Fix python module building

.gitignore

@@ -12,6 +12,9 @@ ITK-*
 libpython-not-needed-symbols-exported-by-interpreter
 tools/
 
+# back-up files when conflicts occur
+*.orig
+
 # Python
 *.py[cod]
 

CMakeLists.txt

@@ -156,6 +156,7 @@ if(ITKPythonPackage_SUPERBUILD)
   endif()
 
   message(STATUS "SuperBuild -   Python3_INCLUDE_DIR: ${Python3_INCLUDE_DIR}")
+  message(STATUS "SuperBuild -   Python3_INCLUDE_DIRS: ${Python3_INCLUDE_DIRS}")
   message(STATUS "SuperBuild -   Python3_LIBRARY: ${Python3_LIBRARY}")
   message(STATUS "SuperBuild -   Python3_EXECUTABLE: ${Python3_EXECUTABLE}")
   message(STATUS "SuperBuild - Searching for python[OK]")

scripts/dockcross-manylinux-download-cache-and-build-module-wheels.sh

@@ -1,18 +1,41 @@
 #!/bin/bash
 
 # This module should be pulled and run from an ITKModule root directory to generate the Linux python wheels of this module,
-# it is used by the circle.yml file contained in ITKModuleTemplate: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate
+# it is used by the azure-pipeline.yml file contained in ITKModuleTemplate: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate
+# First download doxygen
+if [[ ! -f doxygen-1.8.11.linux.bin.tar.gz ]]; then
+  mkdir tools
+  curl https://data.kitware.com/api/v1/file/5c0aa4b18d777f2179dd0a71/download -o doxygen-1.8.11.linux.bin.tar.gz
+  tar -xvzf doxygen-1.8.11.linux.bin.tar.gz -C tools
+fi
+if [[ ! -f ./tools/doxygen-1.8.11/bin/doxygen ]]; then
+  echo "ERROR: can not find required binary './tools/doxygen-1.8.11/bin/doxygen'"
+  exit 255
+fi
 
-curl https://data.kitware.com/api/v1/file/592dd8068d777f16d01e1a92/download -o zstd-1.2.0-linux.tar.gz
-gunzip -d zstd-1.2.0-linux.tar.gz
-tar xf zstd-1.2.0-linux.tar
+# Packages distributed by github are in zstd format, so we need to download that binary to uncompress
+if [[ ! -f zstd-1.2.0-linux.tar.gz ]]; then
+  curl https://data.kitware.com/api/v1/file/592dd8068d777f16d01e1a92/download -o zstd-1.2.0-linux.tar.gz
+  gunzip -d zstd-1.2.0-linux.tar.gz
+  tar xf zstd-1.2.0-linux.tar
+fi
+if [[ ! -f ./zstd-1.2.0-linux/bin/unzstd ]]; then
+  echo "ERROR: can not find required binary './zstd-1.2.0-linux/bin/unzstd'"
+  exit 255
+fi
 
-curl -L https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.0.1}/ITKPythonBuilds-linux.tar.zst -O
-./zstd-1.2.0-linux/bin/unzstd ITKPythonBuilds-linux.tar.zst -o ITKPythonBuilds-linux.tar
-tar xf ITKPythonBuilds-linux.tar
-
-mkdir tools
-curl https://data.kitware.com/api/v1/file/5c0aa4b18d777f2179dd0a71/download -o doxygen-1.8.11.linux.bin.tar.gz
-tar -xvzf doxygen-1.8.11.linux.bin.tar.gz -C tools
+if [[ ! -f ITKPythonBuilds-linux.tar.zst ]]; then
+  curl -L https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.1rc02}/ITKPythonBuilds-linux.tar.zst -O
+  ./zstd-1.2.0-linux/bin/unzstd ./ITKPythonBuilds-linux.tar.zst -o ITKPythonBuilds-linux.tar
+  tar xf ITKPythonBuilds-linux.tar
+fi
+if [[ ! -f ./ITKPythonBuilds-linux.tar.zst ]]; then
+  echo "ERROR: can not find required binary './ITKPythonBuilds-linux.tar.zst'"
+  exit 255
+fi
+if [[ ! -f ./ITKPythonPackage/scripts/dockcross-manylinux-build-module-wheels.sh ]]; then
+  echo "ERROR: can not find required binary './ITKPythonPackage/scripts/dockcross-manylinux-build-module-wheels.sh'"
+  exit 255
+fi
 
