merge the Master branch into the Main branch

SofaDefrost · Oct 21, 2023 · 2590b3a · 2590b3a
2 parents d39af29 + 635c963
commit 2590b3a
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,29 @@
+name: Build
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
+      - uses: sonarsource/sonarqube-scan-action@master
+        env:
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+          SONAR_HOST_URL: ${{ secrets.SONAR_HOST_URL }}
+      # If you wish to fail your job when the Quality Gate is red, uncomment the
+      # following lines. This would typically be used to fail a deployment.
+      # We do not recommend to use this in a pull request. Prefer using pull request
+      # decoration instead.
+      # - uses: sonarsource/sonarqube-quality-gate-action@master
+      #   timeout-minutes: 5
+      #   env:
+      #     SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -54,7 +54,7 @@ jobs:
           SofaPython3_ROOT="$GITHUB_WORKSPACE/SofaPython3"
           mkdir -p "${{ runner.temp }}/sp3_tmp/zip" "${{ runner.temp }}/sp3_tmp/binaries" "$SofaPython3_ROOT"
           url="https://github.com/sofa-framework/SofaPython3/releases/download"
-          url="${url}/release-master-nightly/SofaPython3_master-nightly_python-${{ matrix.python_version }}_for-SOFA-${{ matrix.sofa_branch }}_${{ runner.os }}.zip"
+          url="${url}/release-${{ matrix.sofa_branch }}/SofaPython3_${{ matrix.sofa_branch }}_python-${{ matrix.python_version }}_for-SOFA-${{ matrix.sofa_branch }}_${{ runner.os }}.zip"
           echo "Getting SofaPython3 from $url"
           curl --output "${{ runner.temp }}/sp3_tmp/SofaPython3.zip" -L $url
           unzip -qq "${{ runner.temp }}/sp3_tmp/SofaPython3.zip" -d "${{ runner.temp }}/sp3_tmp/binaries"
@@ -168,7 +168,9 @@ jobs:
           with:
             name: ${{ github.ref_name }}
             tag_name: release-${{ github.ref_name }}
-            fail_on_unmatched_files: true 
+            fail_on_unmatched_files: false
+            target_commitish: ${{ github.ref_name }}
             files: |
               artifacts/CosseratPlugin_*_Linux.zip
               artifacts/CosseratPlugin_*_Windows.zip
+              artifacts/CosseratPlugin_*_macOS.zip
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.12)
-project(CosseratPlugin VERSION 21.12.0)
+project(Cosserat VERSION 21.12.0)
 
 include(cmake/environment.cmake)
 
@@ -47,7 +47,7 @@ set(HEADER_FILES
     ${SRC_ROOT_DIR}/constraint/CosseratNeedleSlidingConstraint.inl
     )
 set(SOURCE_FILES
-    ${SRC_ROOT_DIR}/initCosseratPlugin.cpp
+    ${SRC_ROOT_DIR}/initCosserat.cpp
     ${SRC_ROOT_DIR}/mapping/BaseCosserat.cpp
     ${SRC_ROOT_DIR}/mapping/DiscreteCosseratMapping.cpp
     ${SRC_ROOT_DIR}/mapping/DiscreteDynamicCosseratMapping.cpp
@@ -122,7 +122,7 @@ if(SofaPython3Tools OR SofaPython3_FOUND)
     add_subdirectory(${SRC_ROOT_DIR}/Binding)
 endif()
 
-#add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/src/CosseratPlugin/Binding)
+
 
 ## Install rules for the library and headers; CMake package configurations files
 sofa_create_package_with_targets(
@@ -131,14 +131,19 @@ sofa_create_package_with_targets(
     TARGETS ${PROJECT_NAME} AUTO_SET_TARGET_PROPERTIES
     INCLUDE_SOURCE_DIR "src"
     INCLUDE_INSTALL_DIR ${PROJECT_NAME}
+    EXAMPLE_INSTALL_DIR "examples"
     RELOCATABLE "plugins"
     )
 
+
 # Tests
 # If SOFA_BUILD_TESTS exists and is OFF, then these tests will be auto-disabled
-cmake_dependent_option(COSSERATPLUGIN_BUILD_TESTS "Compile the tests" ON "SOFA_BUILD_TESTS OR NOT DEFINED SOFA_BUILD_TESTS" OFF)
-if(COSSERATPLUGIN_BUILD_TESTS)
+cmake_dependent_option(COSSERAT_BUILD_TESTS "Compile the tests" ON "SOFA_BUILD_TESTS OR NOT DEFINED SOFA_BUILD_TESTS" OFF)
+if(COSSERAT_BUILD_TESTS)
     add_subdirectory(Tests)
 endif()
 
