Enhancement/dependency

.gitignore

@@ -31,3 +31,5 @@ TAGS
 *.m~
 python/*.egg-info/
 /doc/_build/
+/build/
+

CMakeLists.txt

@@ -1,8 +1,8 @@
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.18)
 project(robin
-        VERSION 0.1
+        VERSION 1.2.0
         DESCRIPTION "Robust outlier rejection based on measurement compatibility graphs"
         LANGUAGES CXX
         )
@@ -32,9 +32,9 @@ include(DownloadExternal)
 #
 option(BUILD_DOCS "Build documentation." OFF)
 option(BUILD_TESTS "Enable testing with ctest." ON)
-option(BUILD_PYTHON_BINDINGS "Build python bindings." ON)
 option(BUILD_MATLAB_BINDINGS "Build MATLAB bindings" OFF)
 option(USE_ASAN "Enable address sanitizer" OFF)
+option(USE_SYSTEM_EIGEN3 "Use system pre-installed Eigen" ON)
 option(ENABLE_DIAGNOSTIC_PRINT "Enable printing of diagnostic messages" OFF)
 
 if (ENABLE_DIAGNOSTIC_PRINT)
@@ -46,7 +46,7 @@ endif ()
 # Dependencies
 #
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-find_package(Eigen3 3.3 QUIET REQUIRED NO_MODULE)
+find_external_dependency("Eigen3" "Eigen3::Eigen" "${CMAKE_CURRENT_LIST_DIR}/cmake/DownloadEigen.cmake")
 find_package(OpenMP QUIET REQUIRED)
 robin_download_pmc()
 robin_download_xenium()
@@ -89,6 +89,7 @@ include(CMakePackageConfigHelpers)
 install(
         TARGETS robin
         EXPORT robinTargets
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
         ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
 )
 
@@ -113,6 +114,7 @@ export(
 install(
     TARGETS xenium pmc
     EXPORT robinTargets
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
     ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
 )
 
@@ -146,13 +148,6 @@ if (BUILD_TESTS)
     add_subdirectory(tests)
 endif ()
 
-# Python bindings
-if (BUILD_PYTHON_BINDINGS)
-    robin_download_pybind11()
-    add_subdirectory(${pybind11_SOURCE_DIR} ${pybind11_BINARY_DIR})
-    add_subdirectory(python)
-endif ()
-
 # MATLAB bindings
 if (BUILD_MATLAB_BINDINGS)
     if (USE_ASAN)
@@ -177,7 +172,6 @@ message(STATUS "==============================================================="
 message(STATUS "============= Robin Configuration Options =====================")
 message(STATUS "Build Type: ${CMAKE_BUILD_TYPE}")
 message(STATUS "BUILD_DOCS: ${BUILD_DOCS}")
-message(STATUS "BUILD_PYTHON_BINDINGS: ${BUILD_PYTHON_BINDINGS}")
 message(STATUS "BUILD_MATLAB_BINDINGS: ${BUILD_MATLAB_BINDINGS}")
 message(STATUS "USE_ASAN: ${USE_ASAN}")
 message(STATUS "ENABLE_DIAGNOSTIC_PRINT: ${ENABLE_DIAGNOSTIC_PRINT}")

README.md

@@ -26,11 +26,24 @@ and
 
 If you are interested in more works from us, please visit our lab page [here](http://web.mit.edu/sparklab/).
 
