Merge pull request #42 from InsightSoftwareConsortium/bump-itk

ENH: Bump to ITK v5.3.0 with reusable workflow

Author: tbirdso

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

@@ -3,279 +3,10 @@ name: Build, test, package
 on: [push,pull_request]
 
 jobs:
-  build-test-cxx:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      max-parallel: 3
-      matrix:
-        os: [ubuntu-18.04, windows-2019, macos-10.15]
-        include:
-          - os: ubuntu-18.04
-            c-compiler: "gcc"
-            cxx-compiler: "g++"
-            itk-git-tag: "c693dbc830859ea10d573301f075e121a4c6c581"
-            cmake-build-type: "MinSizeRel"
-          - os: windows-2019
-            c-compiler: "cl.exe"
-            cxx-compiler: "cl.exe"
-            itk-git-tag: "c693dbc830859ea10d573301f075e121a4c6c581"
-            cmake-build-type: "Release"
-          - os: macos-10.15
-            c-compiler: "clang"
-            cxx-compiler: "clang++"
-            itk-git-tag: "c693dbc830859ea10d573301f075e121a4c6c581"
-            cmake-build-type: "MinSizeRel"
+  cxx-build-workflow:
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@36e33ec40332bb8fd85bfcd3ee899f82aa108e79
 
