CI: test docker CIL (#838)

Co-authored-by: Casper da Costa-Luis <casper.dcl@physics.org> Co-authored-by: Kris Thielemans <KrisThielemans@users.noreply.github.com>
SyneRBI · Oct 13, 2023 · 5f394eb · 5f394eb
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diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
@@ -23,19 +23,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-      
+
       - name: Install docker and pre-reqs and clean some disk-space
         shell: bash -l {0}
         run: |
          sudo .github/workflows/install_docker.sh
          sudo .github/workflows/GHA_increase_disk_space.sh
-         
+
       - name: Build docker core image
         # Builds docker image from Docker file.
         shell: bash -l {0}
         run: |
-          docker-compose -f docker/docker-compose.yml build --pull core 
-          
+          docker-compose -f docker/docker-compose.yml build --pull core
+
       - name : docker save core
         # https://docs.docker.com/engine/reference/commandline/save/
         shell: bash -l {0}
@@ -44,14 +44,14 @@ jobs:
           docker image ls
           docker save synerbi/sirf:core | gzip > core.tar.gz
           ls -l
-          
+
       - name: Upload artifact of the core image.
         uses: actions/upload-artifact@v3.1.2
         with:
           name: sirf-core
           path: core.tar.gz
-          
-          
+
+
   build-core-gpu:
     runs-on: ubuntu-latest
     steps:
@@ -61,27 +61,27 @@ jobs:
         run: |
          sudo .github/workflows/install_docker.sh
          sudo .github/workflows/GHA_increase_disk_space.sh
-          
+
       - name: Build docker core-gpu image
         # Builds docker image from Docker file.
         shell: bash -l {0}
         run: |
           docker-compose -f docker/docker-compose.yml -f docker/docker-compose.srv-gpu.yml build --pull core
-          
+
       - name : docker save core-gpu
         # https://docs.docker.com/engine/reference/commandline/save/
         shell: bash -l {0}
         run: |
           docker image ls
           docker save synerbi/sirf:core-gpu | gzip > core-gpu.tar.gz
           ls -l
-          
+
       - name: Upload artifact of the core image.
         uses: actions/upload-artifact@v3.1.2
         with:
           name: sirf-core-gpu
           path: core-gpu.tar.gz
-      
+
   build-devel-and-latest:
     runs-on: ubuntu-latest
     needs: build-core
@@ -95,7 +95,7 @@ jobs:
         run: |
          sudo .github/workflows/install_docker.sh
          sudo .github/workflows/GHA_increase_disk_space.sh
-          
+
       - name: Download artifact of core image
         uses: actions/download-artifact@v3
         with:
@@ -106,18 +106,18 @@ jobs:
         shell: bash -l {0}
         run: |
           docker load --input /tmp/core.tar.gz
-      
+
       - name: Build docker image
         # Builds docker image from Docker file.
         shell: bash -l {0}
         run: |
           set -ex;
-          compose_command="docker-compose -f docker/docker-compose.yml" 
+          compose_command="docker-compose -f docker/docker-compose.yml"
           if [[ ${{ matrix.tag }} == 'devel' ]]; then compose_command="$compose_command -f docker/docker-compose.devel.yml"; fi
           # $compose_command pull core
           $compose_command build --pull sirf
           echo "compose_command=$compose_command" >> $GITHUB_ENV
-          
+
       - name : docker save image
         # https://docs.docker.com/engine/reference/commandline/save/
         shell: bash -l {0}
@@ -126,13 +126,13 @@ jobs:
           sirf_image=`docker image ls | grep ${{ matrix.tag }} | awk '/sirf/ { print $3}'`
           docker history "$sirf_image"
           docker save  synerbi/sirf:${{ matrix.tag }} | gzip > ${{ matrix.tag }}.tar.gz
-          
+
       - name: Upload artifact of image.
         uses: actions/upload-artifact@v3.1.2
         with:
           name: sirf-${{ matrix.tag }}
           path: ${{ matrix.tag }}.tar.gz
-          
+
   build-service-gpu:
       runs-on: ubuntu-latest
       needs: build-core-gpu
@@ -160,9 +160,9 @@ jobs:
           shell: bash -l {0}
           run: |
             set -ex;
-            # docker-compose -f docker/docker-compose.yml -f docker/docker-compose.srv-gpu.yml pull core 
+            # docker-compose -f docker/docker-compose.yml -f docker/docker-compose.srv-gpu.yml pull core
             docker-compose -f docker/docker-compose.yml -f docker/docker-compose.srv-gpu.yml build --pull sirf
-            
+
         # Temporarily disabling the save and upload of the image as it is too big.
         # see https://github.com/SyneRBI/SIRF-SuperBuild/issues/770
 
