Merge branch 'release' into itk-6.0-b1

thewtex · thewtex · commit f25b92614ccd · 2025-07-17T15:23:41.000-04:00
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -94,8 +94,8 @@ if(ITKPythonPackage_SUPERBUILD)
 
   set(ITK_REPOSITORY "https://github.com/InsightSoftwareConsortium/ITK.git")
 
-  # main branch, 2025-07-16
-  set(ITK_GIT_TAG "ff4ff13ec295595cab2edbb3173a39ef798e4c7d")
+  # release-5.4 branch, 2025-06-23
+  set(ITK_GIT_TAG "46f39a0ea702247628036fc3cffdb009caa463cf")
 
   #-----------------------------------------------------------------------------
   # A separate project is used to download ITK, so that it can reused
diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -1,5 +1,5 @@
 ninja==1.11.1.1
-scikit-build-core==0.9.5
+scikit-build-core==0.10.7
 build==1.2.1
 pyproject-metadata
 pathspec
diff --git a/scripts/dockcross-manylinux-build-module-deps.sh b/scripts/dockcross-manylinux-build-module-deps.sh
@@ -74,7 +74,7 @@ for MODULE_INFO in ${ITK_MODULE_PREQ_TOPLEVEL//:/ }; do
 
   echo "Cleaning up module dependency"
   cp ./${MODULE_NAME}/include/* include/
-  find ${MODULE_NAME}/_skbuild -type f -wholename "**/cmake-build/include/*" -print -exec cp {} include \;
+  find ${MODULE_NAME}/*build/*/include -type f -print -exec cp {} include \;
 
   # Cache build archive
   if [[ `(compgen -G ./ITKPythonBuilds-linux*.tar.zst)` ]]; then
diff --git a/scripts/dockcross-manylinux-build-tarball.sh b/scripts/dockcross-manylinux-build-tarball.sh
@@ -4,16 +4,9 @@
 # downloaded by the external module build scripts and used to build their
 # Python package on GitHub CI services.
 
-if test -d /home/kitware/Packaging; then
-  cd /home/kitware/Packaging
-fi
-
 # -----------------------------------------------------------------------
 
 zstd_exe=`(which zstd)`
-if [[ -z ${zstd_exe} && -e /home/kitware/Support/zstd-build/programs/zstd ]]; then
-  zstd_exe=/home/kitware/Support/zstd-build/programs/zstd
-fi
 
 # Find an appropriately versioned zstd.
 #
@@ -38,11 +31,11 @@ fi
 
 # -----------------------------------------------------------------------
 
-tar -c --to-stdout \
+tar -cf ITKPythonBuilds-linux.tar \
   ITKPythonPackage/ITK-* \
   ITKPythonPackage/oneTBB* \
   ITKPythonPackage/requirements-dev.txt \
-  ITKPythonPackage/scripts > ITKPythonBuilds-linux.tar
+  ITKPythonPackage/scripts
 $zstd_exe -f \
   -10 \
   -T6 \
diff --git a/scripts/dockcross-manylinux-cleanup.sh b/scripts/dockcross-manylinux-cleanup.sh
@@ -31,7 +31,7 @@ fi
 unlink oneTBB-prefix
 ${rm_prefix} rm -rf ITKPythonPackage/
 ${rm_prefix} rm -rf tools/
-${rm_prefix} rm -rf _skbuild/
+${rm_prefix} rm -rf _skbuild/ build/
 ${rm_prefix} rm -rf ./*.egg-info/
 ${rm_prefix} rm -rf ./ITK-*-manylinux${MANYLINUX_VERSION}_${TARGET_ARCH}/
 ${rm_prefix} rm -rf ./ITKPythonBuilds-linux-manylinux*${MANYLINUX_VERSION}*.tar.zst
diff --git a/scripts/internal/manylinux-build-common.sh b/scripts/internal/manylinux-build-common.sh
@@ -12,7 +12,7 @@ if [[ $# -eq 0 ]]; then
   PYBIN=(/opt/python/*/bin)
   PYBINARIES=()
   for version in "${PYBIN[@]}"; do
-    if [[ ${version} == *"cp38"* || ${version} == *"cp39"* || ${version} == *"cp310"* || ${version} == *"cp311"* ]]; then
+    if [[ ${version} == *"cp39"* || ${version} == *"cp310"* || ${version} == *"cp311"* ]]; then
       PYBINARIES+=(${version})
     fi
   done
diff --git a/scripts/internal/manylinux-build-module-wheels.sh b/scripts/internal/manylinux-build-module-wheels.sh
@@ -167,6 +167,6 @@ done
 