 ./ITKPythonPackage/scripts/dockcross-manylinux-build-module-wheels.sh

scripts/internal/manylinux-build-module-wheels.sh

@@ -15,10 +15,12 @@ source "${script_dir}/manylinux-build-common.sh"
 for PYBIN in "${PYBINARIES[@]}"; do
     Python3_EXECUTABLE=${PYBIN}/python
     Python3_INCLUDE_DIR=$( find -L ${PYBIN}/../include/ -name Python.h -exec dirname {} \; )
+    Python3_INCLUDE_DIRS=${Python3_INCLUDE_DIR}
 
     echo ""
     echo "Python3_EXECUTABLE:${Python3_EXECUTABLE}"
     echo "Python3_INCLUDE_DIR:${Python3_INCLUDE_DIR}"
+    echo "Python3_INCLUDE_DIRS:${Python3_INCLUDE_DIRS}"
     echo "Python3_LIBRARY:${Python3_LIBRARY}"
 
     if [[ -e /work/requirements-dev.txt ]]; then
@@ -48,6 +50,7 @@ for PYBIN in "${PYBINARIES[@]}"; do
       -DBUILD_TESTING:BOOL=OFF \
       -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
       -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+      -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
       -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
     || exit 1
     ${PYBIN}/python setup.py clean

scripts/internal/manylinux-build-wheels.sh

@@ -30,10 +30,12 @@ SINGLE_WHEEL=0
 for PYBIN in "${PYBINARIES[@]}"; do
     export Python3_EXECUTABLE=${PYBIN}/python3
     Python3_INCLUDE_DIR=$( find -L ${PYBIN}/../include/ -name Python.h -exec dirname {} \; )
+    Python3_INCLUDE_DIRS=${Python3_INCLUDE_DIR}
 
     echo ""
     echo "Python3_EXECUTABLE:${Python3_EXECUTABLE}"
     echo "Python3_INCLUDE_DIR:${Python3_INCLUDE_DIR}"
+    echo "Python3_INCLUDE_DIRS:${Python3_INCLUDE_DIRS}"
     echo "Python3_LIBRARY:${Python3_LIBRARY}"
 
     # Install dependencies
@@ -67,6 +69,7 @@ for PYBIN in "${PYBINARIES[@]}"; do
             -DCMAKE_CXX_COMPILER_TARGET:STRING=$(uname -p)-linux-gnu \
             -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
             -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+            -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
             -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
             -DITK_WRAP_DOC:BOOL=ON \
             -DDOXYGEN_EXECUTABLE:FILEPATH=/work/tools/doxygen-1.8.11/bin/doxygen
@@ -90,6 +93,7 @@ for PYBIN in "${PYBINARIES[@]}"; do
           -DBUILD_TESTING:BOOL=OFF \
           -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
           -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+          -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
           -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
           -DCMAKE_CXX_COMPILER_TARGET:STRING=$(uname -p)-linux-gnu \
           -DWRAP_ITK_INSTALL_COMPONENT_IDENTIFIER:STRING=PythonWheel \
@@ -121,6 +125,7 @@ for PYBIN in "${PYBINARIES[@]}"; do
           -DITK_WRAP_double:BOOL=ON \
           -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
           -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+          -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
           -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
           -DITK_WRAP_DOC:BOOL=ON \
           -DDOXYGEN_EXECUTABLE:FILEPATH=/work/tools/doxygen-1.8.11/bin/doxygen \

