Build VMTK with VTK 9 and ITK 5. Update python versions to all supported

hemelb-codes · Mar 7, 2023 · 0881221 · 0881221
1 parent 05f30e4
commit 0881221
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diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -2,43 +2,46 @@ on:
   push:
     branches: [main]
 
+  pull_request:
+
   release:
     types: [created]
 
 env:
-  VTK_VERSION: 8.2.0
-  ITK_VERSION: 4.13.3
-  VMTK_VERSION: 1.4.1-rc4
-  VMTK_HASH: 63a3b990328d8dfaa6ffd31968fc341cad9dbe67
+  VTK_VERSION: 9.1.0
+  ITK_VERSION: 5.2.1
+  VMTK_VERSION: 1.5.0
+  VMTK_FORK: vmtk
+  VMTK_HASH: 30b0fdad5674d6f134e8a8b601bcef7917671b0a
   PLATFORM: ubuntu
 
 jobs:
 
   VTK-build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version:
-          - "3.6"
-          - "3.7"
           - "3.8"
           - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
       - name: Checkout this repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: builder
 
       - name: Cache
         id: cache-vtk
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /opt/vtk
           key: VTK-${{ env.VTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}-${{ hashFiles('builder/configure-vtk-ubuntu.sh') }}
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         if: steps.cache-vtk.outputs.cache-hit != 'true'
         with:
           python-version: ${{ matrix.python-version }}
@@ -49,17 +52,12 @@ jobs:
 
       - name: Checkout VTK
         if: steps.cache-vtk.outputs.cache-hit != 'true'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: kitware/vtk
           path: vtk
           ref: v${{ env.VTK_VERSION }}
 
-      - name: Patch (to support python >= 3.8)
-        if: steps.cache-vtk.outputs.cache-hit != 'true'
-        working-directory: vtk
-        run: patch -p1 < ${{ github.workspace }}/builder/vtk-py38.patch
-
       - name: Configure
         if: steps.cache-vtk.outputs.cache-hit != 'true'
         env:
@@ -72,17 +70,17 @@ jobs:
         if: steps.cache-vtk.outputs.cache-hit != 'true'
         run: cmake --build build -j 4
 
+      - name: Get failed build tree
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          path: build
+          name: vtk-${{ env.VTK_VERSION }}-failed-build
+
       - name: Install
         if: steps.cache-vtk.outputs.cache-hit != 'true'
         run: cmake --install build
 
-      - name: Un-hardcode the python location in CMake config
-        if: steps.cache-vtk.outputs.cache-hit != 'true'
-        env:
-          BUILD_DIR: build
-          CMAKE_CONFIG_DIR: /opt/vtk/lib/cmake
-        run: builder/unhardcode-python-location.sh
-
       - name: Make visible to setuptools
         env:
           SITE_PACKAGES_DIR: /opt/vtk/lib/python${{ matrix.python-version }}/site-packages
@@ -96,36 +94,35 @@ jobs:
           ${{ github.workspace }}/VTK-${{ env.VTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz
           *
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: VTK-${{ env.VTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
           path: VTK-${{ env.VTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz
 
   ITK-build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version:
-          - "3.6"
-          - "3.7"
           - "3.8"
           - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
-
       - name: Checkout this repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: builder
 
       - name: Cache
         id: cache-itk
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /opt/itk
           key: ITK-${{ env.ITK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}-${{ hashFiles('builder/configure-itk-ubuntu.sh') }}
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         if: steps.cache-itk.outputs.cache-hit != 'true'
         with:
           python-version: ${{ matrix.python-version }}
@@ -136,7 +133,7 @@ jobs:
 
       - name: Checkout ITK
         if: steps.cache-itk.outputs.cache-hit != 'true'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: InsightSoftwareConsortium/ITK
           path: itk
@@ -165,39 +162,38 @@ jobs:
           ${{ github.workspace }}/ITK-${{ env.ITK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz
           *
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: ITK-${{ env.ITK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
           path: ITK-${{ env.ITK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz
 
   VMTK-build:
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     needs: [VTK-build, ITK-build]
 
     strategy:
       matrix:
         python-version:
-          - "3.6"
-          - "3.7"
           - "3.8"
           - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
-
       - name: Checkout this repo
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: builder
 
       - name: Cache VMTK
         id: cache-vmtk
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /opt/vmtk
           key: VMTK-${{ env.VMTK_HASH }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}-vtk${{ env.VTK_VERSION }}-itk${{ env.ITK_VERSION }}-${{ hashFiles('builder/configure-vmtk-ubuntu.sh') }}
 
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
         if: steps.cache-vmtk.outputs.cache-hit != 'true'
         with:
           python-version: ${{ matrix.python-version }}
@@ -208,15 +204,15 @@ jobs:
 