+# Config files and install rules for pythons scripts
+sofa_install_pythonscripts(PLUGIN_NAME ${PROJECT_NAME} PYTHONSCRIPTS_SOURCE_DIR "examples/python3/")
+
 include(cmake/packaging.cmake)
diff --git a/CosseratPluginConfig.cmake.in → CosseratConfig.cmake.in b/CosseratPluginConfig.cmake.in → CosseratConfig.cmake.in
diff --git a/Tests/CMakeLists.txt b/Tests/CMakeLists.txt
@@ -4,7 +4,7 @@ set(This Cosserat_test)
 
 project(${This} C CXX)
 
-#find_package(CosseratPlugin REQUIRED)
+#find_package(Cosserat REQUIRED)
 find_package(Sofa.Testing REQUIRED)
 
 enable_testing()
@@ -25,7 +25,7 @@ add_executable(${This} ${SOURCE_FILES} ${HEADER_FILES})
 
 target_link_libraries(${PROJECT_NAME} 
         Sofa.Testing
-        CosseratPlugin
+        Cosserat
 )
 
 target_include_directories(${This} 

diff --git a/Tests/constraint/CMakeLists.txt b/Tests/constraint/CMakeLists.txt
@@ -13,7 +13,7 @@ target_link_libraries(${This} PUBLIC
         SofaTest 
         gtest 
         gtest_main 
-        CosseratPlugin
+        Cosserat
         Example
 )
 

diff --git a/Tests/constraint/CosseratUnilateralInteractionConstraintTest.cpp b/Tests/constraint/CosseratUnilateralInteractionConstraintTest.cpp
@@ -50,7 +50,7 @@ struct CosseratUnilateralInteractionConstraintTest : public NumericTest<>
         x = new int(42);
 
         sofa::simpleapi::importPlugin("Sofa.Component");
-        sofa::simpleapi::importPlugin("CosseratPlugin");
+        sofa::simpleapi::importPlugin("Cosserat");
 
         //create the context for
         if(simulation==nullptr)

diff --git a/Tests/forcefield/BeamHookeLawForceFieldTest.cpp b/Tests/forcefield/BeamHookeLawForceFieldTest.cpp
@@ -2,7 +2,7 @@
 // Created by younes on 07/06/2021.
 //
 
-#include <CosseratPlugin/config.h>
+#include <Cosserat/config.h>
 
 #include <gtest/gtest.h>
 #include <sofa/testing/BaseTest.h>
@@ -18,7 +18,7 @@
 #include <sofa/core/behavior/ForceField.inl>
 #include <sofa/helper/system/PluginManager.h>
 
-#include <CosseratPlugin/forcefield/BeamHookeLawForceField.inl>
+#include <Cosserat/forcefield/BeamHookeLawForceField.inl>
 #include <sofa/testing/NumericTest.h>
 
 using sofa::testing::BaseTest ;
@@ -45,11 +45,7 @@ struct BeamHookeLawForceFieldTest : public testing::NumericTest<> {
         // initialization or some code to run before each test
         fprintf(stderr, "Starting up ! \n");
         sofa::simpleapi::importPlugin("Sofa.Component");
-        sofa::simpleapi::importPlugin("CosseratPlugin");
-
-        //create the context for
-        if(simulation==nullptr)
-            sofa::simulation::setSimulation(simulation = new sofa::simulation::graph::DAGSimulation());
+        sofa::simpleapi::importPlugin("Cosserat");
     }
 
     // Tears down the test fixture.
@@ -58,7 +54,7 @@ struct BeamHookeLawForceFieldTest : public testing::NumericTest<> {
         // can be used instead of a destructor,
         // but exceptions can be handled in this function only
         if(root) {
-            simulation->unload(root);
+            sofa::simulation::node::unload(root);
         }
         fprintf(stderr, "Starting down ! \n");
     }
@@ -105,8 +101,6 @@ struct BeamHookeLawForceFieldTest : public testing::NumericTest<> {
 protected:
     ///< Root of the scene graph, created by the constructor an re-used in the tests
     simulation::Node::SPtr root;
-    ///< created by the constructor an re-used in the tests
-    simulation::Simulation* simulation {nullptr};
 
     void testFonctionnel();
 };
@@ -131,10 +125,9 @@ void BeamHookeLawForceFieldTest<defaulttype::Vec3Types>::testFonctionnel() {
     EXPECT_NE(root.get(), nullptr) ;
     root->init(sofa::core::execparams::defaultInstance()) ;
 