scripts/macpython-build-module-wheels.sh

@@ -36,10 +36,12 @@ for VENV in "${VENVS[@]}"; do
     py_mm=$(basename ${VENV})
     Python3_EXECUTABLE=${VENV}/bin/python
     Python3_INCLUDE_DIR=$( find -L ${MACPYTHON_PY_PREFIX}/${py_mm}/include -name Python.h -exec dirname {} \; )
+    Python3_INCLUDE_DIRS=${Python3_INCLUDE_DIR}
 
     echo ""
     echo "Python3_EXECUTABLE:${Python3_EXECUTABLE}"
     echo "Python3_INCLUDE_DIR:${Python3_INCLUDE_DIR}"
+    echo "Python3_INCLUDE_DIRS:${Python3_INCLUDE_DIRS}"
     echo "Python3_LIBRARY:${Python3_LIBRARY}"
 
     if [[ -e $PWD/requirements-dev.txt ]]; then
@@ -57,6 +59,7 @@ for VENV in "${VENVS[@]}"; do
       -DBUILD_TESTING:BOOL=OFF \
       -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
       -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+      -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
       -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
     || exit 1
     ${Python3_EXECUTABLE} setup.py clean

scripts/macpython-build-wheels.sh

@@ -65,10 +65,12 @@ for VENV in "${VENVS[@]}"; do
     py_mm=$(basename ${VENV})
     export Python3_EXECUTABLE=${VENV}/bin/python
     Python3_INCLUDE_DIR=$( find -L ${MACPYTHON_PY_PREFIX}/${py_mm}/include -name Python.h -exec dirname {} \; )
+    Python3_INCLUDE_DIRS=${Python3_INCLUDE_DIR}
 
     echo ""
     echo "Python3_EXECUTABLE:${Python3_EXECUTABLE}"
     echo "Python3_INCLUDE_DIR:${Python3_INCLUDE_DIR}"
+    echo "Python3_INCLUDE_DIRS:${Python3_INCLUDE_DIRS}"
     echo "Python3_LIBRARY:${Python3_LIBRARY}"
 
     # Install dependencies
@@ -103,6 +105,7 @@ for VENV in "${VENVS[@]}"; do
         -DITK_WRAP_double:BOOL=ON \
         -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
         -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+        -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
         -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
         -DITK_WRAP_DOC:BOOL=ON
       # Cleanup
@@ -129,6 +132,7 @@ for VENV in "${VENVS[@]}"; do
           -DITK_WRAP_double:BOOL=ON \
           -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
           -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+          -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
           -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
           -DWRAP_ITK_INSTALL_COMPONENT_IDENTIFIER:STRING=PythonWheel \
           -DWRAP_ITK_INSTALL_COMPONENT_PER_MODULE:BOOL=ON \
@@ -158,6 +162,7 @@ for VENV in "${VENVS[@]}"; do
           -DITK_WRAP_double:BOOL=ON \
           -DPython3_EXECUTABLE:FILEPATH=${Python3_EXECUTABLE} \
           -DPython3_INCLUDE_DIR:PATH=${Python3_INCLUDE_DIR} \
+          -DPython3_INCLUDE_DIRS:PATH=${Python3_INCLUDE_DIRS} \
           -DPython3_LIBRARY:FILEPATH=${Python3_LIBRARY} \
           -DITK_WRAP_DOC:BOOL=ON \
         || exit 1

scripts/macpython-download-cache-and-build-module-wheels.sh

@@ -12,7 +12,7 @@ SDK_PATH='/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/D
 if test ! -e $SDK_PATH; then
   sudo ln -s /Applications/Xcode_9.4.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk
 fi
-aria2c -c --file-allocation=none -o ITKPythonBuilds-macosx.tar.zst -s 10 -x 10 https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.0.1}/ITKPythonBuilds-macosx.tar.zst
+aria2c -c --file-allocation=none -o ITKPythonBuilds-macosx.tar.zst -s 10 -x 10 https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.1rc02}/ITKPythonBuilds-macosx.tar.zst
 unzstd ITKPythonBuilds-macosx.tar.zst -o ITKPythonBuilds-macosx.tar
 PATH="/usr/local/opt/gnu-tar/libexec/gnubin:$PATH"
 tar xf ITKPythonBuilds-macosx.tar --checkpoint=10000 --checkpoint-action=dot

