Merge pull request #140 from epernod/v22.06

Fix headers includes and namespaces to follow changes in SOFA

.github/workflows/macos.yml

@@ -145,11 +145,17 @@ jobs:
         run:  |
           if [ "$SOFA_VERSION" = "master" ]; then
               curl --output sofa.zip -L "https://ci.inria.fr/sofa-ci-dev/job/nightly-generate-binaries/CI_BRANCH=master,CI_SCOPE=standard/lastSuccessfulBuild/artifact/MacOS/*zip*/MacOS.zip"
+              unzip sofa.zip -d temp
+              mv temp/MacOS/`ls temp/MacOS` sofa.zip
+              rm -rf temp
+              unzip sofa.zip -d temp
+              mv temp/`ls temp` $SOFA_ROOT
           else
               curl --output sofa.zip -L "https://github.com/sofa-framework/sofa/releases/download/$SOFA_VERSION/SOFA_"$SOFA_VERSION"_MacOS.zip"
+              unzip sofa.zip -d temp
+              sudo mv temp/`ls temp` $SOFA_ROOT
           fi
-          unzip sofa.zip -d temp
-          sudo mv temp/`ls temp` $SOFA_ROOT
+
 
 
 #     CCACHE

.github/workflows/ubuntu.yml

@@ -22,22 +22,27 @@ jobs:
             SOFA_VERSION_I: 999999
             CONTAINER: jnbrunet/caribou-ubuntu-2004-builder:latest
             PYTHON_VERSION: 3.8
+            PYBIND11_VERSION: 2.6
           - sofa_version: v21.12.00
             SOFA_VERSION_I: 211200
             CONTAINER: jnbrunet/caribou-ubuntu-2004-builder:latest
             PYTHON_VERSION: 3.8
+            PYBIND11_VERSION: 2.4
           - sofa_version: v21.06.03
             SOFA_VERSION_I: 210603
             CONTAINER: jnbrunet/caribou-ubuntu-1804-builder:latest
             PYTHON_VERSION: 3.7
+            PYBIND11_VERSION: 2.4
           - sofa_version: v20.12.03
             SOFA_VERSION_I: 201203
             CONTAINER: jnbrunet/caribou-ubuntu-1804-builder:latest
             PYTHON_VERSION: 3.7
+            PYBIND11_VERSION: 2.4
           - sofa_version: v20.06.01
             SOFA_VERSION_I: 200601
             CONTAINER: jnbrunet/caribou-ubuntu-1804-builder:latest
             PYTHON_VERSION: 3.7
+            PYBIND11_VERSION: 2.4
     env:
       SOFA_VERSION: ${{ matrix.sofa_version }}
       SOFA_ROOT: /opt/sofa
@@ -54,6 +59,14 @@ jobs:
           git fetch origin
           git rebase origin/master
 
+      - name: Install pybind11
+        if: ${{ matrix.PYBIND11_VERSION != '2.4' }}
+        run: |
+          git clone --depth 1 -b v${{ matrix.PYBIND11_VERSION }}  https://github.com/pybind/pybind11.git /tmp/pybind11
+          cmake -GNinja -S/tmp/pybind11 -B/tmp/pybind11/build -DPYBIND11_TEST=OFF -DCMAKE_BUILD_TYPE=Release
+          cmake --install /tmp/pybind11/build
+          rm -rf /tmp/pybind11
+
       - name: Download SOFA Release
         run:  |
           if [ "$SOFA_VERSION" = "master" ]; then
@@ -217,6 +230,8 @@ jobs:
         if: ${{ always() }}
         run: |
             [ "$SOFA_VERSION" = "v20.06.01" ] && export LD_LIBRARY_PATH="$SOFA_ROOT/lib:$LD_LIBRARY_PATH"
+            export LD_LIBRARY_PATH="$SOFA_ROOT/collections/SofaBaseMechanics/lib:$LD_LIBRARY_PATH"
+            export LD_LIBRARY_PATH="$SOFA_ROOT/collections/SofaBaseUtils/lib:$LD_LIBRARY_PATH"
             $CARIBOU_ROOT/bin/Caribou.unittests.SofaCaribou
 
       - name: SofaCaribou.PyTest

Benchmark/SofaCaribou/Forcefield/RecomputeOrStore/HyperelasticForcefieldRecomputeF.h

