Remove pmc dependency

CMakeLists.txt

@@ -36,6 +36,7 @@ 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)
+option(WITH_PMC "Enable usage of pmc (GPL License - see notice)" OFF)
 
 if (ENABLE_DIAGNOSTIC_PRINT)
     message(STATUS "Enable printing of diagnostic messages.")
@@ -46,11 +47,34 @@ endif ()
 # Dependencies
 #
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-find_external_dependency("Eigen3" "Eigen3::Eigen" "${CMAKE_CURRENT_LIST_DIR}/cmake/DownloadEigen.cmake")
-find_package(OpenMP QUIET REQUIRED)
-robin_download_pmc()
-robin_download_xenium()
-add_subdirectory(${pmc_SOURCE_DIR} ${pmc_BINARY_DIR})
+find_package(Eigen3)
+if(NOT Eigen3_FOUND)
+    message(STATUS "Eigen3 not found. Downloading Eigen3.")
+    find_external_dependency("Eigen3" "Eigen3::Eigen" "${CMAKE_CURRENT_LIST_DIR}/cmake/DownloadEigen.cmake")
+endif()
+
+find_package(OpenMP REQUIRED)
+
+# pmc
+if(WITH_PMC)
+    message(WARNING "PMC is licensed under the GPL.  Enabling WITH_PMC will cause the resulting 'robin' library to be licensed under the GPL.")
+    find_package(pmc QUIET)
+    if(NOT pmc_FOUND)
+        robin_download_pmc()
+        add_subdirectory(${pmc_SOURCE_DIR} ${pmc_BINARY_DIR})
+    endif()
+
+endif()
+
+find_package(xenium QUIET)
+if(NOT xenium_FOUND)
+    message(STATUS "Xenium not found. Downloading Xenium.")
+    robin_download_xenium()
+    #  Set the flag after downloading
+    set(XENIUM_DOWNLOADED TRUE)
+else()
+    set(XENIUM_DOWNLOADED FALSE)
+endif()
 
 #
 # Add robin target
@@ -63,19 +87,34 @@ file(GLOB
 
 add_library(robin STATIC ${SOURCE_FILES})
 add_library(robin::robin ALIAS robin)
+
+if(WITH_PMC)
 target_link_libraries(robin
         PUBLIC Eigen3::Eigen
-               xenium
+        xenium
         PRIVATE OpenMP::OpenMP_CXX
         PRIVATE pmc)
+        target_compile_definitions(robin PRIVATE USE_PMC) # CHANGED THIS LINE
+else()
+target_link_libraries(robin
+        PUBLIC Eigen3::Eigen
+        xenium
+        PRIVATE OpenMP::OpenMP_CXX)
+endif()
+
 target_include_directories(
         robin
         PUBLIC
         $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/include>
         $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
         $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+        ${Eigen3_INCLUDE_DIRS}
+        ${xenium_INCLUDE_DIRS}
 )
 
+
+
+
 if (USE_ASAN)
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=address -fPIC")
     set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -fsanitize=address")
@@ -111,13 +150,23 @@ export(
         NAMESPACE robin::
 )
 
-install(
-    TARGETS xenium pmc
-    EXPORT robinTargets
-    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-)
+if(xenium_FOUND AND XENIUM_DOWNLOADED)
+    install(
+        TARGETS xenium
+        EXPORT robinTargets
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    )
+endif()
 
+if(WITH_PMC AND pmc_FOUND)
+    install(
+        TARGETS pmc
+        EXPORT robinTargets
+        LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+        ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    )
+endif()
 
 install(
         EXPORT robinTargets
@@ -135,10 +184,12 @@ install(
 
 install(DIRECTORY include/robin DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 
-# To set forcibly xeniumConfig.cmake
-install(FILES cmake/xeniumConfig.cmake
-        DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xenium
-        )
+if(xenium_FOUND)
+    # To set forcibly xeniumConfig.cmake
+    install(FILES cmake/xeniumConfig.cmake
+            DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/xenium
+            )
+endif()
 
 export(PACKAGE robin)
 
@@ -175,4 +226,4 @@ message(STATUS "BUILD_DOCS: ${BUILD_DOCS}")
 message(STATUS "BUILD_MATLAB_BINDINGS: ${BUILD_MATLAB_BINDINGS}")
 message(STATUS "USE_ASAN: ${USE_ASAN}")
 message(STATUS "ENABLE_DIAGNOSTIC_PRINT: ${ENABLE_DIAGNOSTIC_PRINT}")
-message(STATUS "===============================================================")
+message(STATUS "===============================================================")

include/robin/core.hpp

@@ -221,7 +221,7 @@ class CompGraphConstructor<Measurements, CompCheckFunc, 2>
       std::queue<EdgeType> edge_buffer;
 
 #pragma omp for
-      for (size_t k = 0; k < N * (N - 1) / 2; ++k) {
+      for (long k = 0; k < N * (N - 1) / 2; ++k) {
         size_t i = k / N;
         size_t j = k % N;
         if (j <= i) {
@@ -293,7 +293,7 @@ class CompGraphConstructor<Measurements, CompCheckFunc, 2>
 