-    steps:
-    - uses: actions/checkout@v1
-
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
-      with:
-        python-version: "3.7"
-
-    - 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/[email protected]
-
-    - name: Download ITK
-      run: |
-        cd ..
-        git clone https://github.com/InsightSoftwareConsortium/ITK.git
-        cd ITK
-        git checkout ${{ matrix.itk-git-tag }}
-
-    - name: Build ITK
-      if: matrix.os != 'windows-2019'
-      run: |
-        cd ..
-        mkdir ITK-build
-        cd ITK-build
-        cmake -DCMAKE_C_COMPILER:FILEPATH="${{ 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'
-      run: |
-        cd ..
-        mkdir ITK-build
-        cd ITK-build
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
-        cmake -DCMAKE_C_COMPILER:FILEPATH="${{ matrix.c-compiler }}" -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_CXX_COMPILER="${{ matrix.cxx-compiler }}" -DCMAKE_BUILD_TYPE:STRING=${{ matrix.cmake-build-type }} -DBUILD_TESTING:BOOL=OFF -GNinja ../ITK
-        ninja
-      shell: cmd
-
-    - name: Fetch CTest driver script
-      run: |
-        curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITK/dashboard/itk_common.cmake -O
-
-    - name: Configure CTest script
-      shell: bash
-      run: |
-        operating_system="${{ matrix.os }}"
-        cat > dashboard.cmake << EOF
-        set(CTEST_SITE "GitHubActions")
-        file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/.." CTEST_DASHBOARD_ROOT)
-        file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/" CTEST_SOURCE_DIRECTORY)
-        file(TO_CMAKE_PATH "\$ENV{GITHUB_WORKSPACE}/../build" CTEST_BINARY_DIRECTORY)
-        set(dashboard_source_name "${GITHUB_REPOSITORY}")
-        if(ENV{GITHUB_REF} MATCHES "master")
-          set(branch "-master")
-          set(dashboard_model "Continuous")
-        else()
-          set(branch "-${GITHUB_REF}")
-          set(dashboard_model "Experimental")
-        endif()
-        set(CTEST_BUILD_NAME "${GITHUB_REPOSITORY}-${operating_system}-\${branch}")
-        set(CTEST_UPDATE_VERSION_ONLY 1)
-        set(CTEST_TEST_ARGS \${CTEST_TEST_ARGS} PARALLEL_LEVEL \${PARALLEL_LEVEL})
-        set(CTEST_BUILD_CONFIGURATION "Release")
-        set(CTEST_CMAKE_GENERATOR "Ninja")
-        set(CTEST_CUSTOM_WARNING_EXCEPTION
-          \${CTEST_CUSTOM_WARNING_EXCEPTION}
-          # macOS Azure VM Warning
-          "ld: warning: text-based stub file"
-          )
-        set(dashboard_no_clean 1)
-        set(ENV{CC} ${{ matrix.c-compiler }})
-        set(ENV{CXX} ${{ matrix.cxx-compiler }})
-        if(WIN32)
-          set(ENV{PATH} "\${CTEST_DASHBOARD_ROOT}/ITK-build/bin;\$ENV{PATH}")
-        endif()
-        set(dashboard_cache "
-        ITK_DIR:PATH=\${CTEST_DASHBOARD_ROOT}/ITK-build
-        BUILD_TESTING:BOOL=ON
-        ")
-        string(TIMESTAMP build_date "%Y-%m-%d")
-        message("CDash Build Identifier: \${build_date} \${CTEST_BUILD_NAME}")
-        message("CTEST_SITE = \${CTEST_SITE}")
-        include(\${CTEST_SCRIPT_DIRECTORY}/itk_common.cmake)
-        EOF
-        cat dashboard.cmake
-
-    - name: Build and test
-      if: matrix.os != 'windows-2019'
-      run: |
-        ctest --output-on-failure -j 2 -V -S dashboard.cmake
-
-    - name: Build and test
-      if: matrix.os == 'windows-2019'
-      run: |
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
-        ctest --output-on-failure -j 2 -V -S dashboard.cmake
-      shell: cmd
-
-  build-linux-python-packages:
-    runs-on: ubuntu-18.04
-    strategy:
-      max-parallel: 2
-      matrix:
-        python-version: ["36", "37", "38", "39"]
-        include:
-          - itk-python-git-tag: "v5.2.1"
-
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: 'Free up disk space'
-      run: |
-        # Workaround for https://github.com/actions/virtual-environments/issues/709
-        df -h
-        sudo apt-get clean
-        sudo rm -rf "/usr/local/share/boost"
-        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-        df -h
-
-    - name: 'Fetch build script'
-      run: |
-        curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/dockcross-manylinux-download-cache-and-build-module-wheels.sh -O
-        chmod u+x dockcross-manylinux-download-cache-and-build-module-wheels.sh
-
-    - name: 'Build 🐍 Python 📦 package'
-      run: |
-        export ITK_PACKAGE_VERSION=${{ matrix.itk-python-git-tag }}
-        ./dockcross-manylinux-download-cache-and-build-module-wheels.sh cp${{ matrix.python-version }}
-
-    - name: Publish Python package as GitHub Artifact
-      uses: actions/upload-artifact@v1
-      with:
-        name: LinuxWheel${{ matrix.python-version }}
-        path: dist
-
-  build-macos-python-packages:
-    runs-on: macos-10.15
-    strategy:
-      max-parallel: 2
-      matrix:
-        include:
-          - itk-python-git-tag: "v5.2.1"
-
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: 'Specific XCode version'
-      run: |
-        sudo xcode-select -s "/Applications/Xcode_11.7.app"
-
-    - name: Get specific version of CMake, Ninja
-      uses: lukka/[email protected]
-
-    - name: 'Fetch build script'
-      run: |
-        curl -L https://raw.githubusercontent.com/InsightSoftwareConsortium/ITKPythonPackage/master/scripts/macpython-download-cache-and-build-module-wheels.sh -O
-        chmod u+x macpython-download-cache-and-build-module-wheels.sh
-
-    - name: 'Build 🐍 Python 📦 package'
-      run: |
-        export ITK_PACKAGE_VERSION=${{ matrix.itk-python-git-tag }}
-        export MACOSX_DEPLOYMENT_TARGET=10.9
-        ./macpython-download-cache-and-build-module-wheels.sh
-
-    - name: Publish Python package as GitHub Artifact
-      uses: actions/upload-artifact@v1
-      with:
-        name: MacOSWheels
-        path: dist
-
-  build-windows-python-packages:
-    runs-on: windows-2019
-    strategy:
-      max-parallel: 2
-      matrix:
-        python-version-minor: ["6", "7", "8", "9"]
-        include:
-          - itk-python-git-tag: "v5.2.1"
-
-    steps:
-    - name: Get specific version of CMake, Ninja
-      uses: lukka/[email protected]
-
-    - uses: actions/checkout@v2
-      with:
-        path: "im"
-
-    - name: 'Install Python'
-      run: |
-        $pythonArch = "64"
-        $pythonVersion = "3.${{ matrix.python-version-minor }}"
-        iex ((new-object net.webclient).DownloadString('https://raw.githubusercontent.com/scikit-build/scikit-ci-addons/master/windows/install-python.ps1'))
-
-    - name: 'Fetch build dependencies'
-      shell: bash
-      run: |
-        mv im ../../
-        cd ../../
-        curl -L "https://github.com/InsightSoftwareConsortium/ITKPythonBuilds/releases/download/${{ matrix.itk-python-git-tag }}/ITKPythonBuilds-windows.zip" -o "ITKPythonBuilds-windows.zip"
-        7z x ITKPythonBuilds-windows.zip -o/c/P -aoa -r
-        curl -L "https://data.kitware.com/api/v1/file/5c0ad59d8d777f2179dd3e9c/download" -o "doxygen-1.8.11.windows.bin.zip"
-        7z x doxygen-1.8.11.windows.bin.zip -o/c/P/doxygen -aoa -r
-        curl -L "https://data.kitware.com/api/v1/file/5bbf87ba8d777f06b91f27d6/download/grep-win.zip" -o "grep-win.zip"
-        7z x grep-win.zip -o/c/P/grep -aoa -r
-
-    - name: 'Build 🐍 Python 📦 package'
-      shell: cmd
-      run: |
-        cd ../../im
-        call "C:\Program Files (x86)\Microsoft Visual Studio\2019\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
-        set PATH="C:\P\grep;%PATH%"
-        set CC=cl.exe
-        set CXX=cl.exe
-        C:\Python3${{ matrix.python-version-minor }}-x64\python.exe C:\P\IPP\scripts\windows_build_module_wheels.py --py-envs "3${{ matrix.python-version-minor }}-x64" --no-cleanup
-
-    - name: Publish Python package as GitHub Artifact
-      uses: actions/upload-artifact@v1
-      with:
-        name: WindowsWheel3.${{ matrix.python-version-minor }}
-        path: ../../im/dist
-
-  publish-python-packages-to-pypi:
-    needs:
-      - build-linux-python-packages
-      - build-macos-python-packages
-      - build-windows-python-packages
-    runs-on: ubuntu-18.04
-
-    steps:
-    - name: Download Python Packages
-      uses: actions/download-artifact@v2
-
-    - name: Prepare packages for upload
-      run: |
-        ls -R
-        for d in */; do
-          mv ${d}/*.whl .
-        done
-        mkdir dist
-        mv *.whl dist/
-        ls dist
-
-    - name: Publish 🐍 Python 📦 package to PyPI
-      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
+  python-build-workflow:
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@36e33ec40332bb8fd85bfcd3ee899f82aa108e79
+    secrets:
+      pypi_password: ${{ secrets.pypi_password }}

