WIP: ENH: migrate to scikit-build-core, linux amd64

Supporting the Stable ABI / Limited API.

Author: thewtex

.gitignore

@@ -43,6 +43,7 @@ lib
 lib64
 MANIFEST
 oneTBB-prefix/
+pyproject.toml
 
 # Installer logs
 pip-log.txt

CMakeLists.txt

@@ -48,6 +48,11 @@ if(ITKPythonPackage_SUPERBUILD)
       -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
       )
   endif()
+  set(ep_download_extract_timestamp_arg )
+  if(CMAKE_VERSION VERSION_EQUAL "3.24" OR CMAKE_VERSION VERSION_GREATER "3.24")
+    # See https://cmake.org/cmake/help/latest/policy/CMP0135.html
+    set(ep_download_extract_timestamp_arg DOWNLOAD_EXTRACT_TIMESTAMP 1)
+  endif()
 
   #-----------------------------------------------------------------------------
   # Options
@@ -124,6 +129,7 @@ if(ITKPythonPackage_SUPERBUILD)
         -DCMAKE_INSTALL_LIBDIR:STRING=lib # Skip default initialization by GNUInstallDirs CMake module
         ${ep_common_cmake_cache_args}
         ${tbb_cmake_cache_args}
+        ${ep_download_extract_timestamp_arg}
         -DCMAKE_BUILD_TYPE:STRING=Release
       BUILD_BYPRODUCTS "${TBB_DIR}/TBBConfig.cmake"
       USES_TERMINAL_DOWNLOAD 1
@@ -276,18 +282,14 @@ if(ITKPythonPackage_SUPERBUILD)
         -DWRAP_ITK_INSTALL_COMPONENT_PER_MODULE:BOOL=${install_component_per_module}
         -DITK_LEGACY_SILENT:BOOL=ON
         -DITK_WRAP_PYTHON:BOOL=ON
-        -DITK_WRAP_unsigned_short:BOOL=ON
-        -DITK_WRAP_double:BOOL=ON
-        -DITK_WRAP_complex_double:BOOL=ON
-        -DITK_WRAP_IMAGE_DIMS:STRING=2;3;4
-        -DITK_WRAP_DOC:BOOL=ON
         -DDOXYGEN_EXECUTABLE:FILEPATH=${DOXYGEN_EXECUTABLE}
         -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR}
         -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY}
         -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE}
         ${ep_common_cmake_cache_args}
         ${tbb_args}
         ${ep_itk_cmake_cache_args}
+        ${ep_download_extract_timestamp_arg}
       USES_TERMINAL_DOWNLOAD 1
       USES_TERMINAL_UPDATE 1
       USES_TERMINAL_CONFIGURE 1

MANIFEST.in

@@ -1,2 +1,2 @@
-ninja==1.11.1
-scikit-build==0.17.6
+ninja==1.11.1.1
+scikit-build-core==0.8.2

requirements-dev.txt

@@ -49,6 +49,7 @@ tbb_dir=/work/oneTBB-prefix/lib/cmake/TBB
 sudo ldconfig
 export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/work/oneTBB-prefix/lib:/usr/lib:/usr/lib64
 
+# TODO: More work is required to re-enable this feature.
 SINGLE_WHEEL=0
 
 # Compile wheels re-using standalone project and archive cache
@@ -67,8 +68,7 @@ for PYBIN in "${PYBINARIES[@]}"; do
     compile_flags="-O3 -DNDEBUG"
     source_path=/work/ITK-source/ITK
     build_path=/work/ITK-$(basename $(dirname ${PYBIN}))-manylinux${MANYLINUX_VERSION}_${ARCH}
-    SETUP_PY_CONFIGURE="${script_dir}/../setup_py_configure.py"
-    SKBUILD_CMAKE_INSTALL_PREFIX=$(${Python3_EXECUTABLE} -c "from skbuild.constants import CMAKE_INSTALL_DIR; print(CMAKE_INSTALL_DIR)")
+    PYPROJECT_CONFIGURE="${script_dir}/../pyproject_configure.py"
 
     # Clean up previous invocations
     rm -rf ${build_path}
@@ -80,28 +80,26 @@ for PYBIN in "${PYBINARIES[@]}"; do
       echo "#"
 
