Migrate to scikit-build-core

.github/workflows/python_wheels_variants.yml

@@ -100,12 +100,30 @@ jobs:
             *.whl
       - name: Audit wheel
         run: |
+          set -euo pipefail
           WHEEL_TAG=manylinux_2_28_x86_64
           echo "--- Audit binary wheel to ensure it's compliant with ${WHEEL_TAG} standard"
-          auditwheel repair --only-plat --plat ${WHEEL_TAG} python-package/dist/*.whl
-          python3 -m wheel tags --python-tag py3 --abi-tag none --platform ${WHEEL_TAG} --remove \
-            wheelhouse/*.whl
-          mv -v wheelhouse/*.whl python-package/dist/
+          raw_wheels=(python-package/dist/*.whl)
+          if [[ ${#raw_wheels[@]} -ne 1 || ! -f "${raw_wheels[0]}" ]]; then
+            echo "error: expected exactly one raw wheel in python-package/dist"
+            exit 1
+          fi
+          raw_wheel="${raw_wheels[0]}"
+          auditwheel repair --only-plat --plat ${WHEEL_TAG} "${raw_wheel}"
+          repaired_wheels=(wheelhouse/*.whl)
+          if [[ ${#repaired_wheels[@]} -ne 1 || ! -f "${repaired_wheels[0]}" ]]; then
+            echo "error: expected exactly one repaired wheel in wheelhouse"
+            exit 1
+          fi
+          python3 -m wheel tags --python-tag cp312 --abi-tag abi3 --platform ${WHEEL_TAG} --remove \
+            "${repaired_wheels[0]}"
+          tagged_wheels=(wheelhouse/*.whl)
+          if [[ ${#tagged_wheels[@]} -ne 1 || ! -f "${tagged_wheels[0]}" ]]; then
+            echo "error: expected exactly one tagged wheel in wheelhouse"
+            exit 1
+          fi
+          rm -v "${raw_wheel}"
+          mv -v "${tagged_wheels[0]}" python-package/dist/
       - name: Stash files
         run: |
           python3 ops/pipeline/manage-artifacts.py upload \

.github/workflows/python_wheels_winarm64.yml

@@ -59,7 +59,7 @@ jobs:
           mkdir -p wheelhouse
           pip wheel --no-deps -v . --wheel-dir wheelhouse/
           $wheelFile = Get-ChildItem wheelhouse/*.whl | Select-Object -First 1 -ExpandProperty FullName
-          python -m wheel tags --python-tag py3 --abi-tag none --platform win_arm64 --remove $wheelFile
+          python -m wheel tags --python-tag cp312 --abi-tag abi3 --platform win_arm64 --remove $wheelFile
 
       - name: Upload Python wheel xgboost
         if: github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')
@@ -85,7 +85,7 @@ jobs:
           cd python-package
           pip wheel --no-deps -v . --wheel-dir wheelhouse/
           $wheelFile = Get-ChildItem wheelhouse/*.whl | Select-Object -First 1 -ExpandProperty FullName
-          python -m wheel tags --python-tag py3 --abi-tag none --platform win_arm64 --remove $wheelFile
+          python -m wheel tags --python-tag cp312 --abi-tag abi3 --platform win_arm64 --remove $wheelFile
 
       - name: Upload Python wheel xgboost-cpu
         if: github.ref == 'refs/heads/master' || contains(github.ref, 'refs/heads/release_')

CMakeLists.txt

@@ -71,6 +71,12 @@ option(USE_NVTX "Build with cuda profiling annotations. Developers only." OFF)
 set(NVTX_HEADER_DIR "" CACHE PATH "Path to the stand-alone nvtx header")
 option(HIDE_CXX_SYMBOLS "Build shared library and hide all C++ symbols" OFF)
 option(KEEP_BUILD_ARTIFACTS_IN_BINARY_DIR "Output build artifacts in CMake binary dir" OFF)
+# When ON, suppress install() rules intended for system installs (headers,
+# xgboost-config.cmake, XGBoostTargets, xgboost.pc, default lib install).
+# Used by python-package/CMakeLists.txt so the Python wheel's install layout
+# is fully controlled there.
+option(XGBOOST_FOR_PYTHON_WHEEL
+  "Building libxgboost embedded inside the Python wheel; skip default installs" OFF)
 ## CUDA
 option(USE_CUDA  "Build with GPU acceleration" OFF)
 option(USE_NCCL  "Build with NCCL to enable distributed GPU support." OFF)
@@ -457,48 +463,50 @@ endif()
 include(CPack)
 
