Merge branch 'master' into release

Author: thewtex

.gitignore

@@ -10,6 +10,7 @@ venvs
 venv-*
 ITK-*
 libpython-not-needed-symbols-exported-by-interpreter
+tools/
 
 # Python
 *.py[cod]

CMakeLists.txt

@@ -73,8 +73,8 @@ if(ITKPythonPackage_SUPERBUILD)
   include(ExternalProject)
 
   set(ITK_REPOSITORY "https://github.com/InsightSoftwareConsortium/ITK.git")
-  # ITK nightly-master 2018-09-05
-  set(ITK_GIT_TAG "v5.0b01")
+  # ITK nightly-master 2018-12-17
+  set(ITK_GIT_TAG "0cdb1dd5b3")
 
   #-----------------------------------------------------------------------------
   # A separate project is used to download ITK, so that it can reused
@@ -153,6 +153,30 @@ if(ITKPythonPackage_SUPERBUILD)
   message(STATUS "SuperBuild - Searching for python[OK]")
   message(STATUS "SuperBuild -   DOXYGEN_EXECUTABLE: ${DOXYGEN_EXECUTABLE}")
 
+  # CMake configuration variables to pass to ITK's build
+  set(ep_itk_cmake_cache_args "")
+  foreach(var
+    BUILD_SHARED_LIBS
+    ITK_BUILD_DEFAULT_MODULES
+    )
+    if(DEFINED ${var})
+      list(APPEND ep_itk_cmake_cache_args "-D${var}=${${var}}")
+    endif()
+  endforeach()
+  function(cached_variables RESULTVAR PATTERN)
+    get_cmake_property(variables CACHE_VARIABLES)
+    set(result)
+    foreach(variable ${variables})
+      if(${variable} AND variable MATCHES "${PATTERN}")
+        list(APPEND result "-D${variable}=${${variable}}")
+      endif()
+    endforeach()
+    set(${RESULTVAR} ${result} PARENT_SCOPE)
+  endfunction()
+  cached_variables(itk_pattern_cached_vars "^(ITK_WRAP_)|(ITKGroup_)|(Module_)")
+  list(APPEND ep_itk_cmake_cache_args ${itk_pattern_cached_vars})
+  # Todo, also pass all Module_* variables
+  message(STATUS "ITK CMake Cache Args -   ${ep_itk_cmake_cache_args}")
   #-----------------------------------------------------------------------------
   # ITK: This project builds ITK and associated Python modules
 
@@ -182,7 +206,11 @@ if(ITKPythonPackage_SUPERBUILD)
       SOURCE_DIR ${ITK_SOURCE_DIR}
       BINARY_DIR ${ITK_BINARY_DIR}
       PREFIX "ITKp"
+<<<<<<< HEAD
       CMAKE_CACHE_ARGS
+=======
+      CMAKE_ARGS
+>>>>>>> master
         -DBUILD_TESTING:BOOL=OFF
         -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
         -DPY_SITE_PACKAGES_PATH:PATH=${CMAKE_INSTALL_PREFIX}
@@ -198,6 +226,7 @@ if(ITKPythonPackage_SUPERBUILD)
         -DPYTHON_LIBRARY:FILEPATH=${PYTHON_LIBRARY}
         -DPYTHON_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}
         ${ep_common_cmake_cache_args}
+        ${ep_itk_cmake_cache_args}
       USES_TERMINAL_DOWNLOAD 1
       USES_TERMINAL_UPDATE 1
       USES_TERMINAL_CONFIGURE 1

docs/Build_ITK_Python_packages.rst

@@ -129,4 +129,4 @@ Here are the steps:
 - Build "flavor" of package using::
 
 	python setup.py bdist_wheel -- \
-	  -DITK_SOURCE_DIR:PATH=/path/to/ITKPythonPackage-core-build/ITK-source
+	  -DITK_SOURCE_DIR:PATH=/path/to/ITKPythonPackage-core-build/ITKs

itkVersion.py

@@ -1,4 +1,4 @@
-VERSION = '5.0b1'
+VERSION = '5.0b01.dev20181217+563.g0cdb1dd5b3'
 
 def get_versions():
     """Returns versions for the ITK Python package.

