlib:
+ - sysroot
+
+c_stdlib_version:
  - "2.17"
 
 # The CTK libraries below are missing from the conda-forge::cudatoolkit package

conda/recipes/libcucim/meta.yaml

@@ -59,7 +59,7 @@ requirements:
  - cmake >=3.23.1,!=3.25.0
  - make
  - ninja
- - sysroot_{{ target_platform }} {{ sysroot_version }}
+ - {{ stdlib("c") }}
  - yasm # [x86_64]
  host:
  - cuda-version ={{ cuda_version }}

cucim.code-workspace

@@ -33,7 +33,7 @@
  "CUCIM_TESTDATA_FOLDER": "${workspaceDirectory}/test_data",
  // Add cuslide plugin's library path to LD_LIBRARY_PATH
  "LD_LIBRARY_PATH": "${workspaceDirectory}/build-debug/lib:${workspaceDirectory}/cpp/plugins/cucim.kit.cuslide/build-debug/lib:${workspaceDirectory}/temp/cuda/lib64:${os_env:LD_LIBRARY_PATH}",
- "CUCIM_TEST_PLUGIN_PATH": "cucim.kit.cuslide@24.04.00.so"
+ "CUCIM_TEST_PLUGIN_PATH": "cucim.kit.cuslide@24.06.00.so"
  },
  "cwd": "${workspaceDirectory}",
  "catch2": {
@@ -226,7 +226,7 @@
  },
  {
  "name": "CUCIM_TEST_PLUGIN_PATH",
- "value": "cucim.kit.cuslide@24.04.00.so"
+ "value": "cucim.kit.cuslide@24.06.00.so"
  }
  ],
  "console": "externalTerminal",
@@ -254,7 +254,7 @@
  },
  {
  "name": "CUCIM_TEST_PLUGIN_PATH",
- "value": "cucim.kit.cuslide@24.04.00.so"
+ "value": "cucim.kit.cuslide@24.06.00.so"
  }
  ],
  "console": "externalTerminal",
@@ -286,7 +286,7 @@
  },
  {
  "name": "CUCIM_TEST_PLUGIN_PATH",
- "value": "cucim.kit.cuslide@24.04.00.so"
+ "value": "cucim.kit.cuslide@24.06.00.so"
  }
  ],
  "console": "externalTerminal",

dependencies.yaml

@@ -247,8 +247,8 @@ dependencies:
  - click
  - lazy_loader>=0.1
  - numpy>=1.23.4,<2.0a0
- - scikit-image>=0.19.0,<0.23.0a0
- - scipy
+ - scikit-image>=0.19.0,<0.24.0a0
+ - scipy>=1.6.0
  - output_types: conda
  packages:
  - cupy>=12.0.0