V21.12 (#16)

* FIX: add ci.yml workflow to compile plugin for different platforms and build/test corrections

.github/workflows/ci.yml

@@ -0,0 +1,202 @@
+name: Benchmark_tests
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+  #schedule:
+  #  - cron:  '00 2 * * *'
+
+
+jobs:
+  build_and_test:
+    name: Building on ${{ matrix.os }} with SOFA ${{ matrix.sofa_branch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, macos-10.15, windows-2019]
+        sofa_branch: [v21.12] # master
+        python-version: ['3.10']
+
+    steps:
+      - name: Setup SOFA and environment
+        id: sofa
+        uses: sofa-framework/sofa-setup-action@v4
+        with:
+          sofa_root: /opt/sofa
+          sofa_version: ${{ matrix.sofa_branch }}
+          sofa_scope: 'standard'
+
+      - name: Checkout source code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install requirements
+        shell: bash
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            EIGEN_VERSION=3.4.0
+            EIGEN_INSTALL_DIR="C:/eigen"
+            if ! ls -a "$EIGEN_INSTALL_DIR"/* >/dev/null 2>&1; then
+              # directory does not exist or is empty
+              mkdir -p "$EIGEN_INSTALL_DIR"
+              curl --output "${{ runner.temp }}/eigen_tmp.zip" -L \
+                "https://gitlab.com/libeigen/eigen/-/archive/${EIGEN_VERSION}/eigen-${EIGEN_VERSION}.zip"
+              unzip -qq "${{ runner.temp }}/eigen_tmp.zip" -d "${{ runner.temp }}/eigen_tmp"
+              mv "${{ runner.temp }}"/eigen_tmp/eigen-*/* $EIGEN_INSTALL_DIR
+            fi
+            mkdir $EIGEN_INSTALL_DIR/build_release \
+            && cmd //c "${{ steps.sofa.outputs.vs_vsdevcmd }} \
+            && cd /d $EIGEN_INSTALL_DIR/build_release \
+            && cmake -GNinja -DCMAKE_BUILD_TYPE=Release .. \
+            && ninja install"
+          elif [[ "$RUNNER_OS" == "macOS" ]]; then
+            brew install eigen
+          elif [[ "$RUNNER_OS" == "Linux" ]]; then
+            sudo apt install -qq libeigen3-dev libblas-dev libglew-dev
+          fi
+          python3 -m pip install --upgrade pip
+          python3 -m pip install numpy pyyaml
+
+      - name: Build pybind11
+        shell: bash
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            PYBIND_INSTALL_PATH="C:/pybind11" \
+            && git clone -b v2.8 --depth 1 https://github.com/pybind/pybind11.git $PYBIND_INSTALL_PATH \
+            && cmd //c "${{ steps.sofa.outputs.vs_vsdevcmd }} \
+            && cd /d $PYBIND_INSTALL_PATH \
+            && cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DPYBIND11_TEST=OFF . \
+            && ninja install"
+          else
+            PYBIND_INSTALL_PATH="/tmp/pybind11"
+            git clone -b v2.8 --depth 1 https://github.com/pybind/pybind11.git $PYBIND_INSTALL_PATH
+            cd $PYBIND_INSTALL_PATH
+            echo "Curent plugin branch is:" && git branch --show-current
+            cmake -DCMAKE_BUILD_TYPE=Release -DPYBIND11_TEST=OFF .
+            make
+            sudo make install
+          fi
+
+      - name: Build python3 plugin
+        shell: bash
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            SOFA_PYTHON3_ROOT="C:/SofaPython3" \
+            && git clone --branch ${{ steps.sofa.outputs.sofa_version }} https://github.com/sofa-framework/SofaPython3.git $SOFA_PYTHON3_ROOT \
+            && mkdir $SOFA_PYTHON3_ROOT/build_release \
+            && cmd //c "${{ steps.sofa.outputs.vs_vsdevcmd }} \
+            && cd /d $SOFA_PYTHON3_ROOT/build_release \
+            && cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DPYTHON_ROOT=$PYTHON_ROOT -DPython_ROOT=$PYTHON_ROOT -DPYTHON_EXECUTABLE=$PYTHON_ROOT/python.exe \
+            -DPython_EXECUTABLE=$PYTHON_ROOT/python.exe -DCMAKE_PREFIX_PATH="$SOFA_ROOT/build_release/install" .. \
+            && ninja install"
+          else
+            export SOFA_PYTHON3_ROOT=/tmp/SofaPython3