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

@@ -3,16 +3,16 @@
 # 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
 
-wget -L https://data.kitware.com/api/v1/file/592dd8068d777f16d01e1a92/download -O zstd-1.2.0-linux.tar.gz
+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
 
-curl -L https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.0a02}/ITKPythonBuilds-linux.tar.zst -O
+curl -L https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.0b01}/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
-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
+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
 
 ./ITKPythonPackage/scripts/dockcross-manylinux-build-module-wheels.sh

scripts/internal/manylinux-build-wheels.sh

@@ -12,7 +12,7 @@ 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
+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
 popd > /dev/null 2>&1
 # -----------------------------------------------------------------------

scripts/internal/windows_build_common.py

@@ -31,8 +31,7 @@ def venv_paths(python_version):
 
     pip = os.path.join(venv_dir, "Scripts", "pip.exe")
 
-    ninja_executable = os.path.join(
-        ROOT_DIR, "venv-35-x64", "Scripts", "ninja.exe")
+    ninja_executable = os.path.join(venv_dir, "Scripts", "ninja.exe")
     print("NINJA_EXECUTABLE:%s" % ninja_executable)
 
     # Update PATH

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

@@ -6,7 +6,7 @@
 brew update
 brew install zstd aria2 gnu-tar doxygen
 brew upgrade cmake
-aria2c -c --file-allocation=none -o ITKPythonBuilds-macosx.tar.zst -s 10 -x 10 https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.0a02}/ITKPythonBuilds-macosx.tar.zst
+aria2c -c --file-allocation=none -o ITKPythonBuilds-macosx.tar.zst -s 10 -x 10 https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${ITK_PACKAGE_VERSION:=v5.0b01}/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

@@ -1,13 +1,15 @@
 trap { Write-Error $_; Exit 1 }
+$AllProtocols = [System.Net.SecurityProtocolType]'Ssl3,Tls,Tls11,Tls12'
+[System.Net.ServicePointManager]::SecurityProtocol = $AllProtocols
 
 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'))
-if (-not (Test-Path env:ITK_PACKAGE_VERSION)) { $env:ITK_PACKAGE_VERSION = 'v5.0a02' }
+if (-not (Test-Path env:APPVEYOR)) { 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)) { $env:ITK_PACKAGE_VERSION = 'v5.0b01' }
 Invoke-WebRequest -Uri "https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/$env:ITK_PACKAGE_VERSION/ITKPythonBuilds-windows.zip" -OutFile "ITKPythonBuilds-windows.zip"
 sz x ITKPythonBuilds-windows.zip -oC:\P -aoa -r
-Invoke-WebRequest -Uri "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.11.windows.bin.zip" -OutFile "doxygen-1.8.11.windows.bin.zip"
+Invoke-WebRequest -Uri "https://data.kitware.com/api/v1/file/5c0ad59d8d777f2179dd3e9c/download" -OutFile "doxygen-1.8.11.windows.bin.zip"
 sz x doxygen-1.8.11.windows.bin.zip -oC:\P\doxygen -aoa -r
-Invoke-WebRequest -Uri "https://midas3.kitware.com/midas/download/bitstream/462235/grep-win.zip" -OutFile "grep-win.zip"
+Invoke-WebRequest -Uri "https://data.kitware.com/api/v1/file/5bbf87ba8d777f06b91f27d6/download/grep-win.zip" -OutFile "grep-win.zip"
 sz x grep-win.zip -oC:\P\grep -aoa -r
 $env:Path += ";C:\P\grep"
 C:\Python35-x64\python.exe C:\P\IPP\scripts\windows_build_module_wheels.py

scripts/windows_build_wheels.py

@@ -1,4 +1,6 @@
+#!/usr/bin/env python
 
+import argparse
 import glob
 import json
 import os
@@ -104,7 +106,8 @@ def build_wrapped_itk(
 
 
 def build_wheel(python_version, single_wheel=False,
-                cleanup=False, wheel_names=None):
+                cleanup=False, wheel_names=None,
+                cmake_options=[]):
 
     python_executable, \
             python_include_dir, \
@@ -148,8 +151,9 @@ def build_wheel(python_version, single_wheel=False,
                 "-DITK_BINARY_DIR:PATH=%s" % build_path,
                 "-DPYTHON_EXECUTABLE:FILEPATH=%s" % python_executable,
                 "-DPYTHON_INCLUDE_DIR:PATH=%s" % python_include_dir,
-                "-DPYTHON_LIBRARY:FILEPATH=%s" % python_library
-            ])
+                "-DPYTHON_LIBRARY:FILEPATH=%s" % python_library,
+                "-DDOXYGEN_EXECUTABLE:FILEPATH=C:/P/doxygen/doxygen.exe",
+            ] + cmake_options)
             # Cleanup
             check_call([python_executable, "setup.py", "clean"])
 
