Merge branch 'branch-25.04' into vendored-binary-morphology-update

rapidsai · Feb 26, 2025 · 2a8b039 · 2a8b039
2 parents efa10ae + 0717baf
commit 2a8b039
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -13,7 +13,7 @@
 # limitations under the License.
 #
 
-cmake_minimum_required(VERSION 3.26.4)
+cmake_minimum_required(VERSION 3.30.4 FATAL_ERROR)
 
 ################################################################################
 # Prerequisite statements
@@ -209,7 +209,6 @@ install(DIRECTORY
 install(DIRECTORY
             ${deps-fmt_SOURCE_DIR}/include/
             ${deps-nvtx3_SOURCE_DIR}/c/include/
-            ${deps-nvtx3_SOURCE_DIR}/cpp/include/
         DESTINATION
             ${CMAKE_INSTALL_INCLUDEDIR}/${CUCIM_PACKAGE_NAME}/3rdparty)
 

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # <div align="left"><img src="https://rapids.ai/assets/images/rapids_logo.png" width="90px"/>&nbsp;cuCIM</div>
 
-[RAPIDS](https://rapids.ai) cuCIM is an open-source, accelerated computer vision and image processing software library for multidimensional images used in biomedical, geospatial, material and life science, and remote sensing use cases.
+[RAPIDS](https://rapids.ai) cuCIM (pronounced "koo-sim", see [here]( https://ipa-reader.com/?text=ku%CB%90%CB%88s%C9%AAm&voice=Joey )) is an open-source, accelerated computer vision and image processing software library for multidimensional images used in biomedical, geospatial, material and life science, and remote sensing use cases.
 
 cuCIM offers:
 

diff --git a/ci/build_cpp.sh b/ci/build_cpp.sh
@@ -21,7 +21,7 @@ conda config --set path_conflict warn
 
 sccache --zero-stats
 
-RAPIDS_PACKAGE_VERSION=$(rapids-generate-version) rapids-conda-retry mambabuild conda/recipes/libcucim
+RAPIDS_PACKAGE_VERSION=$(rapids-generate-version) rapids-conda-retry build conda/recipes/libcucim
 
 sccache --show-adv-stats
 

diff --git a/ci/build_python.sh b/ci/build_python.sh
@@ -27,7 +27,7 @@ sccache --zero-stats
 
 # TODO: Remove `--no-test` flag once importing on a CPU
 # node works correctly
-RAPIDS_PACKAGE_VERSION=$(head -1 ./VERSION) rapids-conda-retry mambabuild \
+RAPIDS_PACKAGE_VERSION=$(head -1 ./VERSION) rapids-conda-retry build \
   --no-test \
   --channel "${CPP_CHANNEL}" \
   conda/recipes/cucim

diff --git a/ci/build_wheel.sh b/ci/build_wheel.sh
@@ -32,6 +32,9 @@ rapids-pip-retry install \
 
 sccache --zero-stats
 
+rapids-logger "pyenv rehash"
+pyenv rehash
+
 # First build the C++ lib using CMake via the run script
 ./run build_local all ${CMAKE_BUILD_TYPE}
 

diff --git a/conda/environments/all_cuda-118_arch-x86_64.yaml b/conda/environments/all_cuda-118_arch-x86_64.yaml
@@ -8,7 +8,7 @@ channels:
 dependencies:
 - c-compiler
 - click
-- cmake>=3.26.4,!=3.30.0
+- cmake>=3.30.4
 - cuda-version=11.8
 - cudatoolkit
 - cupy>=12.0.0
@@ -42,7 +42,7 @@ dependencies:
 - recommonmark
 - scikit-image>=0.19.0,<0.26.0a0
 - scipy>=1.11.2
-- sphinx>=8.0.0
+- sphinx>=8.0.0,<8.2.0
 - sysroot_linux-64==2.28
 - tifffile>=2022.8.12
 - yasm

diff --git a/conda/environments/all_cuda-128_arch-x86_64.yaml b/conda/environments/all_cuda-128_arch-x86_64.yaml
@@ -8,7 +8,7 @@ channels:
 dependencies:
 - c-compiler
 - click
-- cmake>=3.26.4,!=3.30.0
+- cmake>=3.30.4
 - cuda-cudart-dev
 - cuda-nvcc
 - cuda-version=12.8
@@ -41,7 +41,7 @@ dependencies:
 - recommonmark
 - scikit-image>=0.19.0,<0.26.0a0
 - scipy>=1.11.2
-- sphinx>=8.0.0
+- sphinx>=8.0.0,<8.2.0
 - sysroot_linux-64==2.28
 - tifffile>=2022.8.12
 - yasm

