Compare revisions

4d8ad72d · 2e0c84f3 · a0838570 · 7945405b · 9a2af18e · 24bb01c6
--- a/.clang-format
+++ b/.clang-format
+BasedOnStyle: Google
+SortIncludes: false
+Standard: Cpp03
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
 # pre-commit run -a (Guilhem Saurel, 2022-07-27)
 4af05ec6781f9da65b81af8e3af8d69213f99e85
+# pre-commit run -a (Guilhem Saurel, 2024-02-17)
+48fb48c83f0456de2fb612ef55df8ad789824d87
+# pre-commit run -a (Guilhem Saurel, 2024-02-19)
+0bae435330ee475f8dbb11bf5e672284d294d9b3
--- a/.gitattributes
+++ b/.gitattributes
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML
--- a/.github/workflows/check-changelog.yml
+++ b/.github/workflows/check-changelog.yml
+name: CI - Check-changelog
+on:
+  pull_request:
+    types: [assigned, opened, synchronize, reopened, labeled, unlabeled, edited]
+    branches:
+      - devel
+jobs:
+  check-changelog:
+    name: Check changelog action
+    runs-on: ubuntu-latest
+    steps:
+      - uses: tarides/changelog-check-action@v2
+        with:
+          changelog: CHANGELOG.md
--- a/.github/workflows/conda/environment.yml
+++ b/.github/workflows/conda/environment.yml
-name: eigenpy
-channels:
-  - conda-forge
-  - defaults
-dependencies:
-  - eigen
-  - cmake
-  - numpy
-  - pkg-config
-  - boost
--- a/.github/workflows/jrl-cmakemodules.yml
+++ b/.github/workflows/jrl-cmakemodules.yml
-name: JRL-cmakemodules
+name: CI - JRL-cmakemodules
-on: [push,pull_request]
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
  with-submodules:
    name: Check configuration with git submodules
    runs-on: ubuntu-latest
    steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
        with:
          submodules: true
-      - run: sudo apt install libboost-all-dev libeigen3-dev python3-numpy
+      - run: sudo apt install libboost-all-dev libeigen3-dev python3-numpy python3-scipy
      - run: cmake .
@@ -17,8 +39,10 @@ jobs:
    name: Check configuration without git submodules
    runs-on: ubuntu-latest
    steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
        with:
          submodules: false
-      - run: sudo apt install libboost-all-dev libeigen3-dev python3-numpy
+          path: eigenpy
-      - run: cmake .
+      - run: sudo apt install libboost-all-dev libeigen3-dev python3-numpy python3-scipy
+      - run: cmake -B build -S eigenpy
+      - run: grep -qvz CMAKE_PROJECT_VERSION:STATIC=0.0 build/CMakeCache.txt
--- a/.github/workflows/linux.yml
+++ b/.github/workflows/linux.yml
-name: Check build on linux
+name: CI - Linux via APT
-on: ["push", "pull_request"]
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
  test:
@@ -9,17 +30,31 @@ jobs:
    strategy:
      matrix:
        python: [3]
-        ubuntu: [18, 20, 22]
+        ubuntu: [20, 22]
-        include:
-          - ubuntu: 18
-            python: 2
    steps:
      - uses: actions/checkout@v3
        with:
          submodules: 'true'
      - run: |
          sudo apt-get update
-          sudo apt-get install cmake libboost-all-dev libeigen3-dev python*-numpy python*-dev
+          sudo apt-get install cmake libboost-all-dev libeigen3-dev python*-numpy python*-dev python*-scipy
-      - run: cmake -DPYTHON_EXECUTABLE=$(which python${{ matrix.python }}) .