+            git clone --branch ${{ steps.sofa.outputs.sofa_version }} https://github.com/sofa-framework/SofaPython3.git $SOFA_PYTHON3_ROOT
+            mkdir $SOFA_PYTHON3_ROOT/build_release
+            cd $SOFA_PYTHON3_ROOT/build_release
+            echo "Curent plugin branch is:" && git branch --show-current
+            cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$SOFA_ROOT/build_release/install ..
+            make -j 8
+            make install
+          fi
+      
+      - name: Build Optimus
+        shell: bash
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            EIGEN_INSTALL_DIR="C:/eigen" \
+            && echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE" \
+            && mkdir $GITHUB_WORKSPACE/build_release \
+            && cmd //c "${{ steps.sofa.outputs.vs_vsdevcmd }} \
+            && cd /d $GITHUB_WORKSPACE/build_release \
+            && cmake -GNinja -DCMAKE_BUILD_TYPE=Release -DUSE_BLAS_FOR_OPTIMUS=0 \
+            -DCMAKE_PREFIX_PATH="$SOFA_ROOT/build_release/install";$EIGEN_INSTALL_DIR/build_release .. \
+            && ninja install"
+          else
+            mkdir $GITHUB_WORKSPACE/build_release
+            cd $GITHUB_WORKSPACE/build_release
+            cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$SOFA_ROOT/build_release/install ..
+            make -j 8
+            make install
+          fi
+
+      - name: Create artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: Optimus_${{ steps.sofa.outputs.run_branch }}_for-SOFA-${{ steps.sofa.outputs.sofa_version }}_${{ runner.os }}
+          path: ${{ github.workspace }}/build_release/install
+
+      - name: Install artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: Optimus_${{ steps.sofa.outputs.run_branch }}_for-SOFA-${{ steps.sofa.outputs.sofa_version }}_${{ runner.os }}
+          path: ${{ github.workspace }}/build_release/install
+
+      - name: Optimus tests
+        shell: bash
+        run: |
+          if [[ "$RUNNER_OS" == "Windows" ]]; then
+            echo "Skip tests for windows system"
+          else
+            export SOFA_PYTHON3_ROOT=/tmp/SofaPython3
+            export LD_LIBRARY_PATH=$GITHUB_WORKSPACE/build_release
+            export SOFA_PLUGIN_PATH=$GITHUB_WORKSPACE/build_release
+            FOLDER_LIST=`find $GITHUB_WORKSPACE/benchmarks -maxdepth 1`
+            for FOLDER in $FOLDER_LIST; do
+                if [ -f $FOLDER/verify.sh ]; then
+                    cd $FOLDER
+                    echo "Perform test: $FOLDER"
+                    if [[ "$RUNNER_OS" == "macOS" ]]; then
+                        $FOLDER/verify.sh $SOFA_ROOT/bin/runSofa $SOFA_PYTHON3_ROOT/build_release/lib/libSofaPython3.dylib
+                    else
+                        $FOLDER/verify.sh $SOFA_ROOT/bin/runSofa $SOFA_PYTHON3_ROOT/build_release/lib/libSofaPython3.so
+                    fi
+                fi
+            done
+            echo "All tests have been executed"
+          fi
+
+
+  deploy:
+    name: Deploy artifacts
+    if: always() && startsWith(github.ref, 'refs/heads/') # we are on a branch (not a PR)
+    needs: [build_and_test]
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - name: Get artifacts
+        uses: actions/download-artifact@v2
+        with:
+          path: artifacts
+
+      - name: Zip artifacts
+        shell: bash
+        run: |
+          cd $GITHUB_WORKSPACE/artifacts
+          for artifact in *; do
+            zip $artifact.zip -r $artifact/*
+          done
+
+      - name: Delete old release
+        uses: dev-drprasad/[email protected]
+        with:
+          delete_release: true
+          tag_name: release-${{ github.ref_name }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Upload release
+        uses: softprops/action-gh-release@v1
+        with:
+          name: ${{ github.ref_name }}
+          tag_name: release-${{ github.ref_name }}
+          fail_on_unmatched_files: true
+          files: |
+            artifacts/Optimus_*_Linux.zip
+            artifacts/Optimus_*_macOS.zip

