Merge pull request #603 from rapidsai/branch-23.08

[RELEASE] cucim v23.08

.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-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.08
     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-action-workflows/.github/workflows/custom-job.yaml@branch-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.08
     with:
       arch: "amd64"
       branch: ${{ inputs.branch }}
@@ -51,7 +51,7 @@ jobs:
   python-build:
     needs: [cpp-build]
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.08
     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-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-upload-packages.yaml@branch-23.08
     with:
       build_type: ${{ inputs.build_type || 'branch' }}
       branch: ${{ inputs.branch }}

.github/workflows/pr.yaml

@@ -18,32 +18,32 @@ jobs:
       - conda-python-tests
       - docs-build
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/pr-builder.yaml@branch-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/pr-builder.yaml@branch-23.08
   checks:
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/checks.yaml@branch-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/checks.yaml@branch-23.08
   conda-cpp-build:
     needs: checks
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-cpp-build.yaml@branch-23.08
     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-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-build.yaml@branch-23.08
     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-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.08
     with:
       build_type: pull-request
   docs-build:
     needs: conda-python-build
     secrets: inherit
-    uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/custom-job.yaml@branch-23.08
     with:
       build_type: pull-request
       node_type: "gpu-v100-latest-1"

.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-23.06
+    uses: rapidsai/shared-action-workflows/.github/workflows/conda-python-tests.yaml@branch-23.08
     with:
       build_type: nightly
       branch: ${{ inputs.branch }}

CHANGELOG.md

@@ -1,3 +1,30 @@
+# 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)
+
+## 🐛 Bug Fixes
+
+- Remove libwebp-base upper bound. ([#599](https://github.com/rapidsai/cucim/pull/599)) [@bdice](https://github.com/bdice)
+- Fix ignore_run_exports_from. ([#596](https://github.com/rapidsai/cucim/pull/596)) [@bdice](https://github.com/bdice)
+- 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)
+
+## 🛠️ Improvements
+
+- 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)
+- Allow scikit-image 0.21.0 ([#580](https://github.com/rapidsai/cucim/pull/580)) [@jakirkham](https://github.com/jakirkham)
+- Drop unneeded selector on `libwebp-base` ([#579](https://github.com/rapidsai/cucim/pull/579)) [@jakirkham](https://github.com/jakirkham)
+- switch from bundled lazy loading code to the public lazy_loader package ([#575](https://github.com/rapidsai/cucim/pull/575)) [@grlee77](https://github.com/grlee77)
+- Sync cuCIM API with scikit-image 0.21 ([#573](https://github.com/rapidsai/cucim/pull/573)) [@grlee77](https://github.com/grlee77)
+- cuCIM: Build CUDA 12 packages ([#572](https://github.com/rapidsai/cucim/pull/572)) [@jakirkham](https://github.com/jakirkham)
+- use rapids-upload-docs script ([#570](https://github.com/rapidsai/cucim/pull/570)) [@AyodeAwe](https://github.com/AyodeAwe)
+- Remove documentation build scripts for Jenkins ([#567](https://github.com/rapidsai/cucim/pull/567)) [@ajschmidt8](https://github.com/ajschmidt8)
+
 # cuCIM 23.06.00 (7 Jun 2023)
 
 ## 🚨 Breaking Changes

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-23.06/notebooks/Welcome.ipynb))
+Please check out our [Welcome](notebooks/Welcome.ipynb) notebook ([NBViewer](https://nbviewer.jupyter.org/github/rapidsai/cucim/blob/branch-23.08/notebooks/Welcome.ipynb))
 
 #### Downloading sample images
 

VERSION

@@ -1 +1 @@
-23.06.00
+23.08.00

ci/build_docs.sh

@@ -18,22 +18,22 @@ rapids-print-env
 rapids-logger "Downloading artifacts from previous jobs"
 CPP_CHANNEL=$(rapids-download-conda-from-s3 cpp)
 PYTHON_CHANNEL=$(rapids-download-conda-from-s3 python)
-VERSION_NUMBER="23.06"
 
 rapids-mamba-retry install \
     --channel "${CPP_CHANNEL}" \
     --channel "${PYTHON_CHANNEL}" \
     cucim libcucim
 
