Merge pull request #402 from thewtex/itk-5.3.0

Itk 5.3.0

.github/workflows/build-test-publish.yml

@@ -3,25 +3,25 @@ name: Build, test, publish
 on: [push,pull_request]
 
 env:
-  itk-git-tag: "v5.3rc04"
+  itk-git-tag: "37c107436f163436d9f9caf015b6f642eacdf651"
 
 jobs:
   build-test-cxx:
     runs-on: ${{ matrix.os }}
     strategy:
       max-parallel: 3
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-22.04, windows-2022, macos-12]
         include:
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             c-compiler: "gcc"
             cxx-compiler: "g++"
             cmake-build-type: "MinSizeRel"
-          - os: windows-2019
+          - os: windows-2022
             c-compiler: "cl.exe"
             cxx-compiler: "cl.exe"
             cmake-build-type: "Release"
-          - os: macos-11
+          - os: macos-12
             c-compiler: "clang"
             cxx-compiler: "clang++"
             cmake-build-type: "MinSizeRel"
@@ -31,18 +31,18 @@ jobs:
         with:
           path: Ex
 
-      - name: Set up Python 3.7
+      - name: Set up Python 3.9
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.9
 
       - name: Install build dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install ninja
 
       - name: Get specific version of CMake, Ninja
-        uses: lukka/get-cmake@v3.18.3
+        uses: lukka/get-cmake@v3.19.2
 
       - name: Download ITK
         run: |
@@ -52,20 +52,20 @@ jobs:
           git checkout ${{ env.itk-git-tag }}
 
       - name: Build ITK
-        if: matrix.os != 'windows-2019'
+        if: matrix.os != 'windows-2022'
         run: |
           cd ..
           mkdir ITK-build
           cd ITK-build
           cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK
           ninja
       - name: Build ITK
-        if: matrix.os == 'windows-2019'
+        if: matrix.os == 'windows-2022'
         run: |
           cd ..
           mkdir ITK-build
           cd ITK-build
-          call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+          call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
           cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK
           ninja
         shell: cmd
@@ -115,13 +115,13 @@ jobs:
           EOF
           cat dashboard.cmake
       - name: Build and test
-        if: matrix.os != 'windows-2019'
+        if: matrix.os != 'windows-2022'
         run: |
           ctest -j 2 -VV -S dashboard.cmake
       - name: Build and test
-        if: matrix.os == 'windows-2019'
+        if: matrix.os == 'windows-2022'
         run: |
-          call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+          call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
           ctest -j 2 -VV -S dashboard.cmake
         shell: cmd
 
@@ -130,38 +130,38 @@ jobs:
     strategy:
       max-parallel: 3
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-22.04, windows-2022, macos-12]
         include:
           - os: ubuntu-20.04
             c-compiler: "gcc"
             cxx-compiler: "g++"
             cmake-build-type: "MinSizeRel"
-          - os: windows-2019
+          - os: windows-2022
             c-compiler: "cl.exe"
             cxx-compiler: "cl.exe"
             cmake-build-type: "Release"
-          - os: macos-11
+          - os: macos-12
             c-compiler: "clang"
             cxx-compiler: "clang++"
             cmake-build-type: "MinSizeRel"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           path: Ex
 
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.7
+          python-version: 3.9
 
       - name: Install build dependencies
         run: |
           python -m pip install --upgrade pip
           python -m pip install ninja
 
       - name: Get specific version of CMake, Ninja
-        uses: lukka/get-cmake@v3.18.3
+        uses: lukka/get-cmake@v3.19.2
 
       - name: Fetch CTest driver script
         run: |
@@ -213,14 +213,14 @@ jobs:
           cat dashboard.cmake
 
       - name: Build and test
-        if: matrix.os != 'windows-2019'
+        if: matrix.os != 'windows-2022'
         run: |
           ctest -j 2 -VV -S dashboard.cmake
 
       - name: Build and test
-        if: matrix.os == 'windows-2019'
+        if: matrix.os == 'windows-2022'
         run: |
-          call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
+          call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
           ctest -j 2 -VV -S dashboard.cmake
         shell: cmd
 
@@ -229,20 +229,20 @@ jobs:
     strategy:
       max-parallel: 3
       matrix:
-        os: [ubuntu-20.04, windows-2019, macos-11]
+        os: [ubuntu-22.04, windows-2022, macos-12]
 
     steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python 3.7
-        uses: actions/setup-python@v1
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v3
         with:
-            python-version: 3.7
+            python-version: 3.9
 
       - name: Install build dependencies
         run: |
             python -m pip install --upgrade pip
             python -m pip install ninja
-            python -m pip install itk>=5.2.0.post2
+            python -m pip install itk>=5.3.0
             python -m pip install matplotlib
             python -m pip install itkwidgets
 