       # Configure setup.py
-      ${PYBIN}/python ${SETUP_PY_CONFIGURE} "itk"
+      ${PYBIN}/python ${PYPROJECT_CONFIGURE} "itk"
       # Generate wheel
-      ${PYBIN}/python setup.py bdist_wheel -G Ninja -- \
-            -DITK_SOURCE_DIR:PATH=${source_path} \
-            -DITK_BINARY_DIR:PATH=${build_path} \
-            -DITKPythonPackage_ITK_BINARY_REUSE:BOOL=OFF \
-            -DITKPythonPackage_WHEEL_NAME:STRING="itk" \
-            -DITK_WRAP_unsigned_short:BOOL=ON \
-            -DITK_WRAP_double:BOOL=ON \
-            -DITK_WRAP_complex_double:BOOL=ON \
-            -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" \
-            -DCMAKE_CXX_COMPILER_TARGET:STRING=$(uname -m)-linux-gnu \
-            -DCMAKE_CXX_FLAGS:STRING="$compile_flags" \
-            -DCMAKE_C_FLAGS:STRING="$compile_flags" \
-            -DCMAKE_BUILD_TYPE:STRING="${build_type}" \
-            -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
-            -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
-            -DModule_ITKTBB:BOOL=ON \
-            -DTBB_DIR:PATH=${tbb_dir} \
-            -DITK_WRAP_DOC:BOOL=ON
-      # Cleanup
-      ${PYBIN}/python setup.py clean
+      ${PYBIN}/python -m pip \
+            --verbose \
+            wheel \
+            --wheel-dir dist \
+            --no-deps \
+            --config-settings=cmake.define.ITK_SOURCE_DIR:PATH=${source_path} \
+            --config-settings=cmake.define.ITK_BINARY_DIR:PATH=${build_path} \
+            --config-settings=cmake.define.ITKPythonPackage_ITK_BINARY_REUSE:BOOL=OFF \
+            --config-settings=cmake.define.ITKPythonPackage_WHEEL_NAME:STRING=itk \
+            --config-settings=cmake.define.CMAKE_CXX_COMPILER_TARGET:STRING=$(uname -m)-linux-gnu \
+            "--config-settings=cmake.define.CMAKE_CXX_FLAGS:STRING=$compile_flags" \
+            "--config-settings=cmake.define.CMAKE_C_FLAGS:STRING=$compile_flags" \
+            "--config-settings=cmake.define.CMAKE_BUILD_TYPE:STRING=${build_type}" \
+            --config-settings=cmake.define.Python3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
+            --config-settings=cmake.define.Python3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+            --config-settings=cmake.define.Module_ITKTBB:BOOL=ON \
+            --config-settings=cmake.define.TBB_DIR:PATH=${tbb_dir} \
+            .
 
     else
 
@@ -145,26 +143,23 @@ for PYBIN in "${PYBINARIES[@]}"; do
       wheel_names=$(cat ${script_dir}/../WHEEL_NAMES.txt)
       for wheel_name in ${wheel_names}; do
         # Configure setup.py
-        ${PYBIN}/python ${SETUP_PY_CONFIGURE} ${wheel_name}
+        ${PYBIN}/python ${PYPROJECT_CONFIGURE} ${wheel_name}
         # Generate wheel
-        ${PYBIN}/python setup.py bdist_wheel -G Ninja -- \
-          -DITK_SOURCE_DIR:PATH=${source_path} \
-          -DITK_BINARY_DIR:PATH=${build_path} \
-          -DITKPythonPackage_ITK_BINARY_REUSE:BOOL=ON \
-          -DITKPythonPackage_WHEEL_NAME:STRING=${wheel_name} \
-          -DITK_WRAP_unsigned_short:BOOL=ON \
-          -DITK_WRAP_double:BOOL=ON \
-          -DITK_WRAP_complex_double:BOOL=ON \
-          -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" \
-          -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
-          -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
-          -DCMAKE_BUILD_TYPE:STRING="${build_type}" \
-          -DCMAKE_CXX_FLAGS:STRING="${compile_flags}" \
-          -DCMAKE_C_FLAGS:STRING="${compile_flags}" \
-          -DITK_WRAP_DOC:BOOL=ON \
+        ${PYBIN}/python -m pip \
+          --verbose \
+          wheel \
+          --wheel-dir dist \
+          --no-deps \
+          --config-settings=cmake.define.ITK_SOURCE_DIR:PATH=${source_path} \
+          --config-settings=cmake.define.ITK_BINARY_DIR:PATH=${build_path} \
+          --config-settings=cmake.define.ITKPythonPackage_ITK_BINARY_REUSE:BOOL=ON \
+          --config-settings=cmake.define.ITKPythonPackage_WHEEL_NAME:STRING=${wheel_name} \
+          --config-settings=cmake.define.Python3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
+          --config-settings=cmake.define.Python3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+          --config-settings=cmake.define.CMAKE_CXX_FLAGS:STRING="${compile_flags}" \
+          --config-settings=cmake.define.CMAKE_C_FLAGS:STRING="${compile_flags}" \
+          . \
           || exit 1
-        # Cleanup
-        ${PYBIN}/python setup.py clean
       done
     fi
 
