ENH: Generate Python docstrings from Doxygen documentation

Author: Francois Budin

CMakeLists.txt

@@ -146,6 +146,7 @@ if(ITKPythonPackage_SUPERBUILD)
   message(STATUS "SuperBuild -   PYTHON_LIBRARY: ${PYTHON_LIBRARY}")
   message(STATUS "SuperBuild -   PYTHON_EXECUTABLE: ${PYTHON_EXECUTABLE}")
   message(STATUS "SuperBuild - Searching for python[OK]")
+  message(STATUS "SuperBuild -   DOXYGEN_EXECUTABLE: ${DOXYGEN_EXECUTABLE}")
 
   #-----------------------------------------------------------------------------
   # ITK: This project builds ITK and associated Python modules
@@ -185,6 +186,8 @@ if(ITKPythonPackage_SUPERBUILD)
         -DITK_WRAP_PYTHON:BOOL=ON
         -DITK_WRAP_PYTHON_LEGACY:BOOL=OFF
         -DITK_WRAP_unsigned_short:BOOL=ON
+        -DITK_WRAP_DOC:BOOL=ON
+        -DDOXYGEN_EXECUTABLE:FILEPATH=${DOXYGEN_EXECUTABLE}
         -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR}
         -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}
         -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}

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

@@ -22,7 +22,7 @@ script_dir=$(cd $(dirname $0) || exit 1; pwd)
 
 # Build wheels
 mkdir -p dist
-DOCKER_ARGS="-v $(pwd)/dist:/work/dist/ -v "$script_dir/..":/ITKPythonPackage"
+DOCKER_ARGS="-v $(pwd)/dist:/work/dist/ -v "$script_dir/..":/ITKPythonPackage -v $(pwd}/tools:/tools"
 /tmp/dockcross-manylinux-x64 \
   -a "$DOCKER_ARGS" \
   "/ITKPythonPackage/scripts/internal/manylinux-build-module-wheels.sh" "$@"

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

@@ -11,4 +11,8 @@ curl -L https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/do
 ./zstd-1.2.0-linux/bin/unzstd ITKPythonBuilds-linux.tar.zst -o ITKPythonBuilds-linux.tar
 tar xf ITKPythonBuilds-linux.tar
 
+mkdir tools
+wget -L http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.11.linux.bin.tar.gz -O doxygen-1.8.11.linux.bin.tar.gz
+tar -xvzf doxygen-1.8.11.linux.bin.tar.gz -C tools
+
 ./ITKPythonPackage/scripts/dockcross-manylinux-build-module-wheels.sh

scripts/internal/manylinux-build-wheels.sh

@@ -9,6 +9,12 @@ PYTHON_LIBRARY=""
 
 script_dir=$(cd $(dirname $0) || exit 1; pwd)
 source "${script_dir}/manylinux-build-common.sh"
+# Install prerequirements
+mkdir -p /work/tools
+pushd /work/tools > /dev/null 2>&1
+wget -L http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.11.linux.bin.tar.gz -O doxygen-1.8.11.linux.bin.tar.gz
+tar -xvzf doxygen-1.8.11.linux.bin.tar.gz
+popd > /dev/null 2>&1
 # -----------------------------------------------------------------------
 
 # Build standalone project and populate archive cache
@@ -64,7 +70,9 @@ for PYBIN in "${PYBINARIES[@]}"; do
             -DCMAKE_CXX_COMPILER_TARGET:STRING=$(uname -p)-linux-gnu \
             -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE} \
             -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR} \
-            -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}
+            -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY} \
+            -DITK_WRAP_DOC:BOOL=ON \
+            -DDOXYGEN_EXECUTABLE:FILEPATH=/work/tools/doxygen-1.8.11/bin/doxygen
       # Cleanup
       ${PYBIN}/python setup.py clean
 