-# Build and Install
+--- 
+
+# :gear: Build & Installation
+
+## :package: Dependency 
+
 ROBIN has the following dependencies:
 1. OpenMP
 2. Eigen3
 
+Thus, follow the below commandline:
+
+```bash
+sudo apt-get install gcc g++ build-essential libeigen3-dev cmake python3-pip python3-dev git ninja-build -y
+```
+
+## C++ Installation 
+
 Run the following to build the library using CMake (inside the repo root directory):
 ```bash
 mkdir build && cd build
@@ -41,16 +54,21 @@ The following CMake options are provided:
 ```
 BUILD_DOCS: Build documentation. Default: OFF
 BUILD_TESTS: Enable testing with ctest. Default: ON
-BUILD_PYTHON_BINDINGS: Build python bindings. Default: ON
 BUILD_MATLAB_BINDINGS: Build MATLAB bindings. Default: OFF
 USE_ASAN: Enable address sanitizer. Default: OFF
 ENABLE_DIAGNOSTIC_PRINT: Enable printing of diagnostic messages. Default: OFF
 ```
-To install Python bindings, after building the library (with `BUILD_PYTHON_BINDINGS=ON`), run:
+
+## Python Installation 
+
+It's simple! To install Python bindings, just run:
+
 ```bash
-cd build/python && pip install .
+pip3 install -e python/
 ```
 
+--- 
+
 # Third-party Data
 Some of the testing data are from the [Network Repository](http://networkrepository.com/index.php). 
 For more information, please refer to: 

cmake/DownloadEigen.cmake

@@ -0,0 +1,17 @@
+include(FetchContent)
+FetchContent_Declare(eigen URL https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
+                     PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_LIST_DIR}/eigen.patch UPDATE_DISCONNECTED 1)
+FetchContent_GetProperties(eigen)
+if(NOT eigen_POPULATED)
+  FetchContent_Populate(eigen)
+  if(${CMAKE_VERSION} GREATER_EQUAL 3.25)
+    add_subdirectory(${eigen_SOURCE_DIR} ${eigen_BINARY_DIR} SYSTEM EXCLUDE_FROM_ALL)
+  else()
+    # Emulate the SYSTEM flag introduced in CMake 3.25. Withouth this flag the compiler will
+    # consider this 3rdparty headers as source code and fail due the -Werror flag.
+    add_subdirectory(${eigen_SOURCE_DIR} ${eigen_BINARY_DIR} EXCLUDE_FROM_ALL)
+    get_target_property(eigen_include_dirs eigen INTERFACE_INCLUDE_DIRECTORIES)
+    set_target_properties(eigen PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "${eigen_include_dirs}")
+  endif()
+endif()
+

cmake/DownloadExternal.cmake

@@ -5,7 +5,7 @@ include(GNUInstallDirs)
 function(robin_download_pybind11)
 	download_project(PROJ pybind11
 		GIT_REPOSITORY https://github.com/pybind/pybind11.git
-		GIT_TAG        v2.5.0
+		GIT_TAG        v2.13.6
 		QUIET
 	)
 	set(pybind11_SOURCE_DIR "${pybind11_SOURCE_DIR}" PARENT_SCOPE)
@@ -89,3 +89,17 @@ function(robin_download_xenium)
 	)
 	install(DIRECTORY ${xenium_SOURCE_DIR}/xenium DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 endfunction()
+
+# For handling Eigen3 library
+function(find_external_dependency PACKAGE_NAME TARGET_NAME INCLUDED_CMAKE_PATH)
+  string(TOUPPER ${PACKAGE_NAME} PACKAGE_NAME_UP)
+  set(USE_FROM_SYSTEM_OPTION "USE_SYSTEM_${PACKAGE_NAME_UP}")
+  if(${${USE_FROM_SYSTEM_OPTION}})
+    find_package(${PACKAGE_NAME} QUIET NO_MODULE)
+  endif()
+  if(NOT ${${USE_FROM_SYSTEM_OPTION}} OR NOT TARGET ${TARGET_NAME})
+    set(${USE_FROM_SYSTEM_OPTION} OFF PARENT_SCOPE)
+    include(${INCLUDED_CMAKE_PATH})
+  endif()
+endfunction()
+