LICENSE

@@ -1,7 +1,7 @@
 
                                  Apache License
                            Version 2.0, January 2004
-                        http://www.apache.org/licenses/
+                        https://www.apache.org/licenses/
 
    TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
 
@@ -193,7 +193,7 @@
    you may not use this file except in compliance with the License.
    You may obtain a copy of the License at
 
-       http://www.apache.org/licenses/LICENSE-2.0
+       https://www.apache.org/licenses/LICENSE-2.0
 
    Unless required by applicable law or agreed to in writing, software
    distributed under the License is distributed on an "AS IS" BASIS,

README.md

@@ -10,7 +10,7 @@ H & E ([hematoxylin](https://en.wikipedia.org/wiki/Haematoxylin) and [eosin](htt
 
 Structure Preserving Color Normalization is a technique described in [Vahadane et al., 2016](https://doi.org/10.1109/TMI.2016.2529665) and modified in [Ramakrishnan et al., 2019](https://arxiv.org/abs/1901.03088).  The idea is to model the color of an image pixel as something close to pure white, which is reduced in intensity in a color-specific way via an optical absorption model that depends upon the amounts of hematoxylin and eosin that are present.  [Non-negative matrix factorization](https://en.wikipedia.org/wiki/Non-negative_matrix_factorization) is used on each analyzed image to simultaneously derive the amount of hematoxylin and eosin stain at each pixel and the image-wide effective colors of each stain.
 
-The implementation in ITK accelerates the non-negative matrix factorization by choosing the initial estimate for the color absorption characteristics using a technique mimicking that presented in [Arora et al., 2013](http://proceedings.mlr.press/v28/arora13.html) and modified in [Newberg et al., 2018](https://doi.org/10.1371/journal.pone.0193067).  This approach finds a good solution for a non-negative matrix factorization by first transforming it to the problem of finding a convex hull for a set of points in a cloud.
+The implementation in ITK accelerates the non-negative matrix factorization by choosing the initial estimate for the color absorption characteristics using a technique mimicking that presented in [Arora et al., 2013](https://proceedings.mlr.press/v28/arora13.html) and modified in [Newberg et al., 2018](https://doi.org/10.1371/journal.pone.0193067).  This approach finds a good solution for a non-negative matrix factorization by first transforming it to the problem of finding a convex hull for a set of points in a cloud.
 
 The lead developer of InsightSoftwareConsortium/ITKColorNormalization is [Lee Newberg](https://github.com/Leengit/).
 

include/itkStructurePreservingColorNormalizationFilter.h

@@ -6,7 +6,7 @@
  *  you may not use this file except in compliance with the License.
  *  You may obtain a copy of the License at
  *
- *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
  *
  *  Unless required by applicable law or agreed to in writing, software
  *  distributed under the License is distributed on an "AS IS" BASIS,

include/itkStructurePreservingColorNormalizationFilter.hxx

@@ -6,7 +6,7 @@
  *  you may not use this file except in compliance with the License.
  *  You may obtain a copy of the License at
  *
- *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
  *
  *  Unless required by applicable law or agreed to in writing, software
  *  distributed under the License is distributed on an "AS IS" BASIS,

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name="itk-spcn",
-    version="0.1.8",
+    version="0.2.0",
     author="Lee Newberg",
     author_email="[email protected]",
     packages=["itk"],
@@ -46,5 +46,5 @@
     license="Apache",
     keywords="ITK InsightToolkit",
     url=r"https://github.com/InsightSoftwareConsortium/ITKColorNormalization/",
-    install_requires=[r"itk>=5.2.1.post1"],
+    install_requires=[r"itk>=5.3.0"],
 )

test/itkStructurePreservingColorNormalizationFilterTest.cxx

@@ -6,7 +6,7 @@
  *  you may not use this file except in compliance with the License.
  *  You may obtain a copy of the License at
  *
- *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *         https://www.apache.org/licenses/LICENSE-2.0.txt
  *
  *  Unless required by applicable law or agreed to in writing, software
  *  distributed under the License is distributed on an "AS IS" BASIS,