.github/workflows/ubuntu.yml → .github/workflows/ubuntu.yml_old

@@ -95,7 +95,7 @@ jobs:
               if [ -f $FOLDER/verify.sh ]; then
                   cd $FOLDER
                   echo "Perform test: $FOLDER"
-                  $FOLDER/verify.sh $SOFA_BUILD_DIRECTORY/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib
+                  $FOLDER/verify.sh $SOFA_BUILD_DIRECTORY/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib/libSofaPython3.so
               fi
           done
           echo "All tests have been executed"

CMakeLists.txt

@@ -1,10 +1,11 @@
-cmake_minimum_required(VERSION 3.1)
-project(Optimus)
+cmake_minimum_required(VERSION 3.8)
 
 set(OPTIMUS_MAJOR_VERSION 1)
 set(OPTIMUS_MINOR_VERSION 1)
 set(OPTIMUS_VERSION ${OPTIMUS_MAJOR_VERSION}.${OPTIMUS_MINOR_VERSION})
 
+project(Optimus VERSION ${OPTIMUS_VERSION})
+
 # required standard
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
@@ -171,9 +172,9 @@ else()
     message("SofaPardisoSolver not found, PardisoSolver component will not work")
 endif()
 
-target_include_directories(${PROJECT_NAME} PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")
+target_include_directories(${PROJECT_NAME} PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>")
 target_include_directories(${PROJECT_NAME} PUBLIC "$<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/include>")
-target_include_directories(${PROJECT_NAME} PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/..>")
+target_include_directories(${PROJECT_NAME} PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/src>")
 set_target_properties(${PROJECT_NAME} PROPERTIES VERSION "${OPTIMUS_VERSION}")
 set_target_properties(${PROJECT_NAME} PROPERTIES COMPILE_FLAGS "${COMPILATION_FLAGS}")
 set_target_properties(${PROJECT_NAME} PROPERTIES PUBLIC_HEADER "${HEADER_FILES}")
@@ -183,9 +184,26 @@ include_directories("${CMAKE_CURRENT_SOURCE_DIR}/src")
 get_target_property(compile_defs ${PROJECT_NAME} COMPILE_FLAGS)
 message(STATUS "Compile definitions: ${compile_defs}")
 
-install(TARGETS Optimus
-        EXPORT  OptimusTargets
-        RUNTIME DESTINATION bin
-        LIBRARY DESTINATION lib
-        ARCHIVE DESTINATION lib
-        PUBLIC_HEADER DESTINATION include/Optimus)
+
+# install rules
+if( CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT )
+    set(CMAKE_INSTALL_PREFIX ${CMAKE_BINARY_DIR}/install CACHE PATH "Install path prefix, prepended onto install directories." FORCE)
+endif()
+message(STATUS "Install prefix: ${CMAKE_INSTALL_PREFIX}")
+
+sofa_create_package_with_targets(
+    PACKAGE_NAME ${PROJECT_NAME}
+    PACKAGE_VERSION ${PROJECT_VERSION}
+    TARGETS ${PROJECT_NAME} AUTO_SET_TARGET_PROPERTIES
+    INCLUDE_SOURCE_DIR "src"
+    INCLUDE_INSTALL_DIR ${PROJECT_NAME}
+    EXAMPLE_INSTALL_DIR "examples"
+    RELOCATABLE "plugins"
+    )
+
+#install(TARGETS Optimus
+#        EXPORT  OptimusTargets
+#        RUNTIME DESTINATION bin
+#        LIBRARY DESTINATION lib
+#        ARCHIVE DESTINATION lib
+#        PUBLIC_HEADER DESTINATION include/Optimus)