 include(GNUInstallDirs)
-# Install all headers.  Please note that currently the C++ headers does not form an "API".
-install(DIRECTORY ${xgboost_SOURCE_DIR}/include/xgboost
-  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
-
-# Install libraries. If `xgboost` is a static lib, specify `objxgboost` also, to avoid the
-# following error:
-#
-#  > install(EXPORT ...) includes target "xgboost" which requires target "objxgboost" that is not
-#  > in any export set.
-#
-# https://github.com/dmlc/xgboost/issues/6085
-if(BUILD_STATIC_LIB)
-  set(INSTALL_TARGETS xgboost objxgboost dmlc)
-else()
-  set(INSTALL_TARGETS xgboost)
-endif()
-
-install(TARGETS ${INSTALL_TARGETS}
-  EXPORT XGBoostTargets
-  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-  INCLUDES DESTINATION ${LIBLEGACY_INCLUDE_DIRS})
-install(EXPORT XGBoostTargets
-  FILE XGBoostTargets.cmake
-  NAMESPACE xgboost::
-  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xgboost)
-
-include(CMakePackageConfigHelpers)
-configure_package_config_file(
-  ${CMAKE_CURRENT_LIST_DIR}/cmake/xgboost-config.cmake.in
-  ${CMAKE_CURRENT_BINARY_DIR}/cmake/xgboost-config.cmake
-  INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xgboost)
-write_basic_package_version_file(
-  ${CMAKE_BINARY_DIR}/cmake/xgboost-config-version.cmake
-  VERSION ${XGBOOST_VERSION}
-  COMPATIBILITY AnyNewerVersion)
-install(
-  FILES
-  ${CMAKE_CURRENT_BINARY_DIR}/cmake/xgboost-config.cmake
-  ${CMAKE_BINARY_DIR}/cmake/xgboost-config-version.cmake
-  DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xgboost)
+if(NOT XGBOOST_FOR_PYTHON_WHEEL)
+  # Install all headers.  Please note that currently the C++ headers does not form an "API".
+  install(DIRECTORY ${xgboost_SOURCE_DIR}/include/xgboost
+    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+  # Install libraries. If `xgboost` is a static lib, specify `objxgboost` also, to avoid the
+  # following error:
+  #
+  #  > install(EXPORT ...) includes target "xgboost" which requires target "objxgboost" that is not
+  #  > in any export set.
+  #
+  # https://github.com/dmlc/xgboost/issues/6085
+  if(BUILD_STATIC_LIB)
+    set(INSTALL_TARGETS xgboost objxgboost dmlc)
+  else()
+    set(INSTALL_TARGETS xgboost)
+  endif()
+
+  install(TARGETS ${INSTALL_TARGETS}
+    EXPORT XGBoostTargets
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+    INCLUDES DESTINATION ${LIBLEGACY_INCLUDE_DIRS})
+  install(EXPORT XGBoostTargets
+    FILE XGBoostTargets.cmake
+    NAMESPACE xgboost::
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xgboost)
+
+  include(CMakePackageConfigHelpers)
+  configure_package_config_file(
+    ${CMAKE_CURRENT_LIST_DIR}/cmake/xgboost-config.cmake.in
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/xgboost-config.cmake
+    INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xgboost)
+  write_basic_package_version_file(
+    ${CMAKE_BINARY_DIR}/cmake/xgboost-config-version.cmake
+    VERSION ${XGBOOST_VERSION}
+    COMPATIBILITY AnyNewerVersion)
+  install(
+    FILES
+    ${CMAKE_CURRENT_BINARY_DIR}/cmake/xgboost-config.cmake
+    ${CMAKE_BINARY_DIR}/cmake/xgboost-config-version.cmake
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xgboost)
+endif()
 
 #-- Test
 if(GOOGLE_TEST)
@@ -519,7 +527,7 @@ if(GOOGLE_TEST)
 endif()
 
 # Add xgboost.pc
-if(ADD_PKGCONFIG)
+if(ADD_PKGCONFIG AND NOT XGBOOST_FOR_PYTHON_WHEEL)
   configure_file(${xgboost_SOURCE_DIR}/cmake/xgboost.pc.in ${xgboost_BINARY_DIR}/xgboost.pc @ONLY)
 
   install(

cmake/Utils.cmake

@@ -65,7 +65,11 @@ function(compute_cmake_cuda_archs archs)
   elseif(CMAKE_CUDA_COMPILER_VERSION MATCHES "^([0-9]+\\.[0-9]+)")
     set(CUDA_VERSION "${CMAKE_MATCH_1}")
   endif()
-  list(SORT archs)
+  # NATURAL sort is needed so that 3-digit archs (100, 120) sort *after*
+  # 2-digit ones (70, 90). With the default STRING sort, "100" precedes "70"
+  # alphabetically, which caused the -virtual (PTX) entry below — applied to
+  # the AT -1 position — to land on the wrong architecture.
+  list(SORT archs COMPARE NATURAL)
   unset(CMAKE_CUDA_ARCHITECTURES CACHE)
   set(CMAKE_CUDA_ARCHITECTURES ${archs})
 

doc/build.rst

@@ -193,23 +193,28 @@ There are several ways to build and install the package from source:
     $ pip install -v . # Builds the shared object automatically.
 
