Index: CMakeLists.txt
===================================================================
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -0,0 +1,98 @@
+cmake_minimum_required(VERSION 2.8.12)
+
+project(voro++)
+
+set(PROJECT_VERSION "0.4.6")
+set(SOVERSION 0)
+
+# Cmake modules/macros are in a subdirectory to keep this file cleaner
+set(CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/CMakeModules)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+  #release comes with -O3 by default
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
+endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+
+enable_language(CXX)
+
+######################################################################
+# compiler tests
+# these need ot be done early (before further tests).
+#####################################################################
+
+include(CheckCXXCompilerFlag)
+
+########################################################################
+# Standard install paths                                               #
+########################################################################
+include(GNUInstallDirs)
+
+########################################################################
+#Find external packages
+########################################################################
+find_package(Doxygen)
+
+########################################################################
+# Basic system tests (standard libraries, headers, functions, types)   #
+########################################################################
+include(CheckIncludeFileCXX)
+foreach(HEADER cmath cstdio cstdlib cstring ctime fstream iostream queue vector)
+  check_include_file_cxx(${HEADER} FOUND_${HEADER})
+  if(NOT FOUND_${HEADER})
+    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
+  endif(NOT FOUND_${HEADER})
+endforeach(HEADER)
+
+set(MATH_LIBRARIES "m" CACHE STRING "math library")
+mark_as_advanced( MATH_LIBRARIES )
+include(CheckLibraryExists)
+foreach(FUNC sqrt)
+  check_library_exists(${MATH_LIBRARIES} ${FUNC} "" FOUND_${FUNC}_${MATH_LIBRARIES})
+  if(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+    message(FATAL_ERROR "Could not find needed math function - ${FUNC}")
+  endif(NOT FOUND_${FUNC}_${MATH_LIBRARIES})
+endforeach(FUNC)
+
+######################################
+# Include the following subdirectory # 
+######################################
+
+file(GLOB VORO_SOURCES src/*.cc)
+file(GLOB NOT_VORO_SOURCES src/v_base_wl.cc src/cmd_line.cc src/voro++.cc)
+list(REMOVE_ITEM VORO_SOURCES ${NOT_VORO_SOURCES})
+add_library(voro++ ${VORO_SOURCES})
+set_target_properties(voro++ PROPERTIES 
+  LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/src"
+  SOVERSION ${SOVERSION})
+install(TARGETS voro++ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+
+add_executable(cmd_line src/cmd_line.cc)
+target_link_libraries(cmd_line voro++)
+#cannot have two target with the same name
+set_target_properties(cmd_line PROPERTIES OUTPUT_NAME voro++ 
+  RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/src") 
+install(TARGETS cmd_line RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+
+#for voto++.hh
+include_directories(${CMAKE_SOURCE_DIR}/src)
+file(GLOB EXAMPLE_SOURCES examples/*/*.cc) 
+foreach(SOURCE ${EXAMPLE_SOURCES})
+  string(REGEX REPLACE "^.*/([^/]*)\\.cc$" "\\1" PROGNAME "${SOURCE}")
+  if (NOT PROGNAME STREQUAL ellipsoid) #ellipsoid is broken
+    string(REGEX REPLACE "^.*/(examples/.*)/${PROGNAME}\\.cc$" "\\1" DIRNAME "${SOURCE}")
+    add_executable(${PROGNAME} ${SOURCE})
+    target_link_libraries(${PROGNAME} voro++)
+    set_target_properties(${PROGNAME} PROPERTIES 
+      RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${DIRNAME}" )
+  endif()
+endforeach(SOURCE)
+
+file(GLOB_RECURSE VORO_HEADERS src/*.hh)
+install(FILES ${VORO_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/voro++)
+install(FILES ${CMAKE_SOURCE_DIR}/man/voro++.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+
+if (DOXYGEN_FOUND)
+  add_custom_target(doxygen COMMAND ${DOXYGEN_EXECUTABLE} src/Doxyfile
+    COMMENT "Build doxygen documentation")
+endif (DOXYGEN_FOUND)
+