[misc] Upgrade C++ and python dependencies.

.github/workflows/linux.yml

@@ -66,17 +66,19 @@ jobs:
         sudo apt install -y gdb gnupg curl wget build-essential cmake doxygen graphviz texlive-latex-base
 
         "${PYTHON_EXECUTABLE}" -m pip install setuptools wheel "pip>=20.3"
-        "${PYTHON_EXECUTABLE}" -m pip install "numpy>=1.23,<2.0"
 
         git config --global advice.detachedHead false
-    - name: Build jiminy dependencies
-      run: |
-        BUILD_TYPE="${{ matrix.BUILD_TYPE }}" ./build_tools/build_install_deps_unix.sh
     - name: Install pre-compiled binaries for additional gym-jiminy dependencies
       if: matrix.PYTHON_VERSION != '3.13'
       run: |
         "${PYTHON_EXECUTABLE}" -m pip install "torch" -f https://download.pytorch.org/whl/torch
         "${PYTHON_EXECUTABLE}" -m pip install "gymnasium>=0.28,<1.0" "stable_baselines3>=2.0"
+    - name: Install latest numpy version at build-time for run-time binary compatibility
+      run: |
+        "${PYTHON_EXECUTABLE}" -m pip install --pre --upgrade "numpy>=1.23,<2.1"
+    - name: Build jiminy dependencies
+      run: |
+        BUILD_TYPE="${{ matrix.BUILD_TYPE }}" ./build_tools/build_install_deps_unix.sh
 
     #####################################################################################
 

.github/workflows/macos.yml

@@ -68,17 +68,19 @@ jobs:
         echo "InstallDir=${GITHUB_WORKSPACE}/install" >> $GITHUB_ENV
 
         "${PYTHON_EXECUTABLE}" -m pip install setuptools wheel "pip>=20.3"
-        "${PYTHON_EXECUTABLE}" -m pip install "numpy>=1.23,<2.0"
         "${PYTHON_EXECUTABLE}" -m pip install delocate twine
-    - name: Build jiminy dependencies
-      run: |
-        OSX_DEPLOYMENT_TARGET=${OSX_DEPLOYMENT_TARGET} OSX_ARCHITECTURES=${OSX_ARCHITECTURES} \
-          BUILD_TYPE="${{ matrix.BUILD_TYPE }}" ./build_tools/build_install_deps_unix.sh
     - name: Install pre-compiled binaries for additional gym-jiminy dependencies
       if: matrix.PYTHON_VERSION != '3.13'
       run: |
         "${PYTHON_EXECUTABLE}" -m pip install "torch" -f https://download.pytorch.org/whl/torch
         "${PYTHON_EXECUTABLE}" -m pip install "gymnasium>=0.28,<1.0" "stable_baselines3>=2.0"
+    - name: Install latest numpy version at build-time for run-time binary compatibility
+      run: |
+        "${PYTHON_EXECUTABLE}" -m pip install --pre --upgrade "numpy>=1.23,<2.1"
+    - name: Build jiminy dependencies
+      run: |
+        OSX_DEPLOYMENT_TARGET=${OSX_DEPLOYMENT_TARGET} OSX_ARCHITECTURES=${OSX_ARCHITECTURES} \
+          BUILD_TYPE="${{ matrix.BUILD_TYPE }}" ./build_tools/build_install_deps_unix.sh
 
     #####################################################################################
 

.github/workflows/manylinux.yml

@@ -62,8 +62,10 @@ jobs:
         echo "InstallDir=${GITHUB_WORKSPACE}/install" >> $GITHUB_ENV
 
         "${PYTHON_EXECUTABLE}" -m pip install setuptools wheel "pip>=20.3"
-        "${PYTHON_EXECUTABLE}" -m pip install "numpy>=1.23,<2.0"
         "${PYTHON_EXECUTABLE}" -m pip install twine cmake
+    - name: Install latest numpy version at build-time for run-time binary compatibility
+      run: |
+        "${PYTHON_EXECUTABLE}" -m pip install --pre --upgrade "numpy>=1.23,<2.1"
     - name: Build project dependencies
       run: |
         ./build_tools/build_install_deps_unix.sh