   which will compile XGBoost's native (C++) code using default CMake flags.  To enable
-  additional compilation options, pass corresponding ``--config-settings``:
+  additional compilation options, pass them as CMake defines through
+  ``scikit-build-core``'s ``--config-settings``:
 
   .. code-block:: console
 
-    $ pip install -v . --config-settings use_cuda=True --config-settings use_nccl=True
+    $ pip install -v . \
+        --config-settings cmake.define.USE_CUDA=ON \
+        --config-settings cmake.define.USE_NCCL=ON
 
   Use Pip 22.1 or later to use ``--config-settings`` option.
 
-  Here are the available options for ``--config-settings``:
+  Common CMake options the Python wheel forwards to the libxgboost build
+  (see :ref:`building-the-shared-library` for the full list):
 
-  .. literalinclude:: ../python-package/packager/build_config.py
-    :language: python
-    :start-at: @dataclasses.dataclass
-    :end-before: def _set_config_setting(
-
-  ``use_system_libxgboost`` is a special option. See Item 4 below for
-  detailed description.
+  - ``USE_CUDA`` — build with CUDA / GPU acceleration
+  - ``USE_NCCL`` — build with NCCL for distributed GPU training
+  - ``USE_DLOPEN_NCCL`` — load NCCL dynamically at runtime
+  - ``PLUGIN_FEDERATED`` — enable the federated learning plugin
+  - ``PLUGIN_RMM`` — build with RAPIDS Memory Manager support
+  - ``HIDE_CXX_SYMBOLS`` — hide all C++ symbols in the shared library
+  - ``USE_OPENMP`` — build with OpenMP (defaults to ON)
+  - ``XGBOOST_USE_SYSTEM_LIBXGBOOST`` — see Item 4 below
 
   .. note:: Verbose flag recommended
 
@@ -252,12 +257,12 @@ There are several ways to build and install the package from source:
     libpath = pathlib.Path(sys.base_prefix).joinpath("lib", "libxgboost.so")
     assert libpath.exists()
 
-  Then pass ``use_system_libxgboost=True`` option to ``pip install``:
+  Then pass ``XGBOOST_USE_SYSTEM_LIBXGBOOST=ON`` to ``pip install`` as a CMake define:
 
   .. code-block:: bash
 
     cd python-package
-    pip install . --config-settings use_system_libxgboost=True
+    pip install . --config-settings cmake.define.XGBOOST_USE_SYSTEM_LIBXGBOOST=ON
 
 
 .. note::

doc/contrib/python_packaging.rst

@@ -75,7 +75,7 @@ completes quickly:
 
 .. code-block:: console
 
-  $ pip install xgboost-2.0.0-py3-none-linux_x86_64.whl  # Completes quickly
+  $ pip install xgboost-2.0.0-cp312-abi3-linux_x86_64.whl  # Completes quickly
 
 .. rubric:: Footnotes
 

ops/conda_env/python_lint.yml

@@ -19,5 +19,4 @@ dependencies:
 - cloudpickle
 - pytest
 - hypothesis
-- hatchling
 - pyspark>=4.0.0