diff --git a/conda/recipes/cucim/conda_build_config.yaml b/conda/recipes/cucim/conda_build_config.yaml
@@ -17,4 +17,4 @@ c_stdlib_version:
   - "2.28"
 
 cmake_version:
-  - ">=3.26.4,!=3.30.0"
+  - ">=3.30.4"
diff --git a/conda/recipes/libcucim/conda_build_config.yaml b/conda/recipes/libcucim/conda_build_config.yaml
@@ -17,7 +17,7 @@ c_stdlib_version:
   - "2.28"
 
 cmake_version:
-  - ">=3.26.4,!=3.30.0"
+  - ">=3.30.4"
 
 # The CTK libraries below are missing from the conda-forge::cudatoolkit package
 # for CUDA 11. The "*_host_*" version specifiers correspond to `11.8` packages

diff --git a/cpp/cmake/deps/abseil.cmake b/cpp/cmake/deps/abseil.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -19,18 +19,16 @@ if (NOT TARGET deps::abseil)
             GIT_REPOSITORY https://github.com/abseil/abseil-cpp.git
             GIT_TAG 20200225.2
             GIT_SHALLOW TRUE
+            EXCLUDE_FROM_ALL
     )
-    FetchContent_GetProperties(deps-abseil)
-    if (NOT deps-abseil_POPULATED)
-        message(STATUS "Fetching abseil sources")
-        FetchContent_Populate(deps-abseil)
-        message(STATUS "Fetching abseil sources - done")
-    endif ()
 
     # Create static library
     cucim_set_build_shared_libs(OFF)
-    set(BUILD_TESTING FALSE) # Disable BUILD_TESTING (cmake-build-debug/_deps/deps-abseil-src/CMakeLists.txt:97)
-    add_subdirectory(${deps-abseil_SOURCE_DIR} ${deps-abseil_BINARY_DIR} EXCLUDE_FROM_ALL)
+         # Disable BUILD_TESTING (cmake-build-debug/_deps/deps-abseil-src/CMakeLists.txt:97)
+    set(BUILD_TESTING FALSE)
+    message(STATUS "Fetching abseil sources")
+    FetchContent_MakeAvailable(deps-abseil)
+    message(STATUS "Fetching abseil sources - done")
 
     # Set PIC to prevent the following error message
     # : /usr/bin/ld: ../lib/libabsl_strings.a(escaping.cc.o): relocation R_X86_64_PC32 against symbol `_ZN4absl14lts_2020_02_2516numbers_internal8kHexCharE' can not be used when making a shared object; recompile with -fPIC

diff --git a/cpp/cmake/deps/boost-header-only.cmake b/cpp/cmake/deps/boost-header-only.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2021, NVIDIA CORPORATION.
+# Copyright (c) 2021-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -14,42 +14,19 @@
 #
 
 if (NOT TARGET deps::boost-header-only)
+    find_package(Git REQUIRED)
     set(Boost_VERSION 1.75.0)
     set(boost_component_list "interprocess" "config" "intrusive" "move" "assert" "static_assert" "container" "core" "date_time" "smart_ptr" "throw_exception" "utility" "type_traits" "numeric/conversion" "mpl" "preprocessor" "container_hash" "integer" "detail")
-    FetchContent_Declare(
-            deps-boost-header-only
-            GIT_REPOSITORY https://github.com/boostorg/boost.git
-            GIT_TAG boost-${Boost_VERSION}
-            GIT_SHALLOW TRUE
-    )
-
-    FetchContent_GetProperties(deps-boost-header-only)
-    if (NOT deps-boost-header-only_POPULATED)
-        message(STATUS "Fetching boost-header-only sources")
-        FetchContent_Populate(deps-boost-header-only)
-        message(STATUS "Fetching boost-header-only sources - done")
 