-# Build Python docs
+export RAPIDS_VERSION_NUMBER="23.08"
+export RAPIDS_DOCS_DIR="$(mktemp -d)"
+
 rapids-logger "Build Python docs"
 pushd docs
 sphinx-build -b dirhtml ./source _html
 sphinx-build -b text ./source _text
+mkdir -p "${RAPIDS_DOCS_DIR}/cucim/"{html,txt}
+mv _html/* "${RAPIDS_DOCS_DIR}/cucim/html"
+mv _text/* "${RAPIDS_DOCS_DIR}/cucim/txt"
 popd
 
-if [[ "${RAPIDS_BUILD_TYPE}" != "pull-request" ]]; then
-  rapids-logger "Upload Docs to S3"
-  aws s3 sync --no-progress --delete docs/_html "s3://rapidsai-docs/cucim/${VERSION_NUMBER}/html"
-  aws s3 sync --no-progress --delete docs/_text "s3://rapidsai-docs/cucim/${VERSION_NUMBER}/txt"
-fi
+rapids-upload-docs

ci/release/update-version.sh

@@ -48,4 +48,4 @@ sed_runner "s#branch-${CURRENT_MAJOR}.${CURRENT_MINOR}#branch-${NEXT_MAJOR}.${NE
 for FILE in .github/workflows/*.yaml; do
   sed_runner "/shared-action-workflows/ s/@.*/@branch-${NEXT_SHORT_TAG}/g" "${FILE}"
 done
-sed_runner "s/VERSION_NUMBER=\".*/VERSION_NUMBER=\"${NEXT_SHORT_TAG}\"/g" ci/build_docs.sh
+sed_runner "s/RAPIDS_VERSION_NUMBER=\".*/RAPIDS_VERSION_NUMBER=\"${NEXT_SHORT_TAG}\"/g" ci/build_docs.sh

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

@@ -10,13 +10,19 @@ dependencies:
 - c-compiler
 - click
 - cmake>=3.23.1,!=3.25.0
-- cudatoolkit=11.8
+- cuda-version=11.8
+- cudatoolkit
 - cupy >=12.0.0
 - cxx-compiler
 - gcc_linux-64=11.*
 - imagecodecs>=2021.6.8
 - ipython
 - jbig
+- lazy_loader >=0.1
+- libcufile-dev=1.4.0.31
+- libcufile=1.4.0.31
+- libnvjpeg-dev=11.6.0.55
+- libnvjpeg=11.6.0.55
 - libwebp-base
 - nbsphinx
 - ninja
@@ -34,7 +40,7 @@ dependencies:
 - pytest>=6.2.4
 - python>=3.8,<3.11
 - recommonmark
-- scikit-image >=0.19.0,<0.21.0a0
+- scikit-image >=0.19.0,<0.22.0a0
 - scipy
 - sphinx<6
 - sysroot_linux-64==2.17

conda/environments/all_cuda-120_arch-x86_64.yaml

@@ -0,0 +1,53 @@
+# This file is generated by `rapids-dependency-file-generator`.
+# To make changes, edit ../../dependencies.yaml and run `rapids-dependency-file-generator`.
+channels:
+- rapidsai
+- rapidsai-nightly
+- conda-forge
+- nvidia
+dependencies:
+- GPUtil>=1.4.0
+- c-compiler
+- click
+- cmake>=3.23.1,!=3.25.0
+- cuda-cudart-dev
+- cuda-nvcc
+- cuda-version=12.0
+- cupy >=12.0.0
+- cxx-compiler
+- gcc_linux-64=11.*
+- imagecodecs>=2021.6.8
+- ipython
+- jbig
+- lazy_loader >=0.1
+- libcufile-dev
+- libnvjpeg-dev
+- libnvjpeg-static
+- libwebp-base
+- nbsphinx
+- ninja
+- numpy >=1.21.3
+- numpydoc
+- openslide-python>=1.1.2
+- pip
+- pre-commit
+- psutil>=5.8.0
+- pydata-sphinx-theme
+- pytest-cov>=2.12.1
+- pytest-lazy-fixture>=0.6.3
+- pytest-xdist
+- pytest>=6.2.4
+- python>=3.8,<3.11
+- recommonmark
+- scikit-image >=0.19.0,<0.22.0a0
+- scipy
+- sphinx<6
+- sysroot_linux-64==2.17
+- tifffile>=2022.7.28
+- xz
+- yasm
+- zlib
+- zstd
+- pip:
+  - opencv-python-headless>=4.6
+name: all_cuda-120_arch-x86_64