@@ -174,16 +174,16 @@ jobs:
         #     docker rmi synerbi/sirf:core-gpu
         #     yes | docker system prune
         #     docker image ls
-        #     docker save synerbi/sirf:service-gpu | gzip > service-gpu.tar.gz 
-          
+        #     docker save synerbi/sirf:service-gpu | gzip > service-gpu.tar.gz
+
         # - name: Upload artifact of image.
         #   uses: actions/upload-artifact@v3.1.2
         #   with:
         #     name: sirf-service-gpu
         #     path: service-gpu.tar.gz
-            
-        
-            
+
+
+
   build-service-images:
     runs-on: ubuntu-latest
     needs: build-devel-and-latest
@@ -197,13 +197,13 @@ jobs:
         run: |
          sudo .github/workflows/install_docker.sh
          sudo .github/workflows/GHA_increase_disk_space.sh
-         
+
       - name: setup variables
         shell: bash -l {0}
         run: |
           compose_command="docker-compose -f docker/docker-compose.yml"
-           
-          if [[ ${{ matrix.tag }} == 'service' ]]; 
+
+          if [[ ${{ matrix.tag }} == 'service' ]];
           then
             echo "prereq_image_name="latest"" >> $GITHUB_ENV
             compose_command="$compose_command -f docker/docker-compose.srv.yml"
@@ -212,9 +212,9 @@ jobs:
           then
             echo "prereq_image_name="devel"" >> $GITHUB_ENV
             compose_command="$compose_command -f docker/docker-compose.devel.yml -f docker/docker-compose.srv.yml"
-          fi    
+          fi
           echo "compose_command=$compose_command" >> $GITHUB_ENV
-          
+
       - name: Download artifact of image
         uses: actions/download-artifact@v3
         with:
@@ -225,15 +225,21 @@ jobs:
         shell: bash -l {0}
         run: |
           docker load --input /tmp/${{ env.prereq_image_name }}.tar.gz
-      
+
       - name: Build docker image
         # Builds docker image from Docker file.
         shell: bash -l {0}
         run: |
           set -ex;
           # ${{ env.compose_command }} pull sirf
           ${{ env.compose_command }} build --pull sirf
-          
+
+      - name: Test CIL
+        shell: bash -l {0}
+        run: |
+          set -ex;
+          docker run --rm -v ./.github/workflows:/gh synerbi/sirf:service /gh/test_cil.sh
+
       - name : docker save image
         # https://docs.docker.com/engine/reference/commandline/save/
         shell: bash -l {0}
@@ -243,14 +249,14 @@ jobs:
           # get rid of everything over 2 days old
           docker system prune -a --filter "until=2d"
           docker image ls
-          docker save synerbi/sirf:service | gzip > ${{ matrix.tag }}.tar.gz 
-          
+          docker save synerbi/sirf:service | gzip > ${{ matrix.tag }}.tar.gz
+
       - name: Upload artifact of image.
         uses: actions/upload-artifact@v3.1.2
         with:
           name: sirf-${{ matrix.tag }}
           path: ${{ matrix.tag }}.tar.gz
-      
+
   # Docker images are not currently uploaded with this action.
   # Disable it for now as it would just waste time.
   # upload-images:
@@ -266,7 +272,7 @@ jobs:
   #       run: |
   #        sudo .github/workflows/install_docker.sh
   #        sudo .github/workflows/GHA_increase_disk_space.sh
-          
+
   #     - name: Download artifact of image
   #       uses: actions/download-artifact@v3
   #       with:
@@ -277,14 +283,14 @@ jobs:
   #       shell: bash -l {0}
   #       run: |
   #         docker load --input /tmp/${{ matrix.tag }}.tar.gz
-      
+
   #     - name: Upload docker image
   #       # Builds docker image from Docker file.
   #       shell: bash -l {0}
   #       run: |
-  #         # TODO requirement to 
+  #         # TODO requirement to
   #         docker image ls
   #         echo "Here we would upload image with name: ${{ matrix.tag }}"
-          
-          
+
+
     # TODO: publish to come later
diff --git a/.github/workflows/test_cil.sh b/.github/workflows/test_cil.sh
@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+[ -f .bashrc ] && . .bashrc
+set -euxo pipefail
+
+mkdir cil_sirf_test
+touch cil_sirf_test/__init__.py
+DEFAULT_CIL_TAG=$(/opt/conda/bin/python -c 'import cil; print(f"v{cil.version.version}" if cil.version.commit_hash == "-1" else cil.version.commit_hash[1:])' | tail -n1)
+for fname in test_SIRF.py utils.py testclass.py; do
+  curl -fsSL https://raw.githubusercontent.com/TomographicImaging/CIL/$DEFAULT_CIL_TAG/Wrappers/Python/test/$fname > cil_sirf_test/$fname
+done
+
+$SIRF_PATH/../../INSTALL/bin/gadgetron >& ~/gadgetron.log&
+/opt/conda/bin/python -m unittest discover -v ./cil_sirf_test -k GradientPET -k BlockDataContainer
+for i in $(jobs -p); do kill -n 15 $i; done 2>/dev/null  # kill gadgetron
diff --git a/CHANGES.md b/CHANGES.md
@@ -22,7 +22,7 @@
   - siemens_to_ismrmrd: 8bb8b08f53ce73c2de9ba5f47f1532f96292d92b
   - ISMRMRD: v1.13.2
   - SIRF: v3.5.0
-  - CIL: 0ba2f8e2935db66ec3dfe8c88e407e8d0eb5609f
+  - CIL: v23.1.0
   - CCPi-Regularisation: v22.0.0
   - TomoPhantom: v2.0.0
 

diff --git a/SuperBuild/External_CIL.cmake b/SuperBuild/External_CIL.cmake
@@ -96,7 +96,7 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_run_*.py
            WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
   add_test(NAME CIL_SIRF_TESTS
-          COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_SIRF*.py
+          COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_SIRF*.py -k GradientPET -k BlockDataContainer
           WORKING_DIRECTORY ${${proj}_SOURCE_DIR}/Wrappers/Python/test)
   add_test(NAME CIL_FRAMEWORK_TESTS_4
            COMMAND ${PYTHON_EXECUTABLE} -m unittest discover -p test_Block_*.py