-    Simulation* simulation = sofa::simulation::getSimulation() ;
     auto total_load = dynamic_cast<sofa::core::objectmodel::Data<double> *>(traction->findData("lengthY"));
     for (unsigned int step = 1; step <= 5; ++step) {
-        simulation->animate(root.get(), 1);
+        sofa::simulation::node::animate(root.get(), 1);
         EXPECT_DOUBLE_EQ(total_load->getValue(), 4*step) << "Total load at time step " << step << " is incorrect.";
     }
 }
@@ -176,10 +169,8 @@ void BeamHookeLawForceFieldTest<defaulttype::Vec3Types>::basicAttributesTest(){
         << "Missing attribute with name '"
         << attrname << "'." ;
 
-    Simulation* simulation = sofa::simulation::getSimulation() ;
-    ASSERT_NE(nullptr, simulation) ;
     for(int i=0; i<10; i++){
-        simulation->animate(root.get(),(double)0.01);
+        sofa::simulation::node::animate(root.get(),(double)0.01);
     }
 }
 

diff --git a/examples/python3/NeedleInsertion-predefinedPath.html b/examples/python3/NeedleInsertion-predefinedPath.html
@@ -0,0 +1,24 @@
+<html>
+<head>
+<link href="../../../../share/sofa/examples/Objects/sofa_white.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+	<div id="contenu">			        
+		<center><h3>Cosserat plugin: needle insertion </h3></center>
+		<br>	
+	<div id="orangeText">Instruments control</div>
+	<br>
+	<div align="controler">
+	You can use the keyboard to move the needle (arrow keys):
+	<ul>
+		<li>ctrl + up: move up the needle</li>
+		<li>ctrl + down: move down the needle</li>
+		<li>ctrl + right: move towards the deformable gel (forward insertion)</li>
+		<li>ctrl + left: move away from the deformable gel (backward insertion)</li>
+	</ul>
+    <br>
+
+	</div>
+</div>
+</body>
+</html>
diff --git a/...n3/cosserat/needle/CosserateLikeNeedle.py → ...python3/NeedleInsertion-predefinedPath.py b/...n3/cosserat/needle/CosserateLikeNeedle.py → ...python3/NeedleInsertion-predefinedPath.py
@@ -8,6 +8,8 @@
 import sys
 sys.path.append('../')
 from cosserat.createFemRegularGrid import createFemCube
+from cosserat.usefulFunctions import pluginList
+
 __authors__ = "younesssss"
 __contact__ = "[email protected], [email protected]"
 __version__ = "1.0.0"
@@ -23,10 +25,6 @@
 
 path = os.path.dirname(os.path.abspath(__file__))+'/../mesh/'
 
-pluginNameList = 'SofaConstraint SofaDeformable SofaImplicitOdeSolver SofaMeshCollision SofaPreconditioner' \
-                 ' SofaGeneralTopology SofaOpenglVisual SofaGeneralRigid SoftRobots SofaSparseSolver' \
-                 ' CosseratPlugin SofaBoundaryCondition'
-
 
 class Animation(Sofa.Core.Controller):
 
@@ -93,8 +91,7 @@ def onKeypressedEvent(self, event):
 
 
 def createScene(rootNode):
-    rootNode.addObject(
-        'RequiredPlugin', pluginName=pluginNameList, printLog='0')
+    rootNode.addObject('RequiredPlugin', name='plugins', pluginName=[pluginList])
 
     rootNode.addObject('VisualStyle', displayFlags='showBehaviorModels hideCollisionModels hideBoundingCollisionModels '
                                                    'showForceFields hideInteractionForceFields showWireframe')

diff --git a/examples/python3/NeedleInsertion.html b/examples/python3/NeedleInsertion.html
@@ -0,0 +1,24 @@
+<html>
+<head>
+<link href="../../../../share/sofa/examples/Objects/sofa_white.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+	<div id="contenu">			        
+		<center><h3>Cosserat plugin: needle insertion </h3></center>
+		<br>	
+	<div id="orangeText">Instruments control</div>
+	<br>
+	<div align="controler">
+	You can use the keyboard to move the needle (arrow keys):
+	<ul>
+		<li>ctrl + up: move up the needle</li>
+		<li>ctrl + down: move down the needle</li>
+		<li>ctrl + right: move towards the deformable gel (forward insertion)</li>
+		<li>ctrl + left: move away from the deformable gel (backward insertion)</li>
+	</ul>
+    <br>
+
+	</div>
+</div>
+</body>
+</html>
diff --git a/...osserat/needle/needleTissueInteraction.py → examples/python3/NeedleInsertion.py b/...osserat/needle/needleTissueInteraction.py → examples/python3/NeedleInsertion.py
@@ -5,7 +5,7 @@
 """
 
 from cosserat.needle.needleController import Animation
-from params import NeedleParameters, GeometryParams, PhysicsParams, FemParams, ContactParams
+from cosserat.needle.params import NeedleParameters, GeometryParams, PhysicsParams, FemParams, ContactParams
 from cosserat.usefulFunctions import pluginList
 from cosserat.createFemRegularGrid import createFemCubeWithParams
 from cosserat.cosseratObject import Cosserat
@@ -23,13 +23,13 @@
 