+          echo $(sudo apt list --installed)
+          echo $(g++ --version)
+      - run: cmake . -DPYTHON_EXECUTABLE=$(which python${{ matrix.python }}) -DBUILD_TESTING_SCIPY=ON
      - run: make -j2
-      - run: make test
+      - run: ctest --output-on-failure
+  check:
+    if: always()
+    name: check-linux
+    needs:
+    - test
+    runs-on: Ubuntu-latest
+    steps:
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
--- a/.github/workflows/macos-linux-conda.yml
+++ b/.github/workflows/macos-linux-conda.yml
-name: Conda-CI
-on: [push,pull_request]
-jobs:
-  eigenpy-conda:
-    name: ${{ matrix.os }} - ${{ matrix.build_type }} ${{ matrix.cxx_options }}
-    runs-on: ${{ matrix.os }}
-    env:
-      CCACHE_DIR: /github/home/.ccache # Enable ccache
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ["ubuntu-latest", "macos-latest"]
-        cxx_options: ['', '-mavx2']
-        build_type: [Release, Debug]
-        exclude:
-          - build_type: Debug
-            cxx_options: -mavx2
-            os: macos-latest
-          - build_type: Release
-            cxx_options: -mavx2
-            os: macos-latest
-    steps:
-    - uses: actions/checkout@v2
-      with:
-        submodules: recursive
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        activate-environment: eigenpy
-        auto-update-conda: true
-        environment-file: .github/workflows/conda/environment.yml
-        python-version: '3.10'
-    - uses: actions/cache@v2
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: ccache-${{ matrix.os }}-${{ matrix.build_type }}-${{ matrix.cxx_options }}
-    - name: Install cmake and update conda
-      shell: bash -l {0}
-      run: |
-        conda activate eigenpy
-        conda install cmake -c main
-        conda list
-    - name: Build EigenPy
-      shell: bash -l {0}
-      run: |
-        conda activate eigenpy
-        echo $CONDA_PREFIX
-        mkdir build
-        cd build
-        cmake .. -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$(which python3) -DGENERATE_PYTHON_STUBS=ON -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_CXX_FLAGS=${{ matrix.cxx_options }}
-        make
-        make build_tests
-        export CTEST_OUTPUT_ON_FAILURE=1
-        make test
-        make install
-    - name: Test packaging
-      shell: bash -l {0}
-      run: |
-        conda activate eigenpy
-        cmake -B test-packaging -S unittest/packaging/cmake -DPYTHON_EXECUTABLE=$(which python3)
-    - name: Configure hpp-fcl
-      shell: bash -l {0}
-      run: |
-        conda activate eigenpy
-        conda install -c conda-forge octomap assimp qhull
-        git clone https://github.com/humanoid-path-planner/hpp-fcl.git --recursive
-        cd hpp-fcl
-        mkdir build && cd build
-        cmake .. -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$(which python3)
-    - name: Uninstall EigenPy
-      shell: bash -l {0}
-      run: |
-        cd build
-        make uninstall
--- a/.github/workflows/macos-linux-windows-pixi.yml
+++ b/.github/workflows/macos-linux-windows-pixi.yml
+name: CI - MacOS/Linux/Windows via Pixi
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+jobs:
+  eigenpy-pixi:
+    name: ${{ matrix.os }} - Env ${{ matrix.environment }} ${{ matrix.build_type }} ${{ matrix.cxx_options }} ${{ matrix.compiler }}
+    runs-on: ${{ matrix.os }}
+    env:
+      CCACHE_BASEDIR: "${GITHUB_WORKSPACE}"
+      CCACHE_DIR: "${GITHUB_WORKSPACE}/.ccache"
+      CCACHE_COMPRESS: true
+      CCACHE_COMPRESSLEVEL: 6
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, macos-13]
+        environment: [all, all-py39]
+        build_type: [Release, Debug]
+        cxx_options: ['', '-mavx2']
+        exclude:
+          - os: macos-latest
+            cxx_options: '-mavx2'
+          - os: macos-13
+            cxx_options: '-mavx2'
+        include:
+          - os: windows-latest
+            environment: all
+            cxx_options: ''
+            build_type: Release
+          - os: windows-latest
+            environment: all-clang-cl
+            cxx_options: ''
+            build_type: Release
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - uses: actions/cache@v4
+      with:
+        path: .ccache
+        key: ccache-macos-linux-windows-pixi-${{ matrix.os }}-${{ matrix.build_type }}-${{ matrix.cxx_options }}-${{ matrix.environment }}-${{ github.sha }}
+        restore-keys: ccache-macos-linux-windows-pixi-${{ matrix.os }}-${{ matrix.build_type }}-${{ matrix.cxx_options }}-${{ matrix.environment }}-
+    - uses: prefix-dev/setup-pixi@v0.8.1
+      with:
+        cache: true
+        environments: ${{ matrix.environment }}
+    - name: Build EigenPy [MacOS/Linux/Windows]
+      env:
+        CMAKE_BUILD_PARALLEL_LEVEL: 2
+        EIGENPY_BUILD_TYPE: ${{ matrix.build_type }}
+        EIGENPY_CXX_FLAGS: ${{ matrix.cxx_options }}
+      run: |
+        pixi run -e ${{ matrix.environment }} test
+  check:
+    if: always()
+    name: check-macos-linux-windows-pixi
+    needs:
+    - eigenpy-pixi
+    runs-on: Ubuntu-latest
+    steps:
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
--- a/.github/workflows/nix.yml
+++ b/.github/workflows/nix.yml
+name: "CI - Nix"
+on:
+  push:
+jobs:
+  nix:
+    runs-on: "${{ matrix.os }}-latest"
+    strategy:
+      matrix:
+        os: [ubuntu, macos]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: cachix/install-nix-action@v27
+      - uses: cachix/cachix-action@v15
+        with:
+          name: gepetto
+          authToken: '${{ secrets.CACHIX_AUTH_TOKEN }}'
+      - run: nix build -L
--- a/.github/workflows/reloc.yml
+++ b/.github/workflows/reloc.yml
-name: Ensure relocatable
+name: CI - Ensure relocatable
-on: [push,pull_request]
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
  relocatable:
@@ -30,7 +51,7 @@ jobs:
      run: git -C /RELOC/SRC clone --recursive $(pwd)
    - name: install dependencies
-      run: sudo apt install libboost-all-dev libeigen3-dev python-is-python3 python3-numpy python3-pip ccache
+      run: sudo apt install libboost-all-dev libeigen3-dev python-is-python3 python3-numpy python3-pip python3-scipy ccache
    - name: update CMake
      run: pip install -U pip && pip install -U cmake

