Msvc compliance

CMakeLists.txt

@@ -0,0 +1,33 @@
+cmake_minimum_required(VERSION 3.6.2)
+
+project(eakmeans)
+
+option(STATIC_LIBRARY "Build static library instead of shared library" OFF)
+if(STATIC_LIBRARY)
+	set(LIB_TYPE "STATIC")
+else()
+	set(LIB_TYPE "SHARED")
+endif()
+add_subdirectory(src)
+
+option(BUILD_MAIN "Build test executable" ON)
+if(BUILD_MAIN)
+	set(EXE_SRC "${CMAKE_CURRENT_SOURCE_DIR}/src/main.cpp")
+	include_directories("${CMAKE_CURRENT_SOURCE_DIR}/src")
+	link_directories("${CMAKE_ARCHIVE_OUTPUT_DIRECTORY}" "${BLAS_FOLDER}/dll")
+	add_executable(${PROJECT_NAME} ${EXE_SRC})
+	target_link_libraries(${PROJECT_NAME} PUBLIC ${LIB_EAKMEANS} ${BLAS})
+	add_dependencies(${PROJECT_NAME} libeakmeans)
+	if(WIN32)
+		set_target_properties(${PROJECT_NAME} PROPERTIES LINK_FLAGS "/WHOLEARCHIVE:libeakmeans")
+	endif()
+endif()
+
+option(PYTHON_KMEANS "Build Python integration of eakmeans." OFF)
+if(PYTHON_KMEANS)
+	execute_process(
+	  COMMAND python "${PROJECT_SOURCE_DIR}/setup.py" build_ext -b lib
+	  WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
+	  RESULT_VARIABLE py_result
+	)
+endif()

src/CMakeLists.txt

@@ -0,0 +1,34 @@
+cmake_minimum_required(VERSION 3.6.2)
+
+project(libeakmeans)
+
+# We enable C++11
+set(CMAKE_CXX_STANDARD 11)
+
+set(TARGET_ARCHI "x64")
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${TARGET_ARCHI}" CACHE PATH "Output library (lib) directory")
+set(LIBEAKMEANS_OUTPUT_DIR ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
+
+option(USEBLAS "Use external BLAS library" OFF)
+if(USEBLAS)
+	set(BLAS_FOLDER "${CMAKE_CURRENT_SOURCE_DIR}/../../OpenBLAS/build" CACHE PATH "Folder where to find BLAS distribution")
+	set(BLAS_NAME "libopenblas" CACHE STRING "Name of BLAS implementation")
+endif()
+
+file(GLOB LIB_SRC *.cpp *.hpp *.h)
+get_filename_component(main_cpp ${CMAKE_CURRENT_SOURCE_DIR}/main.cpp ABSOLUTE)
+list(REMOVE_ITEM LIB_SRC "${main_cpp}")
+
+if(USEBLAS)
+	include_directories("${BLAS_FOLDER}/include")
+	find_library(BLAS ${BLAS_NAME} PATHS "${BLAS_FOLDER}" PATH_SUFFIXES lib;dll)
+endif()
+
+add_library(${PROJECT_NAME} ${LIB_TYPE} ${LIB_SRC})
+set_target_properties(${PROJECT_NAME} PROPERTIES LINKER_LANGUAGE CXX)
+target_include_directories (${PROJECT_NAME} PUBLIC {CMAKE_CURRENT_SOURCE_DIR}/src)
+
+if(USEBLAS)
+	target_link_libraries(${PROJECT_NAME} PRIVATE ${BLAS})
+	target_compile_definitions(${PROJECT_NAME} PUBLIC "WITHBLAS")
+endif()

src/arrutilv2l0.h

@@ -54,5 +54,19 @@ COPYING for more details.
 #include "arrutilv2l0blasless.h"
 #endif
 
+#ifdef _MSC_VER
+// add setenv under Windows
+int setenv(const char *name, const char *value, int overwrite)
+{
+	int errcode = 0;
+	if (!overwrite) {
+		size_t envsize = 0;
+		errcode = getenv_s(&envsize, NULL, 0, name);
+		if (errcode || envsize) return errcode;
+	}
+	return _putenv_s(name, value);
+}
+#endif // _MSC_VER
+
 #endif
 

src/barrierutil.cpp

@@ -20,6 +20,7 @@ COPYING for more details.
 