 
 def createScene(rootNode):
-    rootNode.addObject(
-        'RequiredPlugin', pluginName=pluginList, printLog='0')
+
+    rootNode.addObject('RequiredPlugin', name='plugins', pluginName=[pluginList])
 
     rootNode.addObject('VisualStyle', displayFlags='showVisualModels showBehaviorModels hideCollisionModels '
                                                    'hideBoundingCollisionModels hideForceFields '
                                                    'hideInteractionForceFields hideWireframe showMechanicalMappings')
-    rootNode.addObject('DefaultPipeline')
+    rootNode.addObject('CollisionPipeline')
     rootNode.addObject("DefaultVisualManagerLoop")
     rootNode.addObject('RuleBasedContactManager',
                        responseParams='mu=0.1', response='FrictionContactConstraint')
@@ -54,8 +54,7 @@ def createScene(rootNode):
     solverNode = rootNode.addChild('solverNode')
     solverNode.addObject('EulerImplicitSolver',
                          rayleighStiffness=PhysicsParams.rayleighStiffness)
-    solverNode.addObject('SparseLDLSolver', name='solver',
-                         template="CompressedRowSparseMatrixd")
+    solverNode.addObject('SparseLDLSolver', name='solver', template="CompressedRowSparseMatrixd")
     solverNode.addObject('GenericConstraintCorrection')
 
     needle = solverNode.addChild(

diff --git a/python3/cosserat/examples/PCS_Example1.py → examples/python3/PCS_Example1.py b/python3/cosserat/examples/PCS_Example1.py → examples/python3/PCS_Example1.py
@@ -26,7 +26,7 @@
 firstOrder = 1
 
 EI = 1.e2
-coeff = 0
+coeff = 1
 
 F1 = [0., 0., 0., 0., (coeff*1.)/sqrt(2), (coeff*1.)/sqrt(2)]  # N
 
@@ -50,7 +50,6 @@ def __init__(self, *args, **kwargs):
         self.size = nonLinearConfig['nbFramesF']
         self.applyForce = True
         self.forceCoeff = coeff
-        # self.cosseratGeometry = kwargs['cosseratGeometry']
 
     def onAnimateEndEvent(self, event):
         if self.applyForce:
@@ -59,7 +58,6 @@ def onAnimateEndEvent(self, event):
                        sqrt(2), (self.forceCoeff * 1.) / sqrt(2)]
                 for i, v in enumerate(vec):
                     force[i] = v
-                # print(f' The new force: {force}')
 
     def onKeypressedEvent(self, event):
         key = event['key']
@@ -72,25 +70,19 @@ def onKeypressedEvent(self, event):
 
 
 def createScene(rootNode):
-    rootNode.addObject('RequiredPlugin', name='plugins', pluginName=[pluginList,
-                                                                     ['SofaEngine', 'SofaLoader', 'SofaSimpleFem',
-                                                                      'SofaExporter']])
+    rootNode.addObject('RequiredPlugin', name='plugins', pluginName=[pluginList])
     rootNode.addObject('VisualStyle', displayFlags='showVisualModels showBehaviorModels hideCollisionModels '
                                                    'hideBoundingCollisionModels hideForceFields '
                                                    'hideInteractionForceFields hideWireframe showMechanicalMappings')
-    rootNode.findData('dt').value = deltaT
-    # rootNode.findData('gravity').value = [0., -9.81, 0.]
-    rootNode.findData('gravity').value = [0., 0., 0.]
-    # rootNode.addObject('BackgroundSetting', color='0 0.168627 0.211765')
-    # rootNode.addObject('FreeMotionAnimationLoop')
-    # rootNode.addObject('GenericConstraintSolver', tolerance=1e-5, maxIterations=5e2)
+    rootNode.dt.value = deltaT
+    rootNode.gravity.value = [0., 0., 0.]
+
     rootNode.addObject('Camera', position="-35 0 280", lookAt="0 0 0")
+    rootNode.addObject('DefaultAnimationLoop')
 
     solverNode = rootNode.addChild('solverNode')
     solverNode.addObject('EulerImplicitSolver', rayleighStiffness=rayleighStiffness, rayleighMass='0.',
                          firstOrder=firstOrder)
-    # solverNode.addObject('SparseLDLSolver', name='solver',
-    #                      template="CompressedRowSparseMatrixd")
     solverNode.addObject('CGLinearSolver', tolerance=1.e-12, iterations=1000, threshold=1.e-18)
 
     # use this if the collision model if the beam will interact with another object