--- a/.github/workflows/ros_ci.yml
+++ b/.github/workflows/ros_ci.yml
 # This config uses industrial_ci (https://github.com/ros-industrial/industrial_ci.git).
 # For troubleshooting, see readme (https://github.com/ros-industrial/industrial_ci/blob/master/README.rst)
-name: ROS-CI
+name: CI - Linux via ROS
 # This determines when this workflow is run
-on: [push, pull_request] # on all pushes and PRs
+on:
+  push:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+  pull_request:
+    paths-ignore:
+      - 'doc/**'
+      - '.gitlab-ci.yml'
+      - '.gitignore'
+      - '*.md'
+      - 'LICENSE'
+      - 'colcon.pkg'
+      - '.pre-commit-config.yaml'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
  CI:
    strategy:
      matrix:
        env:
-          - {ROS_DISTRO: melodic, PRERELEASE: false}
+          # ROS1
          - {ROS_DISTRO: noetic}
-          - {ROS_DISTRO: foxy}
+          # ROS2
-          - {ROS_DISTRO: rolling}
+          - {ROS_DISTRO: iron}
          - {ROS_DISTRO: humble}
+          - {ROS_DISTRO: jazzy}
+          - {ROS_DISTRO: rolling}
    env:
-      CCACHE_DIR: /github/home/.ccache # Enable ccache
+      # PRERELEASE: true  # Fails due to issues in the underlying Docker image
-      PRERELEASE: true
      BUILDER: colcon
    runs-on: ubuntu-latest
    steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
        with:
          submodules: recursive
-      # This step will fetch/store the directory used by ccache before/after the ci run
-      - uses: actions/cache@v3
-        with:
-          path: ${{ env.CCACHE_DIR }}
-          key: ccache-${{ matrix.env.ROS_DISTRO }}-${{ matrix.env.ROS_REPO }}
      # Run industrial_ci
-      - uses: 'ros-industrial/industrial_ci@master'
+      - uses: 'ros-industrial/industrial_ci@875c2aebfd634eebaa84dbe5198f2fdb4c5f1b7e'
        env: ${{ matrix.env }}
+  check:
+    if: always()
+    name: check-ros-ci
+    needs:
+    - CI
+    runs-on: Ubuntu-latest
+    steps:
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}
--- a/.github/workflows/update-flake-lock.yml
+++ b/.github/workflows/update-flake-lock.yml
+name: update-flake-lock
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 15 3 * *'
+jobs:
+  lockfile:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Install Nix
+        uses: DeterminateSystems/nix-installer-action@main
+      - name: Update flake.lock
+        uses: DeterminateSystems/update-flake-lock@main
+        with:
+          pr-labels: "no changelog"
+          token: ${{ secrets.GH_TOKEN_FOR_UPDATES }}
--- a/.github/workflows/update_pixi_lockfile.yml
+++ b/.github/workflows/update_pixi_lockfile.yml
+name: CI - Update Pixi lockfile
+permissions:
+  contents: write
+  pull-requests: write
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: 0 5 1 * *
+jobs:
+  pixi-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/create-github-app-token@v1
+        id: generate-token
+        with:
+          app-id: ${{ secrets.APP_ID }}
+          private-key: ${{ secrets.APP_PRIVATE_KEY }}
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          ref: devel
+          # Make sure the value of GITHUB_TOKEN will not be persisted in repo's config
+          persist-credentials: false
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+        with:
+          run-install: false
+      - name: Update lockfile
+        run: |
+          set -o pipefail
+          pixi update --json | pixi exec pixi-diff-to-markdown >> diff.md
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ steps.generate-token.outputs.token }}
+          commit-message: 'pixi: Update pixi lockfile'
+          title: Update pixi lockfile
+          body-path: diff.md
+          branch: topic/update-pixi
+          base: devel
+          labels: |
+            pixi
+            no changelog
+          delete-branch: true
+          add-paths: pixi.lock
--- a/.github/workflows/windows-conda.yml
+++ b/.github/workflows/windows-conda.yml
-name: Build Eigenpy on Windows via Conda
-on: [push,pull_request]
-jobs:
-  build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-          os: [windows-latest]
-    steps:
-    - uses: actions/checkout@v2
-    - name: Checkout submodules
-      run: |
-        git submodule update --init
-    - uses: goanpeca/setup-miniconda@v1
-      env:
-        ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
-      with:
-        activate-environment: eigenpy
-        environment-file: .github/workflows/conda/environment.yml
-        python-version: 3.7
-    - name: Build Eigenpy
-      shell: cmd /C CALL {0}
-      env:
-        ACTIONS_ALLOW_UNSECURE_COMMANDS: 'true'
-      run: |
-        :: unset extra Boost envs
-        set Boost_ROOT=
-        set BOOST_ROOT_1_69_0=
-        set BOOST_ROOT_1_72_0=
-        set PATH=%PATH:C:\hostedtoolcache\windows\Boost\1.72.0;=%
-        if errorlevel 1 exit 1
-        :: start building
-        call "%programfiles%\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" amd64
-        if errorlevel 1 exit 1
-        mkdir build
-        pushd build
-        cmake ^
-          -G "NMake Makefiles" ^
-          -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX%\Library ^
-          -DCMAKE_BUILD_TYPE=Release ^
-          -DGENERATE_PYTHON_STUBS=ON ^
-          -DPYTHON_SITELIB=%CONDA_PREFIX%\Lib\site-packages ^
-          -DPYTHON_EXECUTABLE=%CONDA_PREFIX%\python.exe ^
-          ..