.github/workflows/win.yml

@@ -56,17 +56,19 @@ jobs:
       run: |
         git config --global advice.detachedHead false
         python -m pip install setuptools wheel "pip>=20.3"
-        python -m pip install "numpy>=1.23,<2.0"
         python -m pip install pefile machomachomangler
-    - name: Build jiminy dependencies
-      run: |
-        ${env:BUILD_TYPE} = "${{ matrix.BUILD_TYPE }}"
-        & "./workspace/build_tools/build_install_deps_windows.ps1"
     - name: Install pre-compiled binaries for additional gym-jiminy dependencies
       if: matrix.PYTHON_VERSION != '3.13'
       run: |
         python -m pip install "torch" -f https://download.pytorch.org/whl/torch
         python -m pip install "gymnasium>=0.28,<1.0" "stable_baselines3>=2.0"
+    - name: Install latest numpy version at build-time for run-time binary compatibility
+      run: |
+        python -m pip install --pre --upgrade "numpy>=1.23,<2.1"
+    - name: Build jiminy dependencies
+      run: |
+        ${env:BUILD_TYPE} = "${{ matrix.BUILD_TYPE }}"
+        & "./workspace/build_tools/build_install_deps_windows.ps1"
 
     #####################################################################################
 

.gitignore

@@ -10,3 +10,4 @@ install
 build
 build_tools/cmake/*cppad*
 **/log
+**/*.trace

INSTALL.md

@@ -50,7 +50,7 @@ python -m pip install --prefer-binary gym-jiminy[all]
 
 ## Excluding dependencies on Ubuntu 18+
 
-First, one must install the pre-compiled libraries of the dependencies. Most of them are available on `robotpkg` APT repository. Just run the bash script to install them automatically for Ubuntu 18 and upward. It should be straightforward to adapt it to any other distribution for which `robotpkg` is available. Note that if you plan to use a virtual environment (`venv`, `pyenv`, ...), you must install the Python dependencies manually using `pip`, i.e. `"wheel", "numpy>=1.23,<2.0"`.
+First, one must install the pre-compiled libraries of the dependencies. Most of them are available on `robotpkg` APT repository. Just run the bash script to install them automatically for Ubuntu 18 and upward. It should be straightforward to adapt it to any other distribution for which `robotpkg` is available. Note that if you plan to use a virtual environment (`venv`, `pyenv`, ...), you must install the Python dependencies manually using `pip`, i.e. `"wheel", "numpy>=1.23,<2.1"`.
 
 ```bash
 sudo env "PATH=$PATH" ./build_tools/easy_install_deps_ubuntu.sh
@@ -79,7 +79,7 @@ make install -j2
 
 ```bash
 sudo apt install -y gnupg curl wget build-essential cmake doxygen graphviz
-python -m pip install "wheel", "numpy>=1.23,<2.0"
+python -m pip install "wheel", "numpy>=1.23,<2.1"
 ```
 
 ### Jiminy dependencies build and install
@@ -121,7 +121,7 @@ You have to preinstall by yourself the (free) MSVC 2019 toolchain.
 Then, install `setuptools`, `wheel` and `numpy`.
 
