Merge pull request #611 from rapidsai/branch-23.10

[RELEASE] cucim v23.10
rapidsai · Oct 11, 2023 · 0a8a829 · 0a8a829
2 parents f3a294b + f3ed533
commit 0a8a829
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Showing 19 changed files with 60 additions and 35 deletions.
diff --git a/.github/copy-pr-bot.yaml b/.github/copy-pr-bot.yaml
@@ -0,0 +1,4 @@
+# Configuration file for `copy-pr-bot` GitHub App
+# https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/
+
+enabled: true
diff --git a/.github/ops-bot.yaml b/.github/ops-bot.yaml
@@ -6,5 +6,4 @@ branch_checker: true
 label_checker: true
 release_drafter: true
 external_contributors: false
-copy_prs: true
 recently_updated: 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-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
@@ -38,20 +38,20 @@ jobs:
     if: github.ref_type == 'branch'
     needs: [python-build]
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.10
     with:
       arch: "amd64"
       branch: ${{ inputs.branch }}
       build_type: ${{ inputs.build_type || 'branch' }}
-      container_image: "rapidsai/ci:latest"
+      container_image: "rapidsai/ci-conda:latest"
       date: ${{ inputs.date }}
       node_type: "gpu-v100-latest-1"
       run_script: "ci/build_docs.sh"
       sha: ${{ inputs.sha }}
   python-build:
     needs: [cpp-build]
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}
@@ -60,7 +60,7 @@ jobs:
   upload-conda:
     needs: [cpp-build, python-build]
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-upload-packages.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-upload-packages.yaml@branch-23.10
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -18,35 +18,35 @@ jobs:
       - conda-python-tests
       - docs-build
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/pr-builder.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/pr-builder.yaml@branch-23.10
   checks:
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/checks.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/checks.yaml@branch-23.10
   conda-cpp-build:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.10
     with:
       build_type: pull-request
   conda-python-build:
     needs: conda-cpp-build
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.10
     with:
       build_type: pull-request
   conda-python-tests:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.10
     with:
       build_type: pull-request
   docs-build:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.10
     with:
       build_type: pull-request
       node_type: "gpu-v100-latest-1"
       arch: "amd64"
-      container_image: "rapidsai/ci:latest"
+      container_image: "rapidsai/ci-conda:latest"
       run_script: "ci/build_docs.sh"
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -16,7 +16,7 @@ on:
 jobs:
   conda-python-tests:
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.08
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.10
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,8 +1,25 @@
+# cuCIM 23.10.00 (11 Oct 2023)
+
+## 🐛 Bug Fixes
+
+- Use `conda mambabuild` not `mamba mambabuild` ([#607](https://github.com/rapidsai/cucim/pull/607)) [@bdice](https://github.com/bdice)
+
+## 📖 Documentation
+
+- minor updates to release 23.08 changelog ([#605](https://github.com/rapidsai/cucim/pull/605)) [@grlee77](https://github.com/grlee77)
+
+## 🛠️ Improvements
+
+- Update image names ([#609](https://github.com/rapidsai/cucim/pull/609)) [@AyodeAwe](https://github.com/AyodeAwe)
+- Use `copy-pr-bot` ([#606](https://github.com/rapidsai/cucim/pull/606)) [@ajschmidt8](https://github.com/ajschmidt8)
+
 # cuCIM 23.08.00 (9 Aug 2023)
 
 ## 🚨 Breaking Changes
 
 - Sync cuCIM API with scikit-image 0.21 ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
+- The `random_state` argument of medial_axis and unsupervised_wiener is now deprecated and will be removed in the future. The new argument name, `seed`, should be used instead. ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
+- The existing function `cucim.skimage.color.get_xyz_coords` has been renamed `cucim.skimage.color.xyz_tristimulus_values`. The former function name is deprecated and will be removed in the future. ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
 