-        if errorlevel 1 exit 1
-        :: Build and Install
-        cmake --build . --config Release --target install
-        if errorlevel 1 exit 1
-        :: Build stubs
-        git clone https://github.com/jcarpent/pybind11-stubgen.git
-        python "%CD%\pybind11-stubgen\pybind11_stubgen\__init__.py" -o %CONDA_PREFIX%\Lib\site-packages\eigenpy eigenpy --boost-python --ignore-invalid signature --no-setup-py --root-module-suffix ""
-        if errorlevel 1 exit 1
-        :: Testing
-        ctest --output-on-failure -C Release -V
-        if errorlevel 1 exit 1
-        :: Test Python import
-        cd ..
-        python -c "import eigenpy"
-        if errorlevel 1 exit 1
-        :: Test packaging
-        cmake -B test-packaging -S unittest/packaging/cmake ^
-          -G "NMake Makefiles" ^
-          -DPYTHON_EXECUTABLE=%CONDA_PREFIX%\python.exe
-        if errorlevel 1 exit 1
-        :: Configure hpp-fcl
-        conda install -c conda-forge octomap assimp qhull
-        git clone --recursive https://github.com/humanoid-path-planner/hpp-fcl.git
-        pushd hpp-fcl
-        mkdir build
-        pushd build
-        cmake ^
-          -G "NMake Makefiles" ^
-          -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX%\Library ^
-          -DCMAKE_BUILD_TYPE=Release ^
-          -DPYTHON_EXECUTABLE=%CONDA_PREFIX%\python.exe ^
-          ..
-        cd ..
-        if errorlevel 1 exit 1
-        :: Uninstall
-        cmake --build . --config Release --target uninstall
-        if errorlevel 1 exit 1
--- a/.gitignore
+++ b/.gitignore
 *~
-*build*
+*build*/
+# pixi environments
+.pixi
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
 ci:
-    autoupdate_branch: 'devel'
+  autoupdate_branch: devel
+  autofix_prs: false
+  autoupdate_schedule: quarterly
 repos:
-   repo: https://github.com/pre-commit/mirrors-clang-format
+- repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v15.0.7
+  rev: v0.8.6
-    hooks:
+  hooks:
-    -   id: clang-format
+  - id: ruff
-        args: ['--style={BasedOnStyle: Google, SortIncludes: false}']
+    args:
-   repo: https://github.com/pre-commit/pre-commit-hooks
+    - --fix
-    rev: v4.4.0
+    - --exit-non-zero-on-fix
-    hooks:
+    - --ignore
-    -   id: trailing-whitespace
+    - UP036
-   repo: https://github.com/psf/black
+  - id: ruff-format
-    rev: 22.12.0
+- repo: https://github.com/cheshirekow/cmake-format-precommit
-    hooks:
+  rev: v0.6.13
-    -   id: black
+  hooks:
-   repo: https://github.com/cheshirekow/cmake-format-precommit
+  - id: cmake-format
-    rev: v0.6.13
+- repo: https://github.com/pappasam/toml-sort
-    hooks:
+  rev: v0.24.2
-    - id: cmake-format
+  hooks:
+  - id: toml-sort-fix
+    exclude: pixi.toml
+- repo: https://github.com/pre-commit/mirrors-clang-format
+  rev: v19.1.6
+  hooks:
+  - id: clang-format
+    args:
+    - '--style={BasedOnStyle: Google, SortIncludes: false, Standard: Cpp03}'
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+  - id: trailing-whitespace
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -2,7 +2,7 @@
 # Copyright (c) 2014-2019 CNRS Copyright (c) 2018-2023 INRIA
 #
-cmake_minimum_required(VERSION 3.1)
+cmake_minimum_required(VERSION 3.10)
 set(PROJECT_NAME eigenpy)
 set(PROJECT_DESCRIPTION "Bindings between Numpy and Eigen using Boost.Python")
@@ -11,14 +11,30 @@ set(PROJECT_USE_CMAKE_EXPORT TRUE)
 set(PROJECT_USE_KEYWORD_LINK_LIBRARIES TRUE)
 set(PROJECT_CUSTOM_HEADER_EXTENSION "hpp")
 set(PROJECT_COMPATIBILITY_VERSION AnyNewerVersion)
+# To enable jrl-cmakemodules compatibility with workspace we must define the two
+# following lines
+set(PROJECT_AUTO_RUN_FINALIZE FALSE)
+set(PROJECT_SOURCE_DIR ${CMAKE_CURRENT_LIST_DIR})
 # Check if the submodule cmake have been initialized
 set(JRL_CMAKE_MODULES "${CMAKE_CURRENT_LIST_DIR}/cmake")
-if(NOT EXISTS "${CMAKE_SOURCE_DIR}/cmake/base.cmake")
+if(EXISTS "${JRL_CMAKE_MODULES}/base.cmake")
-  if(${CMAKE_VERSION} VERSION_LESS "3.14.0")
+  message(STATUS "JRL cmakemodules found in 'cmake/' git submodule")
+else()
+  find_package(jrl-cmakemodules QUIET CONFIG)