ops/pipeline/audit-cuda-wheel.sh

@@ -40,18 +40,43 @@ WHEEL_TAG=manylinux_2_28_${arch}
 set -x
 
 echo "--- Audit binary wheel to ensure it's compliant with ${WHEEL_TAG} standard"
-auditwheel repair --only-plat --plat ${WHEEL_TAG} python-package/dist/*.whl
-python3 -m wheel tags --python-tag py3 --abi-tag none --platform ${WHEEL_TAG} --remove \
-  wheelhouse/*.whl
-mv -v wheelhouse/*.whl python-package/dist/
+raw_wheels=(python-package/dist/*.whl)
+if [[ ${#raw_wheels[@]} -ne 1 || ! -f "${raw_wheels[0]}" ]]; then
+  echo "error: expected exactly one raw wheel in python-package/dist"
+  exit 1
+fi
+raw_wheel="${raw_wheels[0]}"
+
+auditwheel repair --only-plat --plat ${WHEEL_TAG} "${raw_wheel}"
+repaired_wheels=(wheelhouse/*.whl)
+if [[ ${#repaired_wheels[@]} -ne 1 || ! -f "${repaired_wheels[0]}" ]]; then
+  echo "error: expected exactly one repaired wheel in wheelhouse"
+  exit 1
+fi
+python3 -m wheel tags --python-tag cp312 --abi-tag abi3 --platform ${WHEEL_TAG} --remove \
+  "${repaired_wheels[0]}"
+tagged_wheels=(wheelhouse/*.whl)
+if [[ ${#tagged_wheels[@]} -ne 1 || ! -f "${tagged_wheels[0]}" ]]; then
+  echo "error: expected exactly one tagged wheel in wheelhouse"
+  exit 1
+fi
+rm -v "${raw_wheel}"
+mv -v "${tagged_wheels[0]}" python-package/dist/
+
+final_wheels=(python-package/dist/*.whl)
+if [[ ${#final_wheels[@]} -ne 1 || ! -f "${final_wheels[0]}" ]]; then
+  echo "error: expected exactly one final wheel in python-package/dist"
+  exit 1
+fi
+final_wheel="${final_wheels[0]}"
 
-if ! unzip -l ./python-package/dist/*.whl | grep libgomp > /dev/null; then
+if ! unzip -l "${final_wheel}" | grep libgomp > /dev/null; then
   echo "error: libgomp.so was not vendored in the wheel"
   exit -1
 fi
 
 # Check size of wheel
-pydistcheck --config python-package/pyproject.toml python-package/dist/*.whl
+pydistcheck --config python-package/pyproject.toml "${final_wheel}"
 
 # Generate meta.json only for the main CUDA variant (not cuda13)
 if [[ $cuda_variant == "cuda" && $arch == "x86_64" ]]
@@ -60,7 +85,7 @@ then
   # TODO(hcho3): Generate meta.json that contains both x86_64 and aarch64 wheels
   echo "--- Generate meta info"
   python3 ops/script/format_wheel_meta.py \
-    --wheel-path python-package/dist/*.whl  \
+    --wheel-path "${final_wheel}"  \
     --commit-hash ${GITHUB_SHA}  \
     --platform-tag ${WHEEL_TAG}  \
     --meta-path python-package/dist/
@@ -72,7 +97,7 @@ then
   python3 ops/pipeline/manage-artifacts.py upload \
     --s3-bucket xgboost-nightly-builds \
     --prefix ${BRANCH_NAME}/${GITHUB_SHA} --make-public \
-    python-package/dist/*.whl
+    "${final_wheel}"
 
   if [[ $cuda_variant == "cuda" && $arch == "x86_64" ]]
   then

ops/pipeline/build-python-wheels-cpu.sh

@@ -41,7 +41,7 @@ python3 ops/docker_run.py \
   --image-uri "${IMAGE_URI}" \
   -- auditwheel repair --only-plat \
   --plat ${WHEEL_TAG} python-package/dist/xgboost_cpu-*.whl
-python3 -m wheel tags --python-tag py3 --abi-tag none --platform ${WHEEL_TAG} --remove \
+python3 -m wheel tags --python-tag cp312 --abi-tag abi3 --platform ${WHEEL_TAG} --remove \
   wheelhouse/xgboost_cpu-*.whl
 rm -v python-package/dist/xgboost_cpu-*.whl
 mv -v wheelhouse/xgboost_cpu-*.whl python-package/dist/

ops/pipeline/build-win64.ps1

@@ -77,7 +77,7 @@ conda activate
 & pip wheel --no-deps -v . --wheel-dir dist/
 if ($LASTEXITCODE -ne 0) { throw "Last command failed" }
 
-python -m wheel tags --python-tag py3 --abi-tag none `
+python -m wheel tags --python-tag cp312 --abi-tag abi3 `
   --platform win_amd64 --remove `
   (Get-ChildItem dist/*.whl | Select-Object -Expand FullName)
 if ($LASTEXITCODE -ne 0) { throw "Last command failed" }

ops/pipeline/test-python-sdist.sh

@@ -3,6 +3,11 @@
 
 set -euox pipefail
 
+# Stage the C++ source tree into python-package/cpp_src/ so the sdist is
+# self-contained (scikit-build-core's sdist cannot reach files above
+# python-package/ by itself).
+python3 ops/script/prepare_sdist.py --clean
+
 cd python-package
 python --version
 python -m build --sdist

ops/pipeline/test-python-with-sysprefix.sh

@@ -19,5 +19,5 @@ cd python-package
 pip install virtualenv
 virtualenv venv
 source venv/bin/activate && \
-  pip install -v . --config-settings use_system_libxgboost=True && \
+  pip install -v . --config-settings cmake.define.XGBOOST_USE_SYSTEM_LIBXGBOOST=ON && \
   python -c 'import xgboost'