 ## 🐛 Bug Fixes
 
@@ -11,9 +28,14 @@
 - Add ignore_run_exports for CUDA 11 ([#593](https://github.com/rapidsai/cucim/pull/593)) [@raydouglass](https://github.com/raydouglass)
 - Use linalg &amp; inline `_get_manders_overlap_coeff` ([#578](https://github.com/rapidsai/cucim/pull/578)) [@jakirkham](https://github.com/jakirkham)
 - Fix canny and butterworth (recent CuPy and NumPy compatibility) ([#574](https://github.com/rapidsai/cucim/pull/574)) [@grlee77](https://github.com/grlee77)
+- A bug was fixed in 2D shear calculations for AffineTransform. ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
+- A bug was fixed in the energy calculation of `cucim.skimage.segmentation.chan_vese`. This fix may result in different output from previous versions. ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
 
 ## 🛠️ Improvements
 
+- The formerly private function `_invariant_denoise` has been renamed `denoise_invariant` and is now part of the public `cucim.skimage.restoration` API ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
+- A new `return_mapping` option was added to `cucim.skimage.segmentation.join_segmentations`. This provides an additional output with a mapping between the labels in the joined segmentation and the original ones. ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
+- Added support for y-axis shear to the 2D AffineTransform. ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
 - Postponed the assessment of GPU memory for testing ([#601](https://github.com/rapidsai/cucim/pull/601)) [@gigony](https://github.com/gigony)
 - Do not use x86_64 GDS binaries for aarch64 ([#590](https://github.com/rapidsai/cucim/pull/590)) [@gigony](https://github.com/gigony)
 - remove checks for versions of scikit-image that are no longer supported ([#587](https://github.com/rapidsai/cucim/pull/587)) [@grlee77](https://github.com/grlee77)

diff --git a/README.md b/README.md
@@ -70,7 +70,7 @@ pip install scipy scikit-image cupy-cuda110
 
 ### Notebooks
 
-Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.08/notebooks/Welcome.ipynb))
+Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.10/notebooks/Welcome.ipynb))
 
 #### Downloading sample images
 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-23.08.00
+23.10.00
diff --git a/ci/build_cpp.sh b/ci/build_cpp.sh
@@ -11,6 +11,6 @@ rapids-print-env
 
 rapids-logger "Begin cpp build"
 
-rapids-mamba-retry mambabuild conda/recipes/libcucim
+rapids-conda-retry mambabuild conda/recipes/libcucim
 
 rapids-upload-conda-to-s3 cpp
diff --git a/ci/build_docs.sh b/ci/build_docs.sh
@@ -24,7 +24,7 @@ rapids-mamba-retry install \
     --channel "${PYTHON_CHANNEL}" \
     cucim libcucim
 
-export RAPIDS_VERSION_NUMBER="23.08"
+export RAPIDS_VERSION_NUMBER="23.10"
 export RAPIDS_DOCS_DIR="$(mktemp -d)"
 
 rapids-logger "Build Python docs"

diff --git a/ci/build_python.sh b/ci/build_python.sh
@@ -15,7 +15,7 @@ CPP_CHANNEL=$(rapids-download-conda-from-s3 cpp)
 
 # TODO: Remove `--no-test` flag once importing on a CPU
 # node works correctly
-rapids-mamba-retry mambabuild \
+rapids-conda-retry mambabuild \
   --no-test \
   --channel "${CPP_CHANNEL}" \
   conda/recipes/cucim