@@ -178,37 +173,15 @@ done
 if test "${ARCH}" == "x64"; then
   sudo /opt/python/cp39-cp39/bin/pip3 install auditwheel wheel
   # This step will fixup the wheel switching from 'linux' to 'manylinux<version>' tag
-  for whl in dist/itk_*linux_$(uname -m).whl; do
+  for whl in dist/itk_*linux_*.whl; do
       /opt/python/cp39-cp39/bin/auditwheel repair --plat manylinux${MANYLINUX_VERSION}_x86_64 ${whl} -w /work/dist/
-      rm ${whl}
   done
 else
   for whl in dist/itk_*$(uname -m).whl; do
       auditwheel repair ${whl} -w /work/dist/
       rm ${whl}
   done
 fi
-itk_core_whl=$(ls dist/itk_core*whl | head -n 1)
-repaired_plat1=$(echo $itk_core_whl | cut -d- -f5 | cut -d. -f1)
-repaired_plat2=$(echo $itk_core_whl | cut -d- -f5 | cut -d. -f2)
-for itk_wheel in dist/itk*-linux*.whl; do
-  mkdir -p unpacked_whl packed_whl
-  /opt/python/cp39-cp39/bin/wheel unpack -d unpacked_whl ${itk_wheel}
-  version=$(echo ${itk_wheel} | cut -d- -f3-4)
-  echo "Wheel-Version: 1.0" > unpacked_whl/itk-*/*.dist-info/WHEEL
-  echo "Generator: skbuild 0.8.1" >> unpacked_whl/itk-*/*.dist-info/WHEEL
-  echo "Root-Is-Purelib: false" >> unpacked_whl/itk-*/*.dist-info/WHEEL
-  echo "Tag: ${version}-${repaired_plat1}" >> unpacked_whl/itk-*/*.dist-info/WHEEL
-  echo "Tag: ${version}-${repaired_plat2}" >> unpacked_whl/itk-*/*.dist-info/WHEEL
-  echo "" >> unpacked_whl/itk-*/*.dist-info/WHEEL
-  /opt/python/cp39-cp39/bin/wheel pack -d packed_whl ./unpacked_whl/itk-*
-  mv packed_whl/*.whl dist/
-  rm -rf unpacked_whl packed_whl ${itk_wheel}
-done
-
-for itk_wheel in dist/itk*.whl.whl; do
-  mv $itk_wheel dist/$(basename $itk_wheel .whl)
-done
 
 # Install packages and test
 for PYBIN in "${PYBINARIES[@]}"; do
@@ -219,3 +192,5 @@ for PYBIN in "${PYBINARIES[@]}"; do
     (cd $HOME && ${PYBIN}/python -c 'import itkConfig; itkConfig.LazyLoading = False; import itk;')
     (cd $HOME && ${PYBIN}/python ${script_dir}/../../docs/code/test.py )
 done
+
+rm -f dist/numpy*.whl