 ```powershell
-python -m pip install setuptools wheel "numpy>=1.23,<2.0"
+python -m pip install setuptools wheel "numpy>=1.23,<2.1"
 ```
 
 ### Jiminy dependencies build and install

build_tools/build_install_deps_unix.sh

@@ -127,7 +127,7 @@ rm -rf "${RootDir}/eigenpy/build"
 mkdir -p "${RootDir}/eigenpy/build"
 cd "${RootDir}/eigenpy"
 git reset --hard
-git fetch origin "v3.3.0" && git checkout --force FETCH_HEAD || true
+git fetch origin "v3.4.0" && git checkout --force FETCH_HEAD || true
 git submodule --quiet foreach --recursive git reset --quiet --hard
 git submodule --quiet update --init --recursive --depth 1 --jobs 8
 git apply --reject --whitespace=fix "${RootDir}/build_tools/patch_deps_unix/eigenpy.patch"
@@ -207,13 +207,12 @@ git fetch origin "v5.2.5" && git checkout --force FETCH_HEAD || true
 ### Checkout hpp-fcl
 if [ ! -d "${RootDir}/hpp-fcl" ]; then
   git clone --depth 1 https://github.com/humanoid-path-planner/hpp-fcl.git "${RootDir}/hpp-fcl"
-  git config --global url."https://".insteadOf git://
 fi
 rm -rf "${RootDir}/hpp-fcl/build"
 mkdir -p "${RootDir}/hpp-fcl/build"
 cd "${RootDir}/hpp-fcl"
 git reset --hard
-git fetch origin "v2.4.1" && git checkout --force FETCH_HEAD || true
+git fetch origin "v2.4.4" && git checkout --force FETCH_HEAD || true
 git submodule --quiet foreach --recursive git reset --quiet --hard
 git submodule --quiet update --init --recursive --depth 1 --jobs 8
 git apply --reject --whitespace=fix "${RootDir}/build_tools/patch_deps_unix/hppfcl.patch"
@@ -224,7 +223,6 @@ git fetch origin "v8.0.2" && git checkout --force FETCH_HEAD || true
 ### Checkout pinocchio and its submodules
 if [ ! -d "${RootDir}/pinocchio" ]; then
   git clone --depth 1 https://github.com/stack-of-tasks/pinocchio.git "${RootDir}/pinocchio"
-  git config --global url."https://".insteadOf git://
 fi
 rm -rf "${RootDir}/pinocchio/build"
 mkdir -p "${RootDir}/pinocchio/build"

build_tools/build_install_deps_windows.ps1

@@ -108,7 +108,7 @@ if (-not (Test-Path -PathType Container "$RootDir/eigenpy")) {
 }
 Push-Location -Path "$RootDir/eigenpy"
 git reset --hard
-git fetch origin "v3.3.0"
+git fetch origin "v3.4.0"
 git checkout --force FETCH_HEAD
 git submodule --quiet foreach --recursive git reset --quiet --hard
 git submodule --quiet update --init --recursive --depth 1 --jobs 8
@@ -191,11 +191,10 @@ Pop-Location
 ### Checkout hpp-fcl, then apply some patches
 if (-not (Test-Path -PathType Container "$RootDir/hpp-fcl")) {
   git clone --depth=1 https://github.com/humanoid-path-planner/hpp-fcl.git "$RootDir/hpp-fcl"
-  git config --global url."https://".insteadOf git://
 }
 Push-Location -Path "$RootDir/hpp-fcl"
 git reset --hard
-git fetch origin "v2.4.1"
+git fetch origin "v2.4.4"
 git checkout --force FETCH_HEAD
 git submodule --quiet foreach --recursive git reset --quiet --hard
 git submodule --quiet update --init --recursive --depth 1 --jobs 8
@@ -210,7 +209,6 @@ Pop-Location
 ### Checkout pinocchio and its submodules, then apply some patches
 if (-not (Test-Path -PathType Container "$RootDir/pinocchio")) {
   git clone --depth=1 https://github.com/stack-of-tasks/pinocchio.git "$RootDir/pinocchio"
-  git config --global url."https://".insteadOf git://
 }
 Push-Location -Path "$RootDir/pinocchio"
 git reset --hard

build_tools/easy_install_deps_ubuntu.sh

@@ -59,7 +59,7 @@ echo "-- Python writable site-packages: ${PYTHON_SITELIB}"
 apt update && \
 apt install -y python3-pip && \
 ${SUDO_CMD} python3 -m pip install setuptools wheel "pip>=20.3" && \
-${SUDO_CMD} python3 -m pip install "numpy>=1.23,<2.0" "numba>=0.54.0"
+${SUDO_CMD} python3 -m pip install "numpy>=1.23,<2.1" "numba>=0.54.0"
 
 # Install standard linux utilities
 apt install -y gnupg curl wget build-essential cmake doxygen graphviz pandoc
@@ -81,8 +81,8 @@ fi