diff --git a/cpp/plugins/cucim.kit.cumed/VERSION b/cpp/plugins/cucim.kit.cumed/VERSION
@@ -1 +1 @@
-23.08.00
+23.10.00
diff --git a/cpp/plugins/cucim.kit.cuslide/VERSION b/cpp/plugins/cucim.kit.cuslide/VERSION
@@ -1 +1 @@
-23.08.00
+23.10.00
diff --git a/cucim.code-workspace b/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:${os_env:LD_LIBRARY_PATH}",
-					"CUCIM_TEST_PLUGIN_PATH": "cucim.kit.cuslide@23.08.00.so"
+					"CUCIM_TEST_PLUGIN_PATH": "cucim.kit.cuslide@23.10.00.so"
 				},
 				"cwd": "${workspaceDirectory}",
 				"catch2": {
@@ -226,7 +226,7 @@
 					},
 					{
 						"name": "CUCIM_TEST_PLUGIN_PATH",
-						"value": "cucim.kit.cuslide@23.08.00.so"
+						"value": "cucim.kit.cuslide@23.10.00.so"
 					}
 				],
 				"console": "externalTerminal",
@@ -254,7 +254,7 @@
 					},
 					{
 						"name": "CUCIM_TEST_PLUGIN_PATH",
-						"value": "cucim.kit.cuslide@23.08.00.so"
+						"value": "cucim.kit.cuslide@23.10.00.so"
 					}
 				],
 				"console": "externalTerminal",
@@ -286,7 +286,7 @@
 					},
 					{
 						"name": "CUCIM_TEST_PLUGIN_PATH",
-						"value": "cucim.kit.cuslide@23.08.00.so"
+						"value": "cucim.kit.cuslide@23.10.00.so"
 					}
 				],
 				"console": "externalTerminal",

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -72,9 +72,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '23.08'
+version = '23.10'
 # The full version, including alpha/beta/rc tags.
-release = '23.08.00'
+release = '23.10.00'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/python/cucim/README.md b/python/cucim/README.md
@@ -70,7 +70,7 @@ pip install scipy scikit-image cupy-cuda110
 
 ### Notebooks
 
-Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.08/notebooks/Welcome.ipynb))
+Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.10/notebooks/Welcome.ipynb))
 
 #### Downloading sample images
 

diff --git a/python/cucim/VERSION b/python/cucim/VERSION
@@ -1 +1 @@
-23.08.00
+23.10.00
diff --git a/python/cucim/docs/getting_started/index.md b/python/cucim/docs/getting_started/index.md
@@ -14,15 +14,15 @@
 
 ## Installation
 
-Please download the latest SDK package (`cuCIM-v23.08.00-linux.tar.gz`).
+Please download the latest SDK package (`cuCIM-v23.10.00-linux.tar.gz`).
 
 Untar the downloaded file.
 
 ```bash
-mkdir -p cuCIM-v23.08.00
-tar -xzvf cuCIM-v23.08.00-linux.tar.gz -C cuCIM-v23.08.00
+mkdir -p cuCIM-v23.10.00
+tar -xzvf cuCIM-v23.10.00-linux.tar.gz -C cuCIM-v23.10.00
 
-cd cuCIM-v23.08.00
+cd cuCIM-v23.10.00
 ```
 
 ## Run command
@@ -147,7 +147,7 @@ Its execution would show some metadata information and create two files -- `outp
 ```
 $ ./bin/tiff_image notebooks/input/image.tif .
 [Plugin: cucim.kit.cuslide] Loading...
-[Plugin: cucim.kit.cuslide] Loading the dynamic library from: cucim.kit.cuslide@23.08.00.so
+[Plugin: cucim.kit.cuslide] Loading the dynamic library from: cucim.kit.cuslide@23.10.00.so
 [Plugin: cucim.kit.cuslide] loaded successfully. Version: 0
 Initializing plugin: cucim.kit.cuslide (interfaces: [cucim::io::IImageFormat v0.1]) (impl: cucim.kit.cuslide)
 is_loaded: true

diff --git a/python/cucim/docs/index.md b/python/cucim/docs/index.md
@@ -18,7 +18,7 @@ development/index -->
 
 # cuCIM Documentation
 
-Current latest version is [Version 23.08.00](release_notes/v23.08.00.md).
+Current latest version is [Version 23.10.00](release_notes/v23.10.00.md).
 
 **cuCIM** a toolkit to provide GPU accelerated I/O, image  processing & computer vision primitives for N-Dimensional images with a focus on biomedical imaging.