conda/recipes/cucim/conda_build_config.yaml

@@ -4,5 +4,11 @@ c_compiler_version:
 cxx_compiler_version:
   - 11
 
+cuda_compiler:
+  - cuda-nvcc
+
+cuda11_compiler:
+  - nvcc
+
 sysroot_version:
   - "2.17"

conda/recipes/cucim/meta.yaml

@@ -1,12 +1,12 @@
 # Copyright (c) 2021-2023, NVIDIA CORPORATION.
 
 {% set version = environ.get('GIT_DESCRIBE_TAG', '0.0.0.dev').lstrip('v') %}
-{% set minor_version = version.split('.')[0] + '.' + version.split('.')[2] %}
 {% set py_version = environ['CONDA_PY'] %}
 {% set cuda_version = '.'.join(environ['RAPIDS_CUDA_VERSION'].split('.')[:2]) %}
 {% set cuda_major = cuda_version.split('.')[0] %}
 {% set date_string = environ['RAPIDS_DATE_STRING'] %}
 
+
 package:
   name: cucim
   version: {{ version }}
@@ -17,6 +17,10 @@ source:
 build:
   number: {{ GIT_DESCRIBE_NUMBER }}
   string: cuda{{ cuda_major }}_py{{ py_version }}_{{ date_string }}_{{ GIT_DESCRIBE_HASH }}_{{ GIT_DESCRIBE_NUMBER }}
+  ignore_run_exports_from:
+    {% if cuda_major == "11" %}
+    - {{ compiler('cuda11') }}
+    {% endif %}
   script_env:
     - AWS_ACCESS_KEY_ID
     - AWS_SECRET_ACCESS_KEY
@@ -38,33 +42,40 @@ requirements:
   build:
     - {{ compiler("c") }}
     - {{ compiler("cxx") }}
+    {% if cuda_major == "11" %}
+    - {{ compiler('cuda11') }} ={{ cuda_version }}
+    {% else %}
+    - {{ compiler('cuda') }}
+    {% endif %}
+    - cuda-version ={{ cuda_version }}
     - cmake >=3.23.1,!=3.25.0
     - make
     - ninja
     - sysroot_{{ target_platform }} {{ sysroot_version }}
   host:
     - click
-    - cudatoolkit ={{ cuda_version }}
+    - cuda-version ={{ cuda_version }}
     - cupy >=12.0.0
     - libcucim ={{ version }}
     - numpy 1.21
     - python
-    - scikit-image >=0.19.0,<0.21.0a0
+    - scikit-image >=0.19.0,<0.22.0a0
     - scipy
   run:
-    - {{ pin_compatible('cudatoolkit', max_pin='x', min_pin='x') }}
+    - {{ pin_compatible('cuda-version', max_pin='x', min_pin='x') }}
     - {{ pin_compatible('numpy') }}
     - click
     - cupy >=12.0.0
+    - lazy_loader >=0.1
     - libcucim ={{ version }}
     # - openslide # skipping here but benchmark binary would need openslide library
     - python
-    - scikit-image >=0.19.0,<0.21.0a0
+    - scikit-image >=0.19.0,<0.22.0a0
     - scipy
 
 tests:
   requirements:
-    - cudatoolkit ={{ cuda_version }}
+    - cuda-version ={{ cuda_version }}
   imports:
     - cucim
 

conda/recipes/libcucim/build.sh

@@ -4,7 +4,6 @@ CUCIM_BUILD_TYPE=${CUCIM_BUILD_TYPE:-release}
 
 echo "CC          : ${CC}"
 echo "CXX         : ${CXX}"
-echo "CUDA        : ${CUDA}"
 
 # CUDA needs to include $PREFIX/include as system include path
 export CUDAFLAGS="-isystem $BUILD_PREFIX/include -isystem $PREFIX/include "