Merge branch 'dev'

CHANGELOG.md

@@ -1,21 +1,21 @@
 # Changelog
 
-## [1.0.2] - 2022 March 3
-* Modified the Makevars file to correctly add an rpath (Runpath Search Path) for Mac OS users with `install_name_tool`. From the manual, the command used is `-change old new` whereby this "Changes  the dependent shared library install name old to new in the specified Mach-O binary.  More than one of these options can be specified.  If the Mach-O binary does not contain the old install name in a specified -change option the option is ignored."
+
+## [1.0.3] - 2022 April 08
+* Install rigraph directly in `/src`. Remove previous linking to `igraph` R package in Makevars.
+
+## [1.0.2] - 2022 March 03
+* Fixed Makevars to use `install_name_tool -change`.
 
 ## [1.0.1] - 2021 Dec 03
 * Modified the Makevars to use SHLIB_EXT to account for both shared library extensions on Mac OS (either *.so or *dylib)
 
 ## [1.0.0] - 2021-11-19
 * `leidenAlg` has gone through no major revisions in over a year. In order to avoid any confusion, this should be released with a major version.
 
-
 ## [0.1.1] - 2021-03-02
-
 * Fixed issue with unweighted graph. In this case, we set all edge weights to 1. 
 
-
 ## [0.1.0] - 2020-11-11
-
 * Version published on CRAN: https://cran.r-project.org/web/packages/leidenAlg/index.html
 * Tagged version on github released on 2 Jan 2021: https://github.com/kharchenkolab/leidenAlg/releases/tag/0.1.0

DESCRIPTION

@@ -8,10 +8,11 @@ License: GPL-3
 Copyright: See the file COPYRIGHTS for various leidenAlg copyright details
 Encoding: UTF-8
 LazyData: true
-Depends: R (>= 3.5.0), Matrix, igraph
+Depends: R (>= 3.5.0), Matrix
 Imports: 
     graphics,
     grDevices,
+    igraph,
     Matrix.utils,
     parallel, 
     Rcpp (>= 1.0.5), 
@@ -21,7 +22,7 @@ Suggests:
     pbapply,
     testthat (>= 3.1.0)
 LinkingTo: Rcpp, RcppArmadillo, RcppEigen
-SystemRequirements: GNU make
+SystemRequirements: C++11, GNU make (optional), libxml2 (optional), glpk (>= 4.57, optional)
 RoxygenNote: 7.1.2
 URL: https://github.com/kharchenkolab/leidenAlg
 BugReports: https://github.com/kharchenkolab/leidenAlg/issues

README.md

@@ -6,9 +6,12 @@
 
 Implements the Leiden algorithm via an R interface
 
-## Note: Leiden Algorithm now in igraph
 
-Since [October 2020](https://github.com/igraph/rigraph/pull/399), the R package [igraph](https://cran.r-project.org/web/packages/igraph/) contains the function `cluster_leiden()` implemented by Vincent Traag ([@vtraag](https://github.com/vtraag)). The usage of this function is detailed in the igraph documentation [here](https://igraph.org/r/html/1.2.7/cluster_leiden.html). We recommend users use this function. 
+#### Note: cluster_leiden() now in igraph
+
+Since [October 2020](https://github.com/igraph/rigraph/pull/399), the R package [igraph](https://cran.r-project.org/package=igraph) contains the function `cluster_leiden()` implemented by Vincent Traag ([@vtraag](https://github.com/vtraag)). The usage of this function is detailed in the igraph documentation [here](https://igraph.org/r/html/1.2.7/cluster_leiden.html). We recommend users use this function. 
+
+There is still no R package which entirely encompasses all of the functionality of the original Python/C++ implementation here from https://github.com/vtraag/leidenalg. We hope interested developers could use this package as a starting point for creating an R package which mirrors the full available functionality of the Python package. See [here](https://github.com/vtraag/leidenalg#usage) for details. 
 
 ## Summary
 

src/Makevars

@@ -1,29 +1,29 @@
 
 ## include OpenMP
 
-PKG_CXXFLAGS= -I"../inst/include"  -I"./leidenalg/igraph-R" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
+PKG_CXXFLAGS= -I"../inst/include"  -I"./rigraph/include" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
 
-PKGB_PATH=`echo 'library(igraph); cat(system.file("libs", package="igraph"))' \
-      | ${R_HOME}/bin/R --vanilla --slave`
 
+PKG_CFLAGS = -pthread 
+PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
+LDFLAGS += -lpthread
 
-PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) $(PKGB_PATH)/igraph$(SHLIB_EXT)
+
+
+PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
 CXX_STD = CXX11
 MkInclude = $(R_HOME)/etc${R_ARCH}/Makeconf
 
 #.PHONY: all sublibs
 
 #OBJECTS = $(.cpp=.o)
-SUBDIRS = leidenalg
-SUBLIBS = leidenalg.a
-
-IGRAPH_LIB = $(PKGB_PATH)/igraph$(SHLIB_EXT)
+SUBDIRS = rigraph leidenalg
+SUBLIBS = librigraph.a leidenalg.a
 