@@ -17,7 +17,7 @@
 #include <SofaCaribou/Topology/CaribouTopology.h>
 
 DISABLE_ALL_WARNINGS_BEGIN
-#include <sofa/defaulttype/BaseMatrix.h>
+#include <SofaCaribou/Algebra/BaseMatrixOperations.h>
 DISABLE_ALL_WARNINGS_END
 
 #if (defined(SOFA_VERSION) && SOFA_VERSION < 201200)
@@ -101,7 +101,7 @@ class HyperelasticForcefieldRecomputeF : public ::SofaCaribou::forcefield::Carib
         const sofa::core::objectmodel::Data<VecCoord>& /* d_x */) const override;
 
 
-    void addKToMatrix(sofa::defaulttype::BaseMatrix * /*matrix*/, SReal /*kFact*/, unsigned int & /*offset*/) override;
+    void addKToMatrix(SofaCaribou::Algebra::BaseMatrix * /*matrix*/, SReal /*kFact*/, unsigned int & /*offset*/) override;
 
     /** Get the set of Gauss integration nodes of an element */
     inline auto gauss_nodes_of(std::size_t element_id) const -> const auto & {

Benchmark/SofaCaribou/Forcefield/RecomputeOrStore/HyperelasticForcefieldRecomputeF.inl

@@ -214,7 +214,7 @@ void HyperelasticForcefieldRecomputeF<Element>::addDForce(
 
 template <typename Element>
 void HyperelasticForcefieldRecomputeF<Element>::addKToMatrix(
-    sofa::defaulttype::BaseMatrix * matrix,
+    SofaCaribou::Algebra::BaseMatrix * matrix,
     SReal kFact, unsigned int & offset)
 {
     if (not K_is_up_to_date) {

Benchmark/SofaCaribou/Forcefield/RecomputeOrStore/HyperelasticForcefieldStoreF.h

@@ -6,6 +6,7 @@
 #include <SofaCaribou/config.h>
 #include <SofaCaribou/Material/HyperelasticMaterial.h>
 #include <SofaCaribou/Forcefield/CaribouForcefield.h>
+#include <SofaCaribou/Algebra/BaseMatrixOperations.h>
 
 #include <Caribou/config.h>
 #include <Caribou/constants.h>
@@ -98,7 +99,7 @@ class HyperelasticForcefieldStoreF : public ::SofaCaribou::forcefield::CaribouFo
         const sofa::core::objectmodel::Data<VecCoord>& /* d_x */) const override;
 
 
-    void addKToMatrix(sofa::defaulttype::BaseMatrix * /*matrix*/, SReal /*kFact*/, unsigned int & /*offset*/) override;
+    void addKToMatrix(SofaCaribou::Algebra::BaseMatrix * /*matrix*/, SReal /*kFact*/, unsigned int & /*offset*/) override;
 
     /** Get the set of Gauss integration nodes of an element */
     auto gauss_nodes_of(std::size_t element_id) const -> const auto & {

Benchmark/SofaCaribou/Forcefield/RecomputeOrStore/HyperelasticForcefieldStoreF.inl

@@ -215,7 +215,7 @@ void HyperelasticForcefieldStoreF<Element>::addDForce(
 
 template <typename Element>
 void HyperelasticForcefieldStoreF<Element>::addKToMatrix(
-    sofa::defaulttype::BaseMatrix * matrix,
+    SofaCaribou::Algebra::BaseMatrix * matrix,
     SReal kFact, unsigned int & offset)
 {
     if (not K_is_up_to_date) {

Benchmark/SofaCaribou/Forcefield/RecomputeOrStore/HyperelasticForcefieldStoreFAndS.h

@@ -6,6 +6,7 @@
 #include <SofaCaribou/config.h>
 #include <SofaCaribou/Material/HyperelasticMaterial.h>
 #include <SofaCaribou/Forcefield/CaribouForcefield.h>
+#include <SofaCaribou/Algebra/BaseMatrixOperations.h>
 
 #include <Caribou/config.h>
 #include <Caribou/constants.h>
@@ -17,7 +18,7 @@
 #include <SofaCaribou/Topology/CaribouTopology.h>
 
 DISABLE_ALL_WARNINGS_BEGIN
-#include <sofa/defaulttype/BaseMatrix.h>
+#include <SofaCaribou/Algebra/BaseMatrixOperations.h>
 DISABLE_ALL_WARNINGS_END
 