 #include "barrierutil.h"
 #include <iostream>
+#include <algorithm>
 
 namespace stdthreadutil{
 

src/initialise2.h

@@ -156,7 +156,11 @@ std::tuple<std::unique_ptr<TFloat []>, std::unique_ptr<TFloat []>, std::unique_p
 	std::unique_ptr<TFloat [] >,
 	std::unique_ptr<TInt [] >,
 	TFloat > 
-	(std::move(C_uptr), std::move(C_l22s_uptr), std::move(ind0), TFloat(mse2));	
+#ifdef _MSC_VER
+	(std::move(C_uptr), std::move(C_l22s_uptr), std::move(ind0), std::move(TFloat(mse2)));	//force forwarding
+#else
+	(std::move(C_uptr), std::move(C_l22s_uptr), std::move(ind0), TFloat(mse2));
+#endif
 }
 
 

src/main.cpp

@@ -23,6 +23,7 @@ COPYING for more details.
 #include <string>
 #include <vector>
 #include <algorithm>
+#include <ctime>
 
 #include "optionsutil.h"
 #include "pllkmeansfuncs_void.h"
@@ -611,7 +612,7 @@ int main(int argc, char* argv[]){
 			return 1;
 		}
 
-		if (!(cout_verbosity > 1) and !(file_verbosity > 0)){
+		if (!(cout_verbosity > 1) && !(file_verbosity > 0)){
 			std::cerr << "problem with options : cmse not requested, thus : valinfn has been set to " << valinfn << " but verbosity is not compatible : cout_verbosity is " << cout_verbosity  << " and file_verbosity is " << file_verbosity << " . It is required that cout_verbosity > 1 or file_verbosirt > 0" << std::endl;
 			return 1;
 		} 		
@@ -628,48 +629,48 @@ int main(int argc, char* argv[]){
 		return 1;
 	}
 
-	if (uopts.options["cinfn"].isset and uopts.options["ioutfn"].isset){
+	if (uopts.options["cinfn"].isset && uopts.options["ioutfn"].isset){
 		std::cerr << "problem with options : cannot set both cinfn and ioutfn" << std::endl;
 		return 1;
 	}
 
-	if ((uopts.options["soutfn"].isset and (file_verbosity != 2 and file_verbosity != 3) )){
+	if ((uopts.options["soutfn"].isset && (file_verbosity != 2 && file_verbosity != 3) )){
 		std::cerr << "problem with options : soutfn is set, but file_verbosity is set to " << file_verbosity << ", either unset soutfn or set file_verbosity to 2 (or 3, but then include voutfn as well)" << std::endl;
 		return 1;
 	}
 
-	if ((uopts.options["voutfn"].isset and file_verbosity != 3)){
+	if ((uopts.options["voutfn"].isset && file_verbosity != 3)){
 		std::cerr << "problem with options : voutfn is set, but file_verbosity is set to " << file_verbosity << ", either unset voutfn or set file_verbosity to 3" << std::endl;
 		return 1;
 	}
 
-	if ((uopts.options["moutfn"].isset and nruns == 1)){
+	if ((uopts.options["moutfn"].isset && nruns == 1)){
 		std::cerr << "problem with options : moutfn is set, nruns is 1, either unset moutfn or set nruns to be greater than 1" << std::endl;
 		return 1;
 	}
 