scripts/windows-download-cache-and-build-module-wheels.ps1

@@ -7,7 +7,7 @@ if (-not (Test-Path env:APPVEYOR)) {
   $pythonArch = "64"
   iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/scikit-build/scikit-ci-addons/master/windows/install-python.ps1'))
 }
-if (-not (Test-Path env:ITK_PACKAGE_VERSION)) { $env:ITK_PACKAGE_VERSION = 'v5.0.1' }
+if (-not (Test-Path env:ITK_PACKAGE_VERSION)) { $env:ITK_PACKAGE_VERSION = 'v5.1rc02' }
 Invoke-WebRequest -Uri "https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/$env:ITK_PACKAGE_VERSION/ITKPythonBuilds-windows.zip" -OutFile "ITKPythonBuilds-windows.zip"
 sz x ITKPythonBuilds-windows.zip -oC:\P -aoa -r
 Invoke-WebRequest -Uri "https://data.kitware.com/api/v1/file/5c0ad59d8d777f2179dd3e9c/download" -OutFile "doxygen-1.8.11.windows.bin.zip"

scripts/windows_build_module_wheels.py

@@ -51,6 +51,7 @@ def build_wheels(py_envs=DEFAULT_PY_ENVS):
                 "-DBUILD_TESTING:BOOL=OFF",
                 "-DPython3_EXECUTABLE:FILEPATH=%s" % python_executable,
                 "-DPython3_INCLUDE_DIR:PATH=%s" % python_include_dir,
+                "-DPython3_INCLUDE_DIRS:PATH=%s" % python_include_dir,
                 "-DPython3_LIBRARY:FILEPATH=%s" % python_library
             ])
             # Cleanup

scripts/windows_build_wheels.py

@@ -91,6 +91,7 @@ def build_wrapped_itk(
             "-DITK_WRAP_unsigned_short:BOOL=ON",
             "-DITK_WRAP_double:BOOL=ON",
             "-DPython3_INCLUDE_DIR:PATH=%s" % python_include_dir,
+            "-DPython3_INCLUDE_DIRS:PATH=%s" % python_include_dir,
             "-DPython3_LIBRARY:FILEPATH=%s" % python_library,
             "-DWRAP_ITK_INSTALL_COMPONENT_IDENTIFIER:STRING=PythonWheel",
             "-DWRAP_ITK_INSTALL_COMPONENT_PER_MODULE:BOOL=ON",
@@ -151,6 +152,7 @@ def build_wheel(python_version, single_wheel=False,
                 "-DITK_BINARY_DIR:PATH=%s" % build_path,
                 "-DPython3_EXECUTABLE:FILEPATH=%s" % python_executable,
                 "-DPython3_INCLUDE_DIR:PATH=%s" % python_include_dir,
+                "-DPython3_INCLUDE_DIRS:PATH=%s" % python_include_dir,
                 "-DPython3_LIBRARY:FILEPATH=%s" % python_library,
                 "-DDOXYGEN_EXECUTABLE:FILEPATH=C:/P/doxygen/doxygen.exe",
             ] + cmake_options)
@@ -192,6 +194,7 @@ def build_wheel(python_version, single_wheel=False,
                     "-DITKPythonPackage_WHEEL_NAME:STRING=%s" % wheel_name,
                     "-DPython3_EXECUTABLE:FILEPATH=%s" % python_executable,
                     "-DPython3_INCLUDE_DIR:PATH=%s" % python_include_dir,
+                    "-DPython3_INCLUDE_DIRS:PATH=%s" % python_include_dir,
                     "-DPython3_LIBRARY:FILEPATH=%s" % python_library
                 ] + cmake_options)