 if compgen -G "dist/itk*-linux*.whl" > /dev/null; then
   for itk_wheel in dist/itk*-linux*.whl; do
-    mv ${itk_wheel} ${itk_wheel/linux/manylinux${MANYLINUX_VERSION}}
+    rm ${itk_wheel}
   done
 fi
diff --git a/scripts/internal/manylinux-build-wheels.sh b/scripts/internal/manylinux-build-wheels.sh
@@ -172,18 +172,35 @@ for PYBIN in "${PYBINARIES[@]}"; do
 
 done
 
+sudo /opt/python/cp311-cp311/bin/pip3 install auditwheel wheel
+
 if test "${ARCH}" == "x64"; then
-  sudo /opt/python/cp39-cp39/bin/pip3 install auditwheel wheel
   # This step will fixup the wheel switching from 'linux' to 'manylinux<version>' tag
   for whl in dist/itk_*linux_*.whl; do
-      /opt/python/cp39-cp39/bin/auditwheel repair --plat manylinux${MANYLINUX_VERSION}_x86_64 ${whl} -w /work/dist/
+      /opt/python/cp311-cp311/bin/auditwheel repair --plat manylinux${MANYLINUX_VERSION}_x86_64 ${whl} -w /work/dist/
   done
 else
   for whl in dist/itk_*$(uname -m).whl; do
-      auditwheel repair ${whl} -w /work/dist/
+      /opt/python/cp311-cp311/bin/auditwheel repair ${whl} -w /work/dist/
   done
 fi
 
+# auditwheel does not process this "metawheel" correctly since it does not
+# have any native SO's.
+mkdir -p metawheel-dist
+for whl in dist/itk-*linux_*.whl; do
+  /opt/python/cp311-cp311/bin/wheel unpack --dest metawheel ${whl}
+  manylinux_version=manylinux${MANYLINUX_VERSION}
+  new_tag=$(basename ${whl/linux/${manylinux_version}} .whl)
+  sed -i "s/Tag: .*/Tag: ${new_tag}/" metawheel/itk-*/itk*.dist-info/WHEEL
+  /opt/python/cp311-cp311/bin/wheel pack --dest metawheel-dist metawheel/itk-*
+  mv metawheel-dist/*.whl dist/${new_tag}.whl
+  rm -rf metawheel
+done
+rm -rf metawheel-dist
+rm dist/itk-*-linux_*.whl
+rm dist/itk_*-linux_*.whl
+
 # Install packages and test
 for PYBIN in "${PYBINARIES[@]}"; do
     ${PYBIN}/pip install --user numpy
diff --git a/scripts/internal/windows_build_common.py b/scripts/internal/windows_build_common.py
@@ -4,7 +4,7 @@
 import os
 import shutil
 
-DEFAULT_PY_ENVS = ["38-x64", "39-x64", "310-x64", "311-x64"]
+DEFAULT_PY_ENVS = ["39-x64", "310-x64", "311-x64"]
 
 SCRIPT_DIR = os.path.dirname(__file__)
 ROOT_DIR = os.path.abspath(os.path.join(SCRIPT_DIR, "..", ".."))
diff --git a/scripts/macpython-build-module-wheels.sh b/scripts/macpython-build-module-wheels.sh
@@ -71,6 +71,7 @@ fi
 
 VENV="${VENVS[0]}"
 Python3_EXECUTABLE=${VENV}/bin/python3
+dot_clean ${VENV}
 ${Python3_EXECUTABLE} -m pip install --no-cache delocate
 DELOCATE_LISTDEPS=${VENV}/bin/delocate-listdeps
 DELOCATE_WHEEL=${VENV}/bin/delocate-wheel
diff --git a/scripts/macpython-build-tarball.sh b/scripts/macpython-build-tarball.sh
@@ -13,6 +13,7 @@ if test $(arch) == "arm64"; then
 fi
 
 pushd /Users/svc-dashboard/D/P > /dev/null
+dot_clean ITKPythonPackage
 tar -cf ITKPythonBuilds-macosx${arch_postfix}.tar \
   ITKPythonPackage/ITK-* \
   ${tbb_contents} \
diff --git a/scripts/macpython-download-cache-and-build-module-wheels.sh b/scripts/macpython-download-cache-and-build-module-wheels.sh
@@ -39,22 +39,36 @@
 
