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[RELEASE] cucim v23.10 #611

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Oct 11, 2023
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4 changes: 4 additions & 0 deletions .github/copy-pr-bot.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
# Configuration file for `copy-pr-bot` GitHub App
# https://docs.gha-runners.nvidia.com/apps/copy-pr-bot/

enabled: true
1 change: 0 additions & 1 deletion .github/ops-bot.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,4 @@ branch_checker: true
label_checker: true
release_drafter: true
external_contributors: false
copy_prs: true
recently_updated: true
10 changes: 5 additions & 5 deletions .github/workflows/build.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
Expand All @@ -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 }}
Expand All @@ -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 }}
Expand Down
14 changes: 7 additions & 7 deletions .github/workflows/pr.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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"
2 changes: 1 addition & 1 deletion .github/workflows/test.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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 }}
Expand Down
22 changes: 22 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -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

Expand All @@ -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 & 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)
Expand Down
2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
2 changes: 1 addition & 1 deletion VERSION
Original file line number Diff line number Diff line change
@@ -1 +1 @@
23.08.00
23.10.00
2 changes: 1 addition & 1 deletion ci/build_cpp.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion ci/build_docs.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
2 changes: 1 addition & 1 deletion ci/build_python.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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 "${CPP_CHANNEL}" \
conda/recipes/cucim
Expand Down
2 changes: 1 addition & 1 deletion cpp/plugins/cucim.kit.cumed/VERSION
Original file line number Diff line number Diff line change
@@ -1 +1 @@
23.08.00
23.10.00
2 changes: 1 addition & 1 deletion cpp/plugins/cucim.kit.cuslide/VERSION
Original file line number Diff line number Diff line change
@@ -1 +1 @@
23.08.00
23.10.00
8 changes: 4 additions & 4 deletions cucim.code-workspace
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@
"CUCIM_TESTDATA_FOLDER": "${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": {
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down
4 changes: 2 additions & 2 deletions docs/source/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
2 changes: 1 addition & 1 deletion python/cucim/README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down
2 changes: 1 addition & 1 deletion python/cucim/VERSION
Original file line number Diff line number Diff line change
@@ -1 +1 @@
23.08.00
23.10.00
10 changes: 5 additions & 5 deletions python/cucim/docs/getting_started/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion python/cucim/docs/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down