cmake/eigen.patch

@@ -0,0 +1,74 @@
+commit cf82186416d04ea5df2a397d8fe09dc78d40ca65
+Author: Antonio Sánchez <[email protected]>
+Date:   Sat Mar 5 05:49:45 2022 +0000
+
+    Adds new CMake Options for controlling build components.
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index de1c23e91..0af36a53a 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -477,6 +477,9 @@ if(EIGEN_BUILD_TESTING)
+   add_subdirectory(failtest)
+ endif()
+
++include(CMakeDetermineFortranCompiler)
++option(EIGEN_BUILD_BLAS "Toggles the building of the Eigen Blas library" ${CMAKE_Fortran_COMPILER})
++option(EIGEN_BUILD_LAPACK "Toggles the building of the included Eigen LAPACK library" ${CMAKE_Fortran_COMPILER})
+ if(EIGEN_LEAVE_TEST_IN_ALL_TARGET)
+   add_subdirectory(blas)
+   add_subdirectory(lapack)
+@@ -611,6 +614,8 @@ set_target_properties (eigen PROPERTIES EXPORT_NAME Eigen)
+
+ install (TARGETS eigen EXPORT Eigen3Targets)
+
++option(EIGEN_BUILD_CMAKE_PACKAGE "Enables the creation of EigenConfig.cmake and related files" ON)
++if(EIGEN_BUILD_CMAKE_PACKAGE)
+ configure_package_config_file (
+   ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Eigen3Config.cmake.in
+   ${CMAKE_CURRENT_BINARY_DIR}/Eigen3Config.cmake
+@@ -655,6 +660,7 @@ install (FILES ${CMAKE_CURRENT_BINARY_DIR}/Eigen3Config.cmake
+ # Add uninstall target
+ add_custom_target ( uninstall
+     COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_SOURCE_DIR}/cmake/EigenUninstall.cmake)
++endif()
+
+ if (EIGEN_SPLIT_TESTSUITE)
+   ei_split_testsuite("${EIGEN_SPLIT_TESTSUITE}")
+diff --git a/blas/CMakeLists.txt b/blas/CMakeLists.txt
+index 8d3cb86dc..c530957fb 100644
+--- a/blas/CMakeLists.txt
++++ b/blas/CMakeLists.txt
+@@ -1,6 +1,7 @@
+
+ project(EigenBlas CXX)
+
++if(EIGEN_BUILD_BLAS)
+ include(CheckLanguage)
+ check_language(Fortran)
+ if(CMAKE_Fortran_COMPILER)
+@@ -59,4 +60,4 @@ if(EIGEN_BUILD_TESTING)
+ endif()
+
+ endif()
+-
++endif()
+diff --git a/lapack/CMakeLists.txt b/lapack/CMakeLists.txt
+index c8ca64001..8d6d75401 100644
+--- a/lapack/CMakeLists.txt
++++ b/lapack/CMakeLists.txt
+@@ -1,5 +1,7 @@
+ project(EigenLapack CXX)
+
++if(EIGEN_BUILD_LAPACK AND EIGEN_BUILD_BLAS)
++
+ include(CheckLanguage)
+ check_language(Fortran)
+ if(CMAKE_Fortran_COMPILER)
+@@ -457,3 +459,6 @@ if(EXISTS ${eigen_full_path_to_testing_lapack})
+
+ endif()
+
++elseif(EIGEN_BUILD_LAPACK AND NOT EIGEN_BUILD_BLAS)
++ message(FATAL_ERROR "EIGEN_BUILD_LAPACK requires EIGEN_BUILD_BLAS")
++endif() #EIGEN_BUILD_LAPACK

python/CMakeLists.txt

@@ -1,37 +1,40 @@
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.18)
 
 project(robin_python_bindings)
 
-pybind11_add_module(robin_py robin_py/robin_py.cpp)
+# Set build type
+set(CMAKE_BUILD_TYPE Release)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-message(STATUS "Python Interpreter Version: ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}")
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+find_package(pybind11 CONFIG REQUIRED)
 
-target_link_libraries(robin_py PUBLIC robin)
+message(STATUS "Python Interpreter Version: ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}")
 
 # fix for clang
 # see: https://github.com/pybind/pybind11/issues/1818
 if (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
-    target_compile_options(robin_py PUBLIC -fsized-deallocation)
