remove leidenalg link

CMakeLists.txt

@@ -18,19 +18,15 @@ list(TRANSFORM srclist PREPEND "${PROJECT_SOURCE_DIR}/src/")
 add_library(rliger2 SHARED ${srclist})
 set_target_properties(rliger2 PROPERTIES PREFIX "")
 if(APPLE)
-    set_target_properties(rliger2 PROPERTIES SUFFIX "so")
+    set_target_properties(rliger2 PROPERTIES SUFFIX ".so")
 endif()
 target_include_directories(rliger2
     PRIVATE "${PROJECT_SOURCE_DIR}/src/")
 
-CPMAddPackage(NAME leidenAlg GITHUB_REPOSITORY kharchenkolab/leidenAlg GIT_TAG 1.1.0 DOWNLOAD_ONLY True)
-target_include_directories(rliger2 PRIVATE "${CMAKE_SOURCE_DIR}/src/_deps/leidenalg-src/src/leidenalg/include")
-target_include_directories(rliger2 PRIVATE "${CMAKE_SOURCE_DIR}/src/_deps/leidenalg-src/src/rigraph/include")
 find_r_module(Rcpp)
 find_r_module(RcppArmadillo)
 find_r_module(RcppProgress)
 find_r_module(RcppEigen)
-find_r_module(leidenAlg)
 
 if(R_INCLUDE_DIR)
     target_include_directories(rliger2 PRIVATE "${R_INCLUDE_DIR}")
@@ -61,15 +57,6 @@ if(R_RCPPEIGEN)
 else()
     message(FATAL_ERROR "missing RcppEigen")
 endif()
-if(R_LEIDENALG)
-    find_library(LEIDENALG_LIB leidenAlg.so leidenAlg.dll PATHS "${R_LEIDENALG}" PATH_SUFFIXES "libs")
-    add_library(leidenAlg UNKNOWN IMPORTED)
-    set_property(TARGET leidenAlg PROPERTY IMPORTED_LOCATION ${LEIDENALG_LIB})
-    target_link_libraries(rliger2 PRIVATE leidenAlg)
-else()
-    message(FATAL_ERROR "missing leidenAlg")
-endif()
-
 
 if(NOT(APPLE AND(CMAKE_HOST_SYSTEM_PROCESSOR MATCHES arm64)))
 if(OpenMP_CXX_FOUND)

DESCRIPTION

@@ -36,7 +36,7 @@ LazyData: true
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
 Encoding: UTF-8
-LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress, leidenAlg
+LinkingTo: Rcpp, RcppArmadillo, RcppEigen, RcppProgress
 Depends:
     Matrix,
     methods,

R/RcppExports.R

@@ -103,21 +103,6 @@ makeFeatureMatrix <- function(bedmat, barcodes) {
     .Call(`_rliger2_makeFeatureMatrix`, bedmat, barcodes)
 }
 
-#' Refer to the R function find_partition()
-#' For notes of the graph object, refer to https://igraph.org/c/doc/igraph-Basic.html
-#'
-#' @param edgelist The graph edge list
-#' @param edgelist_length integer The length of the graph edge list
-#' @param num_vertices integer The number of vertices in the graph
-#' @param direction boolean Whether the graph is directed or undirected
-#' @param edge_weights Vector of edge weights. In weighted graphs, a real number is assigned to each (directed or undirected) edge. For an unweighted graph, this is set to 1. Refer to igraph, weighted graphs.
-#' @param resolution Integer resoluiton parameter controlling communities detected (default=1.0) Higher resolutions lead to more communities, while lower resolutions lead to fewer communities.
-#' @param niter Number of iterations that the algorithm should be run for (default=2)
-#' @return A vector of membership values
-find_partition_rcpp <- function(edgelist, edgelist_length, num_vertices, direction, edge_weights, resolution = 1.0, nIter = 2L) {
-    .Call(`_rliger2_find_partition_rcpp`, edgelist, edgelist_length, num_vertices, direction, edge_weights, resolution, nIter)
-}
-
 cluster_vote <- function(nn_ranked, clusts) {
     .Call(`_rliger2_cluster_vote`, nn_ranked, clusts)
 }

src/RcppExports.cpp

@@ -305,23 +305,6 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-// find_partition_rcpp
-std::vector<size_t> find_partition_rcpp(std::vector<int>& edgelist, int edgelist_length, int num_vertices, bool direction, std::vector<double>& edge_weights, double resolution, int nIter);
-RcppExport SEXP _rliger2_find_partition_rcpp(SEXP edgelistSEXP, SEXP edgelist_lengthSEXP, SEXP num_verticesSEXP, SEXP directionSEXP, SEXP edge_weightsSEXP, SEXP resolutionSEXP, SEXP nIterSEXP) {
-BEGIN_RCPP
-    Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
-    Rcpp::traits::input_parameter< std::vector<int>& >::type edgelist(edgelistSEXP);
-    Rcpp::traits::input_parameter< int >::type edgelist_length(edgelist_lengthSEXP);
-    Rcpp::traits::input_parameter< int >::type num_vertices(num_verticesSEXP);
-    Rcpp::traits::input_parameter< bool >::type direction(directionSEXP);
-    Rcpp::traits::input_parameter< std::vector<double>& >::type edge_weights(edge_weightsSEXP);
-    Rcpp::traits::input_parameter< double >::type resolution(resolutionSEXP);
-    Rcpp::traits::input_parameter< int >::type nIter(nIterSEXP);
-    rcpp_result_gen = Rcpp::wrap(find_partition_rcpp(edgelist, edgelist_length, num_vertices, direction, edge_weights, resolution, nIter));
-    return rcpp_result_gen;
-END_RCPP
-}
 // cluster_vote
 IntegerVector cluster_vote(const Eigen::MatrixXd& nn_ranked, IntegerVector clusts);
 RcppExport SEXP _rliger2_cluster_vote(SEXP nn_rankedSEXP, SEXP clustsSEXP) {
@@ -434,7 +417,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"_rliger2_cpp_rank_matrix_dense", (DL_FUNC) &_rliger2_cpp_rank_matrix_dense, 1},
     {"_rliger2_cpp_nnzeroGroups_dgc_T", (DL_FUNC) &_rliger2_cpp_nnzeroGroups_dgc_T, 6},
     {"_rliger2_makeFeatureMatrix", (DL_FUNC) &_rliger2_makeFeatureMatrix, 2},
-    {"_rliger2_find_partition_rcpp", (DL_FUNC) &_rliger2_find_partition_rcpp, 7},
     {"_rliger2_cluster_vote", (DL_FUNC) &_rliger2_cluster_vote, 2},
     {"_rliger2_scale_columns_fast", (DL_FUNC) &_rliger2_scale_columns_fast, 3},
     {"_rliger2_max_factor", (DL_FUNC) &_rliger2_max_factor, 3},