-	if ((uopts.options["moutdir"].isset and nruns == 1)){
+	if ((uopts.options["moutdir"].isset && nruns == 1)){
 		std::cerr << "problem with options : moutdir is set, nruns is 1, either unset moutdir or set nruns to be greater than 1" << std::endl;
 		return 1;
 	}
 
-	if ((uopts.options["voutfn"].isset and nruns != 1)){
+	if ((uopts.options["voutfn"].isset && nruns != 1)){
 		std::cerr << "problem with options : voutfn is set, nruns is " << nruns << ", either unset voutfn or set nruns to 1" << std::endl;
 		return 1;
 	}
 
-	if ((uopts.options["soutfn"].isset and nruns != 1)){
+	if ((uopts.options["soutfn"].isset && nruns != 1)){
 		std::cerr << "problem with options : soutfn is set, nruns is " << nruns << ", this combination is currently not supported, either unset soutfn or set nruns to 1" << std::endl;
 		return 1;
 	}
 
 
-	if ((uopts.options["voutfn"].isset == false and file_verbosity == 3)){
+	if ((uopts.options["voutfn"].isset == false && file_verbosity == 3)){
 		std::cerr << "problem with options : voutfn is not set, but file_verbosity is set to 3, either lower file_verbosity to 0 or 2, or set voutfn" << std::endl;
 		return 1;
 	}
 
-	if (nruns != 1 and (uopts.options["cinfn"].isset || uopts.options["ind0fn"].isset )){
+	if (nruns != 1 && (uopts.options["cinfn"].isset || uopts.options["ind0fn"].isset )){
 		std::cerr << "problem with options : nruns is set to " << nruns << ", but either cinfn or ind0fn is set. For nruns > 1, it is currently not possible to initialise from prespecified centroids or indices. Either reduce nruns to 1, or make sure neither cinfn nor indofn are set. With nruns > 1, init0 may be set. " << std::endl;
 		return 1;
 	}
@@ -682,8 +683,8 @@ int main(int argc, char* argv[]){
 
 
 	if (
-	(uopts.options["cmsewritefn"].isset and !(uopts.options["cmserate"].isset)) ||
-	(!(uopts.options["cmsewritefn"].isset) and uopts.options["cmserate"].isset))
+	(uopts.options["cmsewritefn"].isset && !(uopts.options["cmserate"].isset)) ||
+	(!(uopts.options["cmsewritefn"].isset) && uopts.options["cmserate"].isset))
 	{
 			std::cerr << "problem with options : either 0 or 2 of cmsewritefn and cmserate need to be set\n";
 			return 1;

src/stringutilbase.cpp

@@ -21,6 +21,8 @@ COPYING for more details.
 #include "stringutilbase.h"
 #include <stdexcept>
 #include <iostream>
+#include <algorithm>
+
 namespace stringutil{
 //split the string tosplit by delim. With x appearances of delim in tosplit, the returned vector will have length x + 1 (even if appearances at the start, end, contiguous.
 std::vector<std::string> split(const std::string & tosplit, const std::string & delim){
@@ -63,12 +65,12 @@ std::vector<std::string> split(const std::string & tosplit){
 	unsigned it = 0;	
 
 	while (it != tosplit.size()){
-		while (isws(tosplit[it]) and it != tosplit.size()){
+		while (isws(tosplit[it]) && it != tosplit.size()){
 			++it;
 		}
 		unsigned start = it;
 
-		while (!isws(tosplit[it]) and it != tosplit.size()){
+		while (!isws(tosplit[it]) && it != tosplit.size()){
 			++it;
 		}
 		unsigned end = it;

src/stringutilfile.cpp

@@ -63,7 +63,7 @@ bool file_has_2int_header(const std::string & filename){
 		return false;
 	}
 	/* next test that they are indeed integers */	
-	if (is_integer(bob[0]) and is_integer(bob[1])){
+	if (is_integer(bob[0]) && is_integer(bob[1])){
 		return true;
 	}