+    target_compile_options(spark_robin PUBLIC -fsized-deallocation)
+endif ()
+
+if (DEFINED SKBUILD)
+    message(STATUS "Building with Scikit-Build")
 endif ()
 
-# make sure to output the build file to robin_py folder
-SET_TARGET_PROPERTIES(robin_py
-        PROPERTIES
-        PREFIX ""
-        LIBRARY_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/robin_py"
-        )
-
-# copy package __init__.py file
-configure_file(robin_py/__init__.py
-        ${CMAKE_CURRENT_BINARY_DIR}/robin_py/__init__.py
-        )
-
-# copy setup.py file
-configure_file(setup.py.in
-        ${CMAKE_CURRENT_BINARY_DIR}/setup.py
-        )
-
-file(COPY .
-        DESTINATION .
-        FILES_MATCHING
-        PATTERN *.py)
+if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../)
+  # 'robin_cpp': user-defined build directory
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/../ ${CMAKE_CURRENT_BINARY_DIR}/robin_cpp)
+else()
+  message(STATUS "Performing out-of-tree build, fetching ROBIN v${CMAKE_PROJECT_VERSION} Release from Github")
+  include(FetchContent)
+  FetchContent_Declare(
+    ext_robin PREFIX robin
+    URL https://github.com/MIT-SPARK/ROBIN/archive/refs/tags/v${CMAKE_PROJECT_VERSION}.tar.gz)
+  FetchContent_MakeAvailable(ext_robin)
+endif()
+
+pybind11_add_module(spark_robin robin_py/robin_py.cpp)
+
+target_link_libraries(spark_robin PUBLIC robin::robin pmc)
+
+install(TARGETS spark_robin DESTINATION .)

python/example.py

@@ -1,22 +1,22 @@
-import robin_py
+import spark_robin
 
 if __name__ == "__main__":
     print("Examples showing usage of robin_py")
 
     # creating a Graph in robin
-    g = robin_py.AdjListGraph()
+    g = spark_robin.AdjListGraph()
 
     for i in range(10):
         g.AddVertex(i)
         g.AddVertex(i+10)
         g.AddEdge(i, i+10)
 
     # find the corresponding inlier structures
-    max_core_indices = robin_py.FindInlierStructure(
-        g, robin_py.InlierGraphStructure.MAX_CORE
+    max_core_indices = spark_robin.FindInlierStructure(
+        g, spark_robin.InlierGraphStructure.MAX_CORE
     )
-    max_clique_indices = robin_py.FindInlierStructure(
-        g, robin_py.InlierGraphStructure.MAX_CLIQUE
+    max_clique_indices = spark_robin.FindInlierStructure(
+        g, spark_robin.InlierGraphStructure.MAX_CLIQUE
     )
 
 

python/pyproject.toml

@@ -0,0 +1,35 @@
+[build-system]
+requires = ["scikit_build_core", "pybind11"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "spark_robin"
+version = "1.2.0"
+requires-python = ">=3.8"
+description ='Python binding for Robin'
+authors = [
+    { name = "Jingnan Shi", email = "[email protected]" },
+]
+classifiers = [
+    "Intended Audience :: Developers",
+    "Intended Audience :: Education",
+    "Intended Audience :: Other Audience",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: Unix",
+    "Programming Language :: C++",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+
+[tool.scikit-build]
+

python/robin_py/__init__.py

@@ -1 +1 @@
-from .robin_py import *
+from .spark_robin import *

python/robin_py/robin_py.cpp

@@ -15,7 +15,7 @@ namespace py = pybind11;
 /**
  * Python interface with pybind11
  */
-PYBIND11_MODULE(robin_py, m) {
+PYBIND11_MODULE(spark_robin, m) {
   m.doc() = "Python binding for Robin";
 
   // GraphStorageType