 #if (defined(SOFA_VERSION) && SOFA_VERSION < 201200)
@@ -105,7 +106,7 @@ class HyperelasticForcefieldStoreFAndS : public ::SofaCaribou::forcefield::Carib
         const sofa::core::objectmodel::Data<VecCoord>& /* d_x */) const override;
 
 
-    void addKToMatrix(sofa::defaulttype::BaseMatrix * /*matrix*/, SReal /*kFact*/, unsigned int & /*offset*/) override;
+    void addKToMatrix(SofaCaribou::Algebra::BaseMatrix * /*matrix*/, SReal /*kFact*/, unsigned int & /*offset*/) override;
 
     /** Get the set of Gauss integration nodes of an element */
     auto gauss_nodes_of(std::size_t element_id) const -> const auto & {

Benchmark/SofaCaribou/Forcefield/RecomputeOrStore/HyperelasticForcefieldStoreFAndS.inl

@@ -214,7 +214,7 @@ void HyperelasticForcefieldStoreFAndS<Element>::addDForce(
 
 template <typename Element>
 void HyperelasticForcefieldStoreFAndS<Element>::addKToMatrix(
-    sofa::defaulttype::BaseMatrix * matrix,
+    SofaCaribou::Algebra::BaseMatrix * matrix,
     SReal kFact, unsigned int & offset)
 {
     if (not K_is_up_to_date) {

CMakeLists.txt

@@ -94,7 +94,9 @@ else()
 endif()
 
 # Python 3 option
-find_package(SofaPython3 QUIET)
+if (CARIBOU_WITH_SOFA)
+    sofa_find_package(SofaPython3 QUIET)
+endif()
 set(CMAKE_CXX_STANDARD 17)
 set(PYBIND11_FINDPYTHON ON)
 set(PYBIND11_PYTHON_VERSION 3)

cmake/FindSOFA.cmake

@@ -65,6 +65,9 @@ endif()
 # Compatibility layer
 set(SOFA_VERSION ${SofaFramework_VERSION})
 foreach(component ${SOFA_FIND_COMPONENTS})
+    if (SOFA_VERSION VERSION_LESS "22.06.99")
+        string(REGEX REPLACE "Sofa.Simulation.*" "SofaSimulation" component ${component})
+    endif()
     if (SOFA_VERSION VERSION_LESS "20.12.99")
         string(REGEX REPLACE "SofaSimpleFem|SofaRigid|SofaDeformable|SofaObjectInteraction|SofaMeshCollision|SofaEngine|SofaExplicitOdeSolver|SofaImplicitOdeSolver|SofaLoader" "SofaCommon" component ${component})
 

src/SofaCaribou/Algebra/BaseMatrixOperations.h

@@ -0,0 +1,26 @@
+#pragma once
+
+#include <SofaCaribou/config.h>
+
+// Various utilities to perform numerical operations on SOFA's BaseMatrix.
+DISABLE_ALL_WARNINGS_BEGIN
+#include <sofa/version.h> // for SOFA_VERSION
+DISABLE_ALL_WARNINGS_END
+
+#if (defined(SOFA_VERSION) && SOFA_VERSION < 211200)
+#include <sofa/defaulttype/BaseMatrix.h>
+#else
+#include <sofa/linearalgebra/BaseMatrix.h>
+#endif // (defined(SOFA_VERSION) && SOFA_VERSION < 211299)
+
+namespace SofaCaribou::Algebra
+{
+
+#if (defined(SOFA_VERSION) && SOFA_VERSION < 211200)
+using BaseMatrix = sofa::defaulttype::BaseMatrix;
+#else
+using BaseMatrix = sofa::linearalgebra::BaseMatrix;
+#endif // (defined(SOFA_VERSION) && SOFA_VERSION < 211299)
+
+
+} // namespace SofaCaribou::Algebra

src/SofaCaribou/Algebra/BaseVectorOperations.cpp

@@ -4,11 +4,10 @@
 DISABLE_ALL_WARNINGS_BEGIN
 #include <sofa/version.h>
 #if (defined(SOFA_VERSION) && SOFA_VERSION < 211299)
-#include <sofa/defaulttype/BaseVector.h>
+#include <SofaBaseLinearSolver/FullVector.h>
 #else
-#include <sofa/linearalgebra/BaseVector.h>
+#include <sofa/linearalgebra/FullVector.h>
 #endif // #if (defined(SOFA_VERSION) && SOFA_VERSION < 211299)
-#include <SofaBaseLinearSolver/FullVector.h>
 DISABLE_ALL_WARNINGS_END
 