 # Note that `apt-get` is used instead of `apt` because it supports wildcard in package names
 apt-mark unhold "robotpkg-py3*-eigenpy" "robotpkg-py3*-hpp-fcl" "robotpkg-py3*-pinocchio"
 apt-get install -y --allow-downgrades --allow-unauthenticated \
-    robotpkg-urdfdom-headers=1.0.4 robotpkg-hpp-fcl=2.4.1 robotpkg-pinocchio=2.7.0 \
-    robotpkg-py3*-eigenpy=3.3.0 robotpkg-py3*-hpp-fcl=2.4.1 robotpkg-py3*-pinocchio=2.7.0
+    robotpkg-urdfdom-headers=1.0.4 robotpkg-hpp-fcl=2.4.4 robotpkg-pinocchio=2.7.0 \
+    robotpkg-py3*-eigenpy=3.4.0 robotpkg-py3*-hpp-fcl=2.4.4 robotpkg-py3*-pinocchio=2.7.0
 apt-mark hold "robotpkg-py3*-eigenpy" "robotpkg-py3*-hpp-fcl" "robotpkg-py3*-pinocchio"
 
 # Add openrobots libraries to python packages search path

build_tools/patch_deps_unix/eigenpy.patch

@@ -46,3 +46,171 @@ diff --git a/cmake/python.cmake b/cmake/python.cmake
      else()
        # No hint was provided. We can then check for first Python 2, then Python
        # 3
+diff --git a/include/eigenpy/numpy-allocator.hpp b/include/eigenpy/numpy-allocator.hpp
+index 6165394..4dd5f7e 100644
+--- a/include/eigenpy/numpy-allocator.hpp
++++ b/include/eigenpy/numpy-allocator.hpp
+@@ -138,7 +138,12 @@ struct numpy_allocator_impl_matrix<Eigen::Ref<MatType, Options, Stride> > {
+                         outer_stride = reverse_strides ? mat.innerStride()
+                                                        : mat.outerStride();
+
++#if NPY_ABI_VERSION < 0x02000000
+       const int elsize = call_PyArray_DescrFromType(Scalar_type_code)->elsize;
++#else
++      const int elsize =
++          PyDataType_ELSIZE(call_PyArray_DescrFromType(Scalar_type_code));
++#endif
+       npy_intp strides[2] = {elsize * inner_stride, elsize * outer_stride};
+
+       PyArrayObject *pyArray = (PyArrayObject *)call_PyArray_New(
+@@ -204,7 +209,12 @@ struct numpy_allocator_impl_matrix<
+                         outer_stride = reverse_strides ? mat.innerStride()
+                                                        : mat.outerStride();
+
++#if NPY_ABI_VERSION < 0x02000000
+       const int elsize = call_PyArray_DescrFromType(Scalar_type_code)->elsize;
++#else
++      const int elsize =
++          PyDataType_ELSIZE(call_PyArray_DescrFromType(Scalar_type_code));
++#endif
+       npy_intp strides[2] = {elsize * inner_stride, elsize * outer_stride};
+
+       PyArrayObject *pyArray = (PyArrayObject *)call_PyArray_New(
+diff --git a/include/eigenpy/numpy.hpp b/include/eigenpy/numpy.hpp
+index 6ab627d..cdcfcf4 100644
+--- a/include/eigenpy/numpy.hpp
++++ b/include/eigenpy/numpy.hpp
+@@ -19,6 +19,37 @@
+ #include <numpy/ndarrayobject.h>
+ #include <numpy/ufuncobject.h>
+
++/* Allow compiling against NumPy 1.x and 2.x. See:
++   https://github.com/numpy/numpy/blob/afea8fd66f6bdbde855f5aff0b4e73eb0213c646/doc/source/reference/c-api/array.rst#L1224
++*/
++#if NPY_ABI_VERSION < 0x02000000
++  /* Define 2.0 feature version as it is needed below to decide whether we
++     compile for both 1.x and 2.x (defining it gaurantees 1.x only). 
++  */
++  #define NPY_2_0_API_VERSION 0x00000012
++  /* If we are compiling with NumPy 1.x, PyArray_RUNTIME_VERSION so we
++     pretend the `PyArray_RUNTIME_VERSION` is `NPY_FEATURE_VERSION`.
++     This allows downstream to use `PyArray_RUNTIME_VERSION` if they need to.
++  */
++  #define PyArray_RUNTIME_VERSION NPY_FEATURE_VERSION
++  // Compiling on NumPy 1.x these are the same
++  #define PyArray_DescrProto PyArray_Descr
++  
++static inline PyArray_ArrFuncs* PyDataType_GetArrFuncs(PyArray_Descr* descr) {
++  return descr->f;
++}
++#endif
++
++/* PEP 674 disallow using macros as l-values
++   see : https://peps.python.org/pep-0674/
++*/
++#if PY_VERSION_HEX < 0x030900A4 && !defined(Py_SET_TYPE)
++static inline void _Py_SET_TYPE(PyObject* o, PyTypeObject* type) {
++  Py_TYPE(o) = type;
++}
++#define Py_SET_TYPE(o, type) _Py_SET_TYPE((PyObject*)(o), type)
