Index: CMakeLists.txt
===================================================================
--- a/CMakeLists.txt	(revision 0)
+++ b/CMakeLists.txt	(working copy)
@@ -0,0 +1,109 @@
+cmake_minimum_required(VERSION 2.6)
+
+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 ${CMAKE_SOURCE_DIR}/CMakeModules)
+
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+  #release comes with -O3 by default
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
+endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
+
+enable_language(CXX)
+
+######################################################################
+# compiler tests
+# these need ot be done early (before further tests).
+#####################################################################
+
+include(CheckCXXCompilerFlag)
+
+########################################################################
+# User input options                                                   #
+########################################################################
+option(BUILD_SHARED_LIBS "Build shared libs" ON)
+if (NOT DEFINED LIB)
+  set(LIB "lib")
+endif(NOT DEFINED LIB)
+if (NOT DEFINED MAN)
+  set(MAN "share/man")
+endif(NOT DEFINED MAN)
+if (NOT DEFINED DATA)
+  set(DATA "share/voro++")
+endif(NOT DEFINED DATA)
+
+########################################################################
+#Find external packages
+########################################################################
+find_package(Doxygen)
+
+########################################################################
+# Basic system tests (standard libraries, headers, functions, types)   #
+########################################################################
+include(CheckIncludeFileCXX)
+foreach(HEADER cmath cstdio cstdlib cstring ctime fstream iostream queue vector)
+  check_include_file_cxx(${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 ${LIB} ARCHIVE DESTINATION ${LIB})
+
+add_executable(cmd_line src/cmd_line.cc)
+target_link_libraries(cmd_line voro++)
+#cannot have two target with the same name
+set_target_properties(cmd_line PROPERTIES OUTPUT_NAME voro++ 
+  RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/src") 
+install(TARGETS cmd_line RUNTIME DESTINATION bin)
+
+#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 include/voro++)
+install(FILES ${CMAKE_SOURCE_DIR}/man/voro++.1 DESTINATION ${MAN}/man1)
+
+if (DOXYGEN_FOUND)
+  add_custom_target(help COMMAND ${DOXYGEN_EXECUTABLE} src/Doxyfile 
+    COMMENT "Build doxygen documentation")
+endif (DOXYGEN_FOUND)
+
+configure_file(${CMAKE_MODULE_PATH}/cmake_uninstall.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake IMMEDIATE @ONLY)
+add_custom_target(uninstall COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)
Index: CMakeModules/cmake_uninstall.cmake.in
===================================================================
--- a/CMakeModules/cmake_uninstall.cmake.in	(revision 0)
+++ b/CMakeModules/cmake_uninstall.cmake.in	(working copy)
@@ -0,0 +1,22 @@
+IF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+  MESSAGE(FATAL_ERROR "Cannot find install manifest: \"@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt\"")
+ENDIF(NOT EXISTS "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt")
+
+FILE(READ "@CMAKE_CURRENT_BINARY_DIR@/install_manifest.txt" files)
+STRING(REGEX REPLACE "\n" ";" files "${files}")
+FOREACH(file ${files})
+  MESSAGE(STATUS "Uninstalling \"$ENV{DESTDIR}${file}\"")
+  IF(EXISTS "$ENV{DESTDIR}${file}")
+    EXEC_PROGRAM(
+      "@CMAKE_COMMAND@" ARGS "-E remove \"$ENV{DESTDIR}${file}\""
+      OUTPUT_VARIABLE rm_out
+      RETURN_VALUE rm_retval
+      )
+    IF(NOT "${rm_retval}" STREQUAL 0)
+      MESSAGE(FATAL_ERROR "Problem when removing \"$ENV{DESTDIR}${file}\"")
+    ENDIF(NOT "${rm_retval}" STREQUAL 0)
+  ELSE(EXISTS "$ENV{DESTDIR}${file}")
+    MESSAGE(STATUS "File \"$ENV{DESTDIR}${file}\" does not exist.")
+  ENDIF(EXISTS "$ENV{DESTDIR}${file}")
+ENDFOREACH(file)
+