 #if (defined(SOFA_VERSION) && SOFA_VERSION < 201200)
@@ -21,14 +20,20 @@ using Index = sofa::defaulttype::BaseVector::Index;
 namespace SofaCaribou::Algebra {
 
 namespace { // Anonymous
+#if (defined(SOFA_VERSION) && SOFA_VERSION < 211299)
+using namespace sofa::component::linearsolver;
+#else
+using namespace sofa::linearalgebra;
+#endif
+
 template <typename Real>
-auto to_full_vector(const sofa::defaulttype::BaseVector* v) -> const sofa::component::linearsolver::FullVector<Real> * {
-    return dynamic_cast<const sofa::component::linearsolver::FullVector<Real> *>(v);
+auto to_full_vector(const BaseVector* v) -> const FullVector<Real> * {
+    return dynamic_cast<const FullVector<Real> *>(v);
 }
 
 // Dot product between a SOFA full vector and any BaseVector
 template <typename ReturnValue, typename Real>
-ReturnValue dot(const sofa::component::linearsolver::FullVector<Real> * v1, const sofa::defaulttype::BaseVector * v2) {
+ReturnValue dot(const FullVector<Real> * v1, const BaseVector * v2) {
     const auto n = static_cast<sofa::Size>(v1->size());
     auto value = static_cast<ReturnValue>(0);
     for (sofa::Index i = 0; i < n; ++i) {
@@ -40,7 +45,7 @@ ReturnValue dot(const sofa::component::linearsolver::FullVector<Real> * v1, cons
 
 // Dot product between a two SOFA full vectors
 template <typename ReturnValue, typename Real1, typename Real2>
-ReturnValue dot(const sofa::component::linearsolver::FullVector<Real1> * v1, const sofa::component::linearsolver::FullVector<Real2> * v2) {
+ReturnValue dot(const FullVector<Real1> * v1, const FullVector<Real2> * v2) {
     const auto n = static_cast<sofa::Size>(v1->size());
     auto value = static_cast<ReturnValue>(0);
     for (sofa::Index i = 0; i < n; ++i) {
@@ -52,7 +57,7 @@ ReturnValue dot(const sofa::component::linearsolver::FullVector<Real1> * v1, con
 }
 
 /** Compute the dot product between two BaseVector, i.e. scalar = v1.dot(v2) */
- double dot(const sofa::defaulttype::BaseVector * v1, const sofa::defaulttype::BaseVector * v2) {
+ double dot(const BaseVector * v1, const BaseVector * v2) {
     caribou_assert(v1->size() == v2->size());
 
     // todo(jnbrunet2000@gmail.com): This function is awful. I'm sure there is a much much cleaner and faster way
@@ -119,4 +124,4 @@ ReturnValue dot(const sofa::component::linearsolver::FullVector<Real1> * v1, con
     return static_cast<double> (value);
 }
 
-} // namespace SofaCaribou::Algebra
+} // namespace SofaCaribou::Algebra

src/SofaCaribou/Algebra/BaseVectorOperations.h

@@ -10,20 +10,18 @@ DISABLE_ALL_WARNINGS_BEGIN
 DISABLE_ALL_WARNINGS_END
 
 #if (defined(SOFA_VERSION) && SOFA_VERSION < 211200)
-namespace sofa::defaulttype {
-    class BaseVector;
-}
+#include <sofa/defaulttype/BaseVector.h>
 #else
-namespace sofa::linearalgebra {
-    class BaseVector;
-}
-namespace sofa::defaulttype {
-    using BaseVector = sofa::linearalgebra::BaseVector;
-}
+#include <sofa/linearalgebra/BaseVector.h>
 #endif // (defined(SOFA_VERSION) && SOFA_VERSION < 211299)
 
 namespace SofaCaribou::Algebra {
 
+#if (defined(SOFA_VERSION) && SOFA_VERSION < 211200)
+using BaseVector = sofa::defaulttype::BaseVector;
+#else
+using BaseVector = sofa::linearalgebra::BaseVector;
+#endif
 