-        message(STATUS "Applying patch for boost-header-only")
-        find_package(Git)
-        if(Git_FOUND OR GIT_FOUND)
-            execute_process(
-                COMMAND bash -c "${GIT_EXECUTABLE} reset HEAD --hard && ${GIT_EXECUTABLE} apply ${CMAKE_CURRENT_LIST_DIR}/boost-header-only.patch"
-                WORKING_DIRECTORY "${deps-boost-header-only_SOURCE_DIR}/libs/interprocess"
-                RESULT_VARIABLE exec_result
-                ERROR_VARIABLE exec_error
-                ERROR_STRIP_TRAILING_WHITESPACE
-                OUTPUT_VARIABLE exec_output
-                OUTPUT_STRIP_TRAILING_WHITESPACE
-                )
-            if(exec_result EQUAL 0)
-                message(STATUS "Applying patch for boost-header-only - done")
-            else()
-                message(STATUS "Applying patch for boost-header-only - failed")
-                message(FATAL_ERROR "${exec_output}\n${exec_error}")
-            endif()
-        endif ()
-    endif ()
+    message(STATUS "Fetching boost-header-only sources")
+    FetchContent_Populate(deps-boost-header-only
+        GIT_REPOSITORY https://github.com/boostorg/boost.git
+        GIT_TAG boost-${Boost_VERSION}
+        GIT_SHALLOW TRUE
+        PATCH_COMMAND ${GIT_EXECUTABLE} apply "${CMAKE_CURRENT_LIST_DIR}/boost-header-only.patch" --directory=libs/interprocess)
+    message(STATUS "Fetching boost-header-only sources - done")
 
+    FetchContent_GetProperties(deps-boost-header-only)
     add_library(deps::boost-header-only INTERFACE IMPORTED GLOBAL)
 
     unset(boost_include_string)

diff --git a/cpp/cmake/deps/boost.cmake b/cpp/cmake/deps/boost.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020-2021, NVIDIA CORPORATION.
+# Copyright (c) 2020-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -14,6 +14,9 @@
 #
 
 if (NOT TARGET deps::boost)
+    cmake_policy(PUSH)
+    cmake_policy(SET CMP0169 OLD)
+
     set(Boost_VERSION 1.75.0)
     set(Boost_BUILD_COMPONENTS container)
     set(Boost_BUILD_OPTIONS "threading=multi cxxflags=-fPIC runtime-link=static variant=release link=static address-model=64 --layout=system")
@@ -72,4 +75,6 @@ if (NOT TARGET deps::boost)
 
     set(deps-boost_SOURCE_DIR ${deps-boost_SOURCE_DIR} CACHE INTERNAL "" FORCE)
     mark_as_advanced(deps-boost_SOURCE_DIR)
+
+    cmake_policy(POP)
 endif ()
diff --git a/cpp/cmake/deps/catch2.cmake b/cpp/cmake/deps/catch2.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -19,15 +19,12 @@ if (NOT TARGET deps::catch2)
             GIT_REPOSITORY https://github.com/catchorg/Catch2.git
             GIT_TAG v3.4.0
             GIT_SHALLOW TRUE
+            EXCLUDE_FROM_ALL
     )
-    FetchContent_GetProperties(deps-catch2)
-    if (NOT deps-catch2_POPULATED)
-        message(STATUS "Fetching catch2 sources")
-        FetchContent_Populate(deps-catch2)
-        message(STATUS "Fetching catch2 sources - done")
-    endif ()
 
-    add_subdirectory(${deps-catch2_SOURCE_DIR} ${deps-catch2_BINARY_DIR} EXCLUDE_FROM_ALL)
+    message(STATUS "Fetching catch2 sources")
+    FetchContent_MakeAvailable(deps-catch2)
+    message(STATUS "Fetching catch2 sources - done")
 
     # Include Append catch2's cmake module path so that we can use `include(Catch)`.
     # https://github.com/catchorg/Catch2/blob/devel/docs/cmake-integration.md#catchcmake-and-catchaddtestscmake

diff --git a/cpp/cmake/deps/cli11.cmake b/cpp/cmake/deps/cli11.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -19,15 +19,14 @@ if (NOT TARGET deps::cli11)
             GIT_REPOSITORY https://github.com/CLIUtils/CLI11.git
             GIT_TAG v1.9.1
             GIT_SHALLOW TRUE
+            EXCLUDE_FROM_ALL
     )
-    FetchContent_GetProperties(deps-cli11)
-    if (NOT deps-cli11_POPULATED)
-        message(STATUS "Fetching cli11 sources")
-        FetchContent_Populate(deps-cli11)
-        message(STATUS "Fetching cli11 sources - done")
-    endif ()
-
-    add_subdirectory(${deps-cli11_SOURCE_DIR} ${deps-cli11_BINARY_DIR} EXCLUDE_FROM_ALL)
+    message(STATUS "Fetching cli11 sources")
+    set(CLI11_BUILD_DOCS OFF)
+    set(CLI11_BUILD_EXAMPLES OFF)
+    set(CLI11_BUILD_TESTS OFF)
+    FetchContent_MakeAvailable(deps-cli11)
+    message(STATUS "Fetching cli11 sources - done")
 