       - name: Checkout VMTK
         if: steps.cache-vmtk.outputs.cache-hit != 'true'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
-          repository: vmtk/vmtk
+          repository: ${{ env.VMTK_FORK }}/vmtk
           path: vmtk
           ref: ${{ env.VMTK_HASH }}
 
       - name: Get VTK
         if: steps.cache-vmtk.outputs.cache-hit != 'true'
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: VTK-${{ env.VTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
           path: deps
@@ -227,7 +223,7 @@ jobs:
 
       - name: Get ITK
         if: steps.cache-vmtk.outputs.cache-hit != 'true'
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: ITK-${{ env.ITK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
           path: deps
@@ -251,7 +247,7 @@ jobs:
 
       - name: Store failed build tree
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: failed-VMTK-${{ env.VMTK_HASH }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
           path: build
@@ -273,39 +269,39 @@ jobs:
           ${{ github.workspace }}/VMTK-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz
           *
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: VMTK-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
           path: VMTK-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz
 
   package:
     needs: [VTK-build, ITK-build, VMTK-build]
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
         python-version:
-          - "3.6"
-          - "3.7"
           - "3.8"
           - "3.9"
+          - "3.10"
+          - "3.11"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Get VTK
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: VTK-${{ env.VTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
 
       - name: Get ITK
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: ITK-${{ env.ITK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
 
       - name: Get VMTK
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: VMTK-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
 
@@ -322,7 +318,7 @@ jobs:
           cd /opt/vmtk
           tar -czf ${{ github.workspace }}/all-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz *
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           name: all-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
           path: all-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}.tar.gz
@@ -332,35 +328,36 @@ jobs:
 
     needs: [package]
 
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     strategy:
       matrix:
         python-version:
-          - "3.6"
-          - "3.7"
           - "3.8"
           - "3.9"
+          - "3.10"
+          - "3.11"
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Get VTK
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: VTK-${{ env.VTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
 
       - name: Get ITK
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: ITK-${{ env.ITK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
 
       - name: Get VMTK
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: VMTK-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
 
       - name: Get All
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v3
         with:
           name: all-${{ env.VMTK_VERSION }}-${{ env.PLATFORM }}-py${{ matrix.python-version }}
 

diff --git a/configure-itk-ubuntu.sh b/configure-itk-ubuntu.sh
@@ -1,14 +1,24 @@
 #!/bin/bash
+thisdir=$(readlink -f $(dirname $BASH_SOURCE))
+. $thisdir/cmake_help.sh
+
+declare -A D
 
-cmake \
-    -B build \
-    -S itk \
-    -DCMAKE_INSTALL_PREFIX=$INSTALL_PREFIX \
-    -DCMAKE_BUILD_TYPE=Release \
-    -DBUILD_SHARED_LIBS=ON \
-    -DBUILD_EXAMPLES:BOOL=OFF \
-    -DBUILD_TESTING:BOOL=OFF \
-    -DITK_USE_REVIEW:BOOL=ON \
-    -DITK_USE_REVIEW_STATISTICS:BOOL=ON \
-    -DITK_USE_OPTIMIZED_REGISTRATION_METHODS:BOOL=ON \
-    -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF
+D[CMAKE_INSTALL_PREFIX]=$INSTALL_PREFIX
+D[CMAKE_BUILD_TYPE]=Release
+D[BUILD_SHARED_LIBS]=ON
+D[BUILD_EXAMPLES]=OFF
+D[BUILD_TESTING]=OFF
+D[CMAKE_BUILD_WITH_INSTALL_RPATH]=OFF
+D[CMAKE_INSTALL_RPATH_USE_LINK_PATH]=TRUE
+
+# From Superbuild ITK 5
+D[ITK_LEGACY_REMOVE]=OFF   #<-- Allow LEGACY ITKv4 features for now.
+D[ITK_LEGACY_SILENT]=ON   #<-- Use of legacy code will produce compiler warnings
+D[Module_ITKDeprecated]=ON #<-- Needed for ITKv5 now. (itkMultiThreader.h and MutexLock backwards compatibility.)
+D[Module_ITKReview]=OFF
+
+mkdir -p build
+cd build
+
+run_cmake D ../itk
diff --git a/configure-vmtk-ubuntu.sh b/configure-vmtk-ubuntu.sh
@@ -17,5 +17,4 @@ cmake \
     -DVMTK_USE_RENDERING:STRING=ON \
     -DITK_DIR:PATH=$ITK_DIR \
     -DVTK_DIR:PATH=$VTK_DIR \
-    -DVMTK_USE_VTK8:BOOL=ON \
     -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF