Merge pull request #1 from Lucas-Haubert/topic/decomps_geometry_solvers

Bindings for Eigen's decompositions, matrix solvers, and geometry module, and add stubs

Author: ManifoldFR

.gersemirc

@@ -1,4 +1,4 @@
-definitions: [./CMakeLists.txt, ./cmake]
+definitions: [./CMakeLists.txt, ./cmake, ./tests]
 line_length: 80
 indent: 2
 warn_about_unknown_commands: false

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# pre-commit run -a (format-all, 2025-03-19)
+98c85ab243b68db680a0a5f1ccbf238aeb6523ba

.github/workflows/macos-linux-windows-pixi.yml

@@ -41,7 +41,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, macos-13, windows-latest]
-        environment: [default, python-oldest]
+        environment: [all, all-python-oldest]
         build_type: [Release, Debug]
 
     steps:

.gitignore

@@ -1,5 +1,6 @@
 build*/
 .cache/
+__pycache__
 
 # pixi environments
 .pixi

.pre-commit-config.yaml

@@ -5,7 +5,7 @@ ci:
   submodules: true
 repos:
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v19.1.7
+    rev: v20.1.0
     hooks:
     - id: clang-format
       types_or: []
@@ -27,8 +27,17 @@ repos:
             (?x)^(
                 doc/doxygen-awesome.*
             )$
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.11.2
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
   - repo: https://github.com/BlankSpruce/gersemi
-    rev: 0.19.0
+    rev: 0.19.2
     hooks:
       - id: gersemi
   - repo: https://github.com/Lucas-C/pre-commit-hooks

CMakeLists.txt

@@ -1,27 +1,77 @@
+#
+# Copyright 2025 INRIA
+#
+
 cmake_minimum_required(VERSION 3.18)
 
 set(PROJECT_NAME nanoeigenpy)
-set(PROJECT_URL https://github.com/ManifoldFR/nanoeigenpy)
+set(PROJECT_URL https://github.com/Simple-Robotics/nanoeigenpy)
 set(PROJECT_DESCRIPTION "Tools for using Eigen with nanobind")
 set(PROJECT_CUSTOM_HEADER_EXTENSION "hpp")
 set(PROJECT_USE_CMAKE_EXPORT True)
 
-include(cmake/base.cmake)
+# 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(EXISTS "${JRL_CMAKE_MODULES}/base.cmake")
+  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
+      "\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.")
+    include(FetchContent)
+    FetchContent_Declare(
+      "jrl-cmakemodules"
+      GIT_REPOSITORY "https://github.com/jrl-umi3218/jrl-cmakemodules.git"
+    )
+    FetchContent_MakeAvailable("jrl-cmakemodules")
+    FetchContent_GetProperties("jrl-cmakemodules" SOURCE_DIR JRL_CMAKE_MODULES)
+  endif()
+endif()
+
+option(INSTALL_DOCUMENTATION "Generate and install the documentation" OFF)
 
+if(POLICY CMP0167)
+  cmake_policy(SET CMP0167 NEW)
+  set(CMAKE_POLICY_DEFAULT_CMP0167 NEW)
+endif()
+if(POLICY CMP0177)
+  cmake_policy(SET CMP0177 NEW)
+  set(CMAKE_POLICY_DEFAULT_CMP0177 NEW)
+endif()
+include("${JRL_CMAKE_MODULES}/base.cmake")
 COMPUTE_PROJECT_ARGS(PROJECT_ARGS LANGUAGES CXX)
+include("${JRL_CMAKE_MODULES}/ide.cmake")
+include("${JRL_CMAKE_MODULES}/apple.cmake")
 project(${PROJECT_NAME} ${PROJECT_ARGS})
 
+string(REPLACE "-pedantic" "" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
+string(REPLACE "-Wcast-qual" "" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
+string(REPLACE "-Wconversion" "" CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
+
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)
 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
 
-find_package(Eigen3 REQUIRED)
-
-add_library(nanoeigenpy_headers INTERFACE)
-target_link_libraries(nanoeigenpy_headers INTERFACE Eigen3::Eigen)
-
-find_package(Python REQUIRED COMPONENTS Interpreter Development)
-
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
   set_property(
@@ -30,6 +80,25 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   )
 endif()
 