+  if(jrl-cmakemodules_FOUND)
+    get_property(
+      JRL_CMAKE_MODULES
+      TARGET jrl-cmakemodules::jrl-cmakemodules
+      PROPERTY INTERFACE_INCLUDE_DIRECTORIES)
+    message(STATUS "JRL cmakemodules found on system at ${JRL_CMAKE_MODULES}")
+  elseif(${CMAKE_VERSION} VERSION_LESS "3.14.0")
    message(
      FATAL_ERROR
-        "\nPlease run the following command first:\ngit submodule update --init\n"
+        "\nCan't find jrl-cmakemodules. Please either:\n"
+        "  - use git submodule: 'git submodule update --init'\n"
+        "  - or install https://github.com/jrl-umi3218/jrl-cmakemodules\n"
+        "  - or upgrade your CMake version to >= 3.14 to allow automatic fetching\n"
    )
  else()
    message(STATUS "JRL cmakemodules not found. Let's fetch it.")
@@ -31,6 +47,14 @@ if(NOT EXISTS "${CMAKE_SOURCE_DIR}/cmake/base.cmake")
  endif()
 endif()
+function(set_standard_output_directory target)
+  set_target_properties(
+    ${target}
+    PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin
+               LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib
+               ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+endfunction()
 # Disable -Werror on Unix for now.
 set(CXX_DISABLE_WERROR True)
 set(CMAKE_VERBOSE_MAKEFILE True)
@@ -41,16 +65,30 @@ set(CMAKE_VERBOSE_MAKEFILE True)
 # ----------------------------------------------------
 option(INSTALL_DOCUMENTATION "Generate and install the documentation" OFF)
 option(SUFFIX_SO_VERSION "Suffix library name with its version" OFF)
+option(BUILD_TESTING_SCIPY
+       "Build the SciPy tests (scipy should be installed on the machine)" ON)
-if(DEFINED BUILD_UNIT_TESTS)
+# ----------------------------------------------------
-  message(
+# --- Policy -----------------------------------------
-    AUTHOR_WARNING
+# CMake Policy setup
-      "BUILD_UNIT_TESTS is deprecated. Use BUILD_TESTING instead.\
+# ----------------------------------------------------
-    If you are manually building EigenPy from source in an existing build folder,\
+# Policy can be removed when cmake_minimum_required is updated.
-    we suggest that you delete your build folder and make a new one.")
-  set(BUILD_TESTING ${BUILD_UNIT_TESTS})
+# We also set CMAKE_POLICY_DEFAULT_CMPXXXX because CMake modules can reset
-endif(DEFINED BUILD_UNIT_TESTS)
+# policy and redefine some macros like `find_dependency` that will not use our
+# policy.
+# Use BoostConfig module distributed by boost library instead of using FindBoost
+# module distributed by CMake (to remove in 3.30).
+if(POLICY CMP0167)
+  cmake_policy(SET CMP0167 NEW)
+  set(CMAKE_POLICY_DEFAULT_CMP0167 NEW)
+endif()
+# install() DESTINATION paths are normalized (to remove in 3.31).
+if(POLICY CMP0177)
+  cmake_policy(SET CMP0177 NEW)
+  set(CMAKE_POLICY_DEFAULT_CMP0177 NEW)
+endif()
 include("${JRL_CMAKE_MODULES}/base.cmake")
 compute_project_args(PROJECT_ARGS LANGUAGES CXX)
 project(${PROJECT_NAME} ${PROJECT_ARGS})
@@ -63,10 +101,20 @@ include("${JRL_CMAKE_MODULES}/apple.cmake")
 option(GENERATE_PYTHON_STUBS
       "Generate the Python stubs associated to the Python library" OFF)
+option(BUILD_WITH_CHOLMOD_SUPPORT "Build EigenPy with the Cholmod support" OFF)
+if(APPLE)
+  option(BUILD_WITH_ACCELERATE_SUPPORT
+         "Build EigenPy with the Accelerate support" OFF)
+else(APPLE)
+  set(BUILD_WITH_ACCELERATE_SUPPORT FALSE)
+endif(APPLE)
 string(REPLACE "-pedantic" "" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
 # If needed, fix CMake policy for APPLE systems
 apply_default_apple_configuration()
+check_minimal_cxx_standard(11 ENFORCE)
 if(WIN32)
  set(LINK copy_if_different)
@@ -105,12 +153,45 @@ export_boost_default_options()
 find_package(Boost REQUIRED)
 search_for_boost_python(REQUIRED)
+if(BUILD_WITH_CHOLMOD_SUPPORT)
+  set(CMAKE_MODULE_PATH ${JRL_CMAKE_MODULES}/find-external/CHOLMOD
+                        ${CMAKE_MODULE_PATH})
+  add_project_dependency(CHOLMOD REQUIRED FIND_EXTERNAL "CHOLMOD")
+  message(
+    STATUS
+      "Build with CHOLDOD support (LGPL). See CHOLMOD/Doc/License.txt for further details."