-all: $(SHLIB)
-	if [ "$(OS)" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -change 'igraph$(SHLIB_EXT)' $(PKGB_PATH)/igraph$(SHLIB_EXT) $(SHLIB); fi
 
+all: $(SHLIB) 
 
-$(SHLIB): $(OBJECTS) sublibs
+$(SHLIB): sublibs
 sublibs: sublibraries
 
 sublibraries: 

src/Makevars.win

@@ -1,34 +1,28 @@
 
 ## include OpenMP
 
-# detect R_arch 
-rarch := $(shell echo 'Sys.getenv("R_ARCH")' | ${R_HOME}/bin/R --vanilla --slave) 
+PKG_CXXFLAGS= -I"../inst/include"  -I"./rigraph/include" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
 
-PKGB_PATH := $(shell echo 'library(igraph); cat(system.file("libs", package="igraph"))' | ${R_HOME}/bin/R --vanilla --slave)
 
+PKG_CFLAGS = -pthread 
+PKG_CFLAGS += -I"./include"  -I"../rigraph/include"
+LDFLAGS += -lpthread
 
-## note: the space in '[1] "/i386" ' is important...
-## else, '[1] "/x64" '
-ifeq ($(rarch),[1] "/i386" )
- IGRAPH_LIB := $(PKGB_PATH)/i386/igraph.dll
-else
- IGRAPH_LIB := $(PKGB_PATH)/x64/igraph.dll
-endif
 
-PKG_CXXFLAGS=-I"../inst/include"  -I"./leidenalg/igraph-R" -I"./leidenalg/include" $(SHLIB_OPENMP_CXXFLAGS) 
-
-PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lm $(shell "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) $(IGRAPH_LIB)
+PKG_LIBS=-L/usr/lib/ -L"." -lpthread -lstdc++ -lleidenalg -lrigraph -lm `$(R_HOME)/bin/Rscript -e "Rcpp:::LdFlags()"` $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) $(SHLIB_OPENMP_CXXFLAGS) 
 CXX_STD = CXX11
 MkInclude = $(R_HOME)/etc${R_ARCH}/Makeconf
 
 #.PHONY: all sublibs
 
 #OBJECTS = $(.cpp=.o)
-SUBDIRS = leidenalg
-SUBLIBS = leidenalg.a
+SUBDIRS = rigraph leidenalg
+SUBLIBS = librigraph.a leidenalg.a
+
 
 all: $(SHLIB) 
-$(SHLIB): $(OBJECTS) sublibs
+
+$(SHLIB): sublibs
 sublibs: sublibraries
 
 sublibraries: 

src/leiden.cpp

@@ -76,4 +76,4 @@ std::vector<size_t> find_partition(SEXP graph, std::vector<double>& edge_weights
   //return(igraph_ecount(&g));
 
 }
-
+

src/leidenalg/CPMVertexPartition.cpp

@@ -1,4 +1,5 @@
 #include "CPMVertexPartition.h"
+#include "igraph.h"
 
 CPMVertexPartition::CPMVertexPartition(Graph* graph,
       vector<size_t> membership, double resolution_parameter) :

src/leidenalg/GraphHelper.cpp

@@ -1,5 +1,8 @@
 #include "GraphHelper.h"
 
+#include "igraph.h"
+
+
 #ifdef DEBUG
   using std::cerr;
   using std::endl;

src/leidenalg/LinearResolutionParameterVertexPartition.cpp

@@ -1,4 +1,6 @@
 #include "LinearResolutionParameterVertexPartition.h"
+#include "igraph.h"
+
 
 LinearResolutionParameterVertexPartition::LinearResolutionParameterVertexPartition(Graph* graph,
       vector<size_t> membership, double resolution_parameter) :

src/leidenalg/Makefile

@@ -1,6 +1,6 @@
 CXX ?= g++
 PKG_CXXFLAGS = -O3 -std=c++11 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
-PKG_CXXFLAGS += -I"./include" -I"./igraph-R"
+PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
 LDFLAGS += -lpthread
 
 

src/leidenalg/Makefile.win

@@ -1,6 +1,6 @@
 CXX ?= g++
 PKG_CXXFLAGS = -O3 -std=c++11 -pthread -fPIC $(SHLIB_OPENMP_CXXFLAGS)
-PKG_CXXFLAGS += -I"./include" -I"./igraph-R"
+PKG_CXXFLAGS += -I"./include" -I"../rigraph/include"
 LDFLAGS += -lpthread
 
 

src/leidenalg/ModularityVertexPartition.cpp

@@ -1,5 +1,7 @@
 #include "ModularityVertexPartition.h"
 
+#include "igraph.h"
+
 #ifdef DEBUG
 #include <iostream>
 using std::cerr;

src/leidenalg/MutableVertexPartition.cpp

@@ -1,5 +1,7 @@
 #include "MutableVertexPartition.h"
 
+#include "igraph.h"
+
 #ifdef DEBUG
   using std::cerr;
   using std::endl;

src/leidenalg/Optimiser.cpp

@@ -1,4 +1,6 @@
 #include "Optimiser.h"
+#include "igraph.h"
+
 
 /****************************************************************************
   Create a new Optimiser object

src/leidenalg/RBConfigurationVertexPartition.cpp

@@ -1,4 +1,6 @@
 #include "RBConfigurationVertexPartition.h"
+#include "igraph.h"
+
 
 RBConfigurationVertexPartition::RBConfigurationVertexPartition(Graph* graph,
       vector<size_t> const& membership, double resolution_parameter) :

src/leidenalg/RBERVertexPartition.cpp

@@ -1,5 +1,7 @@
 #include "RBERVertexPartition.h"
 
+#include "igraph.h"
+
 RBERVertexPartition::RBERVertexPartition(Graph* graph,
       vector<size_t> const& membership, double resolution_parameter) :
         LinearResolutionParameterVertexPartition(graph,

src/leidenalg/ResolutionParameterVertexPartition.cpp

@@ -1,4 +1,6 @@
 #include "ResolutionParameterVertexPartition.h"
+#include "igraph.h"
+
 
 ResolutionParameterVertexPartition::ResolutionParameterVertexPartition(Graph* graph,
       vector<size_t> membership, double resolution_parameter) :

src/leidenalg/SignificanceVertexPartition.cpp

@@ -1,5 +1,7 @@
 #include "SignificanceVertexPartition.h"
 
+#include "igraph.h"
+
 #ifdef DEBUG
 #include <iostream>
 using std::cerr;

src/leidenalg/SurpriseVertexPartition.cpp

@@ -1,5 +1,7 @@
 #include "SurpriseVertexPartition.h"
 
+#include "igraph.h"
+
 SurpriseVertexPartition::SurpriseVertexPartition(Graph* graph,
       vector<size_t> const& membership) :
         MutableVertexPartition(graph,

src/leidenalg/include/CPMVertexPartition.h

@@ -2,6 +2,7 @@
 #define CPMVERTEXPARTITION_H
 
 #include <LinearResolutionParameterVertexPartition.h>
+#include "igraph.h"
 
 class CPMVertexPartition : public LinearResolutionParameterVertexPartition
 {

src/leidenalg/include/GraphHelper.h

@@ -1,7 +1,7 @@
 #ifndef GRAPHHELPER_INCLUDED
 #define GRAPHHELPER_INCLUDED
 
-#include <igraph.h>
+#include "igraph.h"
 #include <vector>
 #include <set>
 #include <exception>
@@ -13,6 +13,8 @@
   using std::endl;
 //#endif
 
+
+
 class MutableVertexPartition;
 
 using std::vector;

src/leidenalg/include/LinearResolutionParameterVertexPartition.h

@@ -2,6 +2,7 @@
 #define LINEARRESOLUTIONPARAMETERVERTEXPARTITION_H
 
 #include <ResolutionParameterVertexPartition.h>
+#include "igraph.h"
 
 class LinearResolutionParameterVertexPartition : public ResolutionParameterVertexPartition
 {

src/leidenalg/include/ModularityVertexPartition.h

@@ -2,6 +2,8 @@
 #define MODULARITYVERTEXPARTITION_H
 
 #include <MutableVertexPartition.h>
+#include "igraph.h"
+
 
 class ModularityVertexPartition : public MutableVertexPartition
 {

src/leidenalg/include/MutableVertexPartition.h

@@ -7,6 +7,8 @@
 #include <set>
 #include <utility>
 #include <algorithm>
+#include "igraph.h"
+
 
 using std::string;
 using std::map;

src/leidenalg/include/Optimiser.h

@@ -5,6 +5,9 @@
 #include <set>
 #include <map>
 
+#include "igraph.h"
+
+
 #include <iostream>
 using std::cerr;
 using std::endl;

src/leidenalg/include/RBConfigurationVertexPartition.h

@@ -3,6 +3,9 @@
 
 #include "LinearResolutionParameterVertexPartition.h"
 
+#include "igraph.h"
+
+
 class RBConfigurationVertexPartition : public LinearResolutionParameterVertexPartition
 {
   public:

src/leidenalg/include/RBERVertexPartition.h

@@ -3,6 +3,8 @@
 
 #include <LinearResolutionParameterVertexPartition.h>
 
+#include "igraph.h"
+
 
 class RBERVertexPartition : public LinearResolutionParameterVertexPartition
 {

src/leidenalg/include/ResolutionParameterVertexPartition.h

@@ -3,6 +3,9 @@
 
 #include <MutableVertexPartition.h>
 
+#include "igraph.h"
+
+
 class ResolutionParameterVertexPartition : public MutableVertexPartition
 {
   public:

src/leidenalg/include/SignificanceVertexPartition.h

@@ -3,6 +3,8 @@
 
 #include <MutableVertexPartition.h>
 
+#include "igraph.h"
+
 
 class SignificanceVertexPartition : public MutableVertexPartition
 {