@@ -94,6 +102,8 @@ for PYBIN in "${PYBINARIES[@]}"; do
           -DITK_LEGACY_SILENT:BOOL=ON \
           -DITK_WRAP_PYTHON:BOOL=ON \
           -DITK_WRAP_PYTHON_LEGACY:BOOL=OFF \
+          -DITK_WRAP_DOC:BOOL=ON \
+          -DDOXYGEN_EXECUTABLE:FILEPATH=/work/tools/doxygen-1.8.11/bin/doxygen \
           -G Ninja \
           ${source_path} \
         && ninja \
@@ -114,6 +124,8 @@ for PYBIN in "${PYBINARIES[@]}"; do
           -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE} \
           -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR} \
           -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY} \
+          -DITK_WRAP_DOC:BOOL=ON \
+          -DDOXYGEN_EXECUTABLE:FILEPATH=/work/tools/doxygen-1.8.11/bin/doxygen \
           || exit 1
         # Cleanup
         ${PYBIN}/python setup.py clean

scripts/macpython-build-wheels.sh

@@ -18,7 +18,10 @@ SCRIPT_DIR=""
 script_dir=$(cd $(dirname $0) || exit 1; pwd)
 source "${script_dir}/macpython-build-common.sh"
 # -----------------------------------------------------------------------
-
+# Ensure that requirements are met
+brew update
+brew install doxygen
+# -----------------------------------------------------------------------
 # Remove previous virtualenv's
 rm -rf ${SCRIPT_DIR}/../venvs
 # Create virtualenv's
@@ -99,7 +102,8 @@ for VENV in "${VENVS[@]}"; do
         -DITK_WRAP_unsigned_short:BOOL=ON \
         -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE} \
         -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR} \
-        -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}
+        -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY} \
+        -DITK_WRAP_DOC:BOOL=ON
       # Cleanup
       ${PYTHON_EXECUTABLE} setup.py clean
 
@@ -130,6 +134,7 @@ for VENV in "${VENVS[@]}"; do
           -DITK_LEGACY_SILENT:BOOL=ON \
           -DITK_WRAP_PYTHON:BOOL=ON \
           -DITK_WRAP_PYTHON_LEGACY:BOOL=OFF \
+          -DITK_WRAP_DOC:BOOL=ON \
           -G Ninja \
           ${source_path} \
         && ninja\
@@ -152,6 +157,7 @@ for VENV in "${VENVS[@]}"; do
           -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE} \
           -DPYTHON_INCLUDE_DIR:PATH=${PYTHON_INCLUDE_DIR} \
           -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY} \
+          -DITK_WRAP_DOC:BOOL=ON \
         || exit 1
         # Cleanup
         ${PYTHON_EXECUTABLE} setup.py clean

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

@@ -4,7 +4,7 @@
 # it is used by the .travis.yml file contained in ITKModuleTemplate: https://github.com/InsightSoftwareConsortium/ITKModuleTemplate
 
 brew update
-brew install zstd aria2 gnu-tar
+brew install zstd aria2 gnu-tar doxygen
 aria2c -c --file-allocation=none -o ITKPythonBuilds-macosx.tar.zst -s 10 -x 10 https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v4.12.0.post1}/ITKPythonBuilds-macosx.tar.zst
 unzstd ITKPythonBuilds-macosx.tar.zst -o ITKPythonBuilds-macosx.tar
 PATH="/usr/local/opt/gnu-tar/libexec/gnubin:$PATH"

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

@@ -4,4 +4,6 @@ set-alias sz "$env:ProgramFiles\7-Zip\7z.exe"
 iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/scikit-build/scikit-ci-addons/master/windows/install-python.ps1'))
 Invoke-WebRequest -Uri "https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/v4.12.0.post1/ITKPythonBuilds-windows.zip" -OutFile "ITKPythonBuilds-windows.zip"
 sz x ITKPythonBuilds-windows.zip -oC:\P -aoa -r
+Invoke-WebRequest -Uri "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.11.windows.bin.zip" -OutFile "doxygen-1.8.11.windows.bin.zip"
+sz x doxygen-1.8.11.windows.bin.zip -oC:\P\doxygen -aoa -r
 C:\Python27-x64\python.exe C:\P\IPP\scripts\windows_build_module_wheels.py

scripts/windows_build_wheels.py

@@ -96,6 +96,8 @@ def build_wrapped_itk(
             "-DITK_LEGACY_SILENT:BOOL=ON",
             "-DITK_WRAP_PYTHON:BOOL=ON",
             "-DITK_WRAP_PYTHON_LEGACY:BOOL=OFF",
+            "-DITK_WRAP_DOC:BOOL=ON",
+            "-DDOXYGEN_EXECUTABLE:FILEPATH=C:/P/doxygen/doxygen.exe",
             "-G", "Ninja",
             source_path
         ])