+  )
+  add_definitions(-DEIGENPY_WITH_CHOLMOD_SUPPORT)
+endif(BUILD_WITH_CHOLMOD_SUPPORT)
+if(BUILD_WITH_ACCELERATE_SUPPORT)
+  if(NOT ${Eigen3_VERSION} VERSION_GREATER_EQUAL "3.4.90")
+    message(
+      FATAL_ERROR
+        "Your version of Eigen is too low. Should be at least 3.4.90. Current version is ${Eigen3_VERSION}."
+    )
+  endif()
+  set(CMAKE_MODULE_PATH ${JRL_CMAKE_MODULES}/find-external/Accelerate
+                        ${CMAKE_MODULE_PATH})
+  find_package(
+    Accelerate REQUIRED # FIND_EXTERNAL "Accelerate" # We don't export yet as
+                        # there might be an issue on AMR64 platforms
+  )
+  message(STATUS "Build with Accelerate support framework.")
+  add_definitions(-DEIGENPY_WITH_ACCELERATE_SUPPORT)
+endif(BUILD_WITH_ACCELERATE_SUPPORT)
 # ----------------------------------------------------
 # --- INCLUDE ----------------------------------------
 # ----------------------------------------------------
 set(${PROJECT_NAME}_UTILS_HEADERS
-    include/eigenpy/utils/scalar-name.hpp include/eigenpy/utils/is-approx.hpp
+    include/eigenpy/utils/scalar-name.hpp
-    include/eigenpy/utils/is-aligned.hpp)
+    include/eigenpy/utils/is-approx.hpp
+    include/eigenpy/utils/is-aligned.hpp
+    include/eigenpy/utils/traits.hpp
+    include/eigenpy/utils/python-compat.hpp
+    include/eigenpy/utils/empty-visitor.hpp)
 set(${PROJECT_NAME}_SOLVERS_HEADERS
    include/eigenpy/solvers/solvers.hpp
@@ -122,20 +203,57 @@ set(${PROJECT_NAME}_SOLVERS_HEADERS
    include/eigenpy/solvers/BasicPreconditioners.hpp
    include/eigenpy/solvers/BFGSPreconditioners.hpp)
+set(${PROJECT_NAME}_EIGEN_HEADERS include/eigenpy/eigen/EigenBase.hpp)
+set(${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_CHOLMOD_HEADERS
+    include/eigenpy/decompositions/sparse/cholmod/CholmodBase.hpp
+    include/eigenpy/decompositions/sparse/cholmod/CholmodDecomposition.hpp
+    include/eigenpy/decompositions/sparse/cholmod/CholmodSimplicialLDLT.hpp
+    include/eigenpy/decompositions/sparse/cholmod/CholmodSimplicialLLT.hpp
+    include/eigenpy/decompositions/sparse/cholmod/CholmodSupernodalLLT.hpp)
+set(${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_ACCELERATE_HEADERS
+    include/eigenpy/decompositions/sparse/accelerate/accelerate.hpp)
+set(${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_HEADERS
+    include/eigenpy/decompositions/sparse/LLT.hpp
+    include/eigenpy/decompositions/sparse/LDLT.hpp
+    include/eigenpy/decompositions/sparse/SimplicialCholesky.hpp
+    include/eigenpy/decompositions/sparse/SparseSolverBase.hpp)
+if(BUILD_WITH_CHOLMOD_SUPPORT)
+  list(APPEND ${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_HEADERS
+       ${${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_CHOLMOD_HEADERS})
+endif(BUILD_WITH_CHOLMOD_SUPPORT)
+if(BUILD_WITH_ACCELERATE_SUPPORT)
+  list(APPEND ${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_HEADERS
+       ${${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_ACCELERATE_HEADERS})
+endif(BUILD_WITH_ACCELERATE_SUPPORT)
 set(${PROJECT_NAME}_DECOMPOSITIONS_HEADERS
+    ${${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_HEADERS}
    include/eigenpy/decompositions/decompositions.hpp
    include/eigenpy/decompositions/EigenSolver.hpp
+    include/eigenpy/decompositions/PermutationMatrix.hpp
    include/eigenpy/decompositions/LDLT.hpp
    include/eigenpy/decompositions/LLT.hpp
+    include/eigenpy/decompositions/QR.hpp
+    include/eigenpy/decompositions/HouseholderQR.hpp
+    include/eigenpy/decompositions/ColPivHouseholderQR.hpp
+    include/eigenpy/decompositions/CompleteOrthogonalDecomposition.hpp