 # Install dependencies
 brew update
-brew install zstd aria2 gnu-tar doxygen ninja
-brew upgrade cmake
+brew install --quiet zstd aria2 gnu-tar doxygen ninja
+brew upgrade --quiet cmake
 
 if [[ $(arch) == "arm64" ]]; then
   tarball_arch="-arm64"
 else
   tarball_arch=""
 fi
 # Fetch ITKPythonBuilds archive containing ITK build artifacts
+rm -fr ITKPythonPackage
 echo "Fetching https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.4.0}/ITKPythonBuilds-macosx${tarball_arch}.tar.zst"
 if [[ ! -f ITKPythonBuilds-macosx${tarball_arch}.tar.zst ]]; then
   aria2c -c --file-allocation=none -o ITKPythonBuilds-macosx${tarball_arch}.tar.zst -s 10 -x 10 https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.4.0}/ITKPythonBuilds-macosx${tarball_arch}.tar.zst
 fi
 unzstd --long=31 ITKPythonBuilds-macosx${tarball_arch}.tar.zst -o ITKPythonBuilds-macosx${tarball_arch}.tar
 PATH="$(dirname $(brew list gnu-tar | grep gnubin)):$PATH"
-tar xf ITKPythonBuilds-macosx${tarball_arch}.tar --checkpoint=10000 --checkpoint-action=dot
+gtar xf ITKPythonBuilds-macosx${tarball_arch}.tar --warning=no-unknown-keyword --checkpoint=10000 --checkpoint-action=dot \
+  ITKPythonPackage/ITK-source \
+  ITKPythonPackageRequiredExtractionDir.txt \
+  ITKPythonPackage/scripts
+
+# Extract subdirectories specific to the compiled python versions
+args=( "$@"  )
+source ITKPythonPackage/scripts/macpython-build-common.sh
+for version in "$PYTHON_VERSIONS"; do
+  gtar xf ITKPythonBuilds-macosx${tarball_arch}.tar --warning=no-unknown-keyword --checkpoint=10000 --checkpoint-action=dot \
+    --wildcards "ITKPythonPackage/ITK-${version}-macosx*" \
+    "ITKPythonPackage/venvs/${version}"
+done
+
 rm ITKPythonBuilds-macosx${tarball_arch}.tar
 
 # Optional: Update build scripts
@@ -72,7 +86,10 @@ if [[ -n ${ITKPYTHONPACKAGE_TAG} ]]; then
 fi
 
 # Run build scripts
-sudo mkdir -p /Users/svc-dashboard/D/P && sudo chown $UID:$GID /Users/svc-dashboard/D/P && mv ITKPythonPackage /Users/svc-dashboard/D/P/
+sudo mkdir -p /Users/svc-dashboard/D/P && sudo chown $UID:$GID /Users/svc-dashboard/D/P
+if [[ ! -d /Users/svc-dashboard/D/P/ITKPythonPackage ]]; then
+  mv ITKPythonPackage /Users/svc-dashboard/D/P/
+fi
 
 # Optionally install baseline Python versions
 if [[ ! ${ITK_USE_LOCAL_PYTHON} ]]; then
@@ -82,4 +99,4 @@ if [[ ! ${ITK_USE_LOCAL_PYTHON} ]]; then
 fi
 