++#endif
++
+ #if defined _WIN32 || defined __CYGWIN__
+ #define EIGENPY_GET_PY_ARRAY_TYPE(array) \
+   call_PyArray_MinScalarType(array)->type_num
+@@ -122,7 +153,7 @@ EIGENPY_DLLAPI PyArray_Descr* call_PyArray_DescrFromType(int typenum);
+
+ EIGENPY_DLLAPI void call_PyArray_InitArrFuncs(PyArray_ArrFuncs* funcs);
+
+-EIGENPY_DLLAPI int call_PyArray_RegisterDataType(PyArray_Descr* dtype);
++EIGENPY_DLLAPI int call_PyArray_RegisterDataType(PyArray_DescrProto* dtype);
+
+ EIGENPY_DLLAPI int call_PyArray_RegisterCanCast(PyArray_Descr* descr,
+                                                 int totype,
+@@ -170,7 +201,7 @@ inline void call_PyArray_InitArrFuncs(PyArray_ArrFuncs* funcs) {
+   PyArray_InitArrFuncs(funcs);
+ }
+
+-inline int call_PyArray_RegisterDataType(PyArray_Descr* dtype) {
++inline int call_PyArray_RegisterDataType(PyArray_DescrProto* dtype) {
+   return PyArray_RegisterDataType(dtype);
+ }
+
+diff --git a/include/eigenpy/user-type.hpp b/include/eigenpy/user-type.hpp
+index e66b2d9..bcca555 100644
+--- a/include/eigenpy/user-type.hpp
++++ b/include/eigenpy/user-type.hpp
+@@ -171,7 +171,8 @@ struct SpecialMethods<T, NPY_USERDEF> {
+     char* srcptr = static_cast<char*>(src);
+
+     PyArrayObject* py_array = static_cast<PyArrayObject*>(array);
+-    PyArray_CopySwapFunc* copyswap = PyArray_DESCR(py_array)->f->copyswap;
++    PyArray_CopySwapFunc* copyswap =
++        PyDataType_GetArrFuncs(PyArray_DESCR(py_array))->copyswap;
+
+     for (npy_intp i = 0; i < n; i++) {
+       copyswap(dstptr, srcptr, swap, array);
+@@ -189,8 +190,8 @@ struct SpecialMethods<T, NPY_USERDEF> {
+       return (npy_bool)(value != ZeroValue);
+     } else {
+       T tmp_value;
+-      PyArray_DESCR(py_array)->f->copyswap(
+-          &tmp_value, ip, PyArray_ISBYTESWAPPED(py_array), array);
++      PyDataType_GetArrFuncs(PyArray_DESCR(py_array))
++          ->copyswap(&tmp_value, ip, PyArray_ISBYTESWAPPED(py_array), array);
+       return (npy_bool)(tmp_value != ZeroValue);
+     }
+   }
+diff --git a/src/numpy.cpp b/src/numpy.cpp
+index 01018ba..0621edc 100644
+--- a/src/numpy.cpp
++++ b/src/numpy.cpp
+@@ -14,7 +14,12 @@ void import_numpy() {
+ }
+
+ int PyArray_TypeNum(PyTypeObject* type) {
+-  return PyArray_TypeNumFromName(const_cast<char*>(type->tp_name));
++  PyArray_Descr* descr =
++      PyArray_DescrFromTypeObject(reinterpret_cast<PyObject*>(type));
++  if (descr == NULL) {
++    return NPY_NOTYPE;
++  }
++  return descr->type_num;
+ }
+
+ #if defined _WIN32 || defined __CYGWIN__
+@@ -52,7 +57,7 @@ void call_PyArray_InitArrFuncs(PyArray_ArrFuncs* funcs) {
+   PyArray_InitArrFuncs(funcs);
+ }
+
+-int call_PyArray_RegisterDataType(PyArray_Descr* dtype) {
++int call_PyArray_RegisterDataType(PyArray_DescrProto* dtype) {
+   return PyArray_RegisterDataType(dtype);
+ }
+
+diff --git a/src/register.cpp b/src/register.cpp
+index 84e84f6..1a8ce77 100644
+--- a/src/register.cpp
++++ b/src/register.cpp
+@@ -63,9 +63,9 @@ int Register::registerNewType(
+     throw std::invalid_argument("PyType_Ready fails to initialize input type.");
+   }
+
+-  PyArray_Descr* descr_ptr =
+-      new PyArray_Descr(*call_PyArray_DescrFromType(NPY_OBJECT));
+-  PyArray_Descr& descr = *descr_ptr;
++  PyArray_DescrProto* descr_ptr = new PyArray_DescrProto();
++  Py_SET_TYPE(descr_ptr, &PyArrayDescr_Type);
++  PyArray_DescrProto& descr = *descr_ptr;
+   descr.typeobj = py_type_ptr;
+   descr.kind = 'V';
+   descr.byteorder = '=';
+@@ -98,7 +98,7 @@ int Register::registerNewType(
+   PyArray_Descr* new_descr = call_PyArray_DescrFromType(code);
+
+   if (PyDict_SetItemString(py_type_ptr->tp_dict, "dtype",
+-                           (PyObject*)descr_ptr) < 0) {
++                           (PyObject*)new_descr) < 0) {
+     throw std::invalid_argument("PyDict_SetItemString fails.");
+   }
+