@@ -189,7 +193,7 @@ def build_wheel(python_version, single_wheel=False,
                     "-DPYTHON_EXECUTABLE:FILEPATH=%s" % python_executable,
                     "-DPYTHON_INCLUDE_DIR:PATH=%s" % python_include_dir,
                     "-DPYTHON_LIBRARY:FILEPATH=%s" % python_library
-                ])
+                ] + cmake_options)
 
                 # Cleanup
                 if cleanup:
@@ -215,24 +219,35 @@ def fixup_wheels():
         fixup_wheel(wheel)
 
 
-def test_wheels(single_wheel=False):
+def test_wheels(python_env):
+    (
+        python_executable,
+        python_include_dir,
+        python_library,
+        pip,
+        ninja_executable,
+        path
+    ) = venv_paths(python_env)
+    check_call([pip, 'install', 'itk', '--no-cache-dir', '--no-index',
+        '-f', 'dist'])
+    print('Wheel successfully installed.')
     check_call([
         python_executable,
         os.path.join(ROOT_DIR, "docs/code/testDriver.py")
     ])
+    print('Documentation tests passed.')
 
 
 def build_wheels(py_envs=DEFAULT_PY_ENVS, single_wheel=False,
-                 cleanup=False, wheel_names=None):
+                 cleanup=False, wheel_names=None, cmake_options=[]):
 
-    prepare_build_env("35-x64")
-    prepare_build_env("36-x64")
-    prepare_build_env("37-x64")
+    for py_env in py_envs:
+        prepare_build_env(py_env)
 
     with push_dir(directory=STANDALONE_DIR, make_directory=True):
 
         cmake_executable = "cmake.exe"
-        tools_venv = os.path.join(ROOT_DIR, "venv-35-x64")
+        tools_venv = os.path.join(ROOT_DIR, "venv-" + py_envs[0])
         pip_install(tools_venv, "ninja")
         ninja_executable = os.path.join(tools_venv, "Scripts", "ninja.exe")
 
@@ -249,19 +264,26 @@ def build_wheels(py_envs=DEFAULT_PY_ENVS, single_wheel=False,
 
     # Compile wheels re-using standalone project and archive cache
     for py_env in py_envs:
-        build_wheel(
-            py_env, single_wheel=single_wheel,
-            cleanup=cleanup, wheel_names=wheel_names)
-
-
-def main(py_envs=DEFAULT_PY_ENVS, wheel_names=None, cleanup=True):
-    single_wheel = False
-
-    build_wheels(
-        single_wheel=single_wheel, cleanup=cleanup,
-        py_envs=py_envs, wheel_names=wheel_names)
+        build_wheel(py_env, single_wheel=single_wheel,
+            cleanup=cleanup, wheel_names=wheel_names,
+            cmake_options=cmake_options)
+
+
+def main(wheel_names=None):
+    parser = argparse.ArgumentParser(description='Driver script to build ITK Python wheels.')
+    parser.add_argument('--single-wheel', action='store_true', help='Build a single wheel as opposed to one wheel per ITK module group.')
+    parser.add_argument('--py-envs', nargs='+', default=DEFAULT_PY_ENVS,
+            help='Target Python environment versions, e.g. "37-x64".')
+    parser.add_argument('--no-cleanup', dest='cleanup', action='store_false', help='Do not clean up temporary build files.')
+    parser.add_argument('cmake_options', nargs='*', help='Extra options to pass to CMake, e.g. -DBUILD_SHARED_LIBS:BOOL=OFF')
+    args = parser.parse_args()
+
+    build_wheels(single_wheel=args.single_wheel, cleanup=args.cleanup,
+        py_envs=args.py_envs, wheel_names=wheel_names,
+        cmake_options=args.cmake_options)
     fixup_wheels()
-    test_wheels(single_wheel=single_wheel)
+    for py_env in args.py_envs:
+        test_wheels(py_env)
 
 
 if __name__ == "__main__":