 /**
  * Compute the dot product between two BaseVector, i.e. scalar = v1.dot(v2) *
@@ -33,6 +31,6 @@ namespace SofaCaribou::Algebra {
  *                                  simply reuse this callback. Hence we avoid the need to do multiple virtual checks
  *                                  each time this function is called
  */
- double dot(const sofa::defaulttype::BaseVector * v1, const sofa::defaulttype::BaseVector * v2);
+ double dot(const BaseVector * v1, const BaseVector * v2);
 
-} // namespace SofaCaribou::Algebra
+} // namespace SofaCaribou::Algebra

src/SofaCaribou/Algebra/EigenMatrix.h

@@ -5,7 +5,7 @@
 
 DISABLE_ALL_WARNINGS_BEGIN
 #include <sofa/version.h>
-#include <sofa/defaulttype/BaseMatrix.h>
+#include <SofaCaribou/Algebra/BaseMatrixOperations.h>
 DISABLE_ALL_WARNINGS_END
 
 #if (defined(SOFA_VERSION) && SOFA_VERSION < 201200)
@@ -68,7 +68,7 @@ namespace SofaCaribou::Algebra {
  * \endcode
  */
 template <typename Derived, typename Enable = void>
-class EigenMatrix : public sofa::defaulttype::BaseMatrix
+class EigenMatrix : public BaseMatrix
 {
     static_assert(
         std::is_base_of_v<Eigen::EigenBase<std::decay_t<Derived> >, std::decay_t<Derived> >,
@@ -77,7 +77,7 @@ class EigenMatrix : public sofa::defaulttype::BaseMatrix
 
 public:
     using EigenType = std::remove_cv_t<std::remove_reference_t<Derived>>;
-    using Base = sofa::defaulttype::BaseMatrix;
+    using Base = BaseMatrix;
     using Index = Base::Index;
     using Real = SReal;
     using Scalar = typename EigenType::Scalar;
@@ -168,12 +168,12 @@ class EigenMatrix : public sofa::defaulttype::BaseMatrix
 /// SparseMatrix specialization ///
 ///////////////////////////////////
 template <typename Derived>
-class EigenMatrix<Derived, CLASS_REQUIRES(std::is_base_of_v<Eigen::SparseMatrixBase<std::decay_t<Derived>>, std::decay_t<Derived>>)> : public sofa::defaulttype::BaseMatrix
+class EigenMatrix<Derived, CLASS_REQUIRES(std::is_base_of_v<Eigen::SparseMatrixBase<std::decay_t<Derived>>, std::decay_t<Derived>>)> : public BaseMatrix
 {
 
 public:
     using EigenType = std::remove_cv_t<std::remove_reference_t<Derived>>;
-    using Base = sofa::defaulttype::BaseMatrix;
+    using Base = BaseMatrix;
     using Index = Base::Index;
     using Real = SReal;
     using Scalar = typename EigenType::Scalar;

src/SofaCaribou/Algebra/EigenVector.h

@@ -5,8 +5,8 @@
 #include <Caribou/traits.h>
 
 DISABLE_ALL_WARNINGS_BEGIN
-#include <sofa/defaulttype/BaseMatrix.h>
-#include <sofa/defaulttype/BaseVector.h>
+#include <SofaCaribou/Algebra/BaseMatrixOperations.h>
+#include <SofaCaribou/Algebra/BaseVectorOperations.h>
 DISABLE_ALL_WARNINGS_END
 
 #include <Eigen/Dense>
@@ -23,7 +23,7 @@ namespace SofaCaribou::Algebra {
  * @tparam Enable
  */
 template <typename Derived, typename Enable = void>
-class EigenVector : public sofa::defaulttype::BaseVector
+class EigenVector : public BaseVector
 {
     static_assert(
             std::is_base_of_v<Eigen::EigenBase<std::decay_t<Derived> >, std::decay_t<Derived> >,
@@ -38,7 +38,7 @@ class EigenVector : public sofa::defaulttype::BaseVector
 
 public:
     using EigenType = std::remove_cv_t<std::remove_reference_t<Derived>>;
-    using Base = sofa::defaulttype::BaseVector;
+    using Base = BaseVector;
     using Index = Base::Index;
     using Real = typename EigenType::Scalar;
 

src/SofaCaribou/CMakeLists.txt

@@ -4,6 +4,7 @@ set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
 
 set(HEADER_FILES
     config.h.in
+    Algebra/BaseMatrixOperations.h
     Algebra/BaseVectorOperations.h
     Algebra/EigenMatrix.h
     Algebra/EigenVector.h