+option(
+  BUILD_WITH_CHOLMOD_SUPPORT
+  "Build NanoEigenPy with the Cholmod support"
+  OFF
+)
+
+if(APPLE)
+  option(
+    BUILD_WITH_ACCELERATE_SUPPORT
+    "Build EigenPy with the Accelerate support"
+    OFF
+  )
+endif(APPLE)
+
+# Find dependencies
+ADD_PROJECT_DEPENDENCY(Eigen3 REQUIRED PKG_CONFIG_REQUIRES "eigen3 >= 3.3.1")
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development)
+
 # Detect the installed nanobind package and import it into CMake
 execute_process(
   COMMAND "${Python_EXECUTABLE}" -m nanobind --cmake_dir
@@ -38,29 +107,133 @@ execute_process(
 )
 find_package(nanobind CONFIG REQUIRED)
 
-file(GLOB nanoeigenpy_SOURCES src/*.cpp)
-nanobind_add_module(nanoeigenpy NB_STATIC NB_SUPPRESS_WARNINGS ${nanoeigenpy_SOURCES})
-target_link_libraries(nanoeigenpy PUBLIC nanoeigenpy_headers)
+# Setup main targets
+file(
+  GLOB_RECURSE ${PROJECT_NAME}_HEADERS
+  CONFIGURE_DEPENDS
+  include/nanoeigenpy/*.hpp
+)
+
+add_library(nanoeigenpy_headers INTERFACE)
+target_include_directories(
+  nanoeigenpy_headers
+  INTERFACE
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+)
+target_link_libraries(nanoeigenpy_headers INTERFACE Eigen3::Eigen)
+
+set(${PROJECT_NAME}_SOURCES src/module.cpp src/solvers.cpp)
+nanobind_add_module(nanoeigenpy NB_STATIC NB_SUPPRESS_WARNINGS ${nanoeigenpy_SOURCES} ${nanoeigenpy_HEADERS})
+target_link_libraries(nanoeigenpy PRIVATE nanoeigenpy_headers)
+
+# Cholmod
+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 CHOLMOD support (LGPL). See CHOLMOD/Doc/License.txt for further details."
+  )
+  file(
+    GLOB ${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_CHOLMOD_HEADERS
+    include/nanoeigenpy/decompositions/sparse/cholmod/*.hpp
+  )
+  list(
+    APPEND
+    ${PROJECT_NAME}_HEADERS
+    ${${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_CHOLMOD_HEADERS}
+  )
+  target_link_libraries(nanoeigenpy PRIVATE CHOLMOD::CHOLMOD)
+else()
+  list(
+    FILTER ${PROJECT_NAME}_HEADERS
+    EXCLUDE
+    REGEX "include/nanoeigenpy/decompositions/sparse/cholmod/.*"
+  )
+endif(BUILD_WITH_CHOLMOD_SUPPORT)
+
+# Apple accelerate
+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)
+  message(STATUS "Build with Accelerate support framework.")
+  target_compile_definitions(
+    nanoeigenpy_headers
+    INTERFACE -DNANOEIGENPY_WITH_ACCELERATE_SUPPORT
+  )
+endif(BUILD_WITH_ACCELERATE_SUPPORT)
+
+if(BUILD_WITH_ACCELERATE_SUPPORT)
+  file(
+    GLOB ${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_ACCELERATE_HEADERS
+    include/nanoeigenpy/decompositions/sparse/accelerate/*.hpp
+  )
+  list(
+    APPEND
+    ${PROJECT_NAME}_HEADERS
+    ${${PROJECT_NAME}_DECOMPOSITIONS_SPARSE_ACCELERATE_HEADERS}
+  )
+else()
+  list(
+    FILTER ${PROJECT_NAME}_HEADERS
+    EXCLUDE
+    REGEX "include/nanoeigenpy/decompositions/sparse/accelerate/.*"
+  )
+endif(BUILD_WITH_ACCELERATE_SUPPORT)
+
+if(BUILD_WITH_ACCELERATE_SUPPORT)
+  target_link_libraries(nanoeigenpy PRIVATE Accelerate)
+endif()
 
 if(BUILD_TESTING)
   add_subdirectory(tests)
 endif()
 