 echo "Building module wheels"
-/Users/svc-dashboard/D/P/ITKPythonPackage/scripts/macpython-build-module-wheels.sh "$@"
+/Users/svc-dashboard/D/P/ITKPythonPackage/scripts/macpython-build-module-wheels.sh "${args[@]}"
diff --git a/scripts/macpython-install-python.sh b/scripts/macpython-install-python.sh
@@ -416,7 +416,7 @@ else
   # Deployment target requirements:
   # * 10.9: Python 3.7
   # * 11: Python >= 3.8
-  for pyversion in $LATEST_3p8 $LATEST_3p9 $LATEST_3p10 $LATEST_3p11; do
+  for pyversion in $LATEST_3p9 $LATEST_3p10 $LATEST_3p11; do
     install_macpython $pyversion 11
     install_virtualenv
   done
diff --git a/scripts/windows_build_module_wheels.py b/scripts/windows_build_module_wheels.py
@@ -86,6 +86,9 @@ def build_wheels(py_envs=DEFAULT_PY_ENVS, cleanup=True, cmake_options=[]):
                     "--config-setting=wheel.py-api=%s" % wheel_py_api,
                     "--config-setting=cmake.define.SKBUILD:BOOL=ON",
                     "--config-setting=cmake.define.PY_SITE_PACKAGES_PATH:PATH=.",
+                    "--config-setting=cmake.args=""-G Ninja""",
+                    "--config-setting=cmake.define.CMAKE_BUILD_TYPE:STRING=""Release""",
+                    "--config-setting=cmake.define.CMAKE_MAKE_PROGRAM:FILEPATH=%s" % ninja_executable,
                     "--config-setting=cmake.define.ITK_DIR:PATH=%s" % itk_build_path,
                     "--config-setting=cmake.define.WRAP_ITK_INSTALL_COMPONENT_IDENTIFIER:STRING=PythonWheel",
                     "--config-setting=cmake.define.SWIG_EXECUTABLE:FILEPATH=%s/Wrapping/Generators/SwigInterface/swig/bin/swig.exe" % itk_build_path,
@@ -122,13 +125,15 @@ def build_wheels(py_envs=DEFAULT_PY_ENVS, cleanup=True, cmake_options=[]):
                 if cleanup:
                     check_call([python_executable, "setup.py", "clean"])
 
-def rename_wheel_init(py_env, filepath):
+def rename_wheel_init(py_env, filepath, add_module_name=True):
     """
-    Rename module __init__ file in wheel.
-    This is required to prevent modules to override ITK's __init__ file on install.
-    If the module ships its own __init__ file, it is automatically renamed to
-    __init_{module_name}__ by this function. The renamed __init__ file will be executed
-    by ITK's __init__ file when loading ITK.
+    Rename module __init__ (if add_module_name is True) or __init_module__ (if
+    add_module_name is False) file in wheel.  This is required to prevent
+    modules to override ITK's __init__ file on install or to prevent delvewheel
+    to override __init_module__ file.  If the module ships its own __init__
+    file, it is automatically renamed to __init_{module_name}__ by this
+    function. The renamed __init__ file will be executed by ITK's __init__ file
+    when loading ITK.
     """
     python_executable, python_include_dir, python_library, pip, ninja_executable, path = venv_paths(py_env)
 
@@ -142,11 +147,15 @@ def rename_wheel_init(py_env, filepath):
     wheel_dir = os.path.join(dist_dir, "itk_" + module_name.replace('-','_') + "-" + module_version)
     init_dir = os.path.join(wheel_dir, "itk")
     init_file = os.path.join(init_dir, "__init__.py")
+    init_file_module = os.path.join(init_dir, "__init_" + module_name.split("-")[0] + "__.py")
 
     # Unpack wheel and rename __init__ file if it exists.
     check_call([python_executable, "-m", "wheel", "unpack", filepath, "-d", dist_dir])
-    if os.path.isfile(init_file):
-        shutil.move(init_file, os.path.join(init_dir, "__init_" + module_name + "__.py"))
+    if add_module_name and os.path.isfile(init_file):
+        shutil.move(init_file, init_file_module)
+    if not add_module_name and os.path.isfile(init_file_module):
+        shutil.move(init_file_module, init_file)
+
     # Pack wheel and clean wheel folder
     check_call([python_executable, "-m", "wheel", "pack", wheel_dir, "-d", dist_dir])
     shutil.rmtree(wheel_dir)
@@ -157,6 +166,10 @@ def fixup_wheel(py_envs, filepath, lib_paths:str='', exclude_libs:str=''):
 
     py_env = py_envs[0]
 
+    # Make sure the module __init_module__.py file has the expected name for
+    # delvewheel, i.e., __init__.py.
+    rename_wheel_init(py_env, filepath, False)
+
     delve_wheel = os.path.join("C:/P/IPP", "venv-" + py_env, "Scripts", "delvewheel.exe")
     check_call([delve_wheel, "repair", "--no-mangle-all", "--add-path",
         lib_paths, "--no-dll", exclude_libs, "--ignore-in-wheel", "-w",