OptimusConfig.cmake.in

@@ -0,0 +1,9 @@
+# Optimus plugin configuration file
+
+@PACKAGE_INIT@
+
+if(NOT TARGET @PROJECT_NAME@)
+	include("${CMAKE_CURRENT_LIST_DIR}/@[email protected]")
+endif()
+
+check_required_components(@PROJECT_NAME@)

benchmarks/assimBC_liver_geomagic_cutting_yaml/verify.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# == "2" ]; then
-        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+        SOFA_EXEC="$1 -l $2"
 elif [ $# == "1" ]; then
         SOFA_EXEC="$1 -l libSofaPython3.so"
 else

benchmarks/assimBC_liver_polynomial_springs_point_cloud_yaml/verify.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# == "2" ]; then
-        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+        SOFA_EXEC="$1 -l $2"
 elif [ $# == "1" ]; then
         SOFA_EXEC="$1 -l libSofaPython3.so"
 else

benchmarks/assimBC_synthBrick/verify.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# == "2" ]; then
-        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+        SOFA_EXEC="$1 -l $2"
 elif [ $# == "1" ]; then
         SOFA_EXEC="$1 -l libSofaPython3.so"
 else

benchmarks/assimStiffness_cylinder_UKFSimCorr_yaml/verify.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# == "2" ]; then
-        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+        SOFA_EXEC="$1 -l $2"
 elif [ $# == "1" ]; then
         SOFA_EXEC="$1 -l libSofaPython3.so"
 else

benchmarks/assimStiffness_cylinder_geomagic_yaml/verify.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# == "2" ]; then
-        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+        SOFA_EXEC="$1 -l $2"
 elif [ $# == "1" ]; then
         SOFA_EXEC="$1 -l libSofaPython3.so"
 else

benchmarks/assimStiffness_cylinder_python3_yaml/verify.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# == "2" ]; then
-        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+        SOFA_EXEC="$1 -l $2"
 elif [ $# == "1" ]; then
         SOFA_EXEC="$1 -l libSofaPython3.so"
 else

benchmarks/assimStiffness_cylinder_yaml/verify.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 if [ $# == "2" ]; then
-        SOFA_EXEC="$1 -l $2/libSofaPython3.so"
+        SOFA_EXEC="$1 -l $2"
 elif [ $# == "1" ]; then
         SOFA_EXEC="$1 -l libSofaPython3.so"
 else

benchmarks/crontask/runOptimusTests.sh

@@ -102,7 +102,7 @@ do
     cd $FOLDER
     if [ -f $FOLDER/verify.sh ]; then
         echo "Perform test: $FOLDER"
-        $FOLDER/verify.sh $BUILD_DIRECTORY/install/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        $FOLDER/verify.sh $BUILD_DIRECTORY/install/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib/libSofaPython3.so >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
     fi
 done
 echo "All tests have been executed"

benchmarks/crontask/runOptimusTests_without_compiling.sh

@@ -36,7 +36,7 @@ do
     cd $FOLDER
     if [ -f $FOLDER/verify.sh ]; then
         echo "Perform test: $FOLDER"
-        $FOLDER/verify.sh $BUILD_DIRECTORY/install/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
+        $FOLDER/verify.sh $BUILD_DIRECTORY/install/bin/runSofa $SOFA_PYTHON3_BUILD_DIRECTORY/lib/libSofaPython3.so >> $GENERAL_DIRECTORY/log_`/bin/date +"%Y_%m_%d"`.txt
     fi
 done
 echo "All tests have been executed"