     add_library(deps::cli11 INTERFACE IMPORTED GLOBAL)
     target_link_libraries(deps::cli11 INTERFACE CLI11::CLI11)

diff --git a/cpp/cmake/deps/fmt.cmake b/cpp/cmake/deps/fmt.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -19,17 +19,16 @@ if (NOT TARGET deps::fmt)
             GIT_REPOSITORY https://github.com/fmtlib/fmt.git
             GIT_TAG 7.0.1
             GIT_SHALLOW TRUE
+            EXCLUDE_FROM_ALL
     )
-    FetchContent_GetProperties(deps-fmt)
-    if (NOT deps-fmt_POPULATED)
-        message(STATUS "Fetching fmt sources")
-        FetchContent_Populate(deps-fmt)
-        message(STATUS "Fetching fmt sources - done")
-    endif ()
+
+    message(STATUS "Fetching fmt sources")
 
     # Create static library
     cucim_set_build_shared_libs(OFF)
-    add_subdirectory(${deps-fmt_SOURCE_DIR} ${deps-fmt_BINARY_DIR} EXCLUDE_FROM_ALL)
+
+    FetchContent_MakeAvailable(deps-fmt)
+    message(STATUS "Fetching fmt sources - done")
 
     # Set PIC to prevent the following error message
     # : /usr/bin/ld: ../lib/libfmtd.a(format.cc.o): relocation R_X86_64_PC32 against symbol `stderr@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC

diff --git a/cpp/cmake/deps/googlebenchmark.cmake b/cpp/cmake/deps/googlebenchmark.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -19,18 +19,17 @@ if (NOT TARGET deps::googlebenchmark)
             GIT_REPOSITORY https://github.com/google/benchmark.git
             GIT_TAG v1.5.1
             GIT_SHALLOW TRUE
+            EXCLUDE_FROM_ALL
     )
-    FetchContent_GetProperties(deps-googlebenchmark)
-    if (NOT deps-googlebenchmark_POPULATED)
-        message(STATUS "Fetching googlebenchmark sources")
-        FetchContent_Populate(deps-googlebenchmark)
-        message(STATUS "Fetching googlebenchmark sources - done")
-    endif ()
+
+    message(STATUS "Fetching googlebenchmark sources")
 
     # Create static library
     cucim_set_build_shared_libs(OFF)
     set(BENCHMARK_ENABLE_GTEST_TESTS OFF)
-    add_subdirectory(${deps-googlebenchmark_SOURCE_DIR} ${deps-googlebenchmark_BINARY_DIR} EXCLUDE_FROM_ALL)
+    FetchContent_MakeAvailable(deps-googlebenchmark)
+    message(STATUS "Fetching googlebenchmark sources - done")
+
     cucim_restore_build_shared_libs()
 
     add_library(deps::googlebenchmark INTERFACE IMPORTED GLOBAL)

diff --git a/cpp/cmake/deps/googletest.cmake b/cpp/cmake/deps/googletest.cmake
@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2025, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -19,17 +19,13 @@ if (NOT TARGET deps::googletest)
             GIT_REPOSITORY https://github.com/google/googletest.git
             GIT_TAG release-1.10.0
             GIT_SHALLOW TRUE
+            EXCLUDE_FROM_ALL
     )
-    FetchContent_GetProperties(deps-googletest)
-    if (NOT deps-googletest_POPULATED)
-        message(STATUS "Fetching googletest sources")
-        FetchContent_Populate(deps-googletest)
-        message(STATUS "Fetching googletest sources - done")
-    endif ()
-
+    message(STATUS "Fetching googletest sources")
     # Create static library
     cucim_set_build_shared_libs(OFF)
-    add_subdirectory(${deps-googletest_SOURCE_DIR} ${deps-googletest_BINARY_DIR} EXCLUDE_FROM_ALL)
+    FetchContent_MakeAvailable(deps-googletest)
+    message(STATUS "Fetching googletest sources - done")
     cucim_restore_build_shared_libs()
 
     add_library(deps::googletest INTERFACE IMPORTED GLOBAL)