-install(
-  TARGETS nanoeigenpy_headers
-  EXPORT ${TARGETS_EXPORT_NAME}
-  INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+nanobind_add_stub(
+  nanoeigenpy_stub
+  INSTALL_TIME
+  VERBOSE
+  MODULE nanoeigenpy
+  OUTPUT nanoeigenpy.pyi
+  PYTHON_PATH $<TARGET_FILE_DIR:nanoeigenpy>
+  DEPENDS nanoeigenpy
 )
 
+# Install targets
 install(
-  DIRECTORY include/nanoeigenpy
-  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
-  FILES_MATCHING
-  PATTERN "*.hpp"
+  TARGETS ${PROJECT_NAME}_headers
+  EXPORT ${TARGETS_EXPORT_NAME}
+  PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+  INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
 )
 
 install(
-  TARGETS nanoeigenpy
+  TARGETS ${PROJECT_NAME}
   EXPORT ${TARGETS_EXPORT_NAME}
   LIBRARY DESTINATION ${Python_SITELIB}
 )
+
+ADD_HEADER_GROUP(${PROJECT_NAME}_HEADERS)
+ADD_SOURCE_GROUP(${PROJECT_NAME}_SOURCES)
+
+SETUP_PROJECT_FINALIZE()

README.md

@@ -1,5 +1,9 @@
 # nanoeigenpy
 
+<p align="left">
+  <a href="https://github.com/astral-sh/ruff"><img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Linter: ruff"></a>
+</p>
+
 This is a collection of tools for using Eigen together with nanobind, as a successor to the [eigenpy](https://github.com/stack-of-tasks/eigenpy) support library. Its aim is to help the transition away from Boost.Python.
 
 It reintroduces a few features (e.g. bindings for Eigen matrix decompositions) which are not in [nanobind](https://github.com/wjakob/nanobind) at time of writing.
@@ -18,6 +22,16 @@ These features were finally added to eigenpy with a lot of developer effort. Thi
 - bindings for Eigen's [Geometry module](https://libeigen.gitlab.io/docs/group__Geometry__Module.html) - quaternions, angle-axis representations...
 - bindings for Eigen's matrix dense and sparse decompositions and solvers
 
+### Optional features
+
+**nanoeigenpy** also provides bindings for Eigen's [Cholmod](https://eigen.tuxfamily.org/dox/group__CholmodSupport__Module.html) and [Apple Accelerate](https://eigen.tuxfamily.org/dox/group__AccelerateSupport__Module.html) modules.
+
+> [!NOTE]
+> The Accelerate module is only available on Eigen's master branch, and not in any official release yet (as of 3/28/2025).
+>
+> Cholmod is part of the [SuiteSparse](https://github.com/DrTimothyAldenDavis/SuiteSparse) algorithms library. It can be installed standalone from [conda](https://anaconda.org/conda-forge/libcholmod).
+
+
 ## Example usage
 
 The features included in **nanoeigenpy** are distributed in a Python module which can be imported, or through standalone headers which can be included in your own Python bindings code using a CMake target.
@@ -92,6 +106,7 @@ f(quat)
 
 - the Eigen C++ template library - [conda-forge](https://anaconda.org/conda-forge/eigen) | [repo](https://gitlab.com/libeigen/eigen/)
 - nanobind - [conda-forge](https://anaconda.org/conda-forge/nanobind) | [repo](https://github.com/wjakob/nanobind)
+- [for testing] pytest - `conda install pytest` or `pip install pytest`
 
 #### Conda
 

cmake

@@ -9,3 +9,4 @@ set CMAKE_COLOR_DIAGNOSTICS=1
 
 :: Set default build value only if not previously set
 if not defined NANOEIGENPY_BUILD_TYPE (set NANOEIGENPY_BUILD_TYPE=Release)
+if not defined NANOEIGENPY_BUILD_WITH_CHOLMOD (set NANOEIGENPY_BUILD_WITH_CHOLMOD=OFF)

development/scripts/pixi/activation.bat

@@ -33,3 +33,4 @@ export CMAKE_COLOR_DIAGNOSTICS=1
 
 # Set default build value only if not previously set
 export NANOEIGENPY_BUILD_TYPE=${NANOEIGENPY_BUILD_TYPE:=Release}
+export NANOEIGENPY_BUILD_WITH_CHOLMOD=${NANOEIGENPY_BUILD_WITH_CHOLMOD:=OFF}