@@ -254,26 +254,26 @@ jobs:
     strategy:
       max-parallel: 3
       matrix:
-        os: [ubuntu-20.04]
+        os: [ubuntu-22.04]
         include:
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             c-compiler: "gcc"
             cxx-compiler: "g++"
             cmake-build-type: "Release"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           path: Ex
           submodules: recursive
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v1
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Get specific version of CMake, Ninja
-        uses: lukka/get-cmake@v3.18.3
+        uses: lukka/get-cmake@v3.19.2
 
       - name: Install build dependencies
         run: |

.github/workflows/label-pr.yml

@@ -8,6 +8,6 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: srvaroa/labeler@v0.8
+    - uses: srvaroa/labeler@v0.9
       env:
             GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

CMake/ITKSphinxExamplesExternalData.cmake

@@ -21,7 +21,8 @@ list(APPEND ExternalData_OBJECT_STORES
   "${CMAKE_SOURCE_DIR}/.ExternalData"
   )
 
-set(ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID bafybeicjaaz3xi2qso3kdirmy5ixoxegvfp3bm7o44ytoh6egj5m6wgeuu)
+set(ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID bafybeib6yijwyl52gkalx6griio2wsibowlrt3v5wmkkuqlnuvku64c3ra)
+
 set(ExternalData_URL_ALGO_CID_lower cid)
 set(ExternalData_URL_TEMPLATES "" CACHE STRING
   "Additional URL templates for the ExternalData CMake script to look for testing data. E.g.
@@ -32,6 +33,10 @@ if(NOT ITK_FORBID_DOWNLOADS)
     # Local IPFS gateway
     "http://127.0.0.1:8080/ipfs/%(hash)"
 
+    # Data published on GitHub Pages (note: not complete due to file size
+    # limit)
+    "https://insightsoftwareconsortium.github.io/ITKTestingData/%(algo)/%(hash)"
+
     # Released data rsync'd to Kitware's Apache web server
     "https://itk.org/files/ExternalData/%(algo)/%(hash)"
 
@@ -45,6 +50,9 @@ if(NOT ITK_FORBID_DOWNLOADS)
     "https://${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}.ipfs.w3s.link/Objects/CID/%(hash)"
 
     # Released data on estuary.tech
+    "https://api.estuary.tech/gw/ipfs/${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}/Objects/CID/%(hash)"
+
+    # Protocol Labs gateway
     "https://${ITK_SPHINX_EXAMPLES_DATA_RELEASED_ROOT_CID}.ipfs.dweb.link/Objects/CID/%(hash)"
 
     # Gateway for arbitrary new files, uploaded to web3.storage

CMakeLists.txt

@@ -10,8 +10,8 @@
 # CMake versions greater than the ITKEX_NEWEST_VALIDATED_POLICIES_VERSION policies will
 # continue to generate policy warnings "CMake Warning (dev)...Policy CMP0XXX is not set:"
 #
-set(ITKEX_OLDEST_VALIDATED_POLICIES_VERSION "3.10.2")
-set(ITKEX_NEWEST_VALIDATED_POLICIES_VERSION "3.14.0")
+set(ITKEX_OLDEST_VALIDATED_POLICIES_VERSION "3.16.3")
+set(ITKEX_NEWEST_VALIDATED_POLICIES_VERSION "3.19.7")
 cmake_minimum_required(VERSION ${ITKEX_OLDEST_VALIDATED_POLICIES_VERSION} FATAL_ERROR)
 if("${CMAKE_VERSION}" VERSION_LESS_EQUAL "${ITKEX_NEWEST_VALIDATED_POLICIES_VERSION}")
   #Set and use the newest available cmake policies that are validated to work
@@ -80,7 +80,7 @@ endif()
 if(NOT ITK_VERSION)
   # To get the ITK version information from external package when building
   # stand alone, ITK is required.
-  find_package(ITK 5.2.0 REQUIRED)
+  find_package(ITK 5.3.0 REQUIRED)
 endif()
 set(ITKSphinxExamples_VERSION_MAJOR ${ITK_VERSION_MAJOR})
 set(ITKSphinxExamples_VERSION_MINOR ${ITK_VERSION_MINOR})

Formatting/conf.py.in

@@ -40,7 +40,9 @@ primary_domain = 'cpp'
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = ['sphinx.ext.todo', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode', 'sphinx.ext.imgconverter', 'breathe', 'doxylink', 'breathelink', 'nbsphinx', 'sphinx_contributors']
+    'sphinx.ext.viewcode', 'sphinx.ext.imgconverter', 'breathe', 'doxylink',
+    'breathelink', 'nbsphinx', 'sphinx_contributors',
+    'IPython.sphinxext.ipython_console_highlighting',]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['templates']