 #pragma omp for
       // visit each edge twice
-      for (size_t i = 0; i < N; ++i) {
+      for (long i = 0; i < N; ++i) {
         for (size_t j = 0; j < N; ++j) {
           subset_indices[0] = i;
           subset_indices[1] = j;
@@ -332,7 +332,7 @@ class CompGraphConstructor<Measurements, CompCheckFunc, 2>
 
 #pragma omp for
       // for loop that goes through each (i,j) edge twice
-      for (size_t i = 0; i < N; ++i) {
+      for (long i = 0; i < N; ++i) {
         for (size_t j = 0; j < N; ++j) {
           subset_indices[0] = i;
           subset_indices[1] = j;
@@ -366,7 +366,7 @@ class CompGraphConstructor<Measurements, CompCheckFunc, 2>
 
 #pragma omp for
       // for loop that goes through each (i,j) edge twice
-      for (size_t i = 0; i < N; ++i) {
+      for (long i = 0; i < N; ++i) {
         for (size_t j = 0; j < N; ++j) {
           subset_indices[0] = i;
           subset_indices[1] = j;
@@ -411,7 +411,7 @@ class CompGraphConstructor<Measurements, CompCheckFunc, 2>
       auto* subset_indices = new size_t[2];
 
 #pragma omp for
-      for (size_t k = 0; k < N * (N - 1) / 2; ++k) {
+      for (long k = 0; k < N * (N - 1) / 2; ++k) {
         size_t i = k / N;
         size_t j = k % N;
         if (j <= i) {
@@ -451,7 +451,7 @@ class CompGraphConstructor<Measurements, CompCheckFunc, 2>
       auto* subset_indices = new size_t[2];
 
 #pragma omp for
-      for (size_t k = 0; k < N * (N - 1) / 2; ++k) {
+      for (long k = 0; k < N * (N - 1) / 2; ++k) {
         size_t i = k / N;
         size_t j = k % N;
         if (j <= i) {

include/robin/graph_solvers.hpp

@@ -68,6 +68,7 @@ class KCoreDecompositionSolver {
   size_t max_k_core_number_ = 0;
 };
 
+#ifdef USE_PMC
 /**
  * A facade to the Parallel Maximum Clique (PMC) library.
  *
@@ -119,5 +120,5 @@ class MaxCliqueSolver {
 private:
   Params params_;
 };
-
+#endif
 }

include/robin/pkc.hpp

@@ -60,24 +60,6 @@ struct graph_t {
  */
 void BZ_kCores(const IGraph& g, std::vector<size_t>* deg);
 
-/**
- * @brief K-core decomposition with parallel PKC. This is the non-optimized version.
- * Each thread has its own queue -- parallel PKC_org for k-core decomposition
- *
- * @param g
- * @param deg
- */
-void PKC_original(const IGraph& g, size_t* deg);
-
-/**
- * @brief K-core decomposition with parallel PKC. This particular function is suitable for large
- * graph, with optimization detailed in the original paper.
- *
- * @param g
- * @param deg
- */
-void PKC_optimized(const IGraph& g, size_t* deg);
-
 /**
  * @brief Interface with robin::Graph for K-core decomposition with parallel PKC.
  * @param g

include/robin/problems.hpp

@@ -5,7 +5,7 @@
 // See LICENSE for the license information
 
 #pragma once
-
+#define M_PI       3.14159265358979323846   // pi
 #define _USE_MATH_DEFINES
 
 #include <cmath>

include/robin/robin.hpp

@@ -25,7 +25,9 @@ namespace robin {
 //
 enum class InlierGraphStructure {
   MAX_CORE = 0,
+#ifdef USE_PMC  
   MAX_CLIQUE = 1,
+#endif
 };
 
 std::vector<size_t> FindInlierStructure(const IGraph* g, InlierGraphStructure graph_structure);

src/graph.cpp

@@ -9,7 +9,9 @@
 #include <omp.h>
 #include <random>
 
+#ifdef USE_PMC
 #include <pmc/pmc.h>
+#endif
 #include <robin/graph.hpp>
 #include <robin/pkc.hpp>
 

src/graph_solvers.cpp

@@ -4,7 +4,9 @@
 // Authors: Jingnan Shi, et al. (see THANKS for the full author list)
 // See LICENSE for the license information
 
+#ifdef USE_PMC
 #include <pmc/pmc.h>
+#endif
 #include <robin/pkc.hpp>
 #include <robin/graph_core.hpp>
 #include <robin/graph_solvers.hpp>
@@ -56,6 +58,7 @@ std::vector<size_t> KCoreDecompositionSolver::GetKCore(const size_t& k) {
   return k_core;
 }
 
+#ifdef USE_PMC
 //
 // Definitions for the MaxCliqueSolver class
 //
@@ -154,5 +157,5 @@ std::vector<size_t> MaxCliqueSolver::FindMaxClique(const IGraph& graph) const {
   vector<size_t> C_result(C.begin(), C.end());
   return C_result;
 }
-
+#endif
 }