+    include/eigenpy/decompositions/FullPivHouseholderQR.hpp
    include/eigenpy/decompositions/SelfAdjointEigenSolver.hpp
    include/eigenpy/decompositions/minres.hpp)
 set(${PROJECT_NAME}_HEADERS
    ${${PROJECT_NAME}_UTILS_HEADERS}
    ${${PROJECT_NAME}_SOLVERS_HEADERS}
+    ${${PROJECT_NAME}_EIGEN_HEADERS}
    ${${PROJECT_NAME}_DECOMPOSITIONS_HEADERS}
    include/eigenpy/alignment.hpp
    include/eigenpy/computation-info.hpp
+    include/eigenpy/deprecation-policy.hpp
    include/eigenpy/eigenpy.hpp
    include/eigenpy/exception.hpp
    include/eigenpy/scalar-conversion.hpp
@@ -147,24 +265,37 @@ set(${PROJECT_NAME}_HEADERS
    include/eigenpy/eigen-to-python.hpp
    include/eigenpy/eigen-from-python.hpp
    include/eigenpy/eigen-typedef.hpp
+    include/eigenpy/id.hpp
    include/eigenpy/numpy-map.hpp
    include/eigenpy/geometry.hpp
    include/eigenpy/geometry-conversion.hpp
+    include/eigenpy/map.hpp
    include/eigenpy/memory.hpp
    include/eigenpy/numpy.hpp
    include/eigenpy/numpy-allocator.hpp
    include/eigenpy/numpy-type.hpp
    include/eigenpy/registration.hpp
+    include/eigenpy/registration_class.hpp
    include/eigenpy/angle-axis.hpp
    include/eigenpy/quaternion.hpp
    include/eigenpy/user-type.hpp
    include/eigenpy/ufunc.hpp
    include/eigenpy/register.hpp
+    include/eigenpy/std-array.hpp
    include/eigenpy/std-map.hpp
+    include/eigenpy/std-pair.hpp
    include/eigenpy/std-vector.hpp
+    include/eigenpy/optional.hpp
    include/eigenpy/pickle-vector.hpp
    include/eigenpy/stride.hpp
+    include/eigenpy/tensor/eigen-from-python.hpp
+    include/eigenpy/sparse/eigen-from-python.hpp
+    include/eigenpy/scipy-allocator.hpp
+    include/eigenpy/scipy-type.hpp
+    include/eigenpy/variant.hpp
+    include/eigenpy/std-unique-ptr.hpp
    include/eigenpy/swig.hpp
+    include/eigenpy/type_info.hpp
    include/eigenpy/version.hpp)
 list(
@@ -181,7 +312,27 @@ set(${PROJECT_NAME}_SOLVERS_SOURCES src/solvers/preconditioners.cpp
                                    src/solvers/solvers.cpp)
 set(${PROJECT_NAME}_DECOMPOSITIONS_SOURCES
-    src/decompositions/decompositions.cpp)
+    src/decompositions/decompositions.cpp
+    src/decompositions/eigen-solver.cpp
+    src/decompositions/llt-solver.cpp
+    src/decompositions/ldlt-solver.cpp
+    src/decompositions/minres-solver.cpp
+    src/decompositions/qr-solvers.cpp
+    src/decompositions/eigen-solver.cpp
+    src/decompositions/self-adjoint-eigen-solver.cpp
+    src/decompositions/permutation-matrix.cpp
+    src/decompositions/simplicial-llt-solver.cpp
+    src/decompositions/simplicial-ldlt-solver.cpp)
+if(BUILD_WITH_CHOLMOD_SUPPORT)
+  list(APPEND ${PROJECT_NAME}_DECOMPOSITIONS_SOURCES
+       src/decompositions/cholmod.cpp)
+endif(BUILD_WITH_CHOLMOD_SUPPORT)
+if(BUILD_WITH_ACCELERATE_SUPPORT)
+  list(APPEND ${PROJECT_NAME}_DECOMPOSITIONS_SOURCES
+       src/decompositions/accelerate.cpp)
+endif(BUILD_WITH_ACCELERATE_SUPPORT)
 set(${PROJECT_NAME}_SOURCES
    ${${PROJECT_NAME}_SOLVERS_SOURCES}
@@ -198,20 +349,39 @@ set(${PROJECT_NAME}_SOURCES
    src/matrix-long-double.cpp
    src/matrix-complex-long-double.cpp
    src/matrix-bool.cpp
-    src/matrix-int.cpp
+    src/matrix-char.cpp
-    src/matrix-long.cpp
+    src/matrix-int8.cpp
+    src/matrix-uint8.cpp
+    src/matrix-int16.cpp
+    src/matrix-uint16.cpp
+    src/matrix-int32.cpp
+    src/matrix-uint32.cpp
+    src/matrix-windows-long.cpp
+    src/matrix-windows-ulong.cpp
+    src/matrix-mac-long.cpp
+    src/matrix-mac-ulong.cpp
+    src/matrix-int64.cpp
+    src/matrix-uint64.cpp
+    src/matrix-linux-long-long.cpp
+    src/matrix-linux-ulong-long.cpp
    src/angle-axis.cpp
    src/quaternion.cpp