scripts/internal/manylinux-build-wheels.sh

@@ -0,0 +1,133 @@
+# Generated using: @PYPROJECT_GENERATOR@
+
+[build-system]
+requires = ["scikit-build-core"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "@PYPROJECT_NAME@"
+version = "@PYPROJECT_VERSION@"
+
+description = "@PYPROJECT_DESCRIPTION@"
+readme = "ITK-source/ITK/README.md"
+license = {file = "LICENSE"}
+authors = [
+    { name = "Insight Software Consortium", email = "[email protected]" },
+]
+keywords = [
+    "ITK",
+    "InsightToolkit",
+    @PYPROJECT_EXTRA_KEYWORDS@
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Healthcare Industry",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: Android",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: POSIX",
+    "Operating System :: Unix",
+    "Programming Language :: C++",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Topic :: Software Development :: Libraries",
+]
+requires-python = ">=3.8"
+dependencies = [
+    @PYPROJECT_DEPENDENCIES@
+]
+
+[project.urls]
+Download = "@PYPROJECT_DOWNLOAD_URL@"
+Home = "https://docs.itk.org/"
+Issues = "https://github.com/InsightSoftwareConsortium/ITK/issues"
+Source = "https://github.com/InsightSoftwareConsortium/ITK"
+
+[tool.scikit-build]
+# The versions of CMake to allow. If CMake is not present on the system or does
+# not pass this specifier, it will be downloaded via PyPI if possible. An empty
+# string will disable this check.
+cmake.version = ">=3.16"
+
+# A list of args to pass to CMake when configuring the project. Setting this in
+# config or envvar will override toml. See also ``cmake.define``.
+cmake.args = [@PYPROJECT_CMAKE_ARGS@]
+
+# A table of defines to pass to CMake when configuring the project. Additive.
+cmake.define = {}
+
+# Verbose printout when building.
+cmake.verbose = true
+
+# The build type to use when building the project. Valid options are: "Debug",
+# "Release", "RelWithDebInfo", "MinSizeRel", "", etc.
+cmake.build-type = "Release"
+
+# The source directory to use when building the project. Currently only affects
+# the native builder (not the setuptools plugin).
+cmake.source-dir = "."
+
+# The versions of Ninja to allow. If Ninja is not present on the system or does
+# not pass this specifier, it will be downloaded via PyPI if possible. An empty
+# string will disable this check.
+ninja.version = ">=1.11"
+
+# If CMake is not present on the system or is older required, it will be
+# downloaded via PyPI if possible. An empty string will disable this check.
+ninja.make-fallback = true
+
+# The logging level to display, "DEBUG", "INFO", "WARNING", and "ERROR" are
+# possible options.
+logging.level = "INFO"
+
+# Files to include in the SDist even if they are skipped by default. Supports
+# gitignore syntax.
+sdist.include = ["CMakeLists.txt", "cmake/*.cmake", "README.md", "itkVersion.py", "pyproject.toml", "itk/__init__.py"]
+
+# Files to exclude from the SDist even if they are included by default. Supports
+# gitignore syntax.
+sdist.exclude = ["scripts"]
+
+# The Python tags. The default (empty string) will use the default Python
+# version. You can also set this to "cp37" to enable the CPython 3.7+ Stable ABI
+# / Limited API (only on CPython and if the version is sufficient, otherwise
+# this has no effect). Or you can set it to "py3" or "py2.py3" to ignore Python
+# ABI compatibility. The ABI tag is inferred from this tag.
+wheel.py-api = "@PYPROJECT_PY_API@"
+
+# A list of license files to include in the wheel. Supports glob patterns.
+wheel.license-files = ["LICEN[CS]E*", "ITK-source/ITK/LICENSE", "ITK-source/ITK/NOTICE"]
+
+# Target the platlib or the purelib. If not set, the default is to target the
+# platlib if wheel.cmake is true, and the purelib otherwise.
+wheel.platlib = "@PYPROJECT_PLATLIB@"
+
+# If CMake is less than this value, backport a copy of FindPython. Set to 0
+# disable this, or the empty string.
+backport.find-python = "3.26.1"
+
+# Select the editable mode to use. Can be "redirect" (default) or "inplace".
+editable.mode = "redirect"
+
+# Rebuild the project when the package is imported. The build-directory must be
+# set.
+editable.rebuild = false
+
+# The components to install. If empty, all default components are installed.
+install.components = []
+
+# Whether to strip the binaries. True for scikit-build-core 0.5+.
+install.strip = true
+
+# If set, this will provide a method for backward compatibility.
+minimum-version = "0.8.2"
+
+# The build directory. Defaults to a temporary directory, but can be set.
+build-dir = "build/{wheel_tag}"