README.rst

@@ -59,7 +59,7 @@ Required
 ^^^^^^^^
 
 - CMake_ ( >= 3.10.2 )
-- ITK_  ( >= 5.2.0 )
+- ITK_  ( >= 5.3.0 )
 
 Optional
 ^^^^^^^^

Superbuild/External-ITK.cmake

@@ -2,7 +2,8 @@
 # Get and build itk
 
 if(NOT ITK_TAG)
-  set(ITK_TAG "e801e637634d1cdf050b358299fd7b3771418f2e")
+  # ITK release 2022-12-05
+  set(ITK_TAG "37c107436f163436d9f9caf015b6f642eacdf651")
 endif()
 
 set(_vtk_args)
@@ -44,14 +45,6 @@ if(APPLE)
     "-DBUILD_SHARED_LIBS:BOOL=ON"
     )
 endif()
-set(_windows_args)
-set(_zlib_deps zlib)
-if(WIN32)
-  set(_windows_args
-    "-DITK_USE_SYSTEM_ZLIB:BOOL=OFF"
-    )
-  set(_zlib_deps )
-endif()
 
 ExternalProject_Add(ITK
   GIT_REPOSITORY "${git_protocol}://github.com/InsightSoftwareConsortium/ITK.git"
@@ -66,19 +59,15 @@ ExternalProject_Add(ITK
     -DBUILD_TESTING:BOOL=OFF
     -DITK_BUILD_DEFAULT_MODULES:BOOL=ON
     -DModule_ITKReview:BOOL=ON
+    -DITK_LEGACY_REMOVE:BOOL=ON
     -DITK_LEGACY_SILENT:BOOL=ON
     -DExternalData_OBJECT_STORES:STRING=${ExternalData_OBJECT_STORES}
-    "-DITK_USE_SYSTEM_ZLIB:BOOL=ON"
-    "-DZLIB_ROOT:PATH=${ZLIB_ROOT}"
-    "-DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR}"
-    "-DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY}"
     ${_vtk_args}
     ${_opencv_args}
     ${_wrap_python_args}
     ${_apple_args}
-    ${_windows_args}
   INSTALL_COMMAND ${CMAKE_COMMAND} -E echo "ITK install skipped"
-  DEPENDS ${ITK_DEPENDENCIES} ${_python_depends} ${_zlib_deps}
+  DEPENDS ${ITK_DEPENDENCIES} ${_python_depends}
   LOG_BUILD 0
 )
 

Superbuild/External-Python.cmake

@@ -17,6 +17,6 @@ ExternalProject_Add(ITKPython
   DOWNLOAD_COMMAND ""
   CONFIGURE_COMMAND ${PYTHON_EXECUTABLE} -m venv "${_itk_venv}"
   BUILD_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --upgrade pip
-  INSTALL_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --ignore-installed itk>=5.3rc4.post2 sphinx==4.4.0 docutils<0.18 six black nbsphinx ipython sphinx-contributors ipykernel matplotlib itkwidgets[lab,notebook]>=1.0a7 pydata-sphinx-theme
+  INSTALL_COMMAND ${ITKPYTHON_EXECUTABLE} -m pip install --ignore-installed itk>=5.3.0 sphinx==4.4.0 docutils<0.18 six black nbsphinx ipywidgets sphinx-contributors ipykernel matplotlib itkwidgets[lab,notebook]>=1.0a21 pydata-sphinx-theme
   COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/ITKBlackConfig.cmake
   )

Superbuild/External-VTK.cmake

@@ -24,14 +24,9 @@ ExternalProject_Add(VTK
     -DVTK_WRAP_PYTHON:BOOL=ON
     -DExternalData_OBJECT_STORES:STRING=${ExternalData_OBJECT_STORES}
     "-DPython3_EXECUTABLE:FILEPATH=${PYTHON_EXECUTABLE}"
-    -DVTK_USE_SYSTEM_ZLIB:BOOL=ON
-    "-DZLIB_ROOT:PATH=${ZLIB_ROOT}"
-    "-DZLIB_INCLUDE_DIR:PATH=${ZLIB_INCLUDE_DIR}"
-    "-DZLIB_LIBRARY:FILEPATH=${ZLIB_LIBRARY}"
   INSTALL_COMMAND ""
   LOG_DOWNLOAD 0
   LOG_UPDATE 0
-  DEPENDS zlib
 )
 
 set(VTK_DIR ${CMAKE_BINARY_DIR}/VTK-build)