    src/geometry-conversion.cpp
+    src/scipy-type.cpp
    src/std-vector.cpp
+    src/optional.cpp
+    src/type_info.cpp
    src/version.cpp)
 add_library(${PROJECT_NAME} SHARED ${${PROJECT_NAME}_SOURCES}
                                   ${${PROJECT_NAME}_HEADERS})
+add_library(${PROJECT_NAME}::${PROJECT_NAME} ALIAS ${PROJECT_NAME})
+set_standard_output_directory(${PROJECT_NAME})
 target_include_directories(
  ${PROJECT_NAME} SYSTEM
  PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
-         $<INSTALL_INTERFACE:include>)
+         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+         $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
 modernize_target_link_libraries(
  ${PROJECT_NAME}
@@ -232,17 +402,30 @@ modernize_target_link_libraries(
  ${NUMPY_INCLUDE_DIRS}
  ${PYTHON_INCLUDE_DIR})
+# Links against CholMod
+if(BUILD_WITH_CHOLMOD_SUPPORT)
+  modernize_target_link_libraries(${PROJECT_NAME} SCOPE PUBLIC TARGETS
+                                  CHOLMOD::CHOLMOD)
+endif(BUILD_WITH_CHOLMOD_SUPPORT)
+# Links against accelerate
+if(BUILD_WITH_ACCELERATE_SUPPORT)
+  # modernize_target_link_libraries(${PROJECT_NAME} SCOPE PUBLIC TARGETS
+  # Accelerate)
+  target_link_libraries(${PROJECT_NAME} PRIVATE "-framework accelerate")
+endif(BUILD_WITH_ACCELERATE_SUPPORT)
 if(SUFFIX_SO_VERSION)
  set_target_properties(${PROJECT_NAME} PROPERTIES SOVERSION ${PROJECT_VERSION})
 endif(SUFFIX_SO_VERSION)
 if(NOT WIN32)
  target_compile_options(
-    ${PROJECT_NAME} PRIVATE $<$<CXX_COMPILER_ID:MSVC>:-bigobj>
+    ${PROJECT_NAME} PRIVATE $<$<CXX_COMPILER_ID:MSVC>:-bigobj -MP>
                            "-Wno-conversion")
 else()
  target_compile_options(${PROJECT_NAME}
-                         PRIVATE $<$<CXX_COMPILER_ID:MSVC>:-bigobj>)
+                         PRIVATE $<$<CXX_COMPILER_ID:MSVC>:-bigobj -MP>)
  target_compile_definitions(${PROJECT_NAME} PUBLIC "HAVE_SNPRINTF")
 endif()
@@ -262,29 +445,6 @@ add_source_group(${PROJECT_NAME}_SOURCES)
 # Install package for ROS
 install(FILES package.xml DESTINATION share/eigenpy)
-# Allows Colcon to find non-Ament packages when using workspace underlays
-file(
-  WRITE
-  ${CMAKE_CURRENT_BINARY_DIR}/share/ament_index/resource_index/packages/${PROJECT_NAME}
-  "")
-install(
-  FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/share/ament_index/resource_index/packages/${PROJECT_NAME}
-  DESTINATION share/ament_index/resource_index/packages)
-file(
-  WRITE
-  ${CMAKE_CURRENT_BINARY_DIR}/share/${PROJECT_NAME}/hook/ament_prefix_path.dsv
-  "prepend-non-duplicate;AMENT_PREFIX_PATH;")
-install(
-  FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/share/${PROJECT_NAME}/hook/ament_prefix_path.dsv
-  DESTINATION share/${PROJECT_NAME}/hook)
-file(WRITE
-     ${CMAKE_CURRENT_BINARY_DIR}/share/${PROJECT_NAME}/hook/python_path.dsv
-     "prepend-non-duplicate;PYTHONPATH;${PYTHON_SITELIB}")
-install(
-  FILES ${CMAKE_CURRENT_BINARY_DIR}/share/${PROJECT_NAME}/hook/python_path.dsv
-  DESTINATION share/${PROJECT_NAME}/hook)
 # ----------------------------------------------------
 # --- PYTHON LIBRARY ---------------------------------
@@ -300,3 +460,5 @@ pkg_config_append_libs(${PROJECT_NAME})
 pkg_config_append_cflags("-I${PYTHON_INCLUDE_DIRS}")
 pkg_config_append_cflags("-I${NUMPY_INCLUDE_DIRS}")
 pkg_config_append_boost_libs(${BOOST_COMPONENTS})
+setup_project_finalize()
--- a/LICENSE
+++ b/LICENSE
 BSD 2-Clause License
 Copyright (c) 2014-2020, CNRS
-Copyright (c) 2018-2023, INRIA
+Copyright (c) 2018-2025, INRIA
 All rights reserved.